Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities

Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome

Deciphering how microbial communities are shaped by environmental variability is fundamental for understanding the structure and function of ocean ecosystems. While seasonal environmental gradients have been shown to structure the taxonomic dynamics of microbiomes over time, little is known about their impact on functional dynamics and the coupling between taxonomy and function. Here, we demonstrate annually recurrent, seasonal structuring of taxonomic and functional dynamics in a pelagic Arctic Ocean microbiome by combining autonomous samplers and in situ sensors with long-read metagenomics and SSU ribosomal metabarcoding. Specifically, we identified five temporal microbiome modules whose succession within each annual cycle represents a transition across different ecological states. For instance, Cand. Nitrosopumilus, Syndiniales, and the machinery to oxidise ammonia and reduce nitrite are signatures of early polar night, while late summer is characterised by Amylibacter and sulfur compound metabolism. Leveraging metatranscriptomes from Tara Oceans, we also demonstrate the consistency in functional dynamics across the wider Arctic Ocean during similar temporal periods. Furthermore, the structuring of genetic diversity within functions over time indicates that environmental selection pressure acts heterogeneously on microbiomes across seasons. By integrating taxonomic, functional and environmental information, our study provides fundamental insights into how microbiomes are structured under pronounced seasonal changes in understudied, yet rapidly changing polar marine ecosystems.

Gene content of seawater microbes is a strong predictor of water chemistry across the Great Barrier Reef

BACKGROUND

Seawater microbes (bacteria and archaea) play essential roles in coral reefs by facilitating nutrient cycling, energy transfer, and overall reef ecosystem functioning. However, environmental disturbances such as degraded water quality and marine heatwaves, can impact these vital functions as seawater microbial communities experience notable shifts in composition and function when exposed to stressors. This sensitivity highlights the potential of seawater microbes to be used as indicators of reef health. Microbial indicator analysis has centered around measuring the taxonomic composition of seawater microbial communities, but this can obscure heterogeneity of gene content between taxonomically similar microbes, and thus, microbial functional genes have been hypothesized to have more scope for predictive potential, though empirical validation for this hypothesis is still pending. Using a metagenomics study framework, we establish a functional baseline of seawater microbiomes across offshore Great Barrier Reef (GBR) sites to compare the diagnostic value between taxonomic and functional information in inferring continuous physico-chemical metrics in the surrounding reef.

RESULTS

Integrating gene-centric metagenomics analyses with 17 physico-chemical variables (temperature, salinity, and particulate and dissolved nutrients) across 48 reefs revealed that associations between microbial functions and environmental parameters were twice as stable compared to taxonomy-environment associations. Distinct seasonal variations in surface water chemistry were observed, with nutrient concentrations up to threefold higher during austral summer, explained by enhanced production of particulate organic matter (POM) by photoautotrophic picocyanobacteria, primarily Synechococcus. In contrast, nutrient levels were lower in winter, and POM production was also attributed to Prochlorococcus. Additionally, heterotrophic microbes (e.g., Rhodospirillaceae, Burkholderiaceae, Flavobacteriaceae, and Rhodobacteraceae) were enriched in reefs with elevated dissolved organic carbon (DOC) and phytoplankton-derived POM, encoding functional genes related to membrane transport, sugar utilization, and energy metabolism. These microbes likely contribute to the coral reef microbial loop by capturing and recycling nutrients derived from Synechococcus and Prochlorococcus, ultimately transferring nutrients from picocyanobacterial primary producers to higher trophic levels.

CONCLUSION

This study reveals that functional information in reef-associated seawater microbes more robustly associates with physico-chemical variables than taxonomic data, highlighting the importance of incorporating microbial function in reef monitoring initiatives. Our integrative approach to mine for stable seawater microbial biomarkers can be expanded to include additional continuous metrics of reef health (e.g., benthic cover of corals and macroalgae, fish counts/biomass) and may be applicable to other large-scale reef metagenomics datasets beyond the GBR. Video Abstract.

The Arctic summer microbiome across Fram Strait: Depth, longitude, and substrate concentrations structure microbial diversity in the euphotic zone

The long-term dynamics of microbial communities across geographic, hydrographic, and biogeochemical gradients in the Arctic Ocean are largely unknown. To address this, we annually sampled polar, mixed, and Atlantic water masses of the Fram Strait (2015-2019; 5-100 m depth) to assess microbiome composition, substrate concentrations, and oceanographic parameters. Longitude and water depth were the major determinants (~30%) of microbial community variability. Bacterial alpha diversity was highest in lower-photic polar waters. Community composition shifted from west to east, with the prevalence of, for example, Dadabacteriales and Thiotrichales in Arctic- and Atlantic-influenced waters, respectively. Concentrations of dissolved organic carbon peaked in the western, compared to carbohydrates in the chlorophyll-maximum of eastern Fram Strait. Interannual differences due to the time of sampling, which varied between early (June 2016/2018) and late (September 2019) phytoplankton bloom stages, illustrated that phytoplankton composition and resulting availability of labile substrates influence bacterial dynamics. We identified 10 species clusters with stable environmental correlations, representing signature populations of distinct ecosystem states. In context with published metagenomic evidence, our microbial-biogeochemical inventory of a key Arctic region establishes a benchmark to assess ecosystem dynamics and the imprint of climate change.

Sea-ice melt determines seasonal phytoplankton dynamics and delimits the habitat of temperate Atlantic taxa as the Arctic Ocean atlantifies

The Arctic Ocean is one of the regions where anthropogenic environmental change is progressing most rapidly and drastically. The impact of rising temperatures and decreasing sea ice on Arctic marine microbial communities is yet not well understood. Microbes form the basis of food webs in the Arctic Ocean, providing energy for larger organisms. Previous studies have shown that Atlantic taxa associated with low light are robust to more polar conditions. We compared to which extent sea ice melt influences light-associated phytoplankton dynamics and biodiversity over two years at two mooring locations in the Fram Strait. One mooring is deployed in pure Atlantic water, and the second in the intermittently ice-covered Marginal Ice Zone. Time-series analysis of amplicon sequence variants abundance over a 2-year period, allowed us to identify communities of co-occurring taxa that exhibit similar patterns throughout the annual cycle. We then examined how alterations in environmental conditions affect the prevalence of species. During high abundance periods of diatoms, polar phytoplankton populations dominated, while temperate taxa were weakly represented. Furthermore, we found that polar pelagic and ice-associated taxa, such as Fragilariopsis cylindrus and Melosira arctica, were more common in Atlantic conditions, while temperate taxa, such as Odontella aurita and Proboscia alata, were less abundant under polar conditions. This suggests that sea ice melt may act as a barrier to the northward expansion of temperate phytoplankton, preventing their dominance in regions still strongly influenced by polar conditions. Our findings highlight the complex interactions between sea ice melt, phytoplankton dynamics, and biodiversity in the Arctic.

Multi-omics for studying and understanding polar life

Polar ecosystems are experiencing amongst the most rapid rates of regional warming on Earth. Here, we discuss 'omics' approaches to investigate polar biodiversity, including the current state of the art, future perspectives and recommendations. We propose a community road map to generate and more fully exploit multi-omics data from polar organisms. These data are needed for the comprehensive evaluation of polar biodiversity and to reveal how life evolved and adapted to permanently cold environments with extreme seasonality. We argue that concerted action is required to mitigate the impact of warming on polar ecosystems via conservation efforts, to sustainably manage these unique habitats and their ecosystem services, and for the sustainable bioprospecting of novel genes and compounds for societal gain.

Biogeographic Analysis Suggests Two Types of Planktonic Prokaryote Communities in the Barents Sea

The Barents Sea is one of the most rapidly changing Arctic regions, with an unprecedented sea ice decline and increase in water temperature and salinity. We have studied the diversity of prokaryotic communities using 16S metabarcoding in the western and northeastern parts of the Barents Sea along the Kola Section and the section from Novaya Zemlya to Franz Joseph Land. The hypothesis-independent clustering method revealed the existence of two distinct types of communities. The most common prokaryotic taxa were shared between two types of communities, but their relative abundance was different. It was found that the geographic location of the sampling sites explained more than 30% of the difference between communities, while no statistically significant correlation between environmental parameters and community composition was found. The representatives of the Psychrobacter, Sulfitobacter and Polaribacter genera were dominant in samples from both types of communities. The first type of community was also dominated by members of Halomonas, Pseudoalteromonas, Planococcaceae and an unclassified representative of the Alteromonadaceae family. The second type of community also had a significant proportion of Nitrincolaceae, SAR92, SAR11 Clade I, NS9, Cryomorphaceae and SUP05 representatives. The origin of these communities can be explained by the influence of environmental factors or by the different origins of water masses. This research highlights the importance of studying biogeographic patterns in the Barents Sea in comparison with those in the North Atlantic and Arctic Ocean prokaryote communities.