Seasonal assemblages and short-lived blooms in coastal north-west Atlantic Ocean bacterioplankton

Impact of wildfire ash on bacterioplankton abundance and community composition in a coastal embayment (Ría de Vigo, NW Spain)

Wildfire ash can have an impact on coastal prokaryotic plankton. To understand the extent to which community composition and abundance of coastal prokaryotes are affected by ash, two ash addition experiments were performed. Ash from a massive wildfire that took place in the Ría de Vigo watershed in October 2017 was added to natural surface water samples collected in the middle sector of the ría during the summer of 2019 and winter of 2020, and incubated for 72 h, under natural water temperature and irradiance conditions. Plankton responses were assessed through chlorophyll a and bacterial abundance measurements. Prokaryotic DNA was analyzed using 16S rRNA gene partial sequencing. In summer, when nutrient concentrations were low in the ría, the addition of ash led to an increase in phytoplankton and bacterial abundance, increasing the proportions of Alteromonadales, Flavobacteriales, and the potentially pathogenic Vibrio, among other taxa. After the winter runoff events, nutrient concentrations in the Ría de Vigo were high, and only minor changes in bacterial abundance were detected. Our findings suggest that the compounds associated with wildfire ash can alter the composition of bacterioplanktonic communities, which is relevant information for the management of coastal ecosystems in fire-prone areas.

Taxonomic and functional stability overrules seasonality in polar benthic microbiomes

Coastal shelf sediments are hot spots of organic matter mineralization. They receive up to 50% of primary production, which, in higher latitudes, is strongly seasonal. Polar and temperate benthic bacterial communities, however, show a stable composition based on comparative 16S rRNA gene sequencing despite different microbial activity levels. Here, we aimed to resolve this contradiction by identifying seasonal changes at the functional level, in particular with respect to algal polysaccharide degradation genes, by combining metagenomics, metatranscriptomics, and glycan analysis in sandy surface sediments from Isfjorden, Svalbard. Gene expressions of diverse carbohydrate-active enzymes changed between winter and spring. For example, β-1,3-glucosidases (e.g. GH30, GH17, GH16) degrading laminarin, an energy storage molecule of algae, were elevated in spring, while enzymes related to α-glucan degradation were expressed in both seasons with maxima in winter (e.g. GH63, GH13_18, and GH15). Also, the expression of GH23 involved in peptidoglycan degradation was prevalent, which is in line with recycling of bacterial biomass. Sugar extractions from bulk sediments were low in concentrations during winter but higher in spring samples, with glucose constituting the largest fraction of measured monosaccharides (84% ± 14%). In porewater, glycan concentrations were ~18-fold higher than in overlying seawater (1107 ± 484 vs. 62 ± 101 μg C l-1) and were depleted in glucose. Our data indicate that microbial communities in sandy sediments digest and transform labile parts of photosynthesis-derived particulate organic matter and likely release more stable, glucose-depleted residual glycans of unknown structures, quantities, and residence times into the ocean, thus modulating the glycan composition of marine coastal waters.

A multiyear time series (2004-2012) of bacterial and archaeal community dynamics in a changing Arctic Ocean

Climate change is profoundly impacting the Arctic, leading to a loss of multiyear sea ice and a warmer, fresher upper Arctic Ocean. The response of microbial communities to these climate-mediated changes is largely unknown. Here, we document the interannual variation in bacterial and archaeal communities across a 9-year time series of the Canada Basin that includes two historic sea ice minima (2007 and 2012). We report an overall loss of bacterial and archaeal community richness and significant shifts in community composition. The magnitude and period of most rapid change differed between the stratified water layers. The most pronounced changes in the upper water layers (surface mixed layer and upper Arctic water) occurred earlier in the time series, while changes in the lower layer (Pacific-origin water) occurred later. Shifts in taxonomic composition across time were subtle, but a decrease in Bacteroidota taxa and increase in Thaumarchaeota and Euryarchaeota taxa were the clearest signatures of change. This time series provides a rare glimpse into the potential influence of climate change on Arctic microbial communities; extension to the present day should contribute to deeper insights into the trajectory of Arctic marine ecosystems in response to warming and freshening.

Decoupling of respiration rates and abundance in marine prokaryoplankton

The ocean-atmosphere exchange of CO2 largely depends on the balance between marine microbial photosynthesis and respiration. Despite vast taxonomic and metabolic diversity among marine planktonic bacteria and archaea (prokaryoplankton)1-3, their respiration usually is measured in bulk and treated as a 'black box' in global biogeochemical models4; this limits the mechanistic understanding of the global carbon cycle. Here, using a technology for integrated phenotype analyses and genomic sequencing of individual microbial cells, we show that cell-specific respiration rates differ by more than 1,000× among prokaryoplankton genera. The majority of respiration was found to be performed by minority members of prokaryoplankton (including the Roseobacter cluster), whereas cells of the most prevalent lineages (including Pelagibacter and SAR86) had extremely low respiration rates. The decoupling of respiration rates from abundance among lineages, elevated counts of proteorhodopsin transcripts in Pelagibacter and SAR86 cells and elevated respiration of SAR86 at night indicate that proteorhodopsin-based phototrophy3,5-7 probably constitutes an important source of energy to prokaryoplankton and may increase growth efficiency. These findings suggest that the dependence of prokaryoplankton on respiration and remineralization of phytoplankton-derived organic carbon into CO2 for its energy demands and growth may be lower than commonly assumed and variable among lineages.

Temporal variation in the prokaryotic community of a nearshore marine environment

Prokaryotic communities inhabiting surface waters of temperate areas exhibit patterns of seasonal succession. Generally, studies describing these temporal changes are not performed in the proximity to the coast. In the present study, temporal variation of these communities was determined in surface waters at two stations located in the close proximity to the eastern shore of the northern Adriatic Sea. Sequencing of the V4 region of the 16S rRNA gene identified the highest community richness in December with distinct shifts in community structure between periods from April to May, June to October, and November to March. Temperature was shown to be the main environmental force explaining community temporal variation. The NS5 marine group, uncultured Cryomorphaceae, SAR86 clade, and Synechococcus were present throughout the year. Members without know relatives within Rhodobacteraceae and the NS4 marine group were more pronounced in the period from April to May, the AEGEAN-169 marine group, SAR11 subclade III, and HIMB11 in the period from June to October, and SAR11 subclade Ia and Archaea in the period from November to March. Litoricola and OM60 (NOR5) clade were characteristic for both the community sampled from April to May and November to March. Taken together, prokaryotic communities inhabiting nearshore surface waters exhibit a general pattern in community structure similar to other surface associated assemblages of temperate areas. However, the identified specific community composition and temporal patterns differ from other coastal areas.

Opportunistic diseases in marine eukaryotes: Could Bacteroidota be the next threat to ocean life?

Bacteria within the phylum Bacteroidota (Bacteroidetes) are known to cause devastating and widespread disease outbreaks in marine eukaryotic hosts. However, with few pathogens described in detail, their prevalence and virulence strategies remain largely unknown. Here, we systematically reviewed the literature to evaluate the current understanding of Bacteroidota that cause disease in marine hosts. Isolates affiliated with the genera Tenacibaculum and Aquimarina (Flavobacteriaceae) were the most widely reported and characterized pathogens. Although cultured isolates were predominantly Flavobacteriia, culture-independent studies also found classes Bacteroidia, Cytophagia and Sphingobacteriia associated with disease. We found that pathogenic marine Bacteroidota largely conformed to an opportunistic lifestyle but could also act as secondary pathogens or were involved in polymicrobial diseases. Many diseases were also associated with an environmental stressor, especially those affecting coral, macroalgae and fish. Key virulence traits included the production of adhesins and host tissue-degrading enzymes. Overall, the nature of disease involving Bacteroidota pathogens appears to be an outcome of complex host-pathogen-environment interactions; however, our understanding of virulence remains limited by the lack of functional characterization studies. This is concerning as Bacteroidota have the potential to emerge as a serious threat to marine ecosystems and aquaculture industries, driven by global changes in ocean conditions.

Seasonal bacterial niche structures and chemolithoautotrophic ecotypes in a North Atlantic fjord

Quantifying the temporal change of bacterial communities is essential to understanding how both natural and anthropogenic pressures impact the functions of coastal marine ecosystems. Here we use weekly microbial DNA sampling across four years to show that bacterial phyla have distinct seasonal niches, with a richness peak in winter (i.e., an inverse relationship with daylength). Our results suggest that seasonal fluctuations, rather than the kinetic energy or resource hypotheses, dominated the pattern of bacterial diversity. These findings supplement those from global analyses which lack temporal replication and present few data from winter months in polar and temperate regions. Centered log-ratio transformed data provided new insights into the seasonal niche partitioning of conditionally rare phyla, such as Modulibacteria, Verrucomicrobiota, Synergistota, Deinococcota, and Fermentibacterota. These patterns could not be identified using the standard practice of ASV generation followed by rarefaction. Our study provides evidence that five globally relevant ecotypes of chemolithoautotrophic bacteria from the SUP05 lineage comprise a significant functional group with varying seasonal dominance patterns in the Bedford Basin.

Highly-resolved interannual phytoplankton community dynamics of the coastal Northwest Atlantic

Microbial observatories can track phytoplankton at frequencies that resolve monthly, seasonal, and multiyear trends in environmental change from short-lived events. Using 4-years of weekly flow cytometry along with chloroplast and cyanobacterial 16S rRNA gene sequence data from a time-series station in the coastal Northwest Atlantic (Bedford Basin, Nova Scotia, Canada), we analyzed temporal observations for globally-relevant genera (e.g., Bolidomonas, Teleaulax, Minidiscus, Chaetoceros, Synechococcus, and Phaeocystis) in an oceanic region that has been recognized as a likely hotspot for phytoplankton diversity. Contemporaneous Scotian Shelf data also collected during our study established that the major phytoplankton within the Bedford Basin were important in the Scotian Shelf during spring and fall, therefore pointing to their broader significance within the coastal Northwest Atlantic (NWA). Temporal trends revealed a subset of indicator taxa along with their DNA signatures (e.g., Eutreptiella and Synechococcus), whose distribution patterns make them essential for timely detection of environmentally-driven shifts in the NWA. High-resolution sampling was key to identifying important community shifts towards smaller phytoplankton under anomalous environmental conditions, while further providing a detailed molecular view of community compositions underpinning general phytoplankton succession within the coastal NWA. Our study demonstrates the importance of accessible coastal time-series sites where high-frequency DNA sampling allows for the detection of shifting baselines in phytoplankton communities.

Physical mixing in coastal waters controls and decouples nitrification via biomass dilution

Changes in both quantity and speciation of nitrogen in coastal waters impact phytoplankton communities, contributing to eutrophication and harmful algal blooms. Multidisciplinary oceanographic time series of high resolution are rare but crucial for identifying complex mechanisms that underlie such anthropogenic impacts. Analysis and modeling of such a time series from a seasonally stratified fjord showed that dilution of nitrifier biomass by variable winter mixing altered the timing and rates of nitrification, which converts ammonia to nitrite and nitrate. This reveals a link among climate-sensitive physical dynamics, nitrifier abundance, and diversity, with controls on phytoplankton ecology. The findings imply that explicit measurement and modeling of microbial communities will be required to project impacts of climate change on coastal ecosystems.

Nitrification is a central process of the aquatic nitrogen cycle that controls the supply of nitrate used in other key processes, such as phytoplankton growth and denitrification. Through time series observation and modeling of a seasonally stratified, eutrophic coastal basin, we demonstrate that physical dilution of nitrifying microorganisms by water column mixing can delay and decouple nitrification. The findings are based on a 4-y, weekly time series in the subsurface water of Bedford Basin, Nova Scotia, Canada, that included measurement of functional (amoA) and phylogenetic (16S rRNA) marker genes. In years with colder winters, more intense winter mixing resulted in strong dilution of resident nitrifiers in subsurface water, delaying nitrification for weeks to months despite availability of ammonium and oxygen. Delayed regrowth of nitrifiers also led to transient accumulation of nitrite (3 to 8 μmol · kg_sw⁻¹) due to decoupling of ammonia and nitrite oxidation. Nitrite accumulation was enhanced by ammonia-oxidizing bacteria (Nitrosomonadaceae) with fast enzyme kinetics, which temporarily outcompeted the ammonia-oxidizing archaea (Nitrosopumilus) that dominated under more stable conditions. The study reveals how physical mixing can drive seasonal and interannual variations in nitrification through control of microbial biomass and diversity. Variable, mixing-induced effects on functionally specialized microbial communities are likely relevant to biogeochemical transformation rates in other seasonally stratified water columns. The detailed study reveals a complex mechanism through which weather and climate variability impacts nitrogen speciation, with implications for coastal ecosystem productivity. It also emphasizes the value of high-frequency, multiparameter time series for identifying complex controls of biogeochemical processes in aquatic systems.

A DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin

Plankton samples have been routinely collected and preserved in formalin in many laboratories and museums for more than 100 years. Recently, attention has turned to use DNA information from formalin-fixed samples to examine changes in plankton diversity over time. However, no molecular ecological studies have evaluated the impact of formalin fixation on the genetic composition of the plankton community structure. Here, we developed a method for extracting DNA from archived formalin-preserved plankton samples to determine their community structure by a DNA metabarcoding approach. We found that a lysis solution consisting of borate-NaOH buffer (pH 11) with SDS and proteinase K effectively cleaved the cross-link formed by formalin fixation. DNA was extracted from samples preserved for decades in formalin, and the diatom community of the extracted DNA was in good agreement with the microscopy analysis. Furthermore, we stored a plankton sample for 1.5 years and demonstrated that 18S rRNA gene community structures did not change significantly from non-formalin-fixed, time-zero samples. These results indicate that our method can be used to describe the original community structure of plankton archived in formalin for years. Our approach will be useful for examining the long-term variation of plankton diversity by metabarcoding analysis of 18S rRNA gene community structure.

Impacts of copper and lead exposure on prokaryotic communities from contaminated contrasted coastal seawaters: the influence of previous metal exposure

Our understanding of environmental factors controlling prokaryotic community is largely hampered by the large environmental variability across spatial scales (e.g. trace metal contamination, nutrient enrichment and physicochemical variations) and the broad diversity of bacterial pre-exposure to environmental factors. In this article, we investigated the specific influence of copper (Cu) and lead (Pb) on prokaryotic communities from the uncontaminated site, using mesocosm experiments. In addition, we studied how pre-exposure (i.e. life history) affects communities, with reference to previous metal exposure on the response of three prokaryotic communities to similar Cu exposition. This study showed a stronger influence of Cu contamination than Pb contamination on prokaryotic diversity and structure. We identified 12 and 34 bacterial families and genera, respectively, contributing to the significant differences observed in community structure between control and spiked conditions. Taken altogether, our results point toward a combination of direct negative responses to Cu contamination and indirect responses mediated by interaction with phytoplankton. These identified responses were largely conditioned by the previous exposure of community to contaminants.

Persistent El Niño driven shifts in marine cyanobacteria populations

In the California Current Ecosystem, El Niño acts as a natural phenomenon that is partially representative of climate change impacts on marine bacteria at timescales relevant to microbial communities. Between 2014–2016, the North Pacific warm anomaly (a.k.a., the “blob”) and an El Niño event resulted in prolonged ocean warming in the Southern California Bight (SCB). To determine whether this “marine heatwave” resulted in shifts in microbial populations, we sequenced the rpoC1 gene from the biogeochemically important picocyanobacteria Prochlorococcus and Synechococcus at 434 time points from 2009–2018 in the MICRO time series at Newport Beach, CA. Across the time series, we observed an increase in the abundance of Prochlorococcus relative to Synechococcus as well as elevated frequencies of ecotypes commonly associated with low-nutrient and high-temperature conditions. The relationships between environmental and ecotype trends appeared to operate on differing temporal scales. In contrast to ecotype trends, most microdiverse populations were static and possibly reflect local habitat conditions. The only exceptions were microdiversity from Prochlorococcous HLI and Synechococcus Clade II that shifted in response to the 2015 El Niño event. Overall, Prochlorococcus and Synechococcus populations did not return to their pre-heatwave composition by the end of this study. This research demonstrates that extended warming in the SCB can result in persistent changes in key microbial populations.

Patiriisocius marinistellae gen. nov., sp. nov., isolated from the starfish Patiria pectinifera, and reclassification of Ulvibacter marinus as a member of the genus Patiriisocius comb. nov

A marine strain, designated KK4T, was isolated from the surface of a starfish, Patiria pectinifera, which was collected from seawater off the coast of Hokkaido, Japan. Strain KK4T is a Gram-stain-negative, non-spore-forming, rod-shaped, aerobic bacterium that forms yellow-pigmented colonies. A phylogenetic relationship analysis, based on 16S rRNA gene sequences, revealed that strain KK4T was closely related to Ulvibacter marinus IMCC12008T, Ulvibacter antarcticus IMCC3101T and Ulvibacter litoralis KMM 3912T, with similarities of 96.9, 95.8 and 95.6 %, respectively, but low sequence similarities (<94 %) among other genera in the family Flavobacteriaceae . Genomic similarities between strain KK4T and the three Ulvibacter type strains based on average nucleotide identity and digital DNA–DNA hybridization values were lower than the species delineation thresholds. Moreover, phylogenetic tree based on genome sequences showed that strain KK4T was clustered with U. marinus IMCC12008T and formed a branch independent from the cluster including type species of the genera Ulvibacter , Marixanthomonas , Marinirhabdus , Aureitalea and Aequorivita . Amino acid identity values between strain KK4T/ U. marinus IMCC12008T and the neighbour type species/strains were 61.9–68.2% and 61.5–67.4 %, which were lower than the genus delineation threshold, implying the novel genus status of strain KK4T. Strain KK4T growth occurred at pH 6.0–9.0, 4–30 °C and in NaCl concentrations of 0.5–5.0 %, and optimally at pH 7.0, 25 °C and 3.0 %, respectively. Unlike Ulvibacter strains, strain KK4T could assimilate glucose, mannose, galactose and acetate. The major quinone and fatty acids were menaquinone-6 and iso-C15 : 0 (27.5 %), iso-C15 : 1 G (22.5 %) and iso-C17 : 0 3-OH (12.8 %), respectively. Based on genetic, phylogenetic and phenotypic properties, strain KK4T represents a novel species of the genus Patiriisocius, for which the name Patiriisocius marinistellae gen. nov., sp. nov. is proposed. The type strain is KK4T (=JCM 33344T=KCTC 72225T). In addition, based on the current data, Ulvibacter marinus should be reclassified as Patiriisocius marinus comb. nov.

Modelling Free-Living and Particle-Associated Bacterial Assemblages across the Deep and Hypoxic Lower St. Lawrence Estuary

The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada is an appealing ecosystem for studying how microbial communities and metabolic processes are related to environmental change. Ocean and climate variability result in large spatiotemporal variations in environmental conditions and oceanographic processes. The EGSL is also exposed to a variety of additional human pressures that threaten its integrity and sustainable use, including shipping, aquiculture, coastal development, and oil exploration. To monitor and perhaps mitigate the impacts of these human activities on the EGSL, a comprehensive understanding of the biological communities is required. In this study, we provide the first comprehensive view of bacterial diversity in the EGSL and describe the distinct bacterial assemblages associated with different environmental habitats. This work therefore provides an important baseline ecological framework for bacterial communities in the EGSL useful for further studies on how these communities may respond to environmental change.

The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada are among the largest and most productive coastal ecosystems in the world. Very little information on bacterial diversity exists, hampering our understanding of the relationships between bacterial community structure and biogeochemical function in the EGSL. During the productive spring period, we investigated free-living and particle-associated bacterial communities across the stratified waters of the Lower St. Lawrence Estuary, including the particle-rich surface and bottom boundary layers. Modelling of community structure based on 16S rRNA gene and transcript diversity identified bacterial assemblages specifically associated with four habitat types defined by water mass (upper water or lower water column) and size fraction (free living or particle associated). Assemblages from the upper waters represent sets of cooccurring bacterial populations that are widely distributed across Lower St. Lawrence Estuary surface waters and likely key contributors to organic matter degradation during the spring. In addition, we provide strong evidence that particles in deep hypoxic waters and the bottom boundary layer support a metabolically active bacterial community that is compositionally distinct from those of surface particles and the free-living communities. Among the distinctive features of the bacterial assemblage associated with lower-water particles was the presence of uncultivated lineages of Deltaproteobacteria, including marine myxobacteria. Overall, these results provide an important ecological framework for further investigations of the biogeochemical contributions of bacterial populations in this important coastal marine ecosystem.

IMPORTANCE The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada is an appealing ecosystem for studying how microbial communities and metabolic processes are related to environmental change. Ocean and climate variability result in large spatiotemporal variations in environmental conditions and oceanographic processes. The EGSL is also exposed to a variety of additional human pressures that threaten its integrity and sustainable use, including shipping, aquiculture, coastal development, and oil exploration. To monitor and perhaps mitigate the impacts of these human activities on the EGSL, a comprehensive understanding of the biological communities is required. In this study, we provide the first comprehensive view of bacterial diversity in the EGSL and describe the distinct bacterial assemblages associated with different environmental habitats. This work therefore provides an important baseline ecological framework for bacterial communities in the EGSL useful for further studies on how these communities may respond to environmental change.

Effects of Vertical Water Mass Segregation on Bacterial Community Structure in the Beaufort Sea

The Arctic Ocean is one of the least well-studied marine microbial ecosystems. Its low-temperature and low-salinity conditions are expected to result in distinct bacterial communities, in comparison to lower latitude oceans. However, this is an ocean currently in flux, with climate change exerting pronounced effects on sea-ice coverage and freshwater inputs. How such changes will affect this ecosystem are poorly constrained. In this study, we characterized the bacterial community compositions at different depths in both coastal, freshwater-influenced, and pelagic, sea-ice-covered locations in the Beaufort Sea in the western Canadian Arctic Ocean. The environmental factors controlling the bacterial community composition and diversity were investigated. Alphaproteobacteria dominated the bacterial communities in samples from all depths and stations. The Pelagibacterales and Rhodobacterales groups were the predominant taxonomic representatives within the Alphaproteobacteria. Bacterial communities in coastal and offshore samples differed significantly, and vertical water mass segregation was the controlling factor of community composition among the offshore samples, regardless of the taxonomic level considered. These data provide an important baseline view of the bacterial community in this ocean system that will be of value for future studies investigating possible changes in the Arctic Ocean in response to global change and/or anthropogenic disturbance.

Bayesian Inference of Microbial Community Structure from Metagenomic Data Using BioMiCo

Microbial samples taken from an environment often represent mixtures of communities, where each community is composed of overlapping assemblages of species. Such data represent a serious analytical challenge, as the community structures will be present as complex mixtures, there will be very large numbers of component species, and the species abundance will often be sparse over samples. The structure and complexity of these samples will vary according to both biotic and abiotic factors, and classical methods of data analysis will have a limited value in this setting. A novel Bayesian modeling framework, called BioMiCo, was developed to meet this challenge. BioMiCo takes abundance data derived from environmental DNA, and models each sample by a two-level mixture, where environmental OTUs contribute community structures, and those structures are related to the known biotic and abiotic features of each sample. The model is constrained by Dirichlet priors, which induces compact structures, minimizes variance, and maximizes model interpretability. BioMiCo is trained on a portion of the data, and once trained a BioMiCo model can be employed to make predictions about the features of new samples. This chapter provides a set of protocols that illustrate the application of BioMiCo to real inference problems. Each protocol is designed around the analysis of a real dataset, which was carefully chosen to illustrate specific aspects of real data analysis. With these protocols, users of BioMiCo will be able to undertake basic research into the properties of complex microbial systems, as well as develop predictive models for applied microbiomics.

Drivers of Regional Bacterial Community Structure and Diversity in the Northwest Atlantic Ocean

The fundamental role of bacteria in global biogeochemical cycles warrants a thorough understanding of the factors controlling bacterial community structure. In this study, the integrated effect of seasonal differences and spatial distribution on bacterial community structure and diversity were investigated at the regional scale. We conducted a comprehensive bacterial survey, with 451 samples of the Scotian Shelf sector of the Northwest Atlantic Ocean during spring and fall of 2014 and 2016, to analyze the effects of physicochemical gradients on bacterial community structure. Throughout the region, Pelagibacteraceae and Rhodobacteraceae were the most common in the free-living fraction, while Flavobacteriia and Deltaproteobacteria were more abundant in the particle-associated fraction. Overall, there was strong covariation of the microbial community diversity from the two size fractions. This relationship existed despite the statistically significant difference in community structure between the free-living and particle-associated size fractions. In both size fractions, distribution patterns of bacterial taxa, and species within taxa, displayed temporal and spatial preferences. Distinct bacterial assemblages specific to season and depth in the water column were identified. These distinct assemblages, consistent for both 2014 and 2016, suggested replicable patterns in microbial communities for spring and fall in this region. Over all sites, temperature and oxygen values were highly correlated with community similarity, and salinity and oxygen values were the most strongly positively- and negatively correlated with alpha diversity, respectively. However, the strengths of these correlations depended on the depth and season sampled. The bathymetry of the Scotian Shelf, the abrupt shelf break to the Scotian Slope and the major ocean currents dominating in the region led to the formation of distinct on-shelf and off-shelf bacterial communities both in spring and fall. The highest species richness was observed at the shelf break, where water masses from the two major currents meet. Our study establishes the baseline for assessing future changes in the bacterial community of the Scotian Shelf waters, a rapidly changing sector of the Atlantic Ocean.

The Environment and Cyanophage Diversity: Insights From Environmental Sequencing of DNA Polymerase

Globally distributed and abundant cyanophages in the family Myoviridae have dsDNA genomes with variable gene content, including host-derived auxiliary metabolic genes (AMGs) that potentially can facilitate viral replication. However, it is not well understood how this variation in gene content interacts with environmental variables to shape cyanomyovirus communities. This project correlated the genetic repertoire of cyanomyoviruses with their phyologeny, and investigated cyanomyovirus ecotype distribution as a function of environmental conditions across locations and seasons. Reference cyanomyovirus genomes were compared for their overlap in gene content to infer phyologenetic distances, and these distances were compared to distances calculated based on DNA polymerase (gp43) gene sequences. In turn, gp43 partial gene sequences amplified from natural cyanophage communities were used to describe cyanomyovirus community composition and to assess the relationship between environmental variables. The results showed the following: (1) DNA polymerase gene phylogeny generally correlated with the similarity in gene content among reference cyanomyoviruses, and thus can be used to describe environmental cyanomyovirus communities; (2) spatial and seasonal patterns in cyanomyovirus communities were related to environmental variables; (3) salinity and temperature, combined with nutrient concentration were predictors of cyanomyovirus richness, diversity and community composition. This study shows that environmental variables shape viral communities by drawing on a diverse seed bank of viral genotypes. From these results it is evident that that viral ecotypes with their corresponding genetic repertoires underlie selection pressures. However, the mechanisms involved in selecting for specific viral genotypes remain to be fully understood.

Vertical and Seasonal Patterns Control Bacterioplankton Communities at Two Horizontally Coherent Coastal Upwelling Sites off Galicia (NW Spain)

Analysis of seasonal patterns of marine bacterial community structure along horizontal and vertical spatial scales can help to predict long-term responses to climate change. Several recent studies have shown predictable seasonal reoccurrence of bacterial assemblages. However, only a few have assessed temporal variability over both horizontal and vertical spatial scales. Here, we simultaneously studied the bacterial community structure at two different locations and depths in shelf waters of a coastal upwelling system during an annual cycle. The most noticeable biogeographic patterns observed were seasonality, horizontal homogeneity, and spatial synchrony in bacterial diversity and community structure related with regional upwelling-downwelling dynamics. Water column mixing eventually disrupted bacterial community structure vertical heterogeneity. Our results are consistent with previous temporal studies of marine bacterioplankton in other temperate regions and also suggest a marked influence of regional factors on the bacterial communities inhabiting this coastal upwelling system. Bacterial-mediated carbon fluxes in this productive region appear to be mainly controlled by community structure dynamics in surface waters, and local environmental factors at the base of the euphotic zone.

Dynamics of Heterotrophic Bacterial Assemblages within Synechococcus Cultures

Interactions between photoautotrophic and heterotrophic microorganisms are central to the marine microbial ecosystem. Lab cultures of one of the dominant marine photoautotrophs, Synechococcus, have historically been difficult to render axenic, presumably because these bacteria depend upon other organisms to grow under these conditions. These tight associations between Synechococcus and heterotrophic bacteria represent a good relevant system to study interspecies interactions. Ten individual Synechococcus strains, isolated from eutrophic and oligotrophic waters, were chosen for investigation. Four to six dominant associated heterotrophic bacteria were detected in the liquid cultures of each Synechococcus isolate, comprising members of the Cytophaga-Flavobacteria-Bacteroides (CFB) group (mainly from Flavobacteriales and Cytophagales), Alphaproteobacteria (mainly from the Roseobacter clade), Gammaproteobacteria (mainly from the Alteromonadales and Pseudomonadales), and Actinobacteria The presence of the CFB group, Gammaproteobacteria, and Actinobacteria showed clear geographic patterns related to the isolation environments of the Synechococcus bacteria. An investigation of the population dynamics within a growing culture (XM-24) of one of the isolates, including an evaluation of the proportions of cells that were free-living versus aggregated/attached, revealed interesting patterns for different bacterial groups. In Synechococcus sp. strain XM-24 culture, flavobacteria, which was the most abundant group throughout the culture period, tended to be aggregated or attached to the Synechococcus cells, whereas the actinobacteria demonstrated a free-living lifestyle, and roseobacters displayed different patterns depending on the culture growth phase. Factors contributing to these succession patterns for the heterotrophs likely include interactions among the culture community members, their relative abilities to utilize different compounds produced by Synechococcus cells and changes in the compounds released as culture growth proceeds, and their responses to other changes in the environmental conditions throughout the culture period.IMPORTANCE Marine microbes exist within an interactive ecological network, and studying their interactions is an important part of understanding their roles in global biogeochemical cycling and the determinants of microbial diversity. In this study, the dynamic relationships between Synechococcus spp. and their associated heterotrophic bacteria were investigated. Synechococcus-associated heterotrophic bacteria had similar geographic distribution patterns as their "host" and displayed different lifestyles (free-living versus attached/aggregated) according to the Synechococcus culture growth phases. Combined organic carbon composition and bacterial lifestyle data indicated a potential for succession in carbon utilization patterns by the dominant associated heterotrophic bacteria. Comprehending the interactions between photoautotrophs and heterotrophs and the patterns of organic carbon excretion and utilization is critical to understanding their roles in oceanic biogeochemical cycling.

Unravelling and Reconstructing the Nexus of Salinity, Electricity, and Microbial Ecology for Bioelectrochemical Desalination

Microbial desalination cells (MDCs) are an emerging concept for simultaneous water/wastewater treatment and energy recovery. The key to developing MDCs is to understand fundamental problems, such as the effects of salinity on system performance and the role of microbial community and functional dynamics. Herein, a tubular MDC was operated under a wide range of salt concentrations (0.05-4 M), and the salinity effects were comprehensively examined. The MDC generated higher current with higher salt concentrations in the desalination chamber. When fed with 4 M NaCl, the MDC achieve a current density of 300 A m^-3 (anode volume), which was one of the highest among bioelectrochemical system studies. Community analysis and electrochemical measurements suggested that electrochemically active bacteria Pseudomonas and Acinetobacter transferred electrons extracellularly via electron shuttles, and the consequent ion migration led to high anode salinities and conductivity that favored their dominance. Predictive functional dynamics and Bayesian networks implied that the taxa putatively not capable of extracellular electron transfer (e.g., Bacteroidales and Clostridiales) might indirectly contribute to bioelectrochemical desalination. By integrating the Bayesian network with logistic regression, current production was successfully predicted from taxonomic data. This study has demonstrated uncompromised system performance under high salinity and thus has highlighted the potential of MDCs as an energy-efficient technology to address water-energy challenges. The statistical modeling approach developed in this study represents a significant step toward understating microbial communities and predicting system performance in engineered biological systems.

Annual community patterns are driven by seasonal switching between closely related marine bacteria

Marine microbes exhibit seasonal cycles in community composition, yet the key drivers of these patterns and microbial population fidelity to specific environmental conditions remain to be determined. To begin addressing these questions, we characterized microbial dynamics weekly for 3 years at a temperate, coastal site with dramatic environmental seasonality. This high-resolution time series reveals that changes in microbial community composition are not continuous; over the duration of the time series, the community instead resolves into distinct summer and winter profiles with rapid spring and fall transitions between these states. Here, we show that these community shifts involve switching between closely related strains that exhibit either summer or winter preferences. Moreover, taxa repeat this process annually in both this and another temperate coastal time series, suggesting that this phenomenon may be widespread in marine ecosystems. To address potential biogeochemical impacts of these community changes, PICRUSt-based metagenomes predict seasonality in transporters, photosynthetic proteins, peptidases and carbohydrate metabolic pathways in spite of closely related summer- and winter-associated taxa. Thus, even small temperature shifts, such as those predicted by climate change models, could affect both the structure and function of marine ecosystems.

Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula

The marine ecosystem along the Western Antarctic Peninsula undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including phytoplankton blooms that support a highly productive food web. Despite having important implications for the movement of energy and materials through this ecosystem, little is known about how these changes impact bacterial succession in this region. Using 16S rRNA gene amplicon sequencing, we measured changes in free-living bacterial community composition and richness during a 9-month period that spanned winter to the end of summer. Chlorophyll a concentrations were relatively low until summer when a major phytoplankton bloom occurred, followed 3 weeks later by a high peak in bacterial production. Richness in bacterial communities varied between ~1,200 and 1,800 observed operational taxonomic units (OTUs) before the major phytoplankton bloom (out of ~43,000 sequences per sample). During peak bacterial production, OTU richness decreased to ~700 OTUs. The significant decrease in OTU richness only lasted a few weeks, after which time OTU richness increased again as bacterial production declined toward pre-bloom levels. OTU richness was negatively correlated with bacterial production and chlorophyll a concentrations. Unlike the temporal pattern in OTU richness, community composition changed from winter to spring, prior to onset of the summer phytoplankton bloom. Community composition continued to change during the phytoplankton bloom, with increased relative abundance of several taxa associated with phytoplankton blooms, particularly Polaribacter. Bacterial community composition began to revert toward pre-bloom conditions as bacterial production declined. Overall, our findings clearly demonstrate the temporal relationship between phytoplankton blooms and seasonal succession in bacterial growth and community composition. Our study highlights the importance of high-resolution time series sampling, especially during the relatively under-sampled Antarctic winter and spring, which enabled us to discover seasonal changes in bacterial community composition that preceded the summertime phytoplankton bloom.

Insensitivity of Diverse and Temporally Variable Particle-Associated Microbial Communities to Bulk Seawater Environmental Parameters

There is a growing recognition of the roles of marine microenvironments as reservoirs of biodiversity and as sites of enhanced biological activity and in facilitating biological interactions. Here, we examine the bacterial community inhabiting free-living and particle-associated seawater microenvironments at the Pivers Island Coastal Observatory (PICO). 16S rRNA gene libraries from monthly samples (July 2013 to August 2014) were used to identify microbes in seawater in four size fractions: >63 μm (zooplankton and large particles), 63 to 5 μm (particles), 5 to 1 μm (small particles/dividing cells), and <1 μm (free-living prokaryotes). Analyses of microbial community composition highlight the importance of the microhabitat (e.g., particle-associated versus free-living lifestyle) as communities cluster by size fraction, and the microhabitat explains more of the community variability than measured environmental parameters, including pH, particle concentration, projected daily insolation, nutrients, and temperature. While temperature is statistically associated with community changes in the <1-μm and 5- to 1-μm fractions, none of the measured bulk seawater environmental variables are statistically significant in the larger-particle-associated fractions. These results, combined with high particle-associated community variability, especially in the largest size fraction (i.e., >63 μm), suggest that particle composition, including eukaryotes and their associated microbiomes, may be an important factor in selecting for specific particle-associated bacteria.

IMPORTANCE

By comparing levels of particle-associated and free-living bacterial diversity at a coastal location over the course of 14 months, we show that bacteria associated with particles are generally more diverse and appear to be less responsive to commonly measured environmental variables than free-living bacteria. These diverse and highly variable particle-associated communities are likely driven by differences in particle substrates both within the water column at a single time point and due to seasonal changes over the course of the year.

Bacterioplankton Biogeography of the Atlantic Ocean: A Case Study of the Distance-Decay Relationship

In order to determine the influence of geographical distance, depth, and Longhurstian province on bacterial community composition and compare it with the composition of photosynthetic micro-eukaryote communities, 382 samples from a depth-resolved latitudinal transect (51°S–47°N) from the epipelagic zone of the Atlantic ocean were analyzed by Illumina amplicon sequencing. In the upper 100 m of the ocean, community similarity decreased toward the equator for 6000 km, but subsequently increased again, reaching similarity values of 40–60% for samples that were separated by ~12,000 km, resulting in a U-shaped distance-decay curve. We conclude that adaptation to local conditions can override the linear distance-decay relationship in the upper epipelagial of the Atlantic Ocean which is apparently not restrained by barriers to dispersal, since the same taxa were shared between the most distant communities. The six Longhurstian provinces covered by the transect were comprised of distinct microbial communities; ~30% of variation in community composition could be explained by province. Bacterial communities belonging to the deeper layer of the epipelagic zone (140–200 m) lacked a distance-decay relationship altogether and showed little provincialism. Interestingly, those biogeographical patterns were consistently found for bacteria from three different size fractions of the plankton with different taxonomic composition, indicating conserved underlying mechanisms. Analysis of the chloroplast 16S rRNA gene sequences revealed that phytoplankton composition was strongly correlated with both free-living and particle associated bacterial community composition (R between 0.51 and 0.62, p < 0.002). The data show that biogeographical patterns commonly found in macroecology do not hold for marine bacterioplankton, most likely because dispersal and evolution occur at drastically different rates in bacteria.

Microbial Surface Colonization and Biofilm Development in Marine Environments

Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.

Weak Coherence in Abundance Patterns Between Bacterial Classes and Their Constituent OTUs Along a Regulated River

Deductions about the ecology of high taxonomic bacterial ranks (i.e., phylum, class, order) are often based on their abundance patterns, yet few studies have quantified how accurately variations in abundance of these bacterial groups represent the dynamics of the taxa within them. Using 454-pyrosequencing of the 16S rRNA gene, we investigated whether the changes in abundance of six dominant bacterial classes (Actinobacteria, Beta-/Alpha-/Gamma-proteobacteria, Flavobacteria, and Sphingobacteria) along a large dam-regulated river are reflected by those of their constituent Operational Taxonomic Units (OTUs; 97% similarity level). The environmental impact generated by the reservoirs promoted clear compositional shifts in all bacterial classes that resulted from changes in the abundance of individual OTUs rather than from the appearance of new taxa along the river. Abundance patterns at the class level represented the dynamics of only a small but variable proportion of their constituting OTUs, which were not necessarily the most abundant ones. Within most classes, we detected sub-groups of OTUs showing contrasting responses to reservoir-induced environmental changes. Overall, we show that the patterns observed at the class level fail to capture the dynamics of a significant fraction of their constituent members, calling for caution when the ecological attributes of high-ranks are to be interpreted.

A network-based approach to disturbance transmission through microbial interactions

Microbes numerically dominate aquatic ecosystems and play key roles in the biogeochemistry and the health of these environments. Due to their short generations times and high diversity, microbial communities are among the first responders to environmental changes, including natural and anthropogenic disturbances such as storms, pollutant releases, and upwelling. These disturbances affect members of the microbial communities both directly and indirectly through interactions with impacted community members. Thus, interactions can influence disturbance propagation through the microbial community by either expanding the range of organisms affected or buffering the influence of disturbance. For example, interactions may expand the number of disturbance-affected taxa by favoring a competitor or buffer the impacts of disturbance when a potentially disturbance-responsive clade’s growth is limited by an essential microbial partner. Here, we discuss the potential to use inferred ecological association networks to examine how disturbances propagate through microbial communities focusing on a case study of a coastal community’s response to a storm. This approach will offer greater insight into how disturbances can produce community-wide impacts on aquatic environments following transient changes in environmental parameters.

An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis

Meta-omic technologies such as metagenomics, metatranscriptomics and metaproteomics can aid in the understanding of microbial community structure and metabolism. Although powerful, metagenomics alone can only elucidate functional potential. On the other hand, metaproteomics enables the description of the expressed in situ metabolism and function of a community. Here we describe a protocol for cell lysis, protein and DNA isolation, as well as peptide digestion and extraction from marine microbial cells collected on a cartridge filter unit (such as the Sterivex filter unit) and preserved in an RNA stabilization solution (like RNAlater). In mass spectrometry-based proteomics studies, the identification of peptides and proteins is performed by comparing peptide tandem mass spectra to a database of translated nucleotide sequences. Including the metagenome of a sample in the search database increases the number of peptides and proteins that can be identified from the mass spectra. Hence, in this protocol DNA is isolated from the same filter, which can be used subsequently for metagenomic analysis.

Metaproteomics of aquatic microbial communities in a deep and stratified estuary

Here we harnessed the power of metaproteomics to assess the metabolic diversity and function of stratified aquatic microbial communities in the deep and expansive Lower St. Lawrence Estuary, located in eastern Canada. Vertical profiling of the microbial communities through the stratified water column revealed differences in metabolic lifestyles and in carbon and nitrogen processing pathways. In productive surface waters, we identified heterotrophic populations involved in the processing of high and low molecular weight organic matter from both terrestrial (e.g. cellulose and xylose) and marine (e.g. organic compatible osmolytes) sources. In the less productive deep waters, chemosynthetic production coupled to nitrification by MG-I Thaumarchaeota and Nitrospina appeared to be a dominant metabolic strategy. Similar to other studies of the coastal ocean, we identified methanol oxidation proteins originating from the common OM43 marine clade. However, we also identified a novel lineage of methanol-oxidizers specifically in the particle-rich bottom (i.e. nepheloid) layer. Membrane transport proteins assigned to the uncultivated MG-II Euryarchaeota were also specifically detected in the nepheloid layer. In total, these results revealed strong vertical structure of microbial taxa and metabolic activities, as well as the presence of specific "nepheloid" taxa that may contribute significantly to coastal ocean nutrient cycling.

BioMiCo: a supervised Bayesian model for inference of microbial community structure

BACKGROUND

Microbiome samples often represent mixtures of communities, where each community is composed of overlapping assemblages of species. Such mixtures are complex, the number of species is huge and abundance information for many species is often sparse. Classical methods have a limited value for identifying complex features within such data.

RESULTS

Here, we describe a novel hierarchical model for Bayesian inference of microbial communities (BioMiCo). The model takes abundance data derived from environmental DNA, and models the composition of each sample by a two-level hierarchy of mixture distributions constrained by Dirichlet priors. BioMiCo is supervised, using known features for samples and appropriate prior constraints to overcome the challenges posed by many variables, sparse data, and large numbers of rare species. The model is trained on a portion of the data, where it learns how assemblages of species are mixed to form communities and how assemblages are related to the known features of each sample. Training yields a model that can predict the features of new samples. We used BioMiCo to build models for three serially sampled datasets and tested their predictive accuracy across different time points. The first model was trained to predict both body site (hand, mouth, and gut) and individual human host. It was able to reliably distinguish these features across different time points. The second was trained on vaginal microbiomes to predict both the Nugent score and individual human host. We found that women having normal and elevated Nugent scores had distinct microbiome structures that persisted over time, with additional structure within women having elevated scores. The third was trained for the purpose of assessing seasonal transitions in a coastal bacterial community. Application of this model to a high-resolution time series permitted us to track the rate and time of community succession and accurately predict known ecosystem-level events.

CONCLUSION

BioMiCo provides a framework for learning the structure of microbial communities and for making predictions based on microbial assemblages. By training on carefully chosen features (abiotic or biotic), BioMiCo can be used to understand and predict transitions between complex communities composed of hundreds of microbial species.