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Although bulk bacterial metabolism in response to temperature has been determined for different oceanic regions, the impact of temperature on the functional diversity of dissolved organic matter (DOM) utilization has been largely unexplored. Here, we hypothesized that besides modifying the rates of carbon utilization, temperature can also alter the diversity of substrates utilized. The patterns of utilization of 31 model DOM compounds (as represented in Biolog EcoPlate™) by bacterioplankton were assessed using inocula from surface waters of the southern Bay of Biscay continental shelf over 1 year. Bacteria utilized more polymers and carbohydrates in late spring and summer than in winter, likely reflecting changes in substrate availability linked to the release and accumulation of DOM in phytoplankton post‐bloom conditions. Seawater temperature correlated positively with the number of substrates utilized (i.e. functional richness) and this relationship was maintained in monthly experimental incubations spanning 3°C below and above in situ values. The enhancement of functional richness with experimental warming displayed a unimodal response to ambient temperature, peaking at 16°C. This temperature acted as a threshold separating nutrient‐sufficient from nutrient‐deficient conditions at the study site, suggesting that trophic conditions will be critical in the response of microbial DOM utilization to future warming. [ABSTRACT FROM AUTHOR]

Pico‐ and nanoplankton are key players in the marine ecosystems due to their implication in the biogeochemical cycles, nutrient recycling and the pelagic food webs. However, the specific dynamics and niches of most bacterial, archaeal and eukaryotic plankton remain unknown, as well as the interactions between them. Better characterization of these is critical for understanding and predicting ecosystem functioning under anthropogenic pressures. We used environmental DNA metabarcoding across a 6‐year time series to explore the structure and seasonality of pico‐ and nanoplankton communities in two sites of the Bay of Biscay, one coastal and one offshore, and construct association networks to reveal potential keystone and connector taxa. Temporal trends in alpha diversity were similar between the two sites, and concurrent communities more similar than within the same site at different times. However, we found differences between the network topologies of the two sites, with both shared and site‐specific keystones and connectors. For example, Micromonas, with lower abundance in the offshore site is a keystone here, indicating a stronger effect of associations such as resource competition. This study provides an example of how time series and association network analysis can reveal how similar communities may function differently despite being geographically close. [ABSTRACT FROM AUTHOR]

A decade after environmental scientists integrated high‐throughput sequencing technologies in their toolbox, the genomics‐based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end‐users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics‐based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy‐based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs. [ABSTRACT FROM AUTHOR]

Routine monitoring of benthic biodiversity is critical for managing and understanding the anthropogenic impacts on marine, transitional and freshwater ecosystems. However, traditional reliance on morphological identification generally makes it cost‐prohibitive to increase the scale of monitoring programmes. Metabarcoding of environmental DNA has clear potential to overcome many of the problems associated with traditional monitoring, with prokaryotes and other microorganisms showing particular promise as bioindicators. However, due to the limited knowledge regarding the ecological roles and responses of environmental microorganisms to different types of pressure, the use of de novo approaches is necessary. Here, we use two such approaches for the prediction of multiple impacts present in estuaries and coastal areas of the Bay of Biscay based on microbial communities. The first (Random Forests) is a machine learning method while the second (Threshold Indicator Taxa Analysis and quantile regression splines) is based on de novo identification of bioindicators. Our results show that both methods overlap considerably in the indicator taxa identified, but less for sequence variants. Both methods also perform well in spite of the complexity of the studied ecosystem, providing predictive models with strong correlation to reference values and fair to good agreement with ecological status groups. The ability to predict several specific types of pressure is especially appealing. The cross‐validated models and biotic indices developed can be directly applied to predict the environmental status of estuaries in the same geographical region, although more work is needed to evaluate and improve them for use in new regions or habitats. [ABSTRACT FROM AUTHOR]

Summary: Ostreococcus is a cosmopolitan marine genus of phytoplankton found in mesotrophic and oligotrophic waters, and the smallest free‐living eukaryotes known to date, with a cell diameter close to 1 μm. Ostreococcus has been extensively studied as a model system to investigate viral–host dynamics in culture, yet the impact of viruses in naturally occurring populations is largely unknown. Here, we used Virus Fluorescence in situ Hybridization (VirusFISH) to visualize and quantify viral‐host dynamics in natural populations of Ostreococcus during a seasonal cycle in the central Cantabrian Sea (Southern Bay of Biscay). Ostreococcus were predominantly found during summer and autumn at surface and 50 m depth, in coastal, mid‐shelf and shelf waters, representing up to 21% of the picoeukaryotic communities. Viral infection was only detected in surface waters, and its impact was variable but highest from May to July and November to December, when up to half of the population was infected. Metatranscriptomic data available from the mid‐shelf station unveiled that the Ostreococcus population was dominated by the species O. lucimarinus. This work represents a proof of concept that the VirusFISH technique can be used to quantify the impact of viruses on targeted populations of key microbes from complex natural communities. [ABSTRACT FROM AUTHOR]

Summary: Despite the widespread distribution of proteorhodopsin (PR)‐containing bacteria in the oceans, the use of light‐derived energy to promote bacterial growth has only been shown in a few bacterial isolates, and there is a paucity of data describing the metabolic effects of light on environmental photoheterotrophic taxa. Here, we assessed the effects of light on the taxonomic composition, cell integrity and growth responses of microbial communities in monthly incubations between spring and autumn under different environmental conditions. The photoheterotrophs expressing PR in situ were dominated by Pelagibacterales and SAR116 in July and November, while members of Euryarchaeota, Gammaproteobacteria and Bacteroidetes dominated the PR expression in spring. Cell‐membrane integrity decreased under dark conditions throughout most of the assessment, with maximal effects in summer, under low‐nutrient conditions. A positive effect of light on growth was observed in one incubation (out of nine), coinciding with a declining phytoplankton bloom. Light‐enhanced growth was found in Gammaproteobacteria (Alteromonadales) and Bacteroidetes (Polaribacter and Tenacibaculum). Unexpectedly, some Pelagibacterales also exhibited higher growth rates under light conditions. We propose that the energy harvested by PRs helps to maintain cell viability in dominant coastal photoheterotrophic oligotrophs while promoting the growth of some widespread taxa benefiting from the decline of phytoplankton blooms. [ABSTRACT FROM AUTHOR]

Summary: Heterotrophic bacteria associated with microphytoplankton, particularly those colonizing the phycosphere, are major players in the remineralization of algal‐derived carbon. Ocean warming might impact dissolved organic carbon (DOC) uptake by microphytoplankton‐associated bacteria with unknown biogeochemical implications. Here, by incubating natural seawater samples at three different temperatures, we analysed the effect of experimental warming on the abundance and C and N uptake activity of Rhodobacteraceae and Flavobacteria, two bacterial groups typically associated with microphytoplankton. Using a nano‐scale secondary ion mass spectrometry (nanoSIMS) single‐cell analysis, we quantified the temperature sensitivity of these two taxonomic groups to the uptake of algal‐derived DOC in the microphytoplankton associated fraction with 13C‐bicarbonate and 15N‐leucine as tracers. We found that cell‐specific 13C uptake was similar for both groups (~0.42 fg C h−1 μm−3), but Rhodobacteraceae were more active in 15N‐leucine uptake. Due to the higher abundance of Flavobacteria associated with microphytoplankton, this group incorporated fourfold more carbon than Rhodobacteraceae. Cell‐specific 13C uptake was influenced by temperature, but no significant differences were found for 15N‐leucine uptake. Our results show that the contribution of Flavobacteria and Rhodobacteraceae to C assimilation increased up to sixfold and twofold, respectively, with an increase of 3°C above ambient temperature, suggesting that warming may differently affect the contribution of distinct copiotrophic bacterial taxa to carbon cycling. [ABSTRACT FROM AUTHOR]

Although temperature is a key driver of bacterioplankton metabolism, the effect of ocean warming on different bacterial phylogenetic groups remains unclear. Here, we conducted monthly short-term incubations with natural coastal bacterial communities over an annual cycle to test the effect of experimental temperature on the growth rates and carrying capacities of four phylogenetic groups: SAR11, Rhodobacteraceae, Gammaproteobacteria and Bacteroidetes. SAR11 was the most abundant group year-round as analysed by CARD-FISH, with maximum abundances in summer, while the other taxa peaked in spring. All groups, including SAR11, showed high temperature-sensitivity of growth rates and/or carrying capacities in spring, under phytoplankton bloom or post-bloom conditions. In that season, Rhodobacteraceae showed the strongest temperature response in growth rates, estimated here as activation energy ( E, 1.43 eV), suggesting an advantage to outcompete other groups under warmer conditions. In summer E values were in general lower than 0.65 eV, the value predicted by the Metabolic Theory of Ecology (MTE). Contrary to MTE predictions, carrying capacity tended to increase with warming for all bacterial groups. Our analysis confirms that resource availability is key when addressing the temperature response of heterotrophic bacterioplankton. We further show that even under nutrient-sufficient conditions, warming differentially affected distinct bacterioplankton taxa. [ABSTRACT FROM AUTHOR]

1. Planktonic bacterial community dynamics over short timescales can be of great importance for food webs and ecosystem functioning but are rarely described when microbial community and composition are assessed. To study the significance of such dynamics we sampled the surface water at the deepest point of a mesotrophic lake (Lake Erken, Sweden) every third hour over two days. 2. By combining 454 pyrosequencing of 16S rRNA genes with bromodeoxyuridine immunocapturing of DNA, replicating populations were identified and compared to the community retrieved from total DNA samples. This comparison revealed a significant difference between the actively replicating and total community. 3. The high-frequency diurnal sampling was compared to a year-long survey conducted in the same lake in order to compare the diurnal and seasonal variation in bacterioplankton community composition. At the diurnal-scale, the variation was significantly higher in the replicating than in the total community. However, variation in both active and total diurnal community was significantly lower than the variation in the seasonal total community. 4. Our analysis revealed pronounced short-term dynamics of individual bacterial populations uncoupled from the diurnal light cycle. For example, the proliferating fraction of the most abundant bacterial tribe (LD12) followed a cyclic pattern that covaried with viral abundance. This implies that environmental factors other than light may act as important drivers of microbial community composition, at least in mesotrophic Lake Erken. [ABSTRACT FROM AUTHOR]

The 'cytometric diversity' of phytoplankton communities has been studied based on single-cell properties, but the applicability of this method to characterize bacterioplankton has been unexplored. Here, we analysed seasonal changes in cytometric diversity of marine bacterioplankton along a decadal time-series at three coastal stations in the Southern Bay of Biscay. Shannon- Weaver diversity estimates and Bray- Curtis similarities obtained by cytometric and molecular (16S rRNA tag sequencing) methods were significantly correlated in samples from a 3.5 year monthly time-series. Both methods showed a consistent cyclical pattern in the diversity of surface bacterial communities with maximal values in winter. The analysis of the highly resolved flow cytometry time-series across the vertical profile showed that water column mixing was a key factor explaining the seasonal changes in bacterial composition and the winter increase in bacterial diversity in coastal surface waters. Due to its low cost and short processing time as compared with genetic methods, the cytometric diversity approach represents a useful complementary tool in the macroecology of aquatic microbes. [ABSTRACT FROM AUTHOR]

Rare microbial taxa are increasingly recognized to play key ecological roles, but knowledge of their spatio-temporal dynamics is lacking. In a time-series study in coastal waters, we detected 83 bacterial lineages with significant seasonality, including environmentally relevant taxa where little ecological information was available. For example, Verrucomicrobia had recurrent maxima in summer, while the Flavobacteria NS4, NS5 and NS2b clades had contrasting seasonal niches. Among the seasonal taxa, only 4 were abundant and persistent, 20 cycled between rare and abundant and, remarkably, most of them (59) were always rare (contributing < 1% of total reads). We thus demonstrate that seasonal patterns in marine bacterioplankton are largely driven by lineages that never sustain abundant populations. A fewer number of rare taxa (20) also produced episodic 'blooms', and these events were highly synchronized, mostly occurring on a single month. The recurrent seasonal growth and loss of rare bacteria opens new perspectives on the temporal dynamics of the rare biosphere, hitherto mainly characterized by dormancy and episodes of 'boom and bust', as envisioned by the seed-bank hypothesis. The predictable patterns of seasonal reoccurrence are relevant for understanding the ecology of rare bacteria, which may include key players for the functioning of marine ecosystems. [ABSTRACT FROM AUTHOR]

Studies on the size-scaling of phytoplankton growth rate are usually based on temperature-corrected growth rates or experiments performed at a fixed temperature, but the effects of differing thermal adaptation of small and large species have not been considered. We use an extensive dataset of phytoplankton growth rate responses to temperature and cell size to show that the unimodal size-scaling of phytoplankton growth depends strongly on temperature, and is not significant at high temperatures where the most common picophytoplankton species grow at their optimum. Furthermore, we show that the unimodality results from the different growth rate scaling of picophytoplankton, which differs phylogenetically from larger phytoplankton taxa. Using ribosomal RNA sequences we recalculated the size-scaling allometry with Phylogenetic Generalized Least Squares regression. After phylogenetic correction, the unimodal relationship is not significant at any temperature, suggesting that the observed curvature reflects the evolutionary adaptation of picophytoplankton to the warm conditions usually encountered in oligotrophic environments. [ABSTRACT FROM AUTHOR]

Summary Archaea are abundant in polar oceans but important ecological aspects of this group remain enigmatic, such as patterns of diversity and biogeography. Here, we provide the first high-throughput sequencing population study of Antarctic archaea based on 198 bp fragments of the 16S rRNA gene, targeting different water masses across the Amundsen and Ross Seas. Our results suggest that archaeal community composition is strongly shaped by hydrography and significantly influenced by environmental parameters. Archaeal communities from cold continental shelf waters (SW) of the Ross Sea were similar over depth with a single thaumarchaeal phylotype dominating Antarctic surface waters (AASW) and deeper SW (contributing up to 80% of reads). However, this phylotype contributed less than 8% of reads in circumpolar deep waters (CDW). A related thaumarchaeon (98% identity) was almost absent in AASW, but contributed up to 30% of reads in CDW, suggesting ecological differentiation of closely related phylotypes. Significantly higher archaeal richness and evenness were observed in CDW, with Shannon indices ( c. 2.5) twice as high as for AASW, and high contributions of Group II Euryarchaeota. Based on these results, we suggest that CDW is a hotspot of archaeal diversity and may play an important role in the dispersal of archaeal phylotypes to other oceanic water masses. [ABSTRACT FROM AUTHOR]

The suitability of applying empirical conversion factors (eCFs) to determine bacterial biomass production remains unclear because seawater cultures are usually overtaken by phylotypes that are not abundant in situ. While eCFs vary across environments, it has not been tested whether differences in eCFs are driven by changes in bacterial community composition or by in situ environmental conditions. We carried out seawater cultures throughout a year to analyse the correlation between eCFs and bacterial community structure, analysed by catalysed reporter deposition fluorescence in situ hybridization. Gammaproteobacteria usually dominated seawater cultures, but their abundance exhibited a wide range (25-73% of cell counts) and significantly increased with inorganic nutrient enrichment. Flavobacteria were less abundant but increased up to 40% of cells counts in winter seawater cultures, when in situ chlorophyll a was high. The correlations between eCFs and the abundance of the main broad phylogenetic groups ( Gamma-, Alphaproteobacteria and Flavobacteria) were significant, albeit weak, while more specific groups ( Alteromonadaceae and Rhodobacteraceae) were not significantly correlated. Our results show that the frequent development of the fast-growing group Alteromonadaceae in seawater cultures does not strongly drive the observed variations in eCFs. Rather, the results imply that environmental conditions and the growth of specific phylotypes interact to determine eCFs. [ABSTRACT FROM AUTHOR]

We collected surface samples in Franklin Bay (Western Arctic) from ice-covered to ice-free conditions, to determine seasonal changes in the identity and in situ activity of the prokaryotic assemblages. Catalysed reported fluorescence in situ hybridization was used to quantify the abundance of different groups, and combined with microautoradiography to determine the fraction of active cells taking up three substrates: glucose, amino acids and ATP. In surface waters, Archaea accounted for 16% of the total cell count in winter, but decreased to almost undetectable levels in summer, when Bacteria made up 97% of the total cell count. Alphaproteobacteria were the most abundant group followed by Bacteroidetes (average of 34% and 14% of total cell counts respectively). Some bacterial groups appearing in low abundances (< 10% of total cell counts), such as Betaproteobacteria, Roseobacter and Gammaproteobacteria, showed a high percentage of active cells. By contrast, more abundant groups, such as SAR11 or Bacteroidetes, had a lower percentage of active cells in the uptake of the substrates tested. Archaea showed low heterotrophic activity throughout the year. In comparison with temperate oceans, the percentage of active Bacteria in the uptake of the substrates was relatively high, even during the winter season. [ABSTRACT FROM AUTHOR]

We present measurements of glucose, amino acids, and adenosine triphosphate (ATP) bacterial uptake at tracer concentrations across an oceanic gradient from the Cape Blanc upwelling to the Northeast Atlantic subtropical gyre. The bulk uptake of the compounds increased in the upwelling, with amino acids being the most actively taken up substrate (up to 20 pmol L-1 h-1). The single-cell activity of the bacterial groups also increased in the upwelling, particularly for Rhodobacteraceae (up to 94% of active cells), but this group had low activity in oligotrophic waters (< 10% of active cells), which suggests it is exclusively adapted to high-nutrient conditions. The percentage of SAR11 active cells was relatively high in the upwelling area, particularly for glucose and amino acid uptake (up to 53% of active cells), which suggests that some members of this group are also adapted to nutrient-rich environments. Of the broad phylogenetic groups tested, Bacteroidetes were the least active and Alpha- and Gammaproteobacteria showed similar percentages of active cells in amino acid uptake (∼ 30%). Alphaproteobacteria had the highest percent of cells involved in glucose uptake, while Gammaproteobacteria dominated ATP uptake. This general pattern was confirmed in a broader analysis that included data from contrasting marine environments, which suggests that major phylogenetic groups of bacteria participate differently in the turnover of these low-molecular-weight organics. Our results support the view that broad phylogenetic groups can be identified within the bacterial 'black box' with different patterns in the cycling of organic matter. Analyzing them may help us understand, and ultimately predict, oceanic carbon processing. [ABSTRACT FROM AUTHOR]

The seasonal variation in the grazing effect of mixotrophic flagellates on bacterioplankton was assessed during an annual cycle in an oligotrophic coastal station in the northwest Mediterranean Sea. Ingestion rates of fluorescently labeled bacteria were estimated for different size categories of phytoflagellates (PF) and heterotrophic flagellates (HF) in short-term experiments and compared with long-term grazing estimates and published empirical models. The mixotrophic flagellates included haptophyte-like cells, cryptophytes, and dinoflagellates. The group-specific grazing rates (SGR) averaged 1.1 (3-5 µm PF), 1.3 (5-20 µm PF), 4.0 (<5 µm HF), and 15.4 bacteria individual-1 h-1 (5-20 µm HF). Lower SGR but higher abundances of PF resulted in an average mixotroph contribution of 50% to the total flagellate grazing. Remarkably, the effect was relatively high all through the year (35-65%). Regardless of the presence of chloroplasts, flagellates <5 mm in size accounted, on average, for about 80% of total flagellate bacterivory and ingested a large percentage of their cell carbon per day from bacteria. Soluble reactive phosphorus concentration was negatively correlated with the ingestion rate of both groups of PF, suggesting that mixotrophic flagellates would be using their phagotrophic capability to obtain phosphorus when this nutrient is limiting. HF grazing activity showed a marked seasonality, with grazing being higher during the warmer seasons, and clearance rates were positively correlated with water temperature. Total bacterivory accounted for most of the bacterial production. Short-term and long-term bacterivory measurements were highly correlated, confirming that the smallest flagellates were the main causative agent of bacterial loss. The bacterivory values were also well correlated to a published empirical model that considers HF as the only bacterivorous. However, this model underestimated (up to 50%) total flagellate grazing during periods of high effect of mixotrophic flagellates. [ABSTRACT FROM AUTHOR]