Diatoms shape the biogeography of heterotrophic prokaryotes in early spring in the Southern Ocean

Differential association of key bacterial groups with diatoms and Phaeocystis spp. during spring blooms in the Southern Ocean

Interactions between phytoplankton and heterotrophic bacteria significantly influence the cycling of organic carbon in the ocean, with many of these interactions occurring at the micrometer scale. We explored potential associations between specific phytoplankton and bacteria in two size fractions, 0.8-3 µm and larger than 3 µm, at three naturally iron-fertilized stations and one high nutrient low chlorophyll station in the Southern Ocean. The composition of phytoplankton and bacterial communities was determined by sequencing the rbcL gene and 16S rRNA gene from DNA and RNA extracts, which represent presence and potential activity, respectively. Diatoms, particularly Thalassiosira, contributed significantly to the DNA sequences in the larger size fractions, while haptophytes were dominant in the smaller size fraction. Correlation analysis between the most abundant phytoplankton and bacterial operational taxonomic units revealed strong correlations between Phaeocystis and picoeukaryotes with SAR11, SAR116, Magnetospira, and Planktomarina. In contrast, most Thalassiosira operational taxonomic units showed the highest correlations with Polaribacter, Sulfitobacteria, Erythrobacter, and Sphingobium, while Fragilariopsis, Haslea, and Thalassionema were correlated with OM60, Fluviicola, and Ulvibacter. Our in-situ observations suggest distinct associations between phytoplankton and bacterial taxa, which could play crucial roles in nutrient cycling in the Southern Ocean.

Taxonomic difference in marine bloom-forming phytoplanktonic species affects the dynamics of both bloom-responding prokaryotes and prokaryotic viruses

The production of dissolved organic matter during phytoplankton blooms and consumption by heterotrophic prokaryotes promote marine carbon biogeochemical cycling. Although prokaryotic viruses presumably affect this process, their dynamics during blooms are not fully understood. Here, we investigated the effects of taxonomic difference in bloom-forming phytoplankton on prokaryotes and their viruses. We analyzed the dynamics of coastal prokaryotic communities and viruses under the addition of dissolved intracellular fractions from taxonomically distinct phytoplankton, the diatom Chaetoceros sp. (CIF) and the raphidophycean alga Heterosigma akashiwo (HIF), using microcosm experiments. Ribosomal RNA gene amplicon and viral metagenomic analyses revealed that particular prokaryotes and prokaryotic viruses specifically increased in either CIF or HIF, indicating that taxonomic difference in bloom-forming phytoplankton promotes distinct dynamics of not only the prokaryotic community but also prokaryotic viruses. Furthermore, combining our microcosm experiments with publicly available environmental data mining, we identified both known and novel possible host-virus pairs. In particular, the growth of prokaryotes associating with phytoplanktonic organic matter, such as Bacteroidetes (Polaribacter and NS9 marine group), Vibrio spp., and Rhodobacteriales (Nereida and Planktomarina), was accompanied by an increase in viruses predicted to infect Bacteroidetes, Vibrio, and Rhodobacteriales, respectively. Collectively, our findings suggest that changes in bloom-forming species can be followed by an increase in a specific group of prokaryotes and their viruses and that elucidating these tripartite relationships among specific phytoplankton, prokaryotes, and prokaryotic viruses improves our understanding of coastal biogeochemical cycling in blooms.IMPORTANCEThe primary production during marine phytoplankton bloom and the consumption of the produced organic matter by heterotrophic prokaryotes significantly contribute to coastal biogeochemical cycles. While the activities of those heterotrophic prokaryotes are presumably affected by viral infection, the dynamics of their viruses during blooms are not fully understood. In this study, we experimentally demonstrated that intracellular fractions of taxonomically distinct bloom-forming phytoplankton species, the diatom Chaetoceros sp. and the raphidophycean alga Heterosigma akashiwo, promoted the growth of taxonomically different prokaryotes and prokaryotic viruses. Based on their dynamics and predicted hosts of those viruses, we succeeded in detecting already-known and novel possible host-virus pairs associating with either phytoplankton species. Altogether, we propose that the succession of bloom-forming phytoplankton would change the composition of the abundant prokaryotes, resulting in an increase in their viruses. These changes in viral composition, depending on bloom-forming species, would alter the dynamics and metabolism of prokaryotes, affecting biogeochemical cycling in blooms.

Niche separation in bacterial communities and activities in porewater, loosely attached, and firmly attached fractions in permeable surface sediments

Heterotrophic microbes are central to organic matter degradation and transformation in marine sediments. Currently, most investigations of benthic microbiomes do not differentiate between processes in the porewater and on the grains and, hence, only show a generalized picture of the community. This limits our understanding of the structure and functions of sediment microbiomes. To address this problem, we fractionated sandy surface sediment microbial communities from a coastal site in Isfjorden, Svalbard, into cells associated with the porewater, loosely attached to grains, and firmly attached to grains; we found dissimilar bacterial communities and metabolic activities in these fractions. Most (84%-89%) of the cells were firmly attached, and this fraction comprised more anaerobes, such as sulfate reducers, than the other fractions. The porewater and loosely attached fractions (3% and 8%-13% of cells, respectively) had more aerobic heterotrophs. These two fractions generally showed a higher frequency of dividing cells, polysaccharide (laminarin) hydrolysis rates, and per-cell O2 consumption than the firmly attached cells. Thus, the different fractions occupy distinct niches within surface sediments: the firmly attached fraction is potentially made of cells colonizing areas on the grain that are protected from abrasion, but might be more diffusion-limited for organic matter and electron acceptors. In contrast, the porewater and loosely attached fractions are less resource-limited and have faster growth. Their cell numbers are kept low possibly through abrasion and exposure to grazers. Differences in community composition and activity of these cell fractions point to their distinct roles and contributions to carbon cycling within surface sediments.

Linking the impact of bacteria on phytoplankton growth with microbial community composition and co-occurrence patterns

The interactions between microalgae and bacteria have recently emerged as key control factors which might contribute to a better understanding on how phytoplankton communities assemble and respond to environmental disturbances. We analyzed partial 16S rRNA and 18S rRNA genes from a total of 42 antibiotic bioassays, where phytoplankton growth was assessed in the presence or absence of an active bacterial community. A significant negative impact of bacteria was observed in 18 bioassays, a significant positive impact was detected in 5 of the cases, and a non-detectable effect occurred in 19 bioassays. Thalasiossira spp., Chlorophytes, Vibrionaceae and Alteromonadales were relatively more abundant in the samples where a positive effect of bacteria was observed compared to those where a negative impact was observed. Phytoplankton diversity was lower when bacteria negatively affect their growth than when the effect was beneficial. The phytoplankton-bacteria co-occurrence subnetwork included many significant Chlorophyta-Alteromonadales and Bacillariophyceae-Alteromonadales positive associations. Phytoplankton-bacteria co-exclusions were not detected in the network, which contrasts with the negative effect of bacteria on phytoplankton growth frequently detected in the bioassays, suggesting strong competitive interactions. Overall, this study adds strong evidence supporting the key role of phytoplankton-bacteria interactions in the microbial communities.

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.

Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean

BACKGROUND

Heterotrophic microbes in the Southern Ocean are challenged by the double constraint of low concentrations of organic carbon (C) and iron (Fe). These essential elements are tightly coupled in cellular processes; however, the prokaryotic requirements of C and Fe under varying environmental settings remain poorly studied. Here, we used a combination of metatranscriptomics and metaproteomics to identify prokaryotic membrane transporters for organic substrates and Fe in naturally iron-fertilized and high-nutrient, low-chlorophyll waters of the Southern Ocean during spring and late summer.

RESULTS

Pronounced differences in membrane transporter profiles between seasons were observed at both sites, both at the transcript and protein level. When specific compound classes were considered, the two approaches revealed different patterns. At the transcript level, seasonal patterns were only observed for subsets of genes belonging to each transporter category. At the protein level, membrane transporters of organic compounds were relatively more abundant in spring as compared to summer, while the opposite pattern was observed for Fe transporters. These observations suggest an enhanced requirement for organic C in early spring and for Fe in late summer. Mapping transcripts and proteins to 50 metagenomic-assembled genomes revealed distinct taxon-specific seasonal differences pointing to potentially opportunistic clades, such as Pseudomonadales and Nitrincolaceae, and groups with a more restricted repertoire of expressed transporters, such as Alphaproteobacteria and Flavobacteriaceae.

CONCLUSION

The combined investigations of C and Fe membrane transporters suggest seasonal changes in the microbial requirements of these elements under different productivity regimes. The taxon-specific acquisition strategies of different forms of C and Fe illustrate how diverse microbes could shape transcript and protein expression profiles at the community level at different seasons. Our results on the C- and Fe-related metabolic capabilities of microbial taxa provide new insights into their potential role in the cycling of C and Fe under varying nutrient regimes in the Southern Ocean. Video Abstract.

Temporal variability in the growth-enhancing effects of different bacteria within the microbiome of the diatom Actinocyclus sp

Reciprocal metabolite exchanges between diatoms and bacteria can enhance the growth of both partners and therefore fundamentally influence aquatic ecosystem productivity. Here, we examined the growth-promoting capabilities of 15 different bacterial isolates from the bacterial community associated with the marine diatom Actinocyclus sp. and investigated the magnitude and timing of their effect on the growth of this diatom. In the presence of its microbiome, Actinocyclus sp. growth was significantly enhanced relative to axenic cultures. Co-culture with each of the 15 bacterial isolates examined here (seven Rhodobacteraceae, four Vibrionaceae, two Pseudoalteromonadaceae, one Oceanospirillaceae and one Alteromonadaceae) increased the growth of the diatom host, with four isolates inducing rates of growth that were similar to those delivered by the diatom's full microbiome. However, the timing and duration of this effect differed between the different bacteria tested. Indeed, one Rhodobacteraceae and one Alteromonadaceae enhanced Actinocyclus sp. cell numbers between days 0-6 after co-incubation, five other Rhodobacteraceae promoted diatom cell numbers the most between days 8-12, whilst four Vibrionaceae, one Oceanospirillaceae and one Rhodobacteraceae enhanced Actinocyclus sp. cell abundance between days 14-16. These results are indicative of a succession of the growth-enhancing effects delivered by diverse bacteria throughout the Actinocyclus sp. life cycle, which will likely deliver sustained growth benefits to the diatom when its full microbiome is present.

SAR11 clade microdiversity and activity during the early spring blooms off Kerguelen Island, Southern Ocean

The ecology of the SAR11 clade, the most abundant bacterial group in the ocean, has been intensively studied in temperate and tropical regions, but its distribution remains largely unexplored in the Southern Ocean. Through amplicon sequencing of the 16S rRNA gene, we assessed the contribution of the SAR11 clade to bacterial community composition in the naturally iron fertilized region off Kerguelen Island. We investigated the upper 300 m at seven sites located in early spring phytoplankton blooms and at one high-nutrient low-chlorophyll site. Despite pronounced vertical patterns of the bacterioplankton assemblages, the SAR11 clade had high relative abundances at all depths and sites, averaging 40% (±15%) of the total community relative abundance. Micro-autoradiography combined with CARD-FISH further revealed that the clade had an overall stable contribution (45%-60% in surface waters) to bacterial biomass production (determined by ³ H-leucine incorporation) during different early bloom stages. The spatio-temporal partitioning of some of the SAR11 subclades suggests a niche specificity and periodic selection of different subclades in response to the fluctuating extreme conditions of the Southern Ocean. These observations improve our understanding of the ecology of the SAR11 clade and its implications in biogeochemical cycles in the rapidly changing Southern Ocean.

Role of Bacterial Community Composition as a Driver of the Small-Sized Phytoplankton Community Structure in a Productive Coastal System

We present here the first detailed description of the seasonal patterns in bacterial community composition (BCC) in shelf waters off the Ría de Vigo (Spain), based on monthly samplings during 2 years. Moreover, we studied the relationship between bacterial and small-sized eukaryotic community composition to identify potential biotic interactions among components of these two communities. Bacterial operational taxonomic unit (OTU) richness and diversity systematically peaked in autumn-winter, likely related to low resource availability during this period. BCC showed seasonal and vertical patterns, with Rhodobacteraceae and Flavobacteriaceae families dominating in surface waters, and SAR11 clade dominating at the base of the photic zone (30 m depth). BCC variability was significantly explained by environmental variables (e.g., temperature of water, solar radiation, or dissolved organic matter). Interestingly, a strong and significant correlation was found between BCC and small-sized eukaryotic community composition (ECC), which suggests that biotic interactions may play a major role as structuring factors of the microbial plankton in this productive area. In addition, co-occurrence network analyses revealed strong and significant, mostly positive, associations between bacteria and small-sized phytoplankton. Positive associations likely result from mutualistic relationships (e.g., between Dinophyceae and Rhodobacteraceae), while some negative correlations suggest antagonistic interactions (e.g., between Pseudo-nitzchia sp. and SAR11). These results support the key role of biotic interactions as structuring factors of the small-sized eukaryotic community, mostly driven by positive associations between small-sized phytoplankton and bacteria.

Microbial ecology of the Southern Ocean

The Southern Ocean (SO) distributes climate signals and nutrients worldwide, playing a pivotal role in global carbon sequestration. Microbial communities are essential mediators of primary productivity and carbon sequestration, yet we lack a comprehensive understanding of microbial diversity and functionality in the SO. Here, we examine contemporary studies in this unique polar system, focusing on prokaryotic communities and their relationships with other trophic levels (i.e. phytoplankton and viruses). Strong seasonal variations and the characteristic features of this ocean are directly linked to community composition and ecosystem functions. Specifically, we discuss characteristics of SO microbial communities and emphasise differences from the Arctic Ocean microbiome. We highlight the importance of abundant bacteria in recycling photosynthetically derived organic matter. These heterotrophs appear to control carbon flux to higher trophic levels when light and iron availability favour primary production in spring and summer. Conversely, during winter, evidence suggests that chemolithoautotrophs contribute to prokaryotic production in Antarctic waters. We conclude by reviewing the effects of climate change on marine microbiota in the SO.

A Winter-to-Summer Transition of Bacterial and Archaeal Communities in Arctic Sea Ice

The Arctic is warming 2-3 times faster than the global average, leading to a decrease in Arctic sea ice extent, thickness, and associated changes in sea ice structure. These changes impact sea ice habitat properties and the ice-associated ecosystems. Sea-ice algal blooms provide various algal-derived carbon sources for the bacterial and archaeal communities within the sea ice. Here, we detail the transition of these communities from winter through spring to early summer during the Norwegian young sea ICE (N-ICE2015) expedition. The winter community was dominated by the archaeon Candidatus Nitrosopumilus and bacteria belonging to the Gammaproteobacteria (Colwellia, Kangiellaceae, and Nitrinocolaceae), indicating that nitrogen-based metabolisms, particularly ammonia oxidation to nitrite by Cand. Nitrosopumilus was prevalent. At the onset of the vernal sea-ice algae bloom, the community shifted to the dominance of Gammaproteobacteria (Kangiellaceae, Nitrinocolaceae) and Bacteroidia (Polaribacter), while Cand. Nitrosopumilus almost disappeared. The bioinformatically predicted carbohydrate-active enzymes increased during spring and summer, indicating that sea-ice algae-derived carbon sources are a strong driver of bacterial and archaeal community succession in Arctic sea ice during the change of seasons. This implies a succession from a nitrogen metabolism-based winter community to an algal-derived carbon metabolism-based spring/ summer community.

Biogeography of Southern Ocean Active Prokaryotic Communities Over a Large Spatial Scale

The activity of marine microorganisms depends on community composition, yet, in some oceans, less is known about the environmental and ecological processes that structure their distribution. The objective of this study was to test the effect of geographical distance and environmental parameters on prokaryotic community structure in the Southern Ocean (SO). We described the total (16S rRNA gene) and the active fraction (16S rRNA-based) of surface microbial communities over a ~6,500 km longitudinal transect in the SO. We found that the community composition of the total fraction was different from the active fraction across the zones investigated. In addition, higher α-diversity and stronger species turnover were displayed in the active community compared to the total community. Oceanospirillales, Alteromonadales, Rhodobacterales, and Flavobacteriales dominated the composition of the bacterioplankton communities; however, there were marked differences at the order level. Temperature, salinity, silicic acid, particulate organic nitrogen, and particulate organic carbon correlated with the composition of bacterioplankton communities. A strong distance–decay pattern between closer and distant communities was observed. We hypothesize that it was related to the different oceanic fronts present in the Antarctic Circumpolar Current. Our findings contribute to a better understanding of the complex arrangement that shapes the structure of bacterioplankton communities in the SO.

Drivers of microbial beta-diversity in wastewater treatment plants in China

As one of the most well-documented biogeographic patterns, the distance-decay relationship provides insights into the underlying mechanisms driving biodiversity distribution. Although wastewater treatment plants (WWTPs) are well-controlled engineered ecosystems, this pattern has been seen among microbial communities in activated sludge (AS). However, little is known about the relative importance of environmental heterogeneity and dispersal limitation in shaping AS microbial community across China; especially they are related to spatial scale and organism types. Here, we assessed the distance-decay relationship based on different spatial scales and microbial phylogenetic groups by analyzing 132 activated sludge (AS) samples across China comprising 3,379,200 16S rRNA sequences. Our results indicated that the drivers of distance-decay pattern in China were scale-dependent. Microbial biogeographic patterns in WWTPs were mainly driven by dispersal limitation at both local and national scales. In contrast, conductivity, SRT, and pH played dominant roles in shaping AS microbial community compositions at the regional scale. Turnover rates and the drivers of beta-diversity also varied with microorganism populations. Moreover, a quantitative relationship between dispersal limitation ratio and AS microbial turnover rate was generated. Collectively, these results highlighted the importance of considering multiple spatial scales and micro-organism types for understanding microbial biogeography in WWTPs and provided new insights into predicting variations in AS community structure in response to environmental disturbance.

Diatom Biogeography, Temporal Dynamics, and Links to Bacterioplankton across Seven Oceanographic Time-Series Sites Spanning the Australian Continent

Diatom communities significantly influence ocean primary productivity and carbon cycling, but their spatial and temporal dynamics are highly heterogeneous and are governed by a complex diverse suite of abiotic and biotic factors. We examined the seasonal and biogeographical dynamics of diatom communities in Australian coastal waters using amplicon sequencing data (18S-16S rRNA gene) derived from a network of oceanographic time-series spanning the Australian continent. We demonstrate that diatom community composition in this region displays significant biogeography, with each site harbouring distinct community structures. Temperature and nutrients were identified as the key environmental contributors to differences in diatom communities at all sites, collectively explaining 21% of the variability observed in diatoms assemblages. However, specific groups of bacteria previously implicated in mutualistic ecological interactions with diatoms (Rhodobacteraceae, Flavobacteriaceae and Alteromonadaceae) also explained a further 4% of the spatial dynamics observed in diatom community structure. We also demonstrate that the two most temperate sites (Port Hacking and Maria Island) exhibited strong seasonality in diatom community and that at these sites, winter diatom communities co-occurred with higher proportion of Alteromonadaceae. In addition, we identified significant co-occurrence between specific diatom and bacterial amplicon sequence variants (ASVs), with members of the Roseobacter and Flavobacteria clades strongly correlated with some of the most abundant diatom genera (Skeletonema, Thalassiosira, and Cylindrotheca). We propose that some of these co-occurrences might be indicative of ecologically important interactions between diatoms and bacteria. Our analyses reveal that in addition to physico-chemical conditions (i.e., temperature, nutrients), the relative abundance of specific groups of bacteria appear to play an important role in shaping the spatial and temporal dynamics of marine diatom communities.

Biogeography of Southern Ocean prokaryotes: a comparison of the Indian and Pacific sectors

We investigated the Southern Ocean (SO) prokaryote community structure via zero‐radius operational taxonomic unit (zOTU) libraries generated from 16S rRNA gene sequencing of 223 full water column profiles. Samples reveal the prokaryote diversity trend between discrete water masses across multiple depths and latitudes in Indian (71–99°E, summer) and Pacific (170–174°W, autumn‐winter) sectors of the SO. At higher taxonomic levels (phylum‐family) we observed water masses to harbour distinct communities across both sectors, but observed sectorial variations at lower taxonomic levels (genus‐zOTU) and relative abundance shifts for key taxa such as Flavobacteria, SAR324/Marinimicrobia, Nitrosopumilus and Nitrosopelagicus at both epi‐ and bathy‐abyssopelagic water masses. Common surface bacteria were abundant in several deep‐water masses and vice‐versa suggesting connectivity between surface and deep‐water microbial assemblages. Bacteria from same‐sector Antarctic Bottom Water samples showed patchy, high beta‐diversity which did not correlate well with measured environmental parameters or geographical distance. Unconventional depth distribution patterns were observed for key archaeal groups: Crenarchaeota was found across all depths in the water column and persistent high relative abundances of common epipelagic archaeon Nitrosopelagicus was observed in deep‐water masses. Our findings reveal substantial regional variability of SO prokaryote assemblages that we argue should be considered in wide‐scale SO ecosystem microbial modelling.

Structure and Long-Term Stability of the Microbiome in Diverse Diatom Cultures

Microalgal cultures are often maintained in xenic conditions, i.e., with associated bacteria, and many studies indicate that these communities both are complex and have significant impacts on the physiology of the target photoautotroph. Here, we investigated the structure and stability of microbiomes associated with a diverse sampling of diatoms during long-term maintenance in serial batch culture. We found that, counter to our initial expectation, evenness diversity increased with time since cultivation, driven by a decrease in dominance by the most abundant taxa in each culture. We also found that the site from which and time at which a culture was initially collected had a stronger impact on microbiome structure than the diatom species; however, some bacterial taxa were commonly present in most cultures despite having widely geographically separated collection sites. Our results support the conclusion that stochastic initial conditions (i.e., the local microbial community at the collection site) are important for the long-term structure of these microbiomes, but deterministic forces such as negative frequency dependence and natural selection exerted by the diatom are also at work.

IMPORTANCE Natural microbial communities are extremely complex, with many more species coexisting in the same place than there are different resources to support them. Understanding the forces that allow this high level of diversity has been a central focus of ecological and evolutionary theory for many decades. Here, we used stock cultures of diatoms, which were maintained for years in continuous growth alongside populations of bacteria, as proxies for natural communities. We show that the bacterial communities remained relatively stable for years, and there is evidence that ecological forces worked to stabilize coexistence instead of favoring competition and exclusion. We also show evidence that, despite some important regional differences in bacterial communities, there was a globally present core microbiome potentially selected for in these diatom cultures. Understanding interactions between bacteria and diatoms is important both for basic ecological science and for practical science, such as industrial biofuel production.

Niche partitioning of bacterial communities along the stratified water column in the Black Sea

The Black Sea is the largest semi‐closed permanently anoxic basin on our planet with long‐term stratification. The study aimed at describing the Black Sea microbial community taxonomic and functional composition within the range of depths spanning across oxic/anoxic interface, and to uncover the factors behind both their vertical and regional differentiation. 16S rRNA gene MiSeq sequencing was applied to get the data on microbial community taxonomy, and the PICRUSt pipeline was used to infer their functional profile. The normoxic zone was mainly inhabited by primary producers and heterotrophic prokaryotes (e.g., Flavobacteriaceae, Rhodobacteraceae, Synechococcaceae) whereas the euxinic zone—by heterotrophic and chemoautotrophic taxa (e.g., MSBL2, Piscirickettsiaceae, and Desulfarculaceae). Assimilatory sulfate reduction and oxygenic photosynthesis were prevailing within the normoxic zone, while the role of nitrification, dissimilatory sulfate reduction, and anoxygenic photosynthesis increased in the oxygen‐depleted water column part. Regional differentiation of microbial communities between the Ukrainian shelf and offshore zone was detected as well, yet it was significantly less pronounced than the vertical one. It is suggested that regional differentiation within a well‐oxygenated zone is driven by the difference in phytoplankton communities providing various substrates for the prokaryotes, whereas redox stratification is the main driving force behind microbial community vertical structure.

Bacteria in the lakes of the Tibetan Plateau and polar regions

The Tibetan Plateau, also termed 'the Third Pole' harbors the largest number of high-altitude lakes in the world. Due to the presence of extreme conditions such as low temperature and oligotrophy, the lakes of the Tibetan Plateau share environmental features in common with lakes in the polar regions. However, the extent to which these environments are analogous, or indeed whether they harbor similar microbial communities or a high level of endemic species is poorly understood. Here we compared high-throughput 16S rRNA gene sequencing data from the lakes of the three different regions in order to characterize their taxonomic diversity, the community composition and biogeography. Our results showed despite the similarity in environmental conditions, the spatial distribution of the bacterial communities was distinct with only 3.1% of all operational taxonomic units (OTUs) being present in all three regions (although these OTUs did account for a considerable proportion of the total sequences, 36.4%). Sequences belonging to Burkholderiales and Actinomycetales dominated the shared OTUs across all three regions. Scale dependent distance decay patterns provided evidence of dispersal limitation. Climatic variables and dispersal limitation were apparently both important in controlling the spatial distribution of bacterial communities across regions. This work expands our understanding of the diversity and biogeography of lake bacterial communities across the Tibetan Plateau and provides insights into how they compare to those of the Antarctic and Arctic.

Predetermined clockwork microbial worlds: Current understanding of aquatic microbial diel response from model systems to complex environments

In the photic zone of aquatic ecosystems, microorganisms with different metabolisms and their viruses form complex interactions and food webs. Within these interactions, phototrophic microorganisms such as eukaryotic microalgae and cyanobacteria interact directly with sunlight, and thereby generate circadian rhythms. Diel cycling originally generated in microbial phototrophs is directly transmitted toward heterotrophic microorganisms utilizing the photosynthetic products as they are excreted or exuded. Such diel cycling seems to be indirectly propagated toward heterotrophs as a result of complex biotic interactions. For example, cell death of phototrophic microorganisms induced by viral lysis and protistan grazing provides additional resources of dissolved organic matter to the microbial community, and so generates diel cycling in other heterotrophs with different nutrient dependencies. Likewise, differences in the diel transmitting pathway via complex interactions among heterotrophs, and between heterotrophs and their viruses, may also generate higher variation and time lag diel rhythms in different heterotrophic taxa. Thus, sunlight and photosynthesis not only contribute energy and carbon supply, but also directly or indirectly control diel cycling of the microbial community through complex interactions in the photic zone of aquatic ecosystems.

Seasonal dynamics of prokaryotes and their associations with diatoms in the Southern Ocean as revealed by an autonomous sampler

The Southern Ocean remains one of the least explored marine environments. The investigation of temporal microbial dynamics has thus far been hampered by the limited access to this remote ocean. We present here high-resolution seasonal observations of the prokaryotic community composition during phytoplankton blooms induced by natural iron fertilization. A total of 18 seawater samples were collected by a moored remote autonomous sampler over 4 months at 5-11 day intervals in offshore surface waters (central Kerguelen Plateau). Illumina sequencing of the 16S rRNA gene revealed that among the most abundant amplicon sequence variants, SAR92 and Aurantivirga were the first bloom responders, Pseudomonadaceae, Nitrincolaceae and Polaribacter had successive peaks during the spring bloom decline, and Amylibacter increased in relative abundance later in the season. SAR11 and SUP05 were abundant prior to and after the blooms. Using network analysis, we identified two groups of diatoms representative of the spring and summer bloom that had opposite correlation patterns with prokaryotic taxa. Our study provides the first seasonal picture of microbial community dynamics in the open Southern Ocean and thereby offers biological insights to the cycling of carbon and iron, and to an important puzzling issue that is the modest nitrate decrease associated to iron fertilization.