Introduction

Front. Microbiol.

Frontiers in Microbiology

Front. Microbiol.

1664-302X

Frontiers Media S.A.

10.3389/fmicb.2026.1755559

Review

The hidden potential of archaea in carbon and nitrogen cycling in agricultural soils: a review

Speek

Brenda M.

¹ ² ³ ^* Conceptualization Writing – original draft Writing – review & editing Suleiman

Afnan Khalil Ahmad

³ Conceptualization Writing – review & editing Keuning

Eline

³ Conceptualization Writing – review & editing Sechi

Valentina

² Conceptualization Writing – review & editing Buisman

Cees J. N.

¹ ² Supervision Writing – review & editing Bezemer

T. Martijn

² ⁴ Conceptualization Writing – review & editing

1Environmental Technology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, Netherlands 2Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands 3Bioclear Earth B.V., Groningen, Netherlands 4Aboveground Belowground Interactions Group, Institute of Biology, Leiden University, Leiden, Netherlands

*Correspondence: Brenda M. Speek, Brenda.Speek@wetsus.nl

03 02 2026

2026

1755559

27 11 2025 14 01 2026 20 01 2026

2026

Speek, Suleiman, Keuning, Sechi, Buisman and Bezemer

https://creativecommons.org/licenses/by/4.0/

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

The soil microbiome drives soil nutrient cycling and is intrinsically linked to plant productivity in agriculture. Archaea are members of many soil microbiomes and play important roles in nutrient cycling, particularly in the carbon and nitrogen cycle. Many archaeal groups contribute to both carbon and nitrogen cycles, but their dual roles are often underappreciated. For instance, ammonia-oxidizing archaea couple ammonia oxidation to carbon fixation, contributing to carbon sequestration in soils. Methanogenic archaea use ATP produced through methanogenesis for nitrogen fixation. N-DAMO archaea directly couple carbon and nitrogen cycling through nitrate-dependent anaerobic methane oxidation, while haloarchaea contribute to carbon sequestration and denitrification. Here, we synthesize the latest research regarding the dual roles of archaea in carbon and nitrogen cycling in agricultural soils. We pay special attention to how nutrient input influences these roles. We show that the relevance of the processes is highly context dependent. In addition, we identify several research directions that will help harness the difference roles of archaea in carbon and nitrogen cycling to increase agricultural productivity and sustainability. Finally, we showcase that abundance and activity of archaea in the soil microbiome could be steered through nutrient input or microbiome engineering strategies.

ammonia-oxidizing archaea haloarchaea methanogenic archaea n-damo archaea nutrient cycling

The author(s) declared that financial support was received for this work and/or its publication. Wetsus is co-funded by the European Union (Horizon Europe, LIFE, Interreg and EDRF), the Province of Fryslân and the Dutch Government: Ministry of Economic Affairs (TTT, SBO & PPS-I/TKI Water Technology), Ministry of Education, Culture and Science (TTT & SBO) and Ministry of Infrastructure and Water Management (National Growth Fund—UPPWATER).

section-at-acceptance

Terrestrial Microbiology

1 Introduction

Nutrient cycling is a central function of agricultural soils, maintaining fertility and supporting crop production (Jiao et al., 2019a). Because soil productivity directly affects food production, agricultural soils are typically closely managed (Tully and Ryals, 2017; Kopittke et al., 2019). Management strategies, such as nutrient input, directly impact biochemical nutrient cycling (Frink et al., 1999; Tully and Ryals, 2017). Understanding which processes drive nutrient cycling and how they increase soil productivity is therefore critical (Nealson and Stahl, 1997).

Key players in biochemical nutrient cycling are microbes (Sahu et al., 2017). These microorganisms contribute to maintain soil functionality and crop growth, by contributing to many different processes in soil nutrient cycling, including nitrification, nitrogen (N) fixation, carbon (C) turnover and phosphorus solubilization (Falkowski et al., 2008; Buée et al., 2009; Hartmann and Six, 2022). Bacteria are generally the most abundant group of microorganisms in soils (Bates et al., 2011; Wang et al., 2020). One bacterial species can perform multiple roles and thereby contribute to different nutrient cycles at the same time (Wang X. et al., 2024). Numerous studies have examined the roles of bacteria in agricultural soils; however, archaea have not received the same attention yet.

While previously considered extremophiles (Mehta and Baross, 2006; Dekas et al., 2009), this view has changed, as archaea have been found in common environments such as soils (Bates et al., 2011). Archaea are important members of the soil microbiome (Chen et al., 2008; Moissl-Eichinger et al., 2018; Naitam et al., 2023) and several archaeal species have been found to interact with plants (Chow et al., 2022). Specifically, archaea can improve plant growth through direct and indirect mechanisms; including contributing to biochemical nutrient cycling, mitigation of stresses in plants, phosphate solubilisation, siderophore production and degradation of pollutants (Odelade and Babalola, 2019; Alori et al., 2020; Singh et al., 2023; Martínez-Espinosa, 2024; Ventura et al., 2025). Particularly haloarchaea, known for their adaptation to saline environments, are frequently mentioned for their plant growth-promoting properties (Naitam et al., 2023), while many other archaeal species are known to play roles in biochemical nutrient cycling (Falkowski et al., 2008; Schleper and Nicol, 2010; Offre et al., 2013; Wright and Lehtovirta-Morley, 2023). The impact of archaea on plant growth and nutrient cycling underlines the importance of archaea in agricultural soils and plant productivity.

Agricultural soils can be divided into drylands, land used for crop growth and grasslands, and wetlands, including paddy fields (Jiao et al., 2019a). Dry- and wetlands typically harbour distinct archaeal communities due to differences in oxygen availability, irrigation and management practices (Jiao et al., 2019b). The most dominant archaeal phyla in soils are often the Thaumarchaeota and Euryarchaeota, recently reclassified as Methanobacteriota (Vaksmaa et al., 2016; Yuan et al., 2018; Clark et al., 2020; Megyes et al., 2021; Liu et al., 2022; Saghaï et al., 2022; Zhang et al., 2023). Both phyla have important roles in C and N turnover (Schleper and Nicol, 2010; Offre et al., 2013; Naitam and Kaushik, 2021).

The C- and N-cycles are essential in agriculture: they provide essential nutrients that support plant growth, but at the same time, can result in the release of several potent greenhouse gases (GHGs) (Shah et al., 2020). N plays an important role in plant development, and its deficiency can decrease plant growth, hinder root development and decrease plant dry mass (Frink et al., 1999). N application, in the form of chemical or organic fertilizer, is therefore essential for plants to obtain sufficient N (Ding et al., 2005; Diaz et al., 2006). Both bacteria and archaea play important roles in the transformation of N into ammonium (NH₄⁺) and NO₃⁻ (Cui et al., 2017), the primary sources of N for plants. Members of the Thaumarchaeota, specifically the ammonia-oxidizing archaea (AOA), are highly abundant in grasslands and crop lands, composing up to 95% of the total archaeal community (Clark et al., 2020; Megyes et al., 2021; Liu et al., 2022; Saghaï et al., 2022; Zhang et al., 2023). However, certain bacteria and archaea can transform nitrate (NO₃⁻) into nitrous oxide (N₂O), a GHG 273 times more potent than carbon dioxide (CO₂), through denitrification (Spiertz, 2010; Hirsch and Mauchline, 2015).

The C-cycle influences key soil functions. Soil organic matter (SOM), which consists of approximately 58% organic C, is crucial for retaining soil structure and the water holding capacity of the soil (Manns et al., 2016). The soil microbiome is essential for the generation of SOM and plays a small role in sequestering atmospheric CO₂ (Kallenbach et al., 2016; Jiang et al., 2022). Through microbial respiration, SOM is returned to the atmosphere as CO₂. Under anoxic conditions, methane (CH₄), another potent GHG with a global warming potential 37 times greater than CO₂, is produced by methanogenic archaea (Derwent, 2020). However, methanotrophic archaea and bacteria can mitigate CH₄ emissions by utilizing CH₄ for energy generation (McGlynn, 2017). Both methanogens and methanotrophs belong to the phylum of Methanobacteriota. Methanobacteriota thrive in anaerobic conditions, comprising more than 50% of the archaeal community in these environments (Vaksmaa et al., 2016; Yuan et al., 2018).

Above, four specific archaeal groups are mentioned: AOA, methanogens, methanotrophs and haloarchaea. These archaeal groups are typically characterized by a single well-known characteristic, i.e., ammonia (NH₃) oxidation in AOA, CH₄ production in methanogens and CH₄ oxidation in methanotrophs, or salt tolerance and plant growth-promoting potential for haloarchaea. Yet, all four of these archaeal groups have the potential to contribute to both C- and N-cycling (Figure 1; Table 1). For example, AOA make contributions to N- and C- cycling through N₂O formation and CO₂ fixation (Pratscher et al., 2011). Methanogens contribute to N-cycling via N₂ fixation (Leigh, 2000; Dekas et al., 2009). A specific subset of the anaerobic methanotrophs, N-DAMO archaea, contribute to NO₃⁻ reduction and DNRA (Dissimilatory Nitrate Reduction to Ammonium) (Raghoebarsing et al., 2006; Wang et al., 2025). In contrast, while haloarchaea are not typically found in agricultural soils, they occupy a niche in saline environments, where they contribute to C turnover and denitrification (Torregrosa-Crespo et al., 2020a; Miralles-Robledillo et al., 2024).

Figure 1

A simplified depiction of the carbon and nitrogen cycle in soil. 1) Biological Nitrogen Fixation (BNF), 2) Ammonia oxidation, 3) Nitrite oxidation, 4) Nitrate reduction, 5) Dissimilatory Nitrate Reduction to Ammonia (DNRA), 6) Nitrite reduction, 7) Nitric oxide reduction, 8) Nitrous oxide reduction, 9) Methane oxidation, 10) Methanogenesis, 11) Carbon assimilation, 12) Methanogenesis, 13) Respiration, and 14) Carbon fixation.

Diagram depicting soil and atmospheric interactions with methanogens, AOA, N-DAMO archaea, and haloarchaea. Arrows indicate gas exchanges, including CO2, CH4, N2O, NO, N2, illustrating nitrogen and carbon cycles. Soil layers include compounds like (CHO)n, NO3−, NO2−, and NH3. Various circles and arrows represent microbiological processes and interactions above and below ground, with a legend identifying different microorganisms involved.

Table 1

Overview of the relevant archaeal groups and their roles in C- and N-cycling.

Archaeal group	Role in C-cycling	Role in N-cycling	References
AOA	CO₂ fixation	Ammonia oxidation, N₂O formation	Könneke et al. (2005), Francis et al. (2007), Pratscher et al. (2011), Jung et al. (2014a), Kobayashi et al. (2018), and Wan et al. (2023)
Haloarchaea	Photoheterotrophy, CO₂ fixation	Denitrification	Grant (2001), Falb et al. (2008), Torregrosa-Crespo et al. (2020b), Torregrosa-Crespo et al. (2020a), and Miralles-Robledillo et al. (2021)
Methanogens	Methanogenesis, CO₂ fixation	N₂ fixation	Reeve et al. (1997), Leigh (2000), Dekas et al. (2009), and Borrel et al. (2016)
N-DAMO archaea	CH₄ oxidation	NO₃⁻ reduction, DNRA, N₂O formation	Raghoebarsing et al. (2006), Haroon et al. (2013), Nie et al. (2021), and Tan et al. (2024)

This review aims to increase the understanding of dual roles of AOA, methanogens, N-DAMO archaea, and haloarchaea in C- and N-cycling in agricultural soils. We highlight the potential ecological significance of their dual roles, with particular emphasis on their contributions to GHG emissions. By synthesizing current knowledge on the dual roles of these four archaeal groups in C- and N-cycling, we address the following questions: (1) Under which agricultural conditions are their roles in C- and N-cycling most relevant? (2) How does nutrient addition influence their activity and function? and (3) How can existing knowledge be used to improve current agricultural management practices or which future research is needed before current management practices can be improved? We aim to contribute to identifying research gaps and new research directions which will help in the development of agricultural strategies that utilize the underrecognized functions of archaea in C- and N-cycling to increase agricultural productivity and sustainability. To address these questions, we first provide an overview of the four archaeal groups that participate in both C- and N-cycling, highlighting their ecological niches and contributions to both nutrient cycles.

2 Archaeal groups with dual roles in C- and N-cycling 2.1 Ammonia-oxidizing archaea (AOA)

AOA catalyse the first and rate-limiting step of nitrification by oxidizing NH₃ to nitrite (NO₂⁻) (Könneke et al., 2005; Francis et al., 2007). AOA are often compared to ammonia-oxidizing bacteria (AOB), their bacterial counterparts that catalyse the same reaction. AOA and AOB occupy different ecological niches, but AOA can dominate in abundance under certain environmental conditions (Leininger et al., 2006; Sterngren et al., 2015; Mukhtar et al., 2019; Clark et al., 2020). All AOA fall into the class of Nitrososphaeria, within the phylum Thermoproteota (Rinke et al., 2021). Nitrososphaeria are often the most dominant archaeal class in soils, composing over 70% of the total archaeal community (Megyes et al., 2021; Liu et al., 2022; Saghaï et al., 2022; W. Hu et al., 2022). The order Nitrososphaeria has been classified into several lineages with different characteristics based on NH₃ affinity, optimum pH and urea usage, which allows the different lineages to occupy specific ecological niches (Lehtovirta-Morley et al., 2024; Zheng et al., 2024).

2.2 Haloarchaea

Haloarchaea thrive in saline and hypersaline environments (Oren, 2002; Baker et al., 2024). All haloarchaea belong to the class of Halobacteria within the phylum Methanobacteriota (Garrity et al., 2001). Halobacteria have been found to compose 46.5–89.5% of the total archaeal community in saline soils (Zhao S. et al., 2024). While typically not dominant in other soil types, they have been detected in drylands, where they can make up 20% of the archaeal community (Hu W. et al., 2022). Due to their reported plant growth–promoting properties, haloarchaea have been proposed as potential inoculants to enhance plant tolerance to different stressors (Yadav et al., 2015; Naitam et al., 2023; Mukhtar et al., 2024).

2.3 Methanogenic archaea

Methanogenic archaea are well-known for their exclusive contribution to CH₄ production, as bacteria do not perform this process (Bapteste et al., 2005). While exceptions have been discovered, many methanogens belong to the phylum of Methanobacteriota (Wu et al., 2024). Due to their anoxic nature, methanogens are important contributors to C-cycling in waterlogged soil such as wetlands and paddy fields (Narrowe et al., 2019; Asakawa, 2021). Methanogenic archaea contribute up to 350–420 Tg of CH₄ emissions per year (Lyu et al., 2018), with approximately 50% of CH₄ emissions originating from wetlands and rice paddy fields (Lyu et al., 2018). Even though methanogens can play a prominent role in CH₄ emissions in aerated soils (Angel et al., 2012; Angle et al., 2017), they have a low abundance compared to other archaeal groups in these environments (Angel et al., 2012; Alves et al., 2022).

2.4 N-DAMO archaea

As this review focuses on archaea that impact C- and N-cycling, here the focus will be specifically on archaea that perform nitrate-dependent anaerobic methane oxidation (N-DAMO). N-DAMO archaea belong to the genus of Candidatus (Ca.) Methanoperedens, within the phylum of Methanobacteriota (Raghoebarsing et al., 2006; Zehnle and Schoelmerich, 2025). N-DAMO archaea were first discovered in a consortium with N-DAMO bacteria, who use NO₂⁻ for anaerobic oxidation of CH₄, producing CO₂ and nitrogen gas (N₂) (Raghoebarsing et al., 2006). N-DAMO archaea reduce NO₃⁻ during anaerobic CH₄ oxidation, forming CO₂ and NO₂⁻ through reverse methanogenesis (Haroon et al., 2013; Wei et al., 2022). N-DAMO archaea are found in wetlands and paddy fields (Ding et al., 2016; Wang et al., 2022). In soils they are often detected in association with NO₂⁻-utilizing bacteria who use the NO₂⁻ produced by N-DAMO archaea (Ding et al., 2016). Many ANME (anaerobic methanotrophic archaea) have partnerships with sulphate reducing bacteria for electron shuttling, however, Ca. Methanoperedens does not need this symbiotic reaction (Zehnle and Schoelmerich, 2025).

3 Archaeal contribution to nitrogen cycling 3.1 Nitrification

AOA contribute to N-cycling in two major ways: (1) through NH₃ oxidization, and (2) by producing N₂O (Santoro et al., 2011). AOA and AOB perform oxidation of NH₃ to hydroxylamine (NH₂OH) using the enzyme ammonia-monooxygenase (AMO) (Zhalnina et al., 2012). In most AOA species, AMO exhibits a higher substrate affinity compared to AOB (Zhalnina et al., 2012). Under conditions with low N availability, AOA can therefore outcompete AOB (Ouyang et al., 2017). Moreover, AOA are known for their tolerance of acidic conditions (Gubry-Rangin et al., 2010; Yao et al., 2011; Zhalnina et al., 2012) and obligate acidophilic AOA species have been described (Lehtovirta-Morley et al., 2024). Under acidic conditions, NH₃ availability is reduced, leading to conditions that favour AOA (Prosser and Nicol, 2012). AOA are however not limited to acid soils and can grow in a wide pH range from acidic to alkaline (Prosser and Nicol, 2012). By contrast, AOB prefer soils at neutral pH (Robinson et al., 2014; Du et al., 2022). Finally, AOA have a higher affinity for oxygen than AOB, which can give them a growth advantage under oxygen-limited conditions (Du et al., 2022).

AMO has been identified as the enzyme catalysing the oxidation of NH₃ to NH₂OH (Vajrala et al., 2013). The process of NH₂OH conversion to NO₂⁻ is less well understood. AOB convert NH₂OH to nitric oxide (NO) using hydroxylamine dehydrogenase (HAO), whereas another unidentified enzyme converts NH₂OH to NO₂⁻ (Caranto and Lancaster, 2017). AOA lack the gene encoding HAO, and this part of the NH₃ oxidation process therefore remains unclear (Walker et al., 2010) (Figure 2).

Figure 2

Key enzymes and simplified pathways involved in carbon and nitrogen cycling, specifically focused on the reactions mentioned in this review. The color of the arrow corresponds to the archaeal group involved in the reaction: Green = methanogens, Orange = AOA, purple = N-DAMO archaea, and blue = Halarchaea. Unidentified enzymes are indicated as “?”. NH₂OH = hydroxylamine, NH₄OH = ammonium hydroxide, 3-HP/4-HB = 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle, RuBisCO = ribulose-1,5-bisphosphate carboxylase/oxygenase, amoA = ammonia monooxygenase, hao = hydroxylamine oxidoreductase, hcp = hydroxylamine reductase, nxr = nitrite oxidoreductase (has not been identified in archaea), nirS/nirK = nitrite reductase, norB = nitric oxide reductase, nosZ = nitrous oxide reductase, narG/narH = nitrate reductase, mcr = methyl-coenzyme M reductase (involved in methanogenesis and reverse methanogenesis).

Flowchart depicting nitrogen cycle processes with chemical reactions. Includes arrows showing conversions among compounds: NO3 to NO2, NO, N2O, and N2; NH2OH to NH3/NH4; CO2 to CH4 and (CHO)n. Enzymes like narG, nirK, and nitrogense are labeled along pathways.

Nevertheless, both groups can produce N₂O during NH₃ oxidation. In AOB, several routes of N₂O formation have been proposed, including: 1) N₂O formation via the oxidation of NH₂OH to NO by HAO, 2) NO₂⁻ reduction to NO via nitrite reductase (NIR) and NO reductase (NOR), and 3) oxidation of NH₂OH by cytochrome P460 (Ritchie and Nicholas, 1972; Poth and Focht, 1985; Shaw et al., 2006; Caranto et al., 2016). Studies into the N₂O production mechanism of marine AOA give several insights into the possible pathways of N₂O production in AOA. Using isotope tracing experiments, Wan et al. (2023) found that AOA have several pathways of N₂O production, depending on environmental conditions (Figure 2). Both NH₂OH and NO were identified as key intermediates in AOA metabolism for N₂O formation. Most notably, N₂O formation was observed via NH₂OH oxidation and reaction of NH₂OH with NO. Under low oxygen conditions, nirK (copper-containing nitrite reductase) might be involved in the process of converting NO₂⁻ to NO and O₂ (Kraft et al., 2022; Hernández-Magaña and Kraft, 2024). O₂ produced during the process can subsequently be used during NH₃ oxidation. NO was further converted into N₂O and N₂ through the action of yet to be identified enzymes. nirK in AOA is likely involved in the generation of NO from both NO₂⁻ and NH₂OH, indicating several pathways for N₂O production (Kobayashi et al., 2018). Jung et al. (2014b) studied the N₂O production by five soil AOA. N₂O production by soil AOA primarily took place via NH₂OH oxidation and via nitrifier denitrification from NO₂⁻, indicating that soil AOA also have different pathways for N₂O production (Jung et al., 2014b).

In two marine AOA species, N₂O production increased with decreasing oxygen concentrations (Qin et al., 2017). It is unclear if this is also the case for soil AOA. When the N₂O production of Nitrososphaera viennensis, a soil AOA, Nitrosopumilus maritimus, a marine AOA, and Nitrosospira multiformis, an AOB, were compared, no increase in N₂O production was observed at lower oxygen concentrations, while more N₂O production was measured for the AOB species (Stieglmeier et al., 2014). Niche differentiation within the AOA can play a role in N₂O emission by different AOA species (Jung et al., 2019). Ca. Nitrosotenuis chungbukensis from the order Nitrosopumilales, demonstrated higher yields of N₂O than Ca. Nitrosocosmicus oleophilus from the order Nitrososphaerales (Jung et al., 2019). The amount of N₂O produced seemed to depend on the environmental pH. At pH 7.5, N₂O production originated largely from NH₂OH. In acidic environments, Ca. N. oleophilus seems to increase N₂O production. Interestingly, an isotope tracing experiment showed that Ca. N. oleophilus produced >50% of N₂O from NO₂⁻, which would suggest N₂O formation through a nitrifier denitrification pathway (Jung et al., 2019). In addition, upregulation of a putative cythochrome P450 NO reductase was observed under acidic conditions. Cytochrome P450 is an enzyme involved in conversion of NO to N₂O (Harris, 2002). This enzyme is also used for NO reduction by other microbial species (Higgins et al., 2018). These results suggest that Ca. N. chungbukensis and Ca. N. oleophilus use different pathways for N₂O formation under acidic conditions. These findings exemplify the importance of studying the N₂O yields of different AOA lineages.

3.2 Denitrification

Denitrification is the reduction of NO₃⁻ to N₂, via NO₂⁻, NO and N₂O (Bakken et al., 2012; Thomson et al., 2012). Some microorganisms possess all genes for denitrification and can carry out the entire pathway, whereas others lack the capacity to reduce NO₃⁻ all the way to N₂ and therefore perform partial denitrification (Babbin et al., 2015). Many haloarchaea are predicted to perform (partial) denitrification (Torregrosa-Crespo et al., 2018; Torregrosa-Crespo et al., 2019; Miralles-Robledillo et al., 2021). Haloarchaea likely perform denitrification through a similar pathway as denitrifying bacteria (Torregrosa-Crespo et al., 2020a; Miralles-Robledillo et al., 2024) (Figure 2). Some haloarchaea, such as Haloferax mediterranei, can reduce NO₃⁻ all the way to N₂, while others are predicted to catalyse partial denitrification potentially contributing to N₂O formation (Torregrosa-Crespo et al., 2020b).

Four enzymes are involved in the reduction reactions of the denitrification pathway: membrane-bound nitrate reductase (NAR) or periplasmic nitrate reductase (NAP), NIR, NOR and nitrous oxide reductase (NOS) (Bothe et al., 2000). Many haloarchaea encode the NarG and NarH subunits of NAR (Miralles-Robledillo et al., 2021). The second step, NO₂⁻ reduction, is performed by one of two main nitrite reductases: nirS (cytochrome-cd1-dependent nitrite reductases) or nirK (Kandeler et al., 2006). Genome analysis by Miralles-Robledillo et al. (2021) indicates that haloarchaea encode nirK and do not have nirS. In addition, the same study reveals that qNOR (norZ) is the main NOR in haloarchaea. Finally, haloarchaea encode NosZ for N₂O reduction.

Considering the high relative abundance of haloarchaea in saline environments and the fact that half of the haloarchaea species are predicted to perform (partial) denitrification, they could significantly contribute to gaseous N-emissions (Shi et al., 2016; Torregrosa-Crespo et al., 2018; Miralles-Robledillo et al., 2021). Based on genome analysis it can be interfered which haloarchaea are complete denitrifiers and which are partial denitrifiers (Miralles-Robledillo et al., 2021). While denitrification by some species has been tested in laboratory environments (Torregrosa-Crespo et al., 2019) and RNA-seq studies are conducted to understand the denitrification process (Miralles-Robledillo et al., 2024), studies regarding their contribution to the release of N gasses in the environment are lacking.

3.3 Biological nitrogen fixation

N is most commonly present in the atmosphere in the form of N₂, which is unavailable for most organisms (Erisman et al., 2008). N₂ fixation, the reduction of N₂ to NH_3, is carried out by a select group of bacteria and archaea known as diazotrophs (Boyd and Peters, 2013). Within the bacterial domain, N₂ fixation is a more widespread ability, and N₂-fixing bacteria can either be free-living, or plant associated (Pi et al., 2022). In the domain of archaea N₂ fixation has, to date, only been demonstrated within methanogenic archaea (Leigh, 2000; Dekas et al., 2009). N₂-fixing methanogens have been identified across several orders, including Methanobacteriales, Methanosarcinales, Methanocellales and Methanomicrobiales (Leigh, 2000; Koirala and Brözel, 2021). Notably, N₂-fixing archaea are exclusively free-living (Pi et al., 2022). It is unclear whether N₂ fixation first evolved in archaea and was subsequently transferred to bacteria or vice versa. Both the archaea-first and, more recently, the bacteria-first hypotheses have been proposed (Pi et al., 2022).

N₂ fixation in methanogens is coupled to methanogenesis, as fixation requires the input of ATP generated through methanogenesis (Bae et al., 2018). N₂ fixation is catalysed by the enzyme nitrogenase, of which three different variants exist (Riyaz and Khan, 2025): Fe-dependent, Vanadium (V)-dependent and molybdenum (Mo)-dependent nitrogenase. Mo-nitrogenase is the common type of nitrogenase, encoded by most, if not all, diazotrophs (Chanderban et al., 2023). In addition, it is the most efficient enzyme requiring the lowest amount of ATP for N₂ fixation (Chanderban et al., 2023; Riyaz and Khan, 2025). Identified N₂-fixing methanogens encode the Mo-dependent nitrogenase (Leigh, 2000). Some species, including Methanosarcina acetivorans, even encode all three variants (Chanderban et al., 2023). As Mo-nitrogenase is the common type of nitrogenase, N₂-fixing microorganisms are often detected using nifH, encoding the Fe protein of Mo-nitrogenase, as a biomarker (Fani et al., 2000).

N₂-fixing methanogens have been detected in a variety of different environments, including hydrothermal vents (Mehta and Baross, 2006), soil (Bae et al., 2018) and inside plant roots (Bao et al., 2025). Bae et al. (2018) used nifH to study activity of N₂-fixating archaea in the Florida everglades, a freshwater wetland affected by the intensification of agricultural practices. They found that in soils unaffected by agricultural effluent, 49% of the nifH mRNA transcripts belong to methanogens. This indicates that there is a significant contribution of methanogenic archaea to N₂ fixation in these wetlands.

Since N is an important element in agriculture, it is unsurprising that many studies have focussed on the effect of agricultural practices on diazotrophs. These studies use nifH as a biomarker for detection of both bacterial and archaeal diazotrophs (Fan et al., 2019; Han et al., 2019; Gao et al., 2021; Li et al., 2023; Zhou et al., 2023). However, the detection of N₂-fixing archaea is often not reported in these studies. Because most samples were collected from the topsoil (0–20 cm), this may explain the absence of N₂-fixing archaea. If N₂-fixing archaea were present, they are not further discussed, potentially due to their low abundance compared to N₂-fixing bacteria (Nepel et al., 2022).

The use of nifH as a biomarker to detect archaeal N₂-fixing methanogens has several limitations. Evaluation of different nifH primers revealed that not all primer pairs detect archaeal N₂-fixers (Gaby and Buckley, 2012; Angel et al., 2018). Furthermore, many microbial species carry pseudo-nifH, they encode nifH but are unable to perform N₂ fixation (Mise et al., 2021). This is the case for some anaerobic microorganisms, such as Clostridia species and some methanogens. Instead, other subunits of nitrogenase have been suggested as more suitable biomarkers, such as nifD, encoding the beta-subunit of nitrogenase (Mise et al., 2021). The occurrence of pseudo-nifD is less likely (Mise et al., 2021). Masuda et al. (2023) used nifD to determine the effect of fertilization on the N₂-fixing community in paddy fields. They found a low abundance of total archaeal nifD compared to bacterial nifD, which indicates that bacteria are the major N₂-fixers in these paddy fields. At genus level, the archaeal genus Ca. Methanoperendens was found amongst the top 5 of most abundant genera, particularly in unfertilized paddy fields (Masuda et al., 2023). The identification of Ca. Methanoperendens as a N₂-fixer is surprising, as this archaeon is a methanotroph and not a methanogen. Since N₂ fixation for archaea has only been identified in methanogens, the results of this study require further clarification and could potentially indicate that N₂ fixation within archaea is not limited to methanogenic archaea. Evidence of possible N₂ fixation by methanotrophic archaea has previously been found in methane seep sediments (Miyazaki et al., 2009).

3.4 Dissimilatory nitrate reduction to ammonium (DNRA)

N-DAMO archaea reduce NO₃⁻ to NO₂⁻ using electrons produced from CH₄ via the reverse methanogenesis pathway (Haroon et al., 2013). This conversion is however not the only contribution N-DAMO archaea make to the N-cycle, as N-DAMO archaea can perform DNRA. In bacteria, DNRA is a two-step process where NO₃⁻ is reduced to NO₂⁻ and subsequently to NH₄⁺ via NH₂OH (Zhao et al., 2025). NO₃⁻ is reduced to NO₂⁻ by NAR or NAP and NO₂⁻ is reduced to NH₄⁺ by pentaheme cytochrome c nitrite reductase (NrfA) (Zhao et al., 2025).

N-DAMO archaea encode both nrfA and narG, indicating a similar pathway for NO₃⁻ reduction as bacteria (Haroon et al., 2013; Nie et al., 2021). However, N-DAMO archaea seem to possess several different pathways for DNRA (Wang et al., 2025). Wang et al. (2025) discovered two possible pathways of DNRA in the presence of manganese (Mn): (1) ammonia-forming nitrite reductase (Nrf) pathway and (2) the reverse hydroxylamine:ubiquinone reductase module pathway. In addition to nrfA, hao and the gene encoding hydroxylamine reductase (hcp) were upregulated in the presence of Mn. This suggests that NO₂⁻ was reduced to NH₂OH by hao and subsequently to NH₄⁺ by hcp (Figure 2).

Furthermore, N-DAMO archaea Ca. Methanoperedens nitroreducens was shown the perform DNRA in the presence of iron and low concentrations of NO₃⁻ (Tan et al., 2024). Under the tested conditions, DNRA was coupled to N₂O emissions. The gene encoding cytochrome P460 was upregulated, suggesting a role in catalysing the oxidation of NH₂OH to N₂O. Additionally, the nitric oxide reductase flavorubredoxin (norV) was upregulated, indicating the presence of a second N₂O formation pathway, in which NO is produced by NrfA and subsequently reduced to N₂O via NorV. The results of these studies suggest that DNRA may take place under specific conditions with different electron acceptors using different pathways.

4 Archaeal contribution to carbon cycling 4.1 Carbon fixation

AOA are generally considered to be obligate autotrophs, relying on atmospheric CO₂ as their sole source of carbon through CO₂ fixation. Pratscher et al. (2011) showed direct evidence of autotrophic growth in soil AOA using RNA-stable isotope probing. While a marine AOA species has been suggested to exhibit mixotrophic growth (Hallam et al., 2006), genomic analysis indicates that not all soil AOA are capable of mixotrophic growth (Lehtovirta-Morley et al., 2024).

CO₂ fixation in AOA is coupled to NH₃ oxidation (Pratscher et al., 2011). Without NH₃ present, no CO₂ fixation will take place. AOA fix CO₂ via the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle (Pratscher et al., 2011), this pathway is conserved within all AOA lineages (Lehtovirta-Morley et al., 2024). The gene encoding acetyl-CoA carboxylase α-submit (accA) is an essential gene involved in CO₂ fixation in AOA (Yakimov et al., 2009). In contrast, AOB perform CO₂ fixation via the Calvin-Benson-Bassham (CBB) cycle (Stein et al., 2007). A difference between the 3-HP/4-HB and CBB cycle is the energy required for CO₂ fixation; the archaeal 3-HP/4-HP pathway requires less ATP then the CBB cycle (Könneke et al., 2014), making the archaeal pathway more efficient for biomass formation.

Most research regarding CO₂ fixation by AOA and its environmental significance has been performed in oceans and deep seas. Due to the oligotrophic conditions in water, AOA make significant contributions to CO₂ fixation (Wu et al., 2022). A study involving marine AOA and AOB found that N. maritimus formed 1.3 g dry biomass per mole NH₃ oxidized, and the marine AOB N. oceani 0.8 g dry mass per mole (Könneke et al., 2014). This indicates that N. maritimus can form biomass more efficiently than N. oceani.

A study on AOA and AOB in forest soils estimated that AOA oxidize 59.8 μg N in the form of NH₃ to fix 1 μg C to their biomass (Norman et al., 2015). For AOB this was 58.2 μg N (Norman et al., 2015). While this study looked at the whole community of AOA and AOB rather than single species, these results indicate that the efficiency of CO₂ fixation is similar between both groups. To our knowledge there are currently no studies that performed similar experiments in agricultural soils.

Microcosm experiments with soils from grassland found that 80% of CO₂ fixed into the SOC pool originated from AOA and AOB combined (Xia et al., 2022). Particularly in water amended soils without N addition, AOA contributed significantly to CO₂ fixation, while AOB made large contributions under urea addition (Xia et al., 2022). This result is in line with the fact that AOA can outcompete AOB when N concentrations are low and may indicate that AOA might significantly contribute to CO₂ fixation in N limited soils.

In contrast to AOA, Haloarchaea are considered photoheterotrophs, as they use organic C compounds as their C source and require light to generate energy (Grant, 2001). For example, Haloarcula hispanica was found to grow on acetate as a sole C source (Falb et al., 2008). However, comparative genomics has revealed exceptions: the haloarchaea Natronomonas pharaonis encodes an archaeal-type RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase), indicating that it might be capable of CO₂ fixation (Falb et al., 2008). Whether other haloarchaea carry RuBisCO remains to be resolved.

Methanogens can also contribute to C-cycling via CO₂ fixation. Specifically, autotrophic hydrogenotrophic methanogens who use CO₂ and H₂ as their sole source for C and energy generation (Borrel et al., 2016). Although heterotrophic hydrogenotrophic methanogens have been discovered as well (Kouzuma et al., 2017). Hydrogenotrophic methanogenic archaea are commonly detected in paddy fields, and several orders have been detected in grassland soils (Table 2).

Table 2

Methanogen groups capable of hydrogenotrophic methanogenesis and their habitats.

Order	Representative genera	Primary pathway of methanogenesis	Environment
Methanobacteriales	Methanobacterium, Methanobrevibacter	Hydrogenotrophic	Paddy soils (Zu et al., 2016; Yuan et al., 2018; Wang S. et al., 2023) and grassland (Hofmann et al., 2016)
Methanomicrobiales	Methanoregula, Methanospirillum	Hydrogenotrophic	Paddy soils (Vaksmaa et al., 2016; Zu et al., 2016; Yuan et al., 2018; Wang S. et al., 2023) and grassland (Hofmann et al., 2016)
Methanocellales	Methanocella	Hydrogenotrophic	Paddy soils (Vaksmaa et al., 2016; Zu et al., 2016; Yuan et al., 2018; Wang S. et al., 2023) and grassland (Hofmann et al., 2016)
Methanosarcinales	Methanosarcina	Methylotrophic, acetoclastic and hydrogenotrophic	Paddy soils (Zu et al., 2016; Yuan et al., 2018; Wang S. et al., 2023) and grassland (Hofmann et al., 2016)
Methanococcales	Methanococcus	Hydrogenotrophic	Grassland (Hofmann et al., 2016)

Most CO₂ reducing methanogens fixate C via the reductive acetyl-CoA cycle, also known as the Wood-Ljungdahl pathway, but there are exceptions: Methanospirillum hungatei was found to encode RuBisCO and PRK (phosphoribulokinase), which are involved in the reductive hexulose-phosphate pathway for CO₂ fixation (Kono et al., 2017; Lemaire et al., 2020). It is not clear if M. hungatei can grow with CO₂ as a C source. For autotrophic hydrogenotrophic methanogens, CO₂ is an important source for C and energy generation. A study by Chen et al. (2019) reports that Methanobacterium congolense converts four moles of CO₂ into CH₄ for each mole CO₂ that was converted into biomass. This experiment included only one strain of M. congolense and was performed under CO₂ limited conditions. Similar experiments could be conducted under ambient CO₂ concentrations and with other methanogen strains to determine whether rates are comparable. In soil environments where methanogens are abundant, CO₂ fixation could potentially contribute to carbon sequestration. However, since CH₄ has a higher global warming potential than CO₂, emissions may outweigh the GHG reduction benefits of CO₂ fixation (Danny Harvey, 1993).

4.2 Methanogenesis

Methanogenesis involves the degradation of organic matter into CO₂ and CH₄ (Conrad, 2020). While methanogenesis was initially thought to be a process solely occurring in anaerobic environments, it can also take place under aerobic conditions (Serrano-Silva et al., 2014; Angle et al., 2017). Methanogens rely on other members of the soil microbiome to obtain their substrates for methanogenesis (Conrad, 2020). Fermenting and hydrogenotrophic microorganisms degrade complex organic matter into CO₂, H₂ and simple organic compounds, which can in turn be utilized by methanogenic archaea (Conrad, 2020). Methanogens perform methanogenesis primarily through one of three pathways: (1) the methylotrophic pathway, (2) the acetoclastic pathway and (3) the hydrogenotrophic pathway (Liu and Whitman, 2008). Methylotrophic methanogenesis involves the utilization of methylated compounds as substrates (Liu and Whitman, 2008; Serrano-Silva et al., 2014). Acetoclastic methanogens use acetate as a substrate and hydrogenotrophic methanogens produce CH₄ from CO₂ and H₂ (Liu and Whitman, 2008; Serrano-Silva et al., 2014). The hydrogenotrophic and acetoclastic pathways are the most common (Enrich-Prast et al., 2014; Kim and Whitman, 2014; Serrano-Silva et al., 2014). All methanogens encode Methyl-coenzyme M reductase (MCR), which is involved in the final step of methane formation (Enzmann et al., 2018). The mcr gene, particularly mcrA, is commonly employed as a molecular marker to detect methanogens in environmental samples. For a schematic overview of the three different pathways, we refer to Enzmann et al. (2018). For more in-depth information regarding enzymes involved in the methanogenesis process, we refer to the review by Reeve et al. (1997).

4.3 Nitrate-dependent anaerobic methane oxidation (N-DAMO)

CH₄ oxidation is the process of oxidizing CH₄ to CO₂ (Serrano-Silva et al., 2014) (Figure 1). CH₄ oxidation has been identified within both bacteria and archaea and can be performed under aerobic and anaerobic conditions (Wei et al., 2022; Zhao Y. et al., 2024). N-DAMO archaea perform CH₄ oxidation anaerobically through the reduction of NO₃⁻ to NO₂⁻ (Raghoebarsing et al., 2006) (Figure 2). Anaerobic methane oxidation in archaea is thought to proceed via reverse methanogenesis, as N-DAMO archaea harbour enzymes used for CH₄ formation in methanogens, including mcr (Hallam et al., 2004; Shima and Thauer, 2005; Haroon et al., 2013; Wei et al., 2022).

The N-DAMO process has been shown to contribute to 12–33% of total CH₄ oxidation, N-DAMO archaea could therefore be promising for CH₄ removal in different environments (Wang et al., 2022). In marsh soil, stable isotope probing was used to determine the contribution of N-DAMO archaea and bacteria to CH₄ oxidation. The activity of N-DAMO bacteria was predicted to be 0.1–3.8 nmol ¹³CO₂ g⁻¹ dry soil day⁻¹ and the activity of N-DAMO archaea 0.1 to 4.1 nmol ¹³CO₂ g⁻¹ dry soil day⁻¹ (Zheng et al., 2020). Interestingly, a recent study showed that anaerobic CH₄ oxidation can be an important source of SOM formation (Zhang et al., 2021). While this study did not distinguish between the different anaerobic CH₄ oxidation pathways, approximately 60% of CH₄ was turned into SOM instead of being respired as CO₂.

5 The impact of nutrient input

Nutrient addition through fertilization is a common management strategy in agriculture, widely used to improve crop yield and quality by supplying essential nutrients, such as N, to soils (Bindraban et al., 2015; Ishfaq et al., 2023). Therefore, it is likely that the functions of the discussed archaeal groups in C- and N-cycling will be impacted by nutrient addition. Not only does nutrient input provide plants with nutrients for growth, the addition of nutrients can also increase emission of several GHGs.

Soil nitrification rates significantly increase with increasing N content in the soil (Li et al., 2020). It is therefore not surprising that fertilization will affect the activity of AOA in nutrient cycling. In particular, the type of fertilizer that is applied seems to be relevant, as growth and activity of AOA is increased under manure addition compared to synthetic fertilizer (Zeng et al., 2024; Wu et al., 2025). This is in line with the preference of AOA for lower levels of NH₃, as manure releases NH₃ slowly over time (Zhang et al., 2012; Prosser et al., 2020). Furthermore, long-term inorganic fertilizer application can reduce the pH of the soil, which can also lead to an increase in AOA (Ding et al., 2020). In addition, the N in fertilizer has the potential to increase the abundance of specific AOA lineages. In fields receiving manure with >900 kg/ha N, Nitrosopumilus was the predominant AOA lineage (Wang Z. et al., 2023). Application of manure with <600 kg/ha N led to higher abundance of Nitrososphaera. Even within the same AOA lineage, taxa can react differently to fertilizer input. For example, in acidic soil under different long-term organic and chemical fertilization regimes, Nitrososphaerales were the predominant AOA (Zhao et al., 2022). These regimes also led to differences in the abundance of Nitrososphaerales clades, likely driven by fertilizer-induced changes in soil pH. In paddy fields fertilized with manure, Nitrosotalea devanaterra-like AOA, from the Ca. Nitrosotaleales lineage, were the predominant AOA (Liu et al., 2018). The Ca. Nitrosotaleales lineage is known for its adaptation to acidic soils (Table 3), therefore its abundance was likely linked to the acidic pH in three out of the four studied soils.

Table 3

Characteristics of AOA lineages detected in soil environments based on cultured representatives.

AOA lineage^a	Isolation source of representatives	Ammonia affinity	Capable of utilizing urea as a nitrogen source	Optimum pH range	N₂O production (site preference value)	References
Nitrosopumilales	Marine water and agricultural soils	High (2.2 and 24.8 nM)	Yes^b	7–8	pH 7.5: 29‰pH 6.0: 27‰	Jung et al. (2019, 2022), Zhao et al. (2023), and Qin et al. (2024)
Ca. Nitrosotaleales	Acidic soil	Very high (0.6–2.8 nM)	No	5.3	Unknown	Jung et al. (2022) and Lehtovirta-Morley et al. (2024)
Nitrososphaerales	Agriculture soil, garden soil and thermal springs	Moderate to low (0.14 to 31.5 μM)	Yes	6.5–8.3	pH 7.5: 26‰pH 5.5: 29‰	Jung et al. (2019, 2022) and Qin et al. (2024)
Ca. Nitrosomirales	East China Sea^c	Unknown	Yes, based on metagenomics	7–8	Unknown	Zheng et al. (2024) and Li et al. (2025)

The order of Ca. Nitrosocaldales contains thermophilic AOA species. The order appears to have limited relevance in soil environments and is consequently not mentioned (Luo et al., 2021).

Not all strains encode urease (Zhao et al., 2023).

Ca. Nitrosomirales is likely abundant in both marine and soil environments. However, contains only one cultured representative isolated from the East China Sea.

As nitrification rates increase, N₂O emissions from AOA are also expected to increase. Several field studies have examined the contribution of AOA and AOB to N₂O emission and the effects of nutrient input on the emission rates (Di et al., 2013; Hink et al., 2017; Hei et al., 2023; Zeng et al., 2024). In general, higher availability of NH₃ and a neutral to alkalic pH are linked to increased contribution of AOB to nitrification (Rütting et al., 2021) and N₂O emissions (Di et al., 2013; Hu L. et al., 2022; Zeng et al., 2024). Under N limiting conditions, AOA can exhibit a higher contribution to N₂O emissions than AOB (Guo et al., 2025), likely because AOA are able to outcompete AOB at low substrate concentrations.

In line with this, the type of fertilizer applied to the soil might affect whether AOB or AOA produce more N₂O. Hei et al. (2023) studied the effect of switching chemical fertilization to fertilization with manure in field plots. The N in the chemical fertilizer was applied in the form of urea and contained the same amount of N as the applied manure. Full substitution of urea with manure reduced N₂O emissions from the plots (Hei et al., 2023). The reduction in N₂O emissions correlated with a reduction in the abundance of AOB and an increase in the abundance of AOA. As the field plots received the same N concentrations, this reduction in AOB was most likely a result of the form of N used as fertilizer. It has been reported that AOB have higher affinity for urea than AOA (Qin et al., 2024), while manure releases N more gradually, favouring AOA (Zhang et al., 2012). It should be mentioned that the authors noted a 16–210% reduction of cumulative N₂O emissions, and that cumulative emissions cannot be reduced more than 100%. Their observations are however supported by Hink et al. (2017), who found that AOA produce ∼0.5 × 10⁻³ N₂O-N per NO₃⁻-N produced and AOB ∼ 0.95 × 10⁻³ N₂O-N per NO₃⁻-N, suggesting that AOA produce less N₂O during NH₃ oxidation.

Likewise, CO₂ fixation by AOA seems to be influenced by nutrient addition. Studies in soil often focus on the detection of CO₂⁻ fixating microorganisms using qPCR and correlate gene abundance and CO₂ fixation rates. accA has been used as an indicator gene for the 3-HP/4-HB pathway of AOA (Mao et al., 2024). In two different studies, one in a Mollisol with wheat-soybean-maize rotation and one in paddy soil, a positive correlation was found between accA abundance, autotrophic archaeal community composition and the CO₂ fixation rate (Liao et al., 2020; Wang Q. et al., 2024). Specifically, in Mollisol, no fertilizer and manure treatment had higher accA copy numbers compared to NPK (nitrogen, phosphorus, and potassium) fertilizer and NPK fertilizer with manure (Liao et al., 2020).

In rice fields, conventional fertilization, consisting of NPK application, decreased the accA copy number, while it increased under conventional treatment combined with manure application (Wang Q. et al., 2024). The effect of manure combined with chemical fertilizer is therefore not in line with the results of Liao et al. (2020). This might indicate that fertilizer application is not the only regulator of the accA copy number. It is important, however, to mention that the gene abundance of the bacterial CO₂ fixation pathway was much higher. Nevertheless, these findings indicate contribution of AOA to CO₂ fixation in these soils.

Similar to AOA, it has been observed that methanogens react to fertilizer application and that different fertilizer treatments affect methanogen groups differently. Chemical and organic N application have been observed to increase CH₄ fluxes (Kong et al., 2019). For example, acetoclastic methanogens increased in relative abundance during organic fertilization, while hydrogenotrophic methanogens decreased (Yuan et al., 2018). Acetoclastic methanogens require acetate as their substrate for methanogenesis, which is provided during fertilization with manure, but not during chemical fertilization. This observation was confirmed by Kong et al. (2019), who observed acetoclastic methanogens only under manure treatment.

The effect of management practices on CO₂ and N₂ fixation by methanogens is still an underexplored subject. The link between CO₂ fixation and biomass formation has only been demonstrated in batch experiments for Methanobacterium congolense so far (Chen et al., 2019). In addition, the low abundance of N₂-fixing methanogens in agriculture soils suggests that they do not play a major role in N₂ fixation.

N-DAMO archaea require NO₃⁻ for the oxidation of CH₄. Hence, it is not surprising that they are affected by fertilizer input (Wang et al., 2022). The activity and abundance of N-DAMO archaea increases with fertilizer addition, and in turn, their increase in abundance leads to higher contributions to NO₃⁻ and CH₄ removal in paddy fields (Wang et al., 2022). In addition, the activity of N-DAMO archaea can potentially be optimized through supplementation of nutrients. Wang S. et al. (2024) demonstrated that through optimization of molybdenum, tungsten and selenium concentrations in growth media, the abundance of mcrA could be upregulated. Therefore, increasing the concentrations of these nutrients through fertilization might increase the CH₄ oxidation rate of N-DAMO archaea.

Nutrient availability was observed to impact community composition of haloarchaea in saltwater samples (Hua et al., 2021). To our knowledge, no studies have been performed to determine the effect of nutrient input on this archaeal group. As haloarchaea are involved in denitrification, it can be speculated that the input of additional N can increase the emission of N gasses. With the potential application of haloarchaea as biofertilizers (Naitam et al., 2023), it will be essential to understand the contribution of haloarchaea to C- and N-cycling in the soil.

6 Detection of archaea in agricultural soils

The main challenge in archaeal research and uncovering their role in nutrient cycling, is the fact that many archaea have not been cultured in a laboratory setting (Sun et al., 2020; Rafiq et al., 2023). Several factors limit their culturability such as, lack of ability to mimic correct environmental conditions, and substrate concentrations and the slow growth rates that are typical for archaea. In addition, several archaeal species rely on other members of the soil microbiome for nutrient acquisition, which makes it extremely challenging to obtain pure cultures of these archaea and uncover their full contribution to nutrient cycling (Rafiq et al., 2023).

Despite the challenges in cultivating archaea, they can be studied in realistic environments such as agricultural soils. This is often done using several primers designed to target specific archaeal groups or functional genes (Table 4). For example, amoA primers are widely used for the detection of AOA and specific primers have been designed for the detection of mcrA from M. nitroreducens. Several accA primers have been used to target accA in AOA. nifH and nifD primers can be used for detecting N₂-fixing methanogens, but these primers have not been specifically designed for the detection of N₂-fixing methanogens.

Table 4

Collection of primers used for detection of archaea in literature cited in this review.

Target group	Gene	Primer name	Nucleotide sequence (5′-3′)	Used in reference	Notes^a
Archaea	16S rRNA V3-V5 region	ARC344F	ACGGGGYGCAGCAGGCGCGA	Clark et al. (2020) and Hu W. et al. (2022)
Archaea	16S rRNA V3-V5 region	ARC915R	GTGCTCCCCCGCCAATTCCT	Clark et al. (2020) and Hu W. et al. (2022)
Archaea	16S rRNA V3-V4 region	S-D-Arch-0349-a-S-17	GYG CAS CAG KCG MGA AW	Saghaï et al. (2022)
Archaea	16S rRNA V3-V4 region	S-D-Bact-0785-a-A-21	GACTACHVGGGTATCTAATCC	Saghaï et al. (2022)
Archaea	16S rRNA V3-V4 region	A519F	CAGCMGCCGCGGTAA	Megyes et al. (2021) and Liu et al. (2022)
Archaea	16S rRNA V3-V4 region	Arch855R	TCCCCCGCCAATTCCTTTAA	Megyes et al. (2021) and Liu et al. (2022)
Archaea	16S rRNA	A109f	ACKGCTCAGTAACACGT	Angel et al. (2012)
Archaea	16S rRNA	A334r	TCGCGCCTGCTGCTCCCCGT	Angel et al. (2012)
Thaumarchaeata	AmoA	CrenamoA23f	ATGGTCTGGCTWAGACG	Hink et al. (2017), Clark et al. (2020), Hei et al. (2023), and Zeng et al. (2024)
Thaumarchaeata	AmoA	CrenamoA616r	GCCATCCATCTGTATGTCCA
AOA	16S rRNA	AP422F	GTCTAAAGGGTCTGTAGCCG	Mukhtar et al. (2019)	Primers were verified using the 16S ribosomal RNA gene of Nitrososphaera and Nitrosopumilus (Mukhtar et al., 2019).
AOA	16S rRNA	AP599R	TTCTGGTGAGACGCCTTCG	Mukhtar et al. (2019)
Thaumarchaeata	accA	Crena529F	GCWATGACWGAYTTTGTY RTAATG	Liao et al. (2020)
Thaumarchaeata	accA	Crena981R	TGGWTKRYTTGCAAYTATWCC	Liao et al. (2020)
Methanogens	Universal mcrA	mlas-mod – F	GGYGGTGTMGGDTTCACMCARTA	Angel et al. (2012)
Methanogens	Universal mcrA	mcrA-rev-R	CGTTCATBGCGTAGTTVGGRTAGT	Angel et al. (2012)
Diazotrophs	nifH	nifH-F	AAA GGY GGW ATC GGY AAR TCC ACC AC	Fan et al. (2019), Li et al. (2023), and Zhou et al. (2023)	Designed for the detection of bacterial diazotrophs (Rösch et al., 2002).
Diazotrophs	nifH	nifH-R	TTG TTS GCS GCR TAC ATS GCC ATC AT	Fan et al. (2019), Li et al. (2023), and Zhou et al. (2023)
Diazotrophs	nifH	PolF	TGCGAYCCSAARGCBGACT C	Han et al. (2019) and Gao et al. (2021)	Designed for the detection of bacterial diazotrophs (Poly et al., 2001). Gaby and Buckley (2012) found low coverage of this primer pair for cluster III sequences, which includes nifH sequences from N₂-fixing archaea.
Diazotrophs	nifH	PolR	CCATCATYTCRCCGGA	Han et al. (2019) and Gao et al. (2021)
Diazotrophs	nifH	IGK3	GCI WTH TAY GGI AAR GGI GGI ATH GGI AA	Nepel et al. (2022)	This primer pair was designed for the detection of bacterial N₂-fixers (Ando et al., 2005). Gaby and Buckley (2012) found high coverage of this primer pair for cluster III sequences. Potentially produces high numbers of unspecific reads in soils (Angel et al., 2018).
Diazotrophs	nifH	DVV	ATI GCR AAI CCI CCR CAI ACI ACR TC	Nepel et al. (2022)
Diazotrophs	nifD	Universal nifD F	TGGGGICCIRTIAARGAYATG	Masuda et al. (2023)	Designed for the detection of bacterial nifD (Stoltzfus et al., 1997).
Diazotrophs	nifD	Universal nifD R	TCRTTIGCIATRTGRTGICC	Masuda et al. (2023)
M. nitroreducens-like archaea	mcrA	McrA159F	AAAGTGCGGAGCAGCAATCAC	Shen et al. (2021) and Wang et al. (2022)
M. nitroreducens-like archaea	mcrA	McrA345R	TCGTCCCATTCCTGCTGCATTGC	Shen et al. (2021) and Wang et al. (2022)
Cluster ANME-2d archaea	16S rRNA	DP397F	TGGCTGTCCAGCTRTYC	Ding et al. (2015)	Variations in amplification efficiency were reported (Ding et al., 2015).
Cluster ANME-2d archaea	16S rRNA	DP569R	GRACGCCTGACGATTRAG	Ding et al. (2015)

Unless otherwise noted in this column, the amplification bias of the primer pair in soil environments has not been determined.

Specific primers for haloarchaea exist. For example, Oxley et al. (2010) designed primers for the detection of haloarchaea in human intestinal tracts. However, such primers have not been tested on soil samples as far as we are aware. While ample primers have been designed for the detection of bacteria involved in denitrification, these primers are not always efficient in detecting archaeal targets due to high sequence divergence (Ma et al., 2019). Specific primers have been designed to detect archaeal denitrification genes (Rusch, 2013), however to our knowledge these primers have not been tested using soil samples.

7 Concluding remarks and perspectives

With the involvement of archaea in both C- and N-cycling, archaea can make a significant contribution to the soil nutrient pool. Most archaeal groups are known to perform a specific role, but current literature suggests that the groups discussed here have a broader relevance in agricultural soils, although evidence in some cases is still limited. Based on available studies on the lesser-known functions of AOA, methanogens, N-DAMO and haloarchaea in C- and N-cycling, it seems that these archaeal groups and their functions mainly occur under specific conditions.

The contribution of AOA to N₂O emissions and CO₂ fixation seem mainly relevant under low N conditions or when N is released slowly, such as under manure fertilization. In conditions of high N availability, AOB dominate NH₃ oxidation and are the primary contributors to N₂O emissions. Replacing mineral fertilizers with manure can potentially favour AOA and reduce N₂O emissions from nitrification, as AOA are suggested to produce less N₂O per NH₃ molecule oxidized. Shifting the balance from AOB to AOA through fertilizer treatment could therefore be a suitable strategy for lowering N₂O emissions from agriculture soils. More specifically, management strategies can focus on shifting the AOA population to enhance the abundance of certain AOA lineages. Fertilizer application has shown to influence the abundance of AOA lineages in soil. To incorporate this knowledge into management strategies, insight is needed on the N₂O production rates of all AOA lineages and how soil conditions such as N availability and pH affect these production rates.

More research is also needed into the CO₂ fixation capabilities of AOA. Further studies, for example using stable isotope probing, are needed to confirm this relationship and to determine the actual rate of CO₂ fixation of AOA in agricultural soils, as data from forest soils and marine environments suggests different fixation rates. If CO₂ fixation by AOA significantly contributes to soil C formation, it would be promising to investigate strategies to increase the CO₂ fixation rate of this archaeal group. Currently, the effect of manure treatments on CO₂ fixation by AOA remains unclear, and manure addition, in the studies that are published on this topic, did not see an increase in accA abundance. This suggests that nutrient input might not be a suitable strategy to increase CO₂ fixation by AOA. In this regard, setting up a field experiment to determine the effect of different fertilizers on the CO₂ fixation rates will be required. In addition, exploring other strategies independent of nutrient input such as microbiome engineering might be a promising future direction. A recent study indicates that the CO₂ fixation rates of bacterial autotrophs could be significantly increased through virus infection (Lu et al., 2025). No such effect has been documented for archaea yet, but this appears to be a promising approach to be explored.

Methanogens are primarily relevant in anaerobic environments. Specifically, hydrogenotrophic methanogens can contribute to CO₂ fixation. Considering CO₂ fixation is linked to CH₄ production, an increase in CO₂ fixation will also lead to an increase in CH₄ emissions. Hence, from a sustainability perspective, methanogens are not a good target for increasing CO₂ sequestration in agricultural soils. The same limitation is true for N₂ fixation by methanogens, as N₂ fixation depends on the ATP produced through methanogenesis. Low detection of N₂-fixing methanogens through nifH targeted qPCR, further raises the question if methanogens are relevant for agricultural environments. Adjusting current primers or designing specific primers targeting nifH of N₂-fixating archaea will help determine the significance of N₂ fixation by this archaeal group.

Overall, due to their specific occurrence, increasing methanogen abundance is likely not an appropriate strategy for increasing C or N in most agricultural soils. Therefore, management strategies in agriculture should prioritize other approaches and focus on other CO₂⁻- or N₂-fixing microorganisms that provide nutrients without environmental costs. A potential alternative could be directed evolution to achieve expression of nitrogenase in crops, which might allow plants to directly carry out N transformation without relying on the soil microbiome. This approach currently has several challenges however, including the anaerobic nature of nitrogenase and potential growth defects in host cells due to high metabolic burden (Bennett et al., 2023).

Recent research revealed that a consortium of N-DAMO archaea and bacteria could be used as a promising strategy to reduce NO₃⁻ and CH₄ emissions in brackish ecosystems (Legierse et al., 2023). Using bioaugmentation, N-DAMO abundance reached 47–73% of the total archaeal population in sediment microcosms (Legierse et al., 2023). Implementation in situ has yet to be tested, however it might be a promising strategy in paddy soils or in other waterlogged environments to increase the removal of CH₄ and NO₃⁻ from the system.

While the abundance of N-DAMO archaea is likely low in most soils, N-DAMO growth could be stimulated through fertilization or potentially through bioaugmentation. Before N-DAMO archaea can be used for bioaugmentation in soil environments, several questions need to be answered first, including: (1) Can N-DAMO archaea survive and remain active in anaerobic soils? and (2) If so, what delivery or inoculation strategies would allow bioaugmentation without disruption of the native microbiome? Soils have different redox potentials and nutrient concentrations compared to sediments (Kalev and Toor, 2018), and survival of N-DAMO under these conditions needs to be tested. After answering these questions, small-scale microcosm and controlled field experiments are needed to determine if N-DAMO archaea meaningfully contribute to CH₄ emission mitigation. As current studies suggest that nutrient input can be used to regulate N-DAMO, microcosm and field experiments should examine the effect of different fertilizers on their activity.

The role of haloarchaea in C- and N-cycling remains ambiguous. Notably, out of the archaeal groups reviewed here, they are the only group that has not yet been detected with a specific primer set in soils. Designing specific primers for detection in soil samples should therefore be a priority. Many primers for bacterial denitrifiers are available, some might be suitable for the detection of archaeal denitrification genes (Wei et al., 2015; Ma et al., 2019). Compared to the other archaeal groups that are reviewed here, establishing molecular detection tools will be needed to further establish the ecological significance of haloarchaea.

Future research on haloarchaea should focus on significance of their contributions to C- and N-cycling. This is both important to understand their role in natural environments and for their usage as biofertilizer. In this regard, their contributions to N₂O formation should be the priority for future research. In saline environments, studies should focus on which microbial groups contribute most to N₂O formation. If haloarchaea are major contributors, management strategies could be incorporated to reduce N input in saline environments. Microcosm and field experiments should be used to determine if using haloarchaea as biofertilizer increases N₂O emissions. If this is the case, mitigation strategies are needed. This could include co-amendment with N-DAMO archaea, to reduce the amount of NO₃⁻ in the soil. In addition, Stachler et al. (2020) showed that the endogenous CRIPSR system of haloarchaeon Haloferax volcani could be used to repress gene expression. This might indicate that a similar system can be used to repress genes involved in denitrification. This would reduce the risk of N₂O emissions from haloarchaea used as biofertilizer.

In summary, archaea have diverse functional potential in agriculture soils, but the significance of their roles seems context dependent. Further development of molecular detection tools, specifically for haloarchaea, and culture dependent tools, such as culturing approaches and tracing studies can bridge knowledge gaps. Steering the composition of the soil microbiome might be possible through changes in nutrient management, such as application of organic fertilizer instead of chemical fertilizer, or through microbiome engineering. To harness the potential of N-DAMO archaea for the removal of CH₄ and NO₃⁻, bioaugmentation might be a suitable strategy. Nutrient cycling depends on contributions of the entire soil microbiome, therefore the specific context of the interactions between different groups of organisms in the microbiome should be further understood to fully leverage the functions of archaea in C- and N-cycling. This can then lead to improved nutrient management strategies in agriculture.

Author contributions

BS: Conceptualization, Writing – original draft, Writing – review & editing. AS: Conceptualization, Writing – review & editing. EK: Conceptualization, Writing – review & editing. VS: Conceptualization, Writing – review & editing. CB: Supervision, Writing – review & editing. TB: Conceptualization, Writing – review & editing.

Acknowledgments

This work was performed in the cooperation framework of Wetsus, European Centre of Excellence for Sustainable Water Technology (www.wetsus.nl). The authors like to thank the participants of the research theme “Soil” for the fruitful discussions and their financial support. The authors would also like to thank Jidske Knigge for their helpful comments on the review.

Conflict of interest

BS, AS, and EK were employed by Bioclear Earth B.V.

The remaining author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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The author(s) declared that Generative AI was not used in the creation of this manuscript.

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References

Alori

E. T.

Emmanuel

O. C.

Glick

B. R.

Babalola

O. O.

(2020). Plant–archaea relationships: a potential means to improve crop production in arid and semi-arid regions. World J. Microbiol. Biotechnol. 36:133. doi: 10.1007/s11274-020-02910-6, 32772189

Alves

K. J.

Pylro

V. S.

Nakayama

C. R.

Vital

V. G.

Taketani

R. G.

Santos

D. G.

. (2022). Methanogenic communities and methane emissions from enrichments of Brazilian Amazonia soils under land-use change. Microbiol. Res. 265:127178. doi: 10.1016/j.micres.2022.127178, 36113308

Ando

Goto

Meunchang

Thongra-ar

Fujiwara

Hayashi

. (2005). Detection of nifH sequences in sugarcane (Saccharum officinarum L.) and pineapple (Ananas comosus [L.] Merr.). Soil Sci. Plant Nutr. 51, 303–308. doi: 10.1111/j.1747-0765.2005.tb00034.x

Angel

Claus

Conrad

(2012). Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. ISME J. 6, 847–862. doi: 10.1038/ismej.2011.141, 22071343

Angel

Nepel

Panhölzl

Schmidt

Herbold

C. W.

Eichorst

S. A.

. (2018). Evaluation of primers targeting the diazotroph functional gene and Development of NifMAP – a bioinformatics pipeline for Analyzing nifH amplicon data. Front. Microbiol. 9:703. doi: 10.3389/fmicb.2018.00703, 29760683

Angle

J. C.

Morin

T. H.

Solden

L. M.

Narrowe

A. B.

Smith

G. J.

Borton

M. A.

. (2017). Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions. Nat. Commun. 8:1567. doi: 10.1038/s41467-017-01753-4, 29146959

Asakawa

(2021). Ecology of methanogenic and methane-oxidizing microorganisms in paddy soil ecosystem. Soil Sci. Plant Nutr. 67, 520–526. doi: 10.1080/00380768.2021.1953355

Babbin

A. R.

Bianchi

Jayakumar

Ward

B. B.

(2015). Rapid nitrous oxide cycling in the suboxic ocean. Science 348, 1127–1129. doi: 10.1126/science.aaa8380, 26045434

Bae

H.-S.

Morrison

Chanton

J. P.

Ogram

(2018). Methanogens are major contributors to nitrogen fixation in soils of the Florida Everglades. Appl. Environ. Microbiol. 84, e02222–e02217. doi: 10.1128/AEM.02222-17, 29374038

Baker

B. A.

Gutiérrez-Preciado

Rodríguez del Río

Á.

McCarthy

López-García

Huerta-Cepas

. (2024). Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments. Nat. Microbiol. 9, 964–975. doi: 10.1038/s41564-024-01647-4, 38519541

Bakken

L. R.

Bergaust

Liu

Frostegård

(2012). Regulation of denitrification at the cellular level: a clue to the understanding of N₂O emissions from soils. Philos. Trans. Royal Soc. B 367, 1226–1234. doi: 10.1098/rstb.2011.0321, 22451108

Bao

. (2025). Metatranscriptomic analysis to reveal the coupling between nitrogen fixation and CH4 oxidation in root tissues of Phragmites australis. Biol. Fertil. Soils 61, 57–70. doi: 10.1007/s00374-024-01869-y

Bapteste

É.

Brochier

Boucher

(2005). Higher-level classification of the Archaea: evolution of methanogenesis and methanogens. Archaea 1, 353–363. doi: 10.1155/2005/859728, 15876569

Bates

S. T.

Berg-Lyons

Caporaso

J. G.

Walters

W. A.

Knight

Fierer

(2011). Examining the global distribution of dominant archaeal populations in soil. ISME J. 5, 908–917. doi: 10.1038/ismej.2010.171, 21085198

Bennett

E. M.

Murray

J. W.

Isalan

(2023). Engineering nitrogenases for synthetic nitrogen fixation: from pathway engineering to directed evolution. BioDesign Res. 5:0005. doi: 10.34133/bdr.0005, 37849466

Bindraban

P. S.

Dimkpa

Nagarajan

Roy

Rabbinge

(2015). Revisiting fertilisers and fertilisation strategies for improved nutrient uptake by plants. Biol. Fertil. Soils 51, 897–911. doi: 10.1007/s00374-015-1039-7

Borrel

Adam

P. S.

Gribaldo

(2016). Methanogenesis and the wood–Ljungdahl pathway: an ancient, versatile, and fragile association. Genome Biol. Evol. 8, 1706–1711. doi: 10.1093/gbe/evw114, 27189979

Bothe

Jost

Schloter

Ward

B. B.

Witzel

(2000). Molecular analysis of ammonia oxidation and denitrification in natural environments. FEMS Microbiol. Rev. 24, 673–690. doi: 10.1111/j.1574-6976.2000.tb00566.x, 11077158

Boyd

E. S.

Peters

J. W.

(2013). New insights into the evolutionary history of biological nitrogen fixation. Front. Microbiol. 4:201. doi: 10.3389/fmicb.2013.00201, 23935594

Buée

De Boer

Martin

Van Overbeek

Jurkevitch

(2009). The rhizosphere zoo: an overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors. Plant Soil 321, 189–212. doi: 10.1007/s11104-009-9991-3

Caranto

J. D.

Lancaster

K. M.

(2017). Nitric oxide is an obligate bacterial nitrification intermediate produced by hydroxylamine oxidoreductase. Proc. Natl. Acad. Sci. 114, 8217–8222. doi: 10.1073/pnas.1704504114, 28716929

Caranto

J. D.

Vilbert

A. C.

Lancaster

K. M.

(2016). Nitrosomonas europaea cytochrome P460 is a direct link between nitrification and nitrous oxide emission. Proc. Natl. Acad. Sci. 113, 14704–14709. doi: 10.1073/pnas.1611051113, 27856762

Chanderban

Hill

C. A.

Dhamad

A. E.

Lessner

D. J.

(2023). Expression of V-nitrogenase and Fe-nitrogenase in Methanosarcina acetivorans is controlled by molybdenum, fixed nitrogen, and the expression of Mo-nitrogenase. Appl. Environ. Microbiol. 89:e0103323. doi: 10.1128/aem.01033-23, 37695043

Chen

Ottosen

L. D. M.

Kofoed

M. V. W.

(2019). How low can You go: methane production of Methanobacterium congolense at low CO2 concentrations. Front. Bioeng. Biotechnol. 7:34. doi: 10.3389/fbioe.2019.00034, 30899758

Chen

Zhu

Y. G.

Xia

Shen

J. P.

J. Z.

(2008). Ammonia-oxidizing archaea: important players in paddy rhizosphere soil? Environ. Microbiol. 10, 1978–1987. doi: 10.1111/j.1462-2920.2008.01613.x, 18430011

Chow

Padda

K. P.

Puri

Chanway

C. P.

(2022). An archaic approach to a modern issue: endophytic Archaea for sustainable agriculture. Curr. Microbiol. 79:322. doi: 10.1007/s00284-022-03016-y, 36125558

Clark

D. R.

McKew

B. A.

Dong

L. F.

Leung

Dumbrell

A. J.

. (2020). Mineralization and nitrification: Archaea dominate ammonia-oxidising communities in grassland soils. Soil Biol. Biochem. 143:107725. doi: 10.1016/j.soilbio.2020.107725

Conrad

(2020). Methane production in soil environments—anaerobic biogeochemistry and microbial Life between flooding and desiccation. Microorganisms 8:881. doi: 10.3390/microorganisms8060881, 32545191

Cui

Qiao

Tian

Ouyang

(2017). Plant preference for NH4+ versus NO3− at different growth stages in an alpine agroecosystem. Field Crop Res. 201, 192–199. doi: 10.1016/j.fcr.2016.11.009

Danny Harvey

L. D.

(1993). A guide to global warming potentials (GWPs). Energy Policy 21, 24–34. doi: 10.1016/0301-4215(93)90205-T

Dekas

A. E.

Poretsky

R. S.

Orphan

V. J.

(2009). Deep-Sea Archaea fix and share nitrogen in methane-consuming microbial consortia. Science 326, 422–426. doi: 10.1126/science.1178223, 19833965

Derwent

R. G.

(2020). Global warming potential (GWP) for methane: Monte Carlo analysis of the uncertainties in global tropospheric model predictions. Atmos. 11:486. doi: 10.3390/atmos11050486

H. J.

Cameron

K. C.

Shen

J. P.

Winefield

C. S.

O’Callaghan

Bowatte

. (2013). “The role of Bacteria and Archaea in nitrification, nitrate leaching and nitrous oxide emissions in nitrogen-rich grassland soils” in Molecular Environmental Soil Science (Dordrecht: Springer Netherlands), 79–89.

Diaz

Saliba-Colombani

Loudet

Belluomo

Moreau

Daniel-Vedele

. (2006). Leaf yellowing and anthocyanin accumulation are two genetically independent strategies in response to nitrogen limitation in Arabidopsis thaliana. Plant Cell Physiol. 47, 74–83. doi: 10.1093/pcp/pci225, 16284408

Ding

Z. W.

Y. Z.

Cheng

S. H.

Zeng

R. J.

(2015). New primers for detecting and quantifying denitrifying anaerobic methane oxidation archaea in different ecological niches. Appl. Microbiol. Biotechnol. 99, 9805–9812. doi: 10.1007/s00253-015-6893-6, 26300291

Ding

Z. W.

Y. Z.

Cheng

S. H.

Zeng

R. J.

(2016). Environmental evaluation of coexistence of denitrifying anaerobic methane-oxidizing archaea and bacteria in a paddy field. Appl. Microbiol. Biotechnol. 100, 439–446. doi: 10.1007/s00253-015-6986-2, 26394860

Ding

Jiang

Liu

Zhang

Suo

. (2020). Effects of applying inorganic fertilizer and organic manure for 35 years on the structure and diversity of ammonia-oxidizing archaea communities in a Chinese Mollisols field. MicrobiologyOpen 9:e00942. doi: 10.1002/mbo3.942, 31568679

Ding

Wang

K. J.

Jiang

G. M.

Biswas

D. K.

L. F.

. (2005). Effects of nitrogen deficiency on photosynthetic traits of maize hybrids released in different years. Ann. Bot. 96, 925–930. doi: 10.1093/aob/mci244, 16103036

Meng

Qiu

Chen

Zhang

Song

. (2022). Ammonia-oxidizing archaea and ammonia-oxidizing bacteria communities respond differently in oxy-gen-limited habitats. Front. Environ. Sci. 10:976618. doi: 10.3389/fenvs.2022.976618

Enrich-Prast

Bastviken

Crill

Santoro

A. L.

Signori

C. N.

Sanseverino

A. M.

(2014). “Chemosynthesis” in Reference module in earth systems and environmental sciences (Elsevier).

Enzmann

Mayer

Rother

Holtmann

(2018). Methanogens: biochemical background and biotechnological applications. AMB Express 8:1. doi: 10.1186/s13568-017-0531-x, 29302756

Erisman

J. W.

Sutton

M. A.

Galloway

Klimont

Winiwarter

(2008). How a century of ammonia synthesis changed the world. Nat. Geosci. 1, 636–639. doi: 10.1038/ngeo325

Falb

Müller

Königsmaier

Oberwinkler

Horn

von Gronau

. (2008). Metabolism of halophilic archaea. Extremophiles 12, 177–196. doi: 10.1007/s00792-008-0138-x, 18278431

Falkowski

P. G.

Fenchel

Delong

E. F.

(2008). The microbial engines that drive earth’s biogeochemical cycles. Science 320, 1034–1039. doi: 10.1126/science.1153213

Fan

Delgado-Baquerizo

Guo

Wang

Zhu

. (2019). Suppressed N fixation and diazotrophs after four decades of fertilization. Microbiome 7:143. doi: 10.1186/s40168-019-0757-8, 31672173

Fani

Gallo

Liò

(2000). Molecular evolution of nitrogen fixation: the evolutionary history of the nifD, nifK, nifE, and nifN genes. J. Mol. Evol. 51, 1–11. doi: 10.1007/s002390010061, 10903367

Francis

C. A.

Beman

J. M.

Kuypers

M. M. M.

(2007). New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J. 1, 19–27. doi: 10.1038/ismej.2007.8, 18043610

Frink

C. R.

Waggoner

P. E.

Ausubel

J. H.

(1999). Nitrogen fertilizer: retrospect and prospect. Proc. Natl. Acad. Sci. 96, 1175–1180. doi: 10.1073/pnas.96.4.1175, 9989997

Gaby

J. C.

Buckley

D. H.

(2012). A comprehensive evaluation of PCR primers to amplify the nifH gene of nitrogenase. PLoS One 7:e42149. doi: 10.1371/journal.pone.0042149, 22848735

Gao

(2021). Impact of intercropping on the diazotrophic Community in the Soils of continuous cucumber cropping systems. Front. Microbiol. 12:630302. doi: 10.3389/fmicb.2021.630302, 33868191

Garrity

G. M.

Holt

J. G.

Whitman

W. B.

Keswani

Boone

D. R.

Koga

. (2001). “Phylum all. Euryarchaeota phy. Nov” in Bergey’s manual^® of systematic bacteriology (Springer New York: New York, NY), 211–355.

Grant

W. D.

(2001). “Class III. Halobacteria” in Bergey’s manual of systematic bacteriology. eds. Boone

D. R.

Castenholz

R. W.

Garrity

G. M.

(Springer New York: New York, NY), 294–333.

Gubry-Rangin

Nicol

G. W.

Prosser

J. I.

(2010). Archaea rather than bacteria control nitrification in two agricultural acidic soils. FEMS Microbiol. Ecol. 74, 566–574. doi: 10.1111/j.1574-6941.2010.00971.x, 21039653

Guo

Bol

Lin

. (2025). Patterns and drivers of soil autotrophic nitrification and associated N2O emissions. Soil Biol. Biochem. 203:109730. doi: 10.1016/j.soilbio.2025.109730

Hallam

S. J.

Mincer

T. J.

Schleper

Preston

C. M.

Roberts

Richardson

P. M.

. (2006). Pathways of carbon assimilation and Ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol. 4:e95. doi: 10.1371/journal.pbio.0040095, 16533068

Hallam

S. J.

Putnam

Preston

C. M.

Detter

J. C.

Rokhsar

Richardson

P. M.

. (2004). Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305, 1457–1462. doi: 10.1126/science.1100025, 15353801

Han

L.-L.

Wang

Shen

J. P.

H. J.

Wang

J. T.

Wei

W. X.

. (2019). Multiple factors drive the abundance and diversity of the diazotrophic community in typical farmland soils of China. FEMS Microbiol. Ecol. 95:fiz113. doi: 10.1093/femsec/fiz113, 31295349

Haroon

M. F.

Shi

Imelfort

Keller

Hugenholtz

. (2013). Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 500, 567–570. doi: 10.1038/nature12375, 23892779

Harris

D. L.

(2002). Cytochrome P450nor: a nitric oxide reductase—structure, spectra, and mechanism. Int. J. Quantum Chem. 88, 183–200. doi: 10.1002/qua.10111

Hartmann

Six

(2022). Soil structure and microbiome functions in agroecosystems. Nat. Rev. Earth Environ. 4, 4–18. doi: 10.1038/s43017-022-00366-w

Hei

Peng

Hao

Yang

Zhu

. (2023). Full substitution of chemical fertilizer by organic manure decreases soil N2O emissions driven by ammonia oxidizers and gross nitrogen transformations. Glob. Chang. Biol. 29, 7117–7130. doi: 10.1111/gcb.16957, 37800353

Hernández-Magaña

Kraft

(2024). Nitrous oxide production and consumption by marine ammonia-oxidizing archaea under oxygen depletion. Front. Microbiol. 15:1410251. doi: 10.3389/fmicb.2024.1410251, 39296305

Higgins

S. A.

Schadt

C. W.

Matheny

P. B.

Löffler

F. E.

(2018). Phylogenomics reveal the dynamic evolution of fungal nitric oxide reductases and their relationship to secondary metabolism. Genome Biol. Evol. 10, 2474–2489. doi: 10.1093/gbe/evy187, 30165640

Hink

Nicol

G. W.

Prosser

J. I.

(2017). Archaea produce lower yields of N2O than bacteria during aerobic ammonia oxidation in soil. Environ. Microbiol. 19, 4829–4837. doi: 10.1111/1462-2920.13282, 26971439

Hirsch

P. R.

Mauchline

T. H.

(2015). The importance of the microbial N cycle in soil for crop plant nutrition. Adv. Appl. Microbiol. 93, 45–71. doi: 10.1016/bs.aambs.2015.09.001, 26505688

Hofmann

Praeg

Mutschlechner

Wagner

A. O.

Illmer

(2016). Abundance and potential metabolic activity of methanogens in well-aerated forest and grassland soils of an alpine region. FEMS Microbiol. Ecol. 92:fiv171. doi: 10.1093/femsec/fiv171, 26712349

Dong

Wang

Xiao

Zhu

(2022). The contributions of ammonia oxidizing bacteria and archaea to nitrification-dependent N2O emission in alkaline and neutral purple soils. Sci. Rep. 12:19928. doi: 10.1038/s41598-022-23084-1, 36402873

Hou

Delgado-Baquerizo

Stegen

J. C.

Dong

. (2022). Continental-scale niche differentiation of dominant topsoil archaea in drylands. Environ. Microbiol. 24, 5483–5497. doi: 10.1111/1462-2920.16099, 35706137

Hua

Ouellette

Makkay

A. M.

Papke

R. T.

Zhaxybayeva

(2021). Nutrient supplementation experiments with saltern microbial communities implicate utilization of DNA as a source of phosphorus. ISME J. 15, 2853–2864. doi: 10.1038/s41396-021-00960-8, 33846564

Ishfaq

Wang

Hassan

M. U.

Yuan

Liu

. (2023). Improvement of nutritional quality of food crops with fertilizer: a global meta-analysis. Agron. Sustain. Dev. 43:74. doi: 10.1007/s13593-023-00923-7

Jiang

Xiao

L. Q.

Wan

Liu

Y. F.

. (2022). Research Progress on microbial carbon sequestration in soil: a review. Eurasian Soil Sci. 55, 1395–1404. doi: 10.1134/S1064229322100064

Jiao

Zhang

Hao

(2019a). Core microbiota in agricultural soils and their potential associations with nutrient cycling. mSystems 4, 10–128. doi: 10.1128/mSystems.00313-18, 30944882

Jiao

Zhang

(2019b). Environmental filtering drives distinct continental atlases of soil archaea between dryland and wetland agricultural ecosystems. Microbiome 7:15. doi: 10.1186/s40168-019-0630-9, 30709414

Jung

M.-Y.

Gwak

J. H.

Rohe

Giesemann

Kim

J. G.

Well

. (2019). Indications for enzymatic denitrification to N2O at low pH in an ammonia-oxidizing archaeon. ISME J. 13, 2633–2638. doi: 10.1038/s41396-019-0460-6, 31227816

Jung

M.-Y.

Park

S.-J.

Kim

S. J.

Kim

J. G.

Sinninghe Damsté

J. S.

Jeon

C. O.

. (2014a). A mesophilic, autotrophic, Ammonia-oxidizing archaeon of Thaumarchaeal group I.1a cultivated from a deep oligotrophic soil horizon. Appl. Environ. Microbiol. 80, 3645–3655. doi: 10.1128/AEM.03730-13, 24705324

Jung

M.-Y.

Sedlacek

C. J.

Kits

K. D.

Mueller

A. J.

Rhee

S. K.

Hink

. (2022). Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities. ISME J. 16, 272–283. doi: 10.1038/s41396-021-01064-z, 34316016

Jung

M.-Y.

Well

Min

Giesemann

Park

S. J.

Kim

J. G.

. (2014b). Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils. ISME J. 8, 1115–1125. doi: 10.1038/ismej.2013.205, 24225887

Kalev

S. D.

Toor

G. S.

(2018). “The composition of soils and sediments” in Green chemistry (Elsevier), 339–357.

Kallenbach

C. M.

Frey

S. D.

Grandy

A. S.

(2016). Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls. Nat. Commun. 7:13630. doi: 10.1038/ncomms13630, 27892466

Kandeler

Deiglmayr

Tscherko

Bru

Philippot

(2006). Abundance of narG, nirS, nirK, and nosZ genes of denitrifying Bacteria during primary successions of a glacier foreland. Appl. Environ. Microbiol. 72, 5957–5962. doi: 10.1128/AEM.00439-06

Kim

Whitman

W. B.

(2014). “Methanogens” in Encyclopedia of food microbiology (Elsevier), 602–606.

Kobayashi

Hira

Yoshida

Toyofuku

Shida

Ogasawara

. (2018). Nitric oxide production from nitrite reduction and hydroxylamine oxidation by copper-containing dissimilatory nitrite reductase (NirK) from the aerobic Ammonia-oxidizing archaeon, Nitrososphaera viennensis. Microbes Environ. 33, 428–434. doi: 10.1264/jsme2.ME18058, 30318500

Koirala

Brözel

V. S.

(2021). Phylogeny of nitrogenase structural and assembly components reveals new insights into the origin and distribution of nitrogen fixation across Bacteria and Archaea. Microorganisms 9:1662. doi: 10.3390/microorganisms9081662, 34442741

Kong

Jin

Chen

. (2019). Linking methane emissions to methanogenic and methanotrophic communities under different fertilization strategies in rice paddies. Geoderma 347, 233–243. doi: 10.1016/j.geoderma.2019.04.008

Könneke

Bernhard

A. E.

de la Torre

J. R.

Walker

C. B.

Waterbury

J. B.

Stahl

D. A.

(2005). Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437, 543–546. doi: 10.1038/nature03911, 16177789

Könneke

Schubert

D. M.

Brown

P. C.

Hügler

Standfest

Schwander

. (2014). Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation. Proc. Natl. Acad. Sci. 111, 8239–8244. doi: 10.1073/pnas.1402028111, 24843170

Kono

Mehrotra

Endo

Kizu

Matusda

Kimura

. (2017). A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea. Nat. Commun. 8:14007. doi: 10.1038/ncomms14007, 28082747

Kopittke

P. M.

Menzies

N. W.

Wang

McKenna

B. A.

Lombi

(2019). Soil and the intensification of agriculture for global food security. Environ. Int. 132:105078. doi: 10.1016/j.envint.2019.105078

Kouzuma

Tsutsumi

Ishii

Ueno

Abe

Watanabe

(2017). Non-autotrophic methanogens dominate in anaerobic digesters. Sci. Rep. 7:1510. doi: 10.1038/s41598-017-01752-x, 28473726

Kraft

Jehmlich

Larsen

Bristow

L. A.

Könneke

Thamdrup

. (2022). Oxygen and nitrogen production by an ammonia-oxidizing archaeon. Science 375, 97–100. doi: 10.1126/science.abe6733, 34990242

Legierse

Struik

Smith

Echeveste Medrano

M. J.

Weideveld

van Dijk

. (2023). Nitrate-dependent anaerobic methane oxidation (N-DAMO) as a bioremediation strategy for waters affected by agricultural runoff. FEMS Microbiol. Lett. 370:fnad041. doi: 10.1093/femsle/fnad041, 37170064

Lehtovirta-Morley

L. E.

Ross

Yao

Hazard

Gubry-Rangin

. (2024). Nitrosotalea devaniterrae gen. Nov., sp. nov. and Nitrosotalea sinensis sp. nov., two acidophilic ammonia oxidising archaea isolated from acidic soil, and proposal of the new order Nitrosotaleales Ord. Nov. within the class Nitrososphaeria of the phylum Nitrososphaerota. Int. J. Syst. Evol. Microbiol. 74:006387. doi: 10.1099/ijsem.0.006387

Leigh

J. A.

(2000). Nitrogen fixation in methanogens: the archaeal perspective. Curr. Issues Mol. Biol. 4, 125–131. doi: 10.21775/cimb.002.125

Leininger

Urich

Schloter

Schwark

Nicol

G. W.

. (2006). Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442, 806–809. doi: 10.1038/nature04983, 16915287

Lemaire

O. N.

Jespersen

Wagner

(2020). CO2-fixation strategies in energy extremophiles: what can we learn from acetogens? Front. Microbiol. 11:486. doi: 10.3389/fmicb.2020.00486, 32318032

Zeng

Tian

Wang

Zhang

. (2020). Global patterns and controlling factors of soil nitrification rate. Glob. Chang. Biol. 26, 4147–4157. doi: 10.1111/gcb.15119, 32301539

Zhuang

Cai

Chu

Chen

. (2025). Nitrosarchaeum haohaiensis sp. Nov. CL1T: isolation and characterisation of a novel Ammonia-oxidising archaeon from aquatic environments. Environ. Microbiol. Rep. 17:e70100. doi: 10.1111/1758-2229.70100, 40402825

. (2023). Control factors of soil diazotrophic community assembly and nitrogen fixation rate across eastern China. Geoderma 432:116410. doi: 10.1016/j.geoderma.2023.116410

Liao

Qin

Wang

Zhang

Hao

Chen

. (2020). Long-term chemical fertilization-driving changes in soil autotrophic microbial community depresses soil CO2 fixation in a Mollisol. Sci. Total Environ. 748:141317. doi: 10.1016/j.scitotenv.2020.141317, 32814290

Liu

Zhao

Xie

Tang

Wang

. (2018). Ammonia oxidizers and nitrite-oxidizing bacteria respond differently to long-term manure application in four paddy soils of south of China. Sci. Total Environ. 633, 641–648. doi: 10.1016/j.scitotenv.2018.03.108, 29597161

Liu

. (2022). Archaeal communities perform an important role in maintaining microbial stability under long term continuous cropping systems. Sci. Total Environ. 838:156413. doi: 10.1016/j.scitotenv.2022.156413, 35660449

Liu

Whitman

W. B.

(2008). Metabolic, phylogenetic, and ecological diversity of the methanogenic Archaea. Ann. N. Y. Acad. Sci. 1125, 171–189. doi: 10.1196/annals.1419.019

Chao

Tian

Zhong

Chen

. (2025). DNA viral community enhances microbial carbon fixation capacity via auxiliary metabolic genes in contaminated soils. Nat. Commun. 16:9984. doi: 10.1038/s41467-025-64938-2, 41233343

Luo

Z.-H.

Narsing Rao

M. P.

Chen

Hua

Z. S.

Hedlund

B. P.

. (2021). Genomic insights of "Candidatus Nitrosocaldaceae" based on nine new metagenome-assembled genomes, including "Candidatus Nitrosothermus" gen Nov. and two new species of "Candidatus Nitrosocaldus". Front. Microbiol. 11:608832. doi: 10.3389/fmicb.2020.608832, 33488549

Lyu

Shao

Akinyemi

Whitman

W. B.

(2018). Methanogenesis. Curr. Biol. 28, R727–R732. doi: 10.1016/j.cub.2018.05.021

Zilles

J. L.

Kent

A. D.

(2019). An evaluation of primers for detecting denitrifiers via their functional genes. Environ. Microbiol. 21, 1196–1210. doi: 10.1111/1462-2920.14555, 30724437

Manns

H. R.

Parkin

G. W.

Martin

R. C.

(2016). Evidence of a union between organic carbon and water content in soil. Can. J. Soil Sci. 96, 305–316. doi: 10.1139/cjss-2015-0084

Mao

Yang

Zhong

. (2024). Novel database for accA gene revealed a vertical variability pattern of autotrophic carbon fixation potential of ammonia oxidizing archaea in a permeable subterranean estuary. Mar. Environ. Res. 194:106342. doi: 10.1016/j.marenvres.2024.106342, 38185001

Martínez-Espinosa

R. M.

(2024). Halophilic archaea as tools for bioremediation technologies. Appl. Microbiol. Biotechnol. 108:401. doi: 10.1007/s00253-024-13241-z, 38951176

Masuda

Satoh

Miyamoto

Takano

Ishii

Ohba

. (2023). Biological nitrogen fixation in the long-term nitrogen-fertilized and unfertilized paddy fields, with special reference to diazotrophic iron-reducing bacteria. Arch. Microbiol. 205:291. doi: 10.1007/s00203-023-03631-8, 37470860

McGlynn

S. E.

(2017). Energy metabolism during anaerobic methane oxidation in ANME Archaea. Microbes Environ. 32, 5–13. doi: 10.1264/jsme2.ME16166, 28321009

Megyes

Borsodi

A. K.

Árendás

Márialigeti

(2021). Variations in the diversity of soil bacterial and archaeal communities in response to different long-term fertilization regimes in maize fields. Appl. Soil Ecol. 168:104120. doi: 10.1016/j.apsoil.2021.104120

Mehta

M. P.

Baross

J. A.

(2006). Nitrogen fixation at 92°C by a hydrothermal vent archaeon. Science 314, 1783–1786. doi: 10.1126/science.1134772, 17170307

Miralles-Robledillo

J. M.

Bernabeu

Giani

Martínez-Serna

Martínez-Espinosa

R. M.

Pire

(2021). Distribution of denitrification among haloarchaea: a comprehensive study. Microorganisms 9:1669. doi: 10.3390/microorganisms9081669, 34442748

Miralles-Robledillo

J. M.

Martínez-Espinosa

R. M.

Pire

(2024). Transcriptomic profiling of haloarchaeal denitrification through RNA-Seq analysis. Appl. Environ. Microbiol. 90:e0057124. doi: 10.1128/aem.00571-24, 38814058

Mise

Masuda

Senoo

Itoh

(2021). Undervalued Pseudo- nifH sequences in public databases distort metagenomic insights into biological nitrogen fixers. mSphere 6, e00785–e00721. doi: 10.1128/msphere.00785-21, 34787447

Miyazaki

Higa

Toki

Ashi

Tsunogai

Nunoura

. (2009). Molecular characterization of potential nitrogen fixation by anaerobic methane-oxidizing Archaea in the methane seep sediments at the number 8 Kumano knoll in the Kumano Basin, offshore of Japan. Appl. Environ. Microbiol. 75, 7153–7162. doi: 10.1128/AEM.01184-09, 19783748

Moissl-Eichinger

Pausan

Taffner

Berg

Bang

Schmitz

R. A.

(2018). Archaea are interactive components of complex microbiomes. Trends Microbiol. 26, 70–85. doi: 10.1016/j.tim.2017.07.004

Mukhtar

Lin

Y. P.

Lin

C. M.

Lin

Y. R.

(2019). Relative abundance of Ammonia oxidizing Archaea and Bacteria influences soil nitrification responses to temperature. Microorganisms 7:526. doi: 10.3390/microorganisms7110526, 31690001

Mukhtar

Zahra Shah

Mehnaz

Abdulla Malik

(2024). Isolation and characterization of plant growth promoting and metal resistant Archaea associated with the rhizosphere of Salsola stocksii and Atriplex amnicola. Geomicrobiol J. 41, 755–768. doi: 10.1080/01490451.2024.2381008

Naitam

M. G.

Kaushik

(2021). Archaea: an Agro-ecological perspective. Curr. Microbiol. 78, 2510–2521. doi: 10.1007/s00284-021-02537-2, 34019119

Naitam

M. G.

Ramakrishnan

Grover

Kaushik

(2023). Rhizosphere-dwelling halophilic archaea: a potential candidate for alleviating salinity-associated stress in agriculture. Front. Microbiol. 14. doi: 10.3389/fmicb.2023.1212349, 37564293

Narrowe

A. B.

Borton

M. A.

Hoyt

D. W.

Smith

G. J.

Daly

R. A.

Angle

J. C.

. (2019). Uncovering the diversity and activity of methylotrophic methanogens in freshwater wetland soils. mSystems 4. doi: 10.1128/msystems.00320-19, 31796563

Nealson

K. H.

Stahl

D. A.

(1997). “Chapter 1. Microorganisms and biogeochemical cycles: what can we learn from layered microbial communities?” in Geomicrobiology (Berlin, Boston: De Gruyter), 5–34.

Nepel

Angel

Borer

E. T.

Frey

MacDougall

McCulley

. (2022). Global grassland diazotrophic communities are structured by combined abiotic, biotic, and spatial distance factors but resilient to fertilization. Front. Microbiol. 13:821030. doi: 10.3389/fmicb.2022.821030, 35418962

Nie

W.-B.

Ding

Xie

G. J.

Yang

Peng

Tan

. (2021). Anaerobic oxidation of methane coupled with dissimilatory nitrate reduction to ammonium fuels anaerobic ammonium oxidation. Environ. Sci. Technol. 55, 1197–1208. doi: 10.1021/acs.est.0c02664, 33185425

Norman

J. S.

Lin

Barrett

J. E.

(2015). Paired carbon and nitrogen metabolism by ammonia-oxidizing bacteria and archaea in temperate forest soils. Ecosphere 6, 1–11. doi: 10.1890/ES14-00299.1

Odelade

Babalola

(2019). Bacteria, Fungi and Archaea domains in Rhizospheric soil and their effects in enhancing agricultural productivity. Int. J. Environ. Res. Public Health 16:3873. doi: 10.3390/ijerph16203873, 31614851

Offre

Spang

Schleper

(2013). Archaea in biogeochemical cycles. Ann. Rev. Microbiol. 67, 437–457. doi: 10.1146/annurev-micro-092412-155614

Oren

(2002). Diversity of halophilic microorganisms: environments, phylogeny, physiology, and applications. J. Ind. Microbiol. Biotechnol. 28, 56–63. doi: 10.1038/sj/jim/7000176, 11938472

Ouyang

Norton

J. M.

Stark

J. M.

(2017). Ammonium availability and temperature control contributions of ammonia oxidizing bacteria and archaea to nitrification in an agricultural soil. Soil Biol. Biochem. 113, 161–172. doi: 10.1016/j.soilbio.2017.06.010

Oxley

A. P. A.

Lanfranconi

M. P.

Würdemann

Ott

Schreiber

McGenity

T. J.

. (2010). Halophilic archaea in the human intestinal mucosa. Environ. Microbiol. 12, 2398–2410. doi: 10.1111/j.1462-2920.2010.02212.x, 20438582

H.-W.

Lin

J. J.

Chen

C. A.

Wang

P. H.

Chiang

Y. R.

Huang

C. C.

. (2022). Origin and evolution of nitrogen fixation in prokaryotes. Mol. Biol. Evol. 39. doi: 10.1093/molbev/msac181, 35993177

Poly

Monrozier

L. J.

Bally

(2001). Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Res. Microbiol. 152, 95–103. doi: 10.1016/S0923-2508(00)01172-4, 11281330

Poth

Focht

D. D.

(1985). 15 N kinetic analysis of N₂O production by Nitrosomonas europaea: an examination of nitrifier denitrification. Appl. Environ. Microbiol. 49, 1134–1141. doi: 10.1128/aem.49.5.1134-1141.1985, 16346787

Pratscher

Dumont

M. G.

Conrad

(2011). Ammonia oxidation coupled to CO2 fixation by archaea and bacteria in an agricultural soil. Proc. Natl. Acad. Sci. 108, 4170–4175. doi: 10.1073/pnas.1010981108, 21368116

Prosser

J. I.

Hink

Gubry-Rangin

Nicol

G. W.

(2020). Nitrous oxide production by ammonia oxidizers: physiological diversity, niche differentiation and potential mitigation strategies. Glob. Chang. Biol. 26, 103–118. doi: 10.1111/gcb.14877, 31638306

Prosser

J. I.

Nicol

G. W.

(2012). Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol. 20, 523–531. doi: 10.1016/j.tim.2012.08.001, 22959489

Qin

Meinhardt

K. A.

Moffett

J. W.

Devol

A. H.

Virginia Armbrust

Ingalls

A. E.

. (2017). Influence of oxygen availability on the activities of ammonia-oxidizing archaea. Environ. Microbiol. Rep. 9, 250–256. doi: 10.1111/1758-2229.12525, 28211189

Qin

Wei

S. P.

Zheng

Choi

Johnston

. (2024). Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences. Nat. Microbiol. 9, 524–536. doi: 10.1038/s41564-023-01593-7, 38297167

Rafiq

Hassan

Rehman

Hayat

Nadeem

Hassan

. (2023). Challenges and approaches of culturing the unculturable Archaea. Biology 12:1499. doi: 10.3390/biology12121499, 38132325

Raghoebarsing

A. A.

Pol

van de Pas-Schoonen

Smolders

A. J.

Ettwig

K. F.

Rijpstra

W. I.

. (2006). A microbial consortium couples anaerobic methane oxidation to denitrification. Nature 440, 918–921. doi: 10.1038/nature04617, 16612380

Reeve

J. N.

Nölling

Morgan

R. M.

Smith

D. R.

(1997). Methanogenesis: genes, genomes, and who’s on first? J. Bacteriol. 179, 5975–5986. doi: 10.1128/jb.179.19.5975-5986.1997, 9324240

Rinke

Chuvochina

Mussig

A. J.

Chaumeil

P. A.

Davín

A. A.

Waite

D. W.

. (2021). A standardized archaeal taxonomy for the genome taxonomy database. Nat. Microbiol. 6, 946–959. doi: 10.1038/s41564-021-00918-8, 34155373

Ritchie

G. A. F.

Nicholas

D. J. D.

(1972). Identification of the sources of nitrous oxide produced by oxidative and reductive processes in Nitrosomonas europaea. Biochem. J. 126, 1181–1191. doi: 10.1042/bj1261181, 5073730

Riyaz

Khan

S. T.

(2025). Nitrogen fixation by methanogenic Archaea, literature review and DNA database-based analysis; significance in face of climate change. Arch. Microbiol. 207:6. doi: 10.1007/s00203-024-04191-1, 39611976

Robinson

H. J.

Cameron

K. C.

Podolyan

(2014). The effect of soil pH and dicyandiamide (DCD) on N2O emissions and ammonia oxidiser abundance in a stimulated grazed pasture soil. J. Soils Sediments 14, 1434–1444. doi: 10.1007/s11368-014-0888-2

Rösch

Mergel

Bothe

(2002). Biodiversity of denitrifying and dinitrogen-fixing Bacteria in an acid Forest soil. Appl. Environ. Microbiol. 68, 3818–3829. doi: 10.1128/AEM.68.8.3818-3829.2002, 12147477

Rusch

(2013). Molecular tools for the detection of nitrogen cycling Archaea. Archaea 2013, 1–10. doi: 10.1155/2013/676450, 23365509

Rütting

. (2021). The contribution of ammonia-oxidizing archaea and bacteria to gross nitrification under different substrate availability. Soil Biol. Biochem. 160:108353. doi: 10.1016/j.soilbio.2021.108353

Saghaï

Banjeree

Degrune

Edlinger

García-Palacios

Garland

. (2022). Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils. Environ. Microbiol. 24, 341–356. doi: 10.1111/1462-2920.15830, 34796612

Sahu

Vasu

Sahu

Lal

Singh

S. K.

(2017). “Strength of microbes in nutrient cycling: a key to soil health” in Agriculturally important microbes for sustainable agriculture (Singapore: Springer Singapore), 69–86.

Santoro

A. E.

Buchwald

McIlvin

Casciotti

K. L.

(2011). Isotopic signature of N2O produced by marine Ammonia-oxidizing Archaea. Science 333, 1282–1285. doi: 10.1126/science.1208239, 21798895

Schleper

Nicol

G. W.

(2010). Ammonia-oxidising Archaea – physiology, ecology and evolution, 1–41. doi: 10.1016/B978-0-12-381045-8.00001-1

Serrano-Silva

. (2014). Methanogenesis and Methanotrophy in soil: a review. Pedosphere 24, 291–307. doi: 10.1016/S1002-0160(14)60016-3

Shah

Lateef

Noor

M. A.

(2020). “Carbon and nitrogen cycling in agroecosystems: an overview” in Carbon and nitrogen cycling in soil (Singapore: Springer Singapore), 1–15.

Shaw

L. J.

Nicol

G. W.

Smith

Fear

Prosser

J. I.

Baggs

E. M.

(2006). Nitrosospira spp. can produce nitrous oxide via a nitrifier denitrification pathway. Environ. Microbiol. 8, 214–222. doi: 10.1111/j.1462-2920.2005.00882.x, 16423010

Shen

Yang

W. T.

Yang

Y. L.

Liu

Tian

M. H.

Jin

J. H.

. (2021). Spatial and temporal variations of the community structure and abundance of Candidatus Methanoperedens nitroreducens-like archaea in paddy soils. Eur. J. Soil Biol. 106:103345. doi: 10.1016/j.ejsobi.2021.103345

Shi

Adams

J. M.

Yang

Jing

Chen

. (2016). The biogeography of soil archaeal communities on the eastern Tibetan plateau. Sci. Rep. 6:38893. doi: 10.1038/srep38893, 27958324

Shima

Thauer

R. K.

(2005). Methyl-coenzyme M reductase and the anaerobic oxidation of methane in methanotrophic Archaea. Curr. Opin. Microbiol. 8, 643–648. doi: 10.1016/j.mib.2005.10.002

Singh

Kaushik

Chakdar

Saxena

A. K.

(2023). Unveiling novel insights into haloarchaea (Halolamina pelagica CDK2) for alleviation of drought stress in wheat. World J. Microbiol. Biotechnol. 39:328. doi: 10.1007/s11274-023-03781-3, 37792124

Spiertz

J. H. J.

(2010). Nitrogen, sustainable agriculture and food security. A review. Agron. Sustain. Dev. 30, 43–55. doi: 10.1051/agro:2008064

Stachler

A.-E.

Schwarz

T. S.

Schreiber

Marchfelder

(2020). CRISPRi as an efficient tool for gene repression in archaea. Methods 172, 76–85. doi: 10.1016/j.ymeth.2019.05.023, 31150759

Stein

L. Y.

Arp

D. J.

Berube

P. M.

Chain

P. S.

Hauser

Jetten

M. S.

. (2007). Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environ. Microbiol. 9, 2993–3007. doi: 10.1111/j.1462-2920.2007.01409.x, 17991028

Sterngren

A. E.

Hallin

Bengtson

(2015). Archaeal Ammonia oxidizers dominate in numbers, but Bacteria drive gross nitrification in N-amended grassland soil. Front. Microbiol. 6:1350. doi: 10.3389/fmicb.2015.01350, 26648926

Stieglmeier

Mooshammer

Kitzler

Wanek

Zechmeister-Boltenstern

Richter

. (2014). Aerobic nitrous oxide production through N-nitrosating hybrid formation in ammonia-oxidizing archaea. ISME J. 8, 1135–1146. doi: 10.1038/ismej.2013.220, 24401864

Stoltzfus

J. R.

R. M. P. P.

Malarvithi

P. P.

Ladha

J. K.

De Bruijn

F. J.

(1997). Isolation of endophytic bacteria from rice and assessment of their potential for supplying rice with biologically fixed nitrogen. Plant Soil 194, 25–36. doi: 10.1023/A:1004298921641

Sun

Liu

Pan

Wang

(2020). Perspectives on cultivation strategies of Archaea. Microb. Ecol. 79, 770–784. doi: 10.1007/s00248-019-01422-7, 31432245

Tan

Nie

W. B.

Evans

Wang

X. W.

Dang

C. C.

. (2024). Nitrate-dependent anaerobic methane oxidation coupled to Fe(III) reduction as a source of ammonium and nitrous oxide. Water Res. 256:121571. doi: 10.1016/j.watres.2024.121571, 38583332

Thomson

A. J.

Giannopoulos

Pretty

Baggs

E. M.

Richardson

D. J.

(2012). Biological sources and sinks of nitrous oxide and strategies to mitigate emissions. Philos. Trans. Royal Soc. B 367, 1157–1168. doi: 10.1098/rstb.2011.0415, 22451101

Torregrosa-Crespo

Bergaust

Pire

Martínez-Espinosa

R. M.

(2018). Denitrifying haloarchaea: sources and sinks of nitrogenous gases. FEMS Microbiol. Lett. 365:fnx270. doi: 10.1093/femsle/fnx270, 29237000

Torregrosa-Crespo

Pire

Bergaust

Martínez-Espinosa

R. M.

(2020b). Haloferax mediterranei, an archaeal model for denitrification in saline systems, characterized through integrated physiological and transcriptional analyses. Front. Microbiol. 11:768. doi: 10.3389/fmicb.2020.00768, 32390995

Torregrosa-Crespo

Pire

Martínez-Espinosa

R. M.

Bergaust

(2019). Denitrifying haloarchaea within the genus Haloferax display divergent respiratory phenotypes, with implications for their release of nitrogenous gases. Environ. Microbiol. 21, 427–436. doi: 10.1111/1462-2920.14474, 30421557

Torregrosa-Crespo

Pire

Richardson

D. J.

Martínez-Espinosa

R. M.

(2020a). Exploring the molecular machinery of denitrification in Haloferax mediterranei through proteomics. Front. Microbiol. 11:605859. doi: 10.3389/fmicb.2020.605859, 33363526

Tully

Ryals

(2017). Nutrient cycling in agroecosystems: balancing food and environmental objectives. Agroecol. Sustain. Food Syst. 41, 761–798. doi: 10.1080/21683565.2017.1336149

Vajrala

Martens-Habbena

Sayavedra-Soto

L. A.

Schauer

Bottomley

P. J.

Stahl

D. A.

. (2013). Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea. Proc. Natl. Acad. Sci. 110, 1006–1011. doi: 10.1073/pnas.1214272110, 23277575

Vaksmaa

Lüke

Van Alen

Valè

Lupotto

Jetten

M. M.

. (2016). Distribution and activity of the anaerobic methanotrophic community in a nitrogen-fertilized Italian paddy soil. FEMS Microbiol. Ecol. 92:fiw181. doi: 10.1093/femsec/fiw181

Ventura

J. P.

Lacerda-Júnior

G. V.

Rados

Bisson

Fernandes-Júnior

P. I.

Melo

I. S.

(2025). Harnessing haloarchaea from halophyte Atriplex nummularia rhizosphere to enhance salt stress tolerance in maize seedlings. Environ. Microb. [Preprint 21:12. doi: 10.1186/s40793-025-00698-2, 41382235

Walker

C. B.

de la Torre

J. R.

Klotz

M. G.

Urakawa

Pinel

Arp

D. J.

. (2010). Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc. Natl. Acad. Sci. 107, 8818–8823. doi: 10.1073/pnas.0913533107, 20421470

Wan

X. S.

Hou

Kao

S. J.

Zhang

Sheng

H. X.

Shen

. (2023). Pathways of N2O production by marine ammonia-oxidizing archaea determined from dual-isotope labeling. Proc. Natl. Acad. Sci. 120:e2220697120. doi: 10.1073/pnas.2220697120, 36888658

Wang

Bier

Zgleszewski

Peipoch

Omondi

Mukherjee

. (2020). Distinct distribution of Archaea from soil to freshwater to estuary: implications of archaeal composition and function in different environments. Front. Microbiol. 11:576661. doi: 10.3389/fmicb.2020.576661, 33193193

Wang

Chi

Song

(2024). Important soil microbiota’s effects on plants and soils: a comprehensive 30-year systematic literature review. Front. Microbiol. 15:1347745. doi: 10.3389/fmicb.2024.1347745, 38591030

Wang

Chong

Wan

Sun

Wang

Lou

. (2024). Optimizing the activity of denitrifying anaerobic methane oxidation archaea by tailoring micronutrient compositions: a strategy for enhanced nitrate reduction. Chem. Eng. J. 502:158113. doi: 10.1016/j.cej.2024.158113

Wang

Chu

Zhao

Zhou

(2024). A study of different agricultural practices over a dozen years: influence on soil CO2 fixation rates and soil autotrophic microbial communities. Soil Tillage Res. 239:106067. doi: 10.1016/j.still.2024.106067

Wang

Zheng

Duan

(2023). Ammonia oxidizing archaea and bacteria respond to different manure application rates during organic vegetable cultivation in Northwest China. Sci. Rep. 13:8064. doi: 10.1038/s41598-023-35134-3, 37202434

Wang

Sun

Liu

Dolfing

(2023). Distribution of methanogenic and methanotrophic consortia at soil-water interfaces in rice paddies across climate zones. iScience 26:105851. doi: 10.1016/j.isci.2022.105851, 36636345

Wang

Tan

Dang

C. C.

Liu

L. Y.

Wang

X. W.

. (2025). Manganese-mediated dissimilatory nitrate reduction to ammonium of nitrate-dependent anaerobic methane oxidation. Chem. Eng. J. 506:159901. doi: 10.1016/j.cej.2025.159901

Wang

Yao

Jia

Zhu

Zheng

Kartal

. (2022). Nitrogen input promotes denitrifying methanotrophs’ abundance and contribution to methane emission reduction in coastal wetland and paddy soil. Environ. Pollut. 302:119090. doi: 10.1016/j.envpol.2022.119090, 35240269

Wei

Isobe

Nishizawa

Zhu

Shiratori

Ohte

. (2015). Higher diversity and abundance of denitrifying microorganisms in environments than considered previously. ISME J. 9, 1954–1965. doi: 10.1038/ismej.2015.9, 25756678

Wei

Wang

(2022). The denitrifying anaerobic methane oxidation process and microorganisms in the environments: a review. Front. Mar. Sci. 9:1038400. doi: 10.3389/fmars.2022.1038400

Wright

C. L.

Lehtovirta-Morley

L. E.

(2023). Nitrification and beyond: metabolic versatility of ammonia oxidising archaea. ISME J. 17, 1358–1368. doi: 10.1038/s41396-023-01467-0, 37452095

Hong

Liu

Jiao

. (2022). Niche differentiation of ammonia-oxidizing archaea and related autotrophic carbon fixation potential in the water column of the South China Sea. iScience 25:104333. doi: 10.1016/j.isci.2022.104333, 35602962

Tang

Tan

Sun

Zeng

Liu

. (2025). Long-term substitution of chemical fertilizer with organic manure enhances the activity and autotrophic growth of ammonia-oxidizing archaea and comammox nitrospira in paddy soil. J. Environ. Manag. 396:127816. doi: 10.1016/j.jenvman.2025.127816, 41313985

Zhou

Tahon

Liu

Zhang

. (2024). Isolation of a methyl-reducing methanogen outside the Euryarchaeota. Nature 632, 1124–1130. doi: 10.1038/s41586-024-07728-y, 39048829

Xia

Bowatte

Jia

Newton

(2022). Offsetting N2O emissions through nitrifying CO2 fixation in grassland soil. Soil Biol. Biochem. 165:108528. doi: 10.1016/j.soilbio.2021.108528

Yadav

A. N.

Sharma

Gulati

Singh

Dey

Pal

K. K.

. (2015). Haloarchaea endowed with phosphorus solubilization attribute implicated in phosphorus cycle. Sci. Rep. 5:12293. doi: 10.1038/srep12293, 26216440

Yakimov

M.M.

Cono

La Denaro

(2009) “A first insight into the occurrence and expression of functional amoA and accA genes of autotrophic and ammonia-oxidizing bathypelagic Crenarchaeota of Tyrrhenian Sea,” Deep-Sea Res. II Top. Stud. Oceanogr., 56, pp. 748–754. doi:10.1016/j.dsr2.2008.07.024.

Yao

Gao

Nicol

G. W.

Campbell

C. D.

Prosser

J. I.

Zhang

. (2011). Links between Ammonia oxidizer community structure, abundance, and nitrification potential in acidic soils. Appl. Environ. Microbiol. 77, 4618–4625. doi: 10.1128/AEM.00136-11, 21571885

Yuan

Zhu

Cao

(2018). Effects of different fertilizers on methane emissions and methanogenic community structures in paddy rhizosphere soil. Sci. Total Environ. 627, 770–781. doi: 10.1016/j.scitotenv.2018.01.233, 29426201

Zehnle

Schoelmerich

M. C.

(2025). Candidatus Methanoperedens. Trends Microbiol. 33, 472–473. doi: 10.1016/j.tim.2025.01.015, 40037956

Zeng

Tan

Zhang

You

Zheng

Chen

. (2024). Long-term addition of organic manure stimulates the growth and activity of comammox in a subtropical Inceptisol. Sci. Total Environ. 948:174839. doi: 10.1016/j.scitotenv.2024.174839, 39025147

Zhalnina

de Quadros

P. D.

Camargo

F. A.

Triplett

E. W.

(2012). Drivers of archaeal ammonia-oxidizing communities in soil. Front. Microbiol. 3:210. doi: 10.3389/fmicb.2012.00210, 22715335

Zhang

Ning

Yuan

M. M.

Zhou

Guo

. (2023). Experimental warming leads to convergent succession of grassland archaeal community. Nat. Clim. Chang. 13, 561–569. doi: 10.1038/s41558-023-01664-x

Zhang

Wang

Xia

Cao

Jia

(2021). Anaerobic methane oxidation sustains soil organic carbon accumulation. Appl. Soil Ecol. 167:104021. doi: 10.1016/j.apsoil.2021.104021

Zhang

J. B.

Zhu

T. B.

Cai

Z. C.

Qin

S. W.

Müller

(2012). Effects of long-term repeated mineral and organic fertilizer applications on soil nitrogen transformations. Eur. J. Soil Sci. 63, 75–85. doi: 10.1111/j.1365-2389.2011.01410.x

Zhao

Chen

Shen

Zhou

Zhang

Zhou

. (2025). Dissimilatory nitrate reduction to ammonia in the natural environment and wastewater treatment facilities: a comprehensive review. Environ. Technol. Innov. 37:104011. doi: 10.1016/j.eti.2024.104011

Zhao

Huang

Chakrabarti

Cooper

Choi

Ganan

. (2023). Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil. ISME J. 17, 1839–1850. doi: 10.1038/s41396-023-01493-y, 37596409

Zhao

Liu

Cao

Hao

Liu

(2024). Anaerobic oxidation of methane driven by different electron acceptors: a review. Sci. Total Environ. 946:174287. doi: 10.1016/j.scitotenv.2024.174287, 38945238

Zhao

van der Heijden

Banerjee

Liu

J. J.

H. D.

Zhou

. (2024). The role of halophyte-induced saline fertile islands in soil microbial biogeochemical cycling across arid ecosystems. Commun. Biol. 7:1061. doi: 10.1038/s42003-024-06741-1, 39209991

Zhao

Wang

Zhou

Alam

M. S.

Fan

Guo

. (2022). Long-term adaptation of acidophilic archaeal Ammonia oxidisers following different soil fertilisation histories. Microb. Ecol. 83, 424–435. doi: 10.1007/s00248-021-01763-2, 33970312

Zheng

Hou

Chen

Zhou

Liu

Yin

. (2020). Denitrifying anaerobic methane oxidation in intertidal marsh soils: occurrence and environmental significance. Geoderma 357:113943. doi: 10.1016/j.geoderma.2019.113943

Zheng

Wang

Gao

Yang

. (2024). Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments. ISME J. 18:wrad002. doi: 10.1093/ismejo/wrad002, 38365232

Zhou

Fan

Gao

Chang

Liang

. (2023). Synergistic effects of diazotrophs and arbuscular mycorrhizal fungi on soil biological nitrogen fixation after three decades of fertilization. iMeta 2:e81. doi: 10.1002/imt2.81, 38868350

Zhong

Deng

Shi

Wang

Jia

. (2016). Geographical distribution of methanogenic Archaea in nine representative Paddy soils in China. Front. Microbiol. 7:1447. doi: 10.3389/fmicb.2016.01447, 27679621

Edited by: Huaihai Chen, Sun Yat-sen University, China

Reviewed by: Aiju Liu, Shandong University of Technology, China

Zhan Wang, Ningxia Academy of Agriculture and Forestry Sciences, China