Climate change is a world-wide environmental problem caused by anthropogenic greenhouse gas emissions that results in an increase in average surface temperature (IPCC et al., 2008). As the largest ecosystem on Earth with an important role in geochemical cycling of key elements such as Fe, S, and Mn, the marine ecosystem is influenced by climate change with associated effects such as an increased ocean surface temperature of 1°C in the last century (IPCC et al., 2008; Abraham et al., 2013; Garcia-Soto et al., 2021) and higher dissolved carbon dioxide (CO₂) concentrations (Connell et al., 2013). This leads to further problems such as acidification, salinity changes, water stratification, deoxygenation, and sea level rise (Connell et al., 2013; Breitburg et al., 2018; Malhi et al., 2020). In addition, mounting evidence indicates that climate change alters the biodiversity and community compositions of marine ecosystems. These include tropical regions experiencing species loss while temperate regions might experience increasing diversity as species migrate to the poles (Alabia et al., 2020) that has potentially far reaching implications for ecosystem services (Staniczenko et al., 2017).

Despite only consisting of 4% of the earth’s total area and 11% of the world’s oceans, coastal zones contain more than a third of the world’s human population and contribute with 90% of the catch from marine fisheries (Barbier, 2017). Coastal areas also provide many additional ecosystem services including carbon storage in estuaries and sediments, contaminant removal, and storm plus flooding buffering (Canuel et al., 2012). The coastal areas are also responsible for the majority of atmospheric methane emission from the marine environment (Borges et al., 2016; Weber et al., 2019). Eukaryotes are abundant in coastal systems and play important ecological roles by serving as both primary producers and consumers (Nagarkar et al., 2018). For example, they graze on prokaryotes (Massana et al., 2004) and deliver energy to higher trophic levels through the food web. Moreover, eukaryotes are also involved in the benthic–pelagic exchange process between the sediment and open water (Marcus and Boero, 1998) with the transfer of individual organisms as well as elements such as phosphorous and nitrogen (Fanning et al., 1982). One important habitat for eukaryotes is the benthic sediment, although it has received less attention compared to the pelagic environment (Salonen et al., 2019). The eukaryotic communities in sediments are complex and diverse, including various benthic macrofauna (e.g., Bivalvia), meiofauna (e.g., nematodes, protists), and algae (e.g., diatoms) (Bik et al., 2012; Broman et al., 2019b). Moreover, sediment acts as a reservoir for resting stages of phytoplankton and zooplankton (Brendonck and De Meester, 2003; Suikkanen et al., 2010) and harbors larvae of semi-aquatic insects for some time before they emerge to the terrestrial phase (Mason et al., 2022). The coastal biodiversity is threated by climate change and anthropogenic activities (Holon et al., 2018), resulting in many species disappearing (Pan et al., 2013), and such that it may correspondingly affect ecosystem processes. For example, low sediment biodiversity can decrease the coastal ecosystem’s stability and resistance, making it vulnerable to invasive species or other forms of disturbance (Levin et al., 2001). Therefore, it is essential to better understand how the structure and activity of coastal benthic eukaryotic communities is influenced by global warming.

The Baltic Sea is one of the largest brackish water areas in the world that it is relatively isolated due to a narrow connection to the North Sea (Stigebrandt, 2001). This sea has suffered from a high level of eutrophication over an extended time due to anthropogenic nutrient loading and atmospheric deposition of primarily nitrogen and phosphorus (Knuuttila et al., 2011). This eutrophication contributes to increased biomass production and elevated oxygen consumption (Reusch et al., 2018). In the last century, the area of year-round hypoxic “dead zones” in the Baltic Sea has expanded ten-fold (Carstensen et al., 2014). Correspondingly, the dead zone eukaryotic community structure has also been modified with an increased abundance of species tolerating low oxygen conditions such as nematodes (Broman et al., 2020) and lower hatching of zooplankton resting stages (Broman et al., 2015). While higher global warming-related oxygen consumption (Schmidtko et al., 2017) will likely magnify the influence of eutrophication and algae blooms (Reusch et al., 2018), it is not well known how the benthic eukaryotic community and especially the active groups will respond.

This research was conducted in a Baltic Sea bay that has been used as a discharge recipient of warm water from a nuclear power plant for more than 50 years, which has raised the average water temperature by approximately 5.1°C above a nearby, unaffected, control bay. This temperature difference is within the same order of magnitude of the expected temperature increase for the Baltic Sea (Andersson et al., 2015). Therefore, this bay can be regarded as a natural laboratory to study the influence of long-term climate change in a Baltic Sea coastal ecosystem (Seidel et al., 2022a). Previous studies of this model system have uncovered that the sediment prokaryote communities in the heated versus the control bay show a weakened resilience with microbial RNA transcripts for stress in the heated bay despite exposure to > 50 years of warming (Seidel et al., 2022a). In addition, the sediment surface microbial community (< 2 cm of depth) in the warmed conditions exhibited a higher diversity due to shallowing of geochemical layers (Seidel et al., 2022b).

In this study, a metatranscriptomic dataset from the heated and control Baltic Sea bay sediments at four seasonal time points over a year was interrogated to investigate whether and how the eukaryotic community composition and their active functions differed between the two bays and change over time. It was hypothesized that heating of coastal marine system leads to a difference in the species composition of sediment-bound eukaryotic communities as well as different seasonal dynamics in their transcriptome signatures, such as overall increased activities in the winter.

This study demonstrated that more than 50 years of heating of a coastal marine system has led to changes in the sediment-bound eukaryotic community structure and activity. Overall, the results showed that long-term warming increased the diversity of the eukaryotic community during spring and triggered changes in the seasonal activity patterns of common sediment eukaryotes. The likely main driver for these changes was temperature with on average 5.1°C higher temperatures in the heated compared to the control bay over an annual cycle (Seidel et al., 2022b). The canonical correspondence analysis separated the eukaryotic communities between the heated and control bay along the salinity differences among sampling sites. Although temperature was not significant, the direction of the temperature and salinity arrows were in the same direction. Other factors such as oxygen concentration is lowered in higher temperatures (Brewer and Peltzer, 2017) such that a lack of oxygen likely limited nitrification in the sediment (Liikanen et al., 2002). This resulted in less nitrite and nitrate, potentially explaining a portion of the observed among-site variation. This study complements and adds a layer of generality to previous studies suggesting significant effects of climate change on the more intensively studied prokaryotic communities (Seidel et al., 2022a,b, 2023).

A highly diversified eukaryote community can act as a reservoir of rare and dormant taxa, which provides ecosystems with a biological buffering capacity to handle climate change and cope with extreme weather events such as marine heat waves (Capo et al., 2016). The Shannon H index was significantly higher in the heated bay in May (Figure 2A). This was potentially explained by an earlier onset of summer conditions in the heated bay, leading to a more diverse active community in the warmer waters in the heated bay compared to the control bay (Salonen et al., 2019). The alpha diversity also varied in November with significantly higher family level alpha diversities in the control bay (Figure 2A). However, the number of statistically increased RNA transcript numbers was still higher in the heated bay (Figures 4, 5). These two opposing patterns may suggest the control bay entered cold winter conditions earlier, which might have caused the community to have a low number of transcripts from a wide range of taxa. While in the heated bay, there were still certain taxa that were more active and dominant while others had a low number of transcripts. In June and March, the active sediment eukaryotic communities in both heated bay and control bay were in summer and spring-bloom conditions. These conditions tended to provide settings for a more similar in alpha diversity. Recent climate change has already altered the marine eukaryotic diversity globally, e.g., in temperate zones and high latitude areas (Gao et al., 2018; Han et al., 2022) and the impacts of climate change can either work directly on the eukaryote’s life-cycle, or indirectly through food web interactions (Przytulska et al., 2015). Eukaryotic diversity in the marine ecosystem generally declines toward the poles, which is suggested to be primarily driven by decreasing of ocean temperatures (Ibarbalz et al., 2019). It is unknown how climate change will affect the sediment-bound eukaryotic diversity, but this study suggested that climate change will alter the community composition, but the magnitude of those changes can vary among different seasons. Other studies have also shown that temporal changes like year and season affect the diversity of sediment eukaryotes (Guardiola et al., 2016; Salonen et al., 2019; Broman et al., 2020; Lalzar et al., 2023). The community composition of sediment eukaryotes also changes in response to annual and seasonal abiotic fluctuations as well as to clines and gradients in environmental variables such as turbidity, nutrients, and human activities (Broman et al., 2015; Salonen et al., 2019; Vause et al., 2019). In all, the data suggested that large scale climate change induced shifts in seasonality that will have major effects on eukaryotic sediment organisms and the overall ecosystem structure and functioning.

Most previous marine sediment bound eukaryote research focuses on spatial variability in community composition (Salonen et al., 2019; Wang et al., 2022; Lalzar et al., 2023) or the temporal variability in the same area (Salonen et al., 2019). This study compared seasonal variability in community composition between two bays in close spatial distance, but with significant differences in water temperatures. This enabled inference of how environmental variation, such as climate change, affects community composition and transcriptomic activity without a significant spatial variance. Furthermore, while most previous studies use 18S rRNA gene data to determine eukaryotic community compositions, this study added the aspect of studying the transcript-based active members. The sediment-bound eukaryote community compositions in this study were dominated by the functionally important Bacillariophyta (diatoms) in both bays, followed by Dinophyceae (dinoflagellates), Ctenophores, and other less abundant taxa. Within these major groups there were both facultative sediment dwellers as well as those organisms that only spend part of their life cycle in the sediment, e.g., as resting stages (Fryxell, 1983; Lewis et al., 1999; McQuoid et al., 2002; Ellegaard and Ribeiro, 2018). This is in line with other studies demonstrating that eukaryotes in sediments have diverse communities with different dominance patterns, e.g., diatoms, maxillopods, or dinoflagellates (Salonen et al., 2019; Iburg et al., 2021; Lalzar et al., 2023). The largest phyla and family level community differences between the bays were present in spring and summer with a tendency toward more diatoms in the control bay (∼75% relative abundance), whereas dinoflagellates contributed more to the relative abundance in the heated bay, albeit not significantly. In contrast, during winter the community compositions between the two bays were more similar. Dinoflagellates are suggested to be favored (Vehmaa et al., 2011) while diatoms have a tendency to decrease (Wasmund et al., 1998) with mild winters. This shift in the relative abundances of diatoms and dinoflagellates is projected to lead to differences in the production of the system (Wei et al., 2004), which might result in lower benthic production and higher pelagic secondary production through energy transfer in the food web (Hjerne et al., 2019). Likewise, differences in the sediment-bound eukaryotic communities in terms of resting stages could lead to an altered benthic-pelagic coupling in coastal systems.

The differential RNA transcript counts showed a similar trend as the alpha diversity, with more increased transcripts in May and November compared to March and June samplings. The most common taxa among those differentially expressed transcripts were the functionally important Bacillariophyta (diatoms) and Dinophyceae (dinoflagellates) that are commonly found in sediments (Broman et al., 2017; Salonen et al., 2019). Bacillariophyta (diatoms) play a vital role in the marine ecosystem (Nelson et al., 1995) and tend to dominate phytoplankton communities in well-mixed coastal areas, where they can access sufficient light and nutrient resources (Morel and Price, 2003). The Bacillariophyta usually bloom in open waters during spring and then sink to the sediment in response to nutrient depletion, but there are also diatoms that solely live on surfaces and in the sediment (Smetacek, 1985; Vyverman, 1992; Dela-Cruz et al., 2006). A previous study found that diatoms dominate a Baltic Sea sediment transcriptome (Broman et al., 2017) with RNA reads associated with diatoms being linked to the thylakoid membrane in the chloroplast and photosynthesis. Furthermore, a low abundance of genes coding for the Calvin-Benson-Bassam cycle (to synthesize Rubisco for photosynthesis) is suggested to indicate that many of these diatoms were in resting stages (Thureborn et al., 2016; Broman et al., 2017). Differential RNA transcripts assigned to diatoms during winter in the heated bay were associated with energy production and protein synthesis, which may indicate an increased metabolism in the heated bay sediment-bound community during winter. In general, the results showed a pattern of early diatom activity in the heated bay suggesting future climate change might decrease the dominance and activity of diatoms in later spring development.

Dinoflagellates were another common component in the sediment eukaryotic community, but only a few genes had differential RNA transcripts that were predominantly in the heated bay. Likewise, the Ctenophores, Spirotrichea, Mamiellophyceae, Zygnemophyceae, and Trebouxiophyceae only had differential transcript numbers in the heated compared to the control bay. These transcripts were associated with various genes and commonly occurring categories included “regulating energy metabolism” and “protein families: metabolism,” which might indicate that the sediment bound eukaryotic community in the heated bay had a more active metabolism throughout the year. The Ctenophores are functionally important gelatinous zooplankton in marine food webs that predate other zooplankton and fish eggs (Gamble, 1994; Mills, 1995; Purcell, 1997). In agreement with this study, they are often abundant during summer phytoplankton blooms and are predicted to be favored by climate change (Mills, 2001; Javidpour et al., 2009). Spirotrichea is a diverse subgroup of the class Ciliophora (commonly termed ciliates) (Gao et al., 2016) that are important components of marine food webs, acting as the food resource for large zooplankton and predators of bacteria and phytoplankton (Weisse and Sonntag, 2016). Other taxa with differential transcripts in the heated bay were Mamiellophyceae, Zygnemophyceae, and Trebouxiophyceae that are phytoplanktonic green algae (Gontcharov et al., 2003; Leliaert et al., 2012). Transcripts from those taxa were mostly involved in photosynthesis and significantly increased in the heated bay especially in May, suggesting the photosynthesizing algal community activities were different between the bays, or due to differences in cell numbers. All these taxa had only differential transcript numbers in the heated bay and their diverse functions suggested that future climate change and warming can trigger more diverse community composition involved in various metabolism pathways.

In summary, this study demonstrated that long-term (> 50 years) heating of coastal waters (average 5°C, i.e., comparable to the expected temperature increase for the Baltic Sea by 2100) altered the community composition, seasonal dynamics, and the transcriptome of sediment-bound eukaryotes. Other studies suggest that sediment eukaryotes show promise to become a tool for environmental monitoring of coastal systems (Gielings et al., 2021). Therefore, the results from this study can help predict the influence of future global warming in sediment communities and their overlaying pelagic systems, with this study suggesting a generally more active metabolism during winter. However, the methodology for characterizing sediment eukaryotes is still under intense development (Reñé et al., 2020), and future work can be extended both spatially and temporally to gain a more comprehensive view of the sediment bound communities.

The RNA transcript raw reads are available on the JGI Integrated Microbial Genomes and Microbiomes (IMG) database with the following references JGI proposal ID 503869. The R code used for analysis is available at GitHub: https://github.com/lsjmouse/eukaryotes_manuscript_R_analysis.

SL: Formal analysis, Methodology, Visualization, Writing – original draft, Writing – review & editing. EN: Formal analysis, Methodology, Software, Supervision, Visualization, Writing – original draft, Writing – review & editing. LS: Data curation, Methodology, Supervision, Writing – original draft, Writing – review & editing. MK: Funding acquisition, Supervision, Writing – original draft, Writing – review & editing. AF: Funding acquisition, Supervision, Writing – original draft, Writing – review & editing. MD: Funding acquisition, Methodology, Supervision, Writing – original draft, Writing – review & editing. SH: Funding acquisition, Methodology, Supervision, Writing – original draft, Writing – review & editing.