Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes

Advances in Diversity, Evolutionary Dynamics and Biotechnological Potential of Restriction-Modification Systems

Restriction-modification systems (RMS) are ubiquitous in prokaryotes and serve as primitive immune-like mechanisms that safeguard microbial genomes against foreign genetic elements. Beyond their well-known role in sequence-specific defense, RMS also contribute significantly to genomic stability, drive evolutionary processes, and mitigate the deleterious effects of mutations. This review provides a comprehensive synthesis of current insights into RMS, emphasizing their structural and functional diversity, ecological and evolutionary roles, and expanding applications in biotechnology. By integrating recent advances with an analysis of persisting challenges, we highlight the critical contributions of RMS to both fundamental microbiology and practical applications in biomedicine and industrial biotechnology. Furthermore, we discuss emerging research directions in RMS, particularly in light of novel technologies and the increasing importance of microbial genetics in addressing global health and environmental issues.

Genome-resolved adaptation strategies of Rhodobacterales to changing conditions in the Chesapeake and Delaware Bays

The abundant and metabolically versatile aquatic bacterial order, Rhodobacterales, influences marine biogeochemical cycles. We assessed Rhodobacterales metagenome-assembled genome (MAG) abundance, estimated growth rates, and potential and expressed functions in the Chesapeake and Delaware Bays, two important US estuaries. Phylogenomics of draft and draft/closed Rhodobacterales genomes from this study and others placed 46 nearly complete MAGs from these bays into 11 genera, many were not well characterized. Their abundances varied between the bays and were influenced by temperature, salinity, and silicate and phosphate concentrations. Rhodobacterales genera possessed unique and shared genes for transporters, photoheterotrophy, complex carbon degradation, nitrogen, and sulfur metabolism reflecting their seasonal differences in abundance and activity. Planktomarina genomospecies were more ubiquitous than the more niche specialists, HIMB11, CPC320, LFER01, and MED-G52. Their estimated growth rates were correlated to various factors including phosphate and silicate concentrations, cell density, and light. Metatranscriptomic analysis of four abundant genomospecies commonly revealed that aerobic anoxygenic photoheterotrophy-associated transcripts were highly abundant at night. These Rhodobacterales also differentially expressed genes for CO oxidation and nutrient transport and use between different environmental conditions. Phosphate concentrations and light penetration in the Chesapeake Bay likely contributed to higher estimated growth rates of HIMB11 and LFER01, respectively, in summer where they maintained higher ribosome concentrations and prevented physiological gene expression constraints by downregulating transporter genes compared to the Delaware Bay. Our study highlights the spatial and temporal shifts in estuarine Rhodobacterales within and between these bays reflected through their abundance, unique metabolisms, estimated growth rates, and activity changes.

IMPORTANCE

In the complex web of global biogeochemical nutrient cycling, the Rhodobacterales emerge as key players, exerting a profound influence through their abundance and dynamic activity. While previous studies have primarily investigated these organisms within marine ecosystems, this study delves into their roles within estuarine environments using a combination of metagenomic and metatranscriptomic analyses. We uncovered a range of Rhodobacterales genera, from generalists to specialists, each exhibiting distinct abundance patterns and gene expression profiles. This diversity equips them with the capacity to thrive amidst the varying environmental conditions encountered within dynamic estuarine habitats. Crucially, our findings illuminate the adaptable nature of estuarine Rhodobacterales, revealing their various energy production pathways and diverse resource management, especially during phytoplankton or algal blooms. Whether adopting a free-living or particle-attached existence, these organisms demonstrate remarkable flexibility in their metabolic strategies, underscoring their pivotal role in driving ecosystem dynamics within estuarine ecosystems.

Freshwater plastisphere: a review on biodiversity, risks, and biodegradation potential with implications for the aquatic ecosystem health

The plastisphere, a unique microbial biofilm community colonizing plastic debris and microplastics (MPs) in aquatic environments, has attracted increasing attention owing to its ecological and public health implications. This review consolidates current state of knowledge on freshwater plastisphere, focussing on its biodiversity, community assembly, and interactions with environmental factors. Current biomolecular approaches revealed a variety of prokaryotic and eukaryotic taxa associated with plastic surfaces. Despite their ecological importance, the presence of potentially pathogenic bacteria and mobile genetic elements (i.e., antibiotic resistance genes) raises concerns for ecosystem and human health. However, the extent of these risks and their implications remain unclear. Advanced sequencing technologies are promising for elucidating the functions of plastisphere, particularly in plastic biodegradation processes. Overall, this review emphasizes the need for comprehensive studies to understand plastisphere dynamics in freshwater and to support effective management strategies to mitigate the impact of plastic pollution on freshwater resources.

Toxigenic Vibrio cholerae can cycle between environmental plastic waste and floodwater: Implications for environmental management of cholera

Globally, there has been a significant rise in cholera cases and deaths, with an increase in the number of low- and middle-income countries (LMICs) reporting outbreaks. In parallel, plastic pollution in LMICs is increasing, and has become a major constituent of urban dump sites. The surfaces of environmental plastic pollution can provide a habitat for complex microbial biofilm communities; this so-called 'plastisphere' can also include human pathogens. Under conditions simulating a peri-urban environmental waste pile, we determine whether toxigenic Vibrio cholerae (O1 classical; O1 El Tor; O139) can colonise and persist on plastic following a simulated flooding event. Toxigenic V. cholerae colonized and persisted on plastic and organic waste for at least 14 days before subsequent transfer to either fresh or brackish floodwater, where they can further persist at concentrations sufficient to cause human infection. Taken together, this study suggests that plastics in the environment can act as significant reservoirs for V. cholerae, whilst subsequent transfer to floodwaters demonstrates the potential for the wider dissemination of cholera. Further understanding of how diseases interact with plastic waste will be central for combating infection, educating communities, and diminishing the public health risk of plastics in the environment.

A Gulf Stream frontal eddy harbors a distinct microbiome compared to adjacent waters

Mesoscale oceanographic features, including eddies, have the potential to alter productivity and other biogeochemical rates in the ocean. Here, we examine the microbiome of a cyclonic, Gulf Stream frontal eddy, with a distinct origin and environmental parameters compared to surrounding waters, in order to better understand the processes dominating microbial community assembly in the dynamic coastal ocean. Our microbiome-based approach identified the eddy as distinct from the surround Gulf Stream waters. The eddy-associated microbial community occupied a larger area than identified by temperature and salinity alone, increasing the predicted extent of eddy-associated biogeochemical processes. While the eddy formed on the continental shelf, after two weeks both environmental parameters and microbiome composition of the eddy were most similar to the Gulf Stream, suggesting the effect of environmental filtering on community assembly or physical mixing with adjacent Gulf Stream waters. In spite of the potential for eddy-driven upwelling to introduce nutrients and stimulate primary production, eddy surface waters exhibit lower chlorophyll a along with a distinct and less even microbial community, compared to the Gulf Stream. At the population level, the eddy microbiome exhibited differences among the cyanobacteria (e.g. lower Trichodesmium and higher Prochlorococcus) and in the heterotrophic alpha Proteobacteria (e.g. lower relative abundances of specific SAR11 phylotypes) versus the Gulf Stream. However, better delineation of the relative roles of processes driving eddy community assembly will likely require following the eddy and surrounding waters since inception. Additionally, sampling throughout the water column could better clarify the contribution of these mesoscale features to primary production and carbon export in the oceans.

Species-specific responses of marine bacteria to environmental perturbation

Environmental perturbations shape the structure and function of microbial communities. Oil spills are a major perturbation and resolving spills often requires active measures like dispersant application that can exacerbate the initial disturbance. Species-specific responses of microorganisms to oil and dispersant exposure during such perturbations remain largely unknown. We merged metatranscriptomic libraries with pangenomes to generate Core-Accessory Metatranscriptomes (CA-Metatranscriptomes) for two microbial hydrocarbon degraders that played important roles in the aftermath of the Deepwater Horizon oil spill. The Colwellia CA-Metatranscriptome illustrated pronounced dispersant-driven acceleration of core (~41%) and accessory gene (~59%) transcription, suggesting an opportunistic strategy. Marinobacter responded to oil exposure by expressing mainly accessory genes (~93%), suggesting an effective hydrocarbon-degrading lifestyle. The CA-Metatranscriptome approach offers a robust way to identify the underlying mechanisms of key microbial functions and highlights differences of specialist-vs-opportunistic responses to environmental disturbance.

Porous marine snow differentially benefits chemotactic, motile, and nonmotile bacteria

Particulate organic carbon settling through the marine water column is a key process that regulates the global climate by sequestering atmospheric carbon. The initial colonization of marine particles by heterotrophic bacteria represents the first step in recycling this carbon back to inorganic constituents-setting the magnitude of vertical carbon transport to the abyss. Here, we demonstrate experimentally using millifluidic devices that, although bacterial motility is essential for effective colonization of a particle leaking organic nutrients into the water column, chemotaxis specifically benefits at intermediate and higher settling velocities to navigate the particle boundary layer during the brief window of opportunity provided by a passing particle. We develop an individual-based model that simulates the encounter and attachment of bacterial cells with leaking marine particles to systematically evaluate the role of different parameters associated with bacterial run-and-tumble motility. We further use this model to explore the role of particle microstructure on the colonization efficiency of bacteria with different motility traits. We find that the porous microstructure facilitates additional colonization by chemotactic and motile bacteria, and fundamentally alters the way nonmotile cells interact with particles due to streamlines intersecting with the particle surface.

You Exude What You Eat: How Carbon-, Nitrogen-, and Sulfur-Rich Organic Substrates Shape Microbial Community Composition and the Dissolved Organic Matter Pool

Phytoplankton is the major source of labile organic matter in the sunlit ocean, and they are therefore key players in most biogeochemical cycles. However, studies examining the heterotrophic bacterial cycling of specific phytoplankton-derived nitrogen (N)- and sulfur (S)-containing organic compounds are currently lacking at the molecular level. Therefore, the present study investigated how the addition of N-containing (glycine betaine [GBT]) and S-containing (dimethylsulfoniopropionate [DMSP]) organic compounds, as well as glucose, influenced the microbial production of new organic molecules and the microbial community composition. The chemical composition of microbial-produced dissolved organic matter (DOM) was analyzed by ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) demonstrating that CHO-, CHON-, and CHOS-containing molecules were enriched in the glucose, GBT, and DMSP experiments, respectively. High-throughput sequencing showed that Alteromonadales was the dominant group in the glucose, while Rhodobacterales was the most abundant group in both the GBT and DMSP experiments. Cooccurrence network analysis furthermore indicated more complex linkages between the microbial community and organic molecules in the GBT compared with the other two experiments. Our results shed light on how different microbial communities respond to distinct organic compounds and mediate the cycling of ecologically relevant compounds. IMPORTANCE Nitrogen (N)- and sulfur (S)-containing compounds are normally considered part of the labile organic matter pool that fuels heterotrophic bacterial activity in the ocean. Both glycine betaine (GBT) and dimethylsulfoniopropionate (DMSP) are representative N- and S-containing organic compounds, respectively, that are important phytoplankton cellular compounds. The present study therefore examined how the microbial community and the organic matter they produce are influenced by the addition of carbohydrate-containing (glucose), N-containing (GBT), and S-containing (DMSP) organic compounds. The results demonstrate that when these carbon-, N-, and S-rich compounds are added separately, the organic molecules produced by the bacteria growing on them are enriched in the same elements. Similarly, the microbial community composition was also distinct when different compounds were added as the substrate. Overall, this study demonstrates how the microbial communities metabolize and transform different substrates thereby, expanding our understanding of the complexity of links between microbes and substrates in the ocean.

Time-series incubations in a coastal environment illuminates the importance of early colonizers and the complexity of bacterial biofilm dynamics on marine plastics

The problematic of microplastics pollution in the marine environment is tightly linked to their colonization by a wide diversity of microorganisms, the so-called plastisphere. The composition of the plastisphere relies on a complex combination of multiple factors including the surrounding environment, the time of incubation along with the polymer type, making it difficult to understand how the biofilm evolves during the microplastic lifetime over the oceans. To better define bacterial community assembly processes on plastics, we performed a 5 months spatio-temporal survey of the plastisphere in an oyster farming area in the Bay of Brest (France). We deployed three types of plastic pellets in two positions in the foreshore and in the water column. Plastic-associated biofilm composition in all these conditions was monitored using 16 S rRNA metabarcoding and compared to free-living and attached bacterial members of seawater. We observed that bacterial families associated to plastic pellets were significantly distinct from the ones found in seawater, with a significant prevalence of filamentous Cyanobacteria on plastics. No convergence towards a unique plastisphere was detected between polymers exposed in the intertidal and subtidal area, emphasizing the central role of the surrounding environment on constantly shaping the plastisphere community diversity. However, we could define a bulk of early-colonizers of marine biofilms such as Alteromonas, Pseudoalteromonas or Vibrio. These early-colonizers could reach high abundances in floating microplastics collected in field-sampling studies, suggesting the plastic-associated biofilms could remain at early development stages across large oceanic scales. Our study raises the hypothesis that most members of the plastisphere, including putative pathogens, could result of opportunistic colonization processes and unlikely long-term transport.

pH mediated assemblage of carbon, nitrogen, and sulfur related microbial communities in petroleum reservoirs

Microorganisms are the core drivers of biogeochemistry processes in petroleum reservoirs and have been widely used to enhance petroleum recovery. However, systematic information about the microbial communities related to the C-N-S cycle in petroleum reservoirs under different pH conditions remains poorly understood. In this study, 16S rRNA gene data from 133 petroleum samples were collected, and 756 C-N-S related genera were detected. The Chao1 richness and Shannon diversity indices for the C-N-S-related microbial communities showed significant differences among different pH conditions and at the lowest levels in acidic conditions with pH values of 4.5-6.5. In addition, pH was the most important factor influencing the C-N-S related microbial communities and contributed to 17.95% of the variation in the methanogenesis community. A total of 55 functional genera were influenced by pH, which accounted for 42.08% of the C-N-S related genera. Among them, the genera Pseudomonas and Arcobacter were the highest and were concentrated in acidic conditions with pH values of 4.5-6.5. In parallel, 56 predicted C-N-S related genes were examined, and pH affected 16 of these genes, including putative chitinase, mcrA, mtrB, cysH, narGHIVYZ, nirK, nirB, nifA, sat, aprAB, and dsrAB. Furthermore, the co-occurrence networks of the C-N-S related microbial communities distinctly varied among the different pH conditions. The acidic environment exhibited the lowest complex network with the lowest keystone taxa number, and Escherichia-Shigella was the only keystone group that existed in all three networks. In summary, this study strengthened our knowledge regarding the C-N-S related microbial communities in petroleum reservoirs under different pH conditions, which is of great significance for understanding the microbial ecology and geochemical cycle of petroleum reservoirs.

Keystone Microorganisms Regulate the Methanogenic Potential in Coals with Different Coal Ranks

Microorganisms are the core drivers of coal biogeochemistry and are closely related to the formation of coalbed methane. However, it remains poorly understood about the network relationship and stability of microbial communities in coals with different ranks. In this study, a high-throughput sequencing data set was analyzed to understand the microbial co-occurrence network in coals with different ranks including anthracite, medium-volatile bituminous, and high-volatile bituminous. The results showed similar topological properties for the microbial networks among coals with different ranks, but a great difference was found in the microbial composition in different large modules among coals with different ranks, and these three networks had three, four, and four large modules with seven, nine, and nine phyla, respectively. Among these networks, a total of 46 keystone taxa were identified in large modules, and these keystone taxa were different in coals with different ranks. Bacteria dominated the keystone taxa in the microbial network, and these bacterial keystone taxa mainly belonged to phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Besides, the removal of the key microbial data could reduce the community stability of microbial communities in bituminous coals. A partial least-squares path model further showed that these bacterial keystone taxa indirectly affected methanogenic potential by maintaining the microbial community stability and bacterial diversity. In summary, these results showed that keystone taxa played an important role in determining the community diversity, maintaining the microbial community stability, and controlling the methanogenic potential, which is of great significance for understanding the microbial ecology and the geochemical cycle of coal seams.

Fate of face masks after being discarded into seawater: Aging and microbial colonization

Billions of discarded masks have entered the oceans since the outbreak of the COVID-19 pandemic. Current reports mostly discuss the potential of masks as plastic pollution, but there has been no study on the fate of this emerging plastic waste in the marine environment. Therefore, we exposed masks in natural seawater and evaluated their aging and effects on the microbial community using a combination of physicochemical and biological techniques. After 30-day exposure in natural seawater, the masks suffered from significant aging. Microbial colonizers such as Rhodobacteraceae Flavobacteriaceae, Vibrionaceae and fouling organisms like calcareous tubeworms Hydroides elegans were massively present on the masks. The roughness and modulus of the mask fiber increased 3 and 5 times, respectively, and the molecular weight decreased 7%. The growth of biofouling organisms caused the masks negatively buoyant after 14-30 days. Our study sheds some light on the fate of discarded masks in a coastal area and provides fundamental data to manage this important plastic waste during COVID-19 pandemic.

Carbon-Nitrogen-Sulfur-Related Microbial Taxa and Genes Maintained the Stability of Microbial Communities in Coals

Coal microbes are the predominant form of life in the subsurface ecosystem, which play a vital role in biogeochemical cycles. However, the systematic information about carbon-nitrogen-sulfur (C-N-S)-related microbial communities in coal seams is limited. In this study, 16S rRNA gene data from a total of 93 microbial communities in coals were collected for meta-analysis. The results showed that 718 functional genera were related to the C-N-S cycle, wherein N₂ fixation, denitrification, and C degradation groups dominated in relative abundance, Chao1 richness, Shannon diversity, and niche width. Genus Pseudomonas having the most C-N-S-related functions showed the highest relative abundance, and genus Herbaspirillum with a higher abundance participated in C degradation, CH₄ oxidation, N₂ fixation, ammoxidation, and denitrification. Such Herbaspirillum was a core genus in the co-occurrence network of microbial prokaryotes and showed higher levels in weight degree, betweenness centrality, and eigenvector centrality. In addition, most of the methanogens could fix N₂ and dominated in the N₂ fixation groups. Among them, genera Methanoculleus and Methanosaeta showed higher levels in the betweenness centrality index. In addition, the genus Clostridium was linked to the methanogenesis co-occurrence network module. In parallel, the S reduction gene was present in the highest total relative abundance of genes, followed by the C degradation and the denitrification genes, and S genes (especially cys genes) were the main genes linked to the co-occurrence network of the C-N-S-related genes. In summary, this study strengthened our knowledge regarding the C-N-S-related coal microbial communities, which is of great significance in understanding the microbial ecology and geochemical cycle of coals.

Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables

Disturbances, here defined as events that directly alter microbial community composition, are commonly studied in host-associated and engineered systems. In spite of global change both altering environmental averages and increasing extreme events, there has been relatively little research into the causes, persistence and population-level impacts of disturbance in the dynamic coastal ocean. Here, we utilize 3 years of observations from a coastal time series to identify disturbances based on the largest week-over-week changes in the microbiome (i.e. identifying disturbance as events that alter the community composition). In general, these microbiome disturbances were not clearly linked to specific environmental factors and responsive taxa largely differed, aside from SAR11, which generally declined. However, several disturbance metagenomes identified increased phage-associated genes, suggesting that unexplained community shifts might be caused by increased mortality. Furthermore, a category 1 hurricane, the only event that would likely be classified a priori as an environmental disturbance, was not an outlier in microbiome composition, but did enhance a bloom in seasonally abundant phytoplankton. Thus, as extreme environmental changes intensify, assumptions of what constitutes a disturbance should be re-examined in the context of ecological history and microbiome responses.

Functional and Seasonal Changes in the Structure of Microbiome Inhabiting Bottom Sediments of a Pond Intended for Ecological King Carp Farming

Simple Summary

Bottom sediments are usually classified as extreme habitats for microorganisms. They are defined as matter deposited on the bottom of water bodies through the sedimentation process. The quality of sediments is extremely important for the good environmental status of water, because they are an integral part of the surface water environment. Microorganisms living in sediments are involved in biogeochemical transformations and play a fundamental role in maintaining water purity, decomposition of organic matter, and primary production. As a rule, studies on bottom sediments focus on monitoring their chemistry and pollution, while little is known about the structure of bacterial communities inhabiting this extreme environment. In this study, Next-Generation Sequencing (NGS) was combined with the Community-Level Physiological Profiling (CLPP) technique to obtain a holistic picture of bacterial biodiversity in the bottom sediments from Cardinal Pond intended for ecological king carp farming. It was evident that the bottom sediments of the studied pond were characterized by a rich microbiota composition, whose structure and activity depended on the season, and the most extensive modifications of the biodiversity and functionality of microorganisms were noted in summer.

Abstract

The main goal of the study was to determine changes in the bacterial structure in bottom sediments occurring over the seasons of the year and to estimate microbial metabolic activity. Bottom sediments were collected four times in the year (spring, summer, autumn, and winter) from 10 different measurement points in Cardinal Pond (Ślesin, NW Poland). The Next-Generation Sequencing (MiSeq Illumina) and Community-Level Physiological Profiling techniques were used for identification of the bacterial diversity structure and bacterial metabolic and functional activities over the four seasons. It was evident that Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant phyla, while representatives of Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria predominated at the class level in the bottom sediments. An impact of the season on biodiversity and metabolic activity was revealed with the emphasis that the environmental conditions in summer modified the studied parameters most strongly. Carboxylic and acetic acids and carbohydrates were metabolized most frequently, whereas aerobic respiration I with the use of cytochrome C was the main pathway used by the microbiome of the studied bottom sediments.

Linkages Among Dissolved Organic Matter Export, Dissolved Metabolites, and Associated Microbial Community Structure Response in the Northwestern Sargasso Sea on a Seasonal Scale

Deep convective mixing of dissolved and suspended organic matter from the surface to depth can represent an important export pathway of the biological carbon pump. The seasonally oligotrophic Sargasso Sea experiences annual winter convective mixing to as deep as 300 m, providing a unique model system to examine dissolved organic matter (DOM) export and its subsequent compositional transformation by microbial oxidation. We analyzed biogeochemical and microbial parameters collected from the northwestern Sargasso Sea, including bulk dissolved organic carbon (DOC), total dissolved amino acids (TDAA), dissolved metabolites, bacterial abundance and production, and bacterial community structure, to assess the fate and compositional transformation of DOM by microbes on a seasonal time-scale in 2016-2017. DOM dynamics at the Bermuda Atlantic Time-series Study site followed a general annual trend of DOC accumulation in the surface during stratified periods followed by downward flux during winter convective mixing. Changes in the amino acid concentrations and compositions provide useful indices of diagenetic alteration of DOM. TDAA concentrations and degradation indices increased in the mesopelagic zone during mixing, indicating the export of a relatively less diagenetically altered (i.e., more labile) DOM. During periods of deep mixing, a unique subset of dissolved metabolites, such as amino acids, vitamins, and benzoic acids, was produced or lost. DOM export and compositional change were accompanied by mesopelagic bacterial growth and response of specific bacterial lineages in the SAR11, SAR202, and SAR86 clades, Acidimicrobiales, and Flavobacteria, during and shortly following deep mixing. Complementary DOM biogeochemistry and microbial measurements revealed seasonal changes in DOM composition and diagenetic state, highlighting microbial alteration of the quantity and quality of DOM in the ocean.

Macroecological distributions of gene variants highlight the functional organization of soil microbial systems

The recent application of macroecological tools and concepts has made it possible to identify consistent patterns in the distribution of microbial biodiversity, which greatly improved our understanding of the microbial world at large scales. However, the distribution of microbial functions remains largely uncharted from the macroecological point of view. Here, we used macroecological models to examine how the genes encoding the functional capabilities of microorganisms are distributed within and across soil systems. Models built using functional gene array data from 818 soil microbial communities showed that the occupancy-frequency distributions of genes were bimodal in every studied site, and that their rank-abundance distributions were best described by a lognormal model. In addition, the relationships between gene occupancy and abundance were positive in all sites. This allowed us to identify genes with high abundance and ubiquitous distribution (core) and genes with low abundance and limited spatial distribution (satellites), and to show that they encode different sets of microbial traits. Common genes encode microbial traits related to the main biogeochemical cycles (C, N, P and S) while rare genes encode traits related to adaptation to environmental stresses, such as nutrient limitation, resistance to heavy metals and degradation of xenobiotics. Overall, this study characterized for the first time the distribution of microbial functional genes within soil systems, and highlight the interest of macroecological models for understanding the functional organization of microbial systems across spatial scales.

Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf

Throughout coastal Antarctica, ice shelves separate oceanic waters from sunlight by hundreds of meters of ice. Historical studies have detected activity of nitrifying microorganisms in oceanic cavities below permanent ice shelves. However, little is known about the microbial composition and pathways that mediate these activities. In this study, we profiled the microbial communities beneath the Ross Ice Shelf using a multi-omics approach. Overall, beneath-shelf microorganisms are of comparable abundance and diversity, though distinct composition, relative to those in the open meso- and bathypelagic ocean. Production of new organic carbon is likely driven by aerobic lithoautotrophic archaea and bacteria that can use ammonium, nitrite, and sulfur compounds as electron donors. Also enriched were aerobic organoheterotrophic bacteria capable of degrading complex organic carbon substrates, likely derived from in situ fixed carbon and potentially refractory organic matter laterally advected by the below-shelf waters. Altogether, these findings uncover a taxonomically distinct microbial community potentially adapted to a highly oligotrophic marine environment and suggest that ocean cavity waters are primarily chemosynthetically-driven systems.

Vertical Inheritance Facilitates Interspecies Diversification in Biosynthetic Gene Clusters and Specialized Metabolites

While specialized metabolites are thought to mediate ecological interactions, the evolutionary processes driving chemical diversification, particularly among closely related lineages, remain poorly understood. Here, we examine the evolutionary dynamics governing the distribution of natural product biosynthetic gene clusters (BGCs) among 118 strains representing all nine currently named species of the marine actinobacterial genus Salinispora. While much attention has been given to the role of horizontal gene transfer (HGT) in structuring BGC distributions, we find that vertical descent facilitates interspecies BGC diversification over evolutionary timescales. Moreover, we identified a distinct phylogenetic signal among Salinispora species at both the BGC and metabolite level, indicating that specialized metabolism represents a conserved phylogenetic trait. Using a combination of genomic analyses and liquid chromatography–high-resolution tandem mass spectrometry (LC-MS/MS) targeting nine experimentally characterized BGCs and their small molecule products, we identified gene gain/loss events, constrained interspecies recombination, and other evolutionary processes associated with vertical inheritance as major contributors to BGC diversification. These evolutionary dynamics had direct consequences for the compounds produced, as exemplified by species-level differences in salinosporamide production. Together, our results support the concept that specialized metabolites, and their cognate BGCs, can represent phylogenetically conserved functional traits with chemical diversification proceeding in species-specific patterns over evolutionary time frames.

Coral mucus rapidly induces chemokinesis and genome-wide transcriptional shifts toward early pathogenesis in a bacterial coral pathogen

Elevated seawater temperatures have contributed to the rise of coral disease mediated by bacterial pathogens, such as the globally distributed Vibrio coralliilyticus, which utilizes coral mucus as a chemical cue to locate stressed corals. However, the physiological events in the pathogens that follow their entry into the coral host environment remain unknown. Here, we present simultaneous measurements of the behavioral and transcriptional responses of V. coralliilyticus BAA-450 incubated in coral mucus. Video microscopy revealed a strong and rapid chemokinetic behavioral response by the pathogen, characterized by a two-fold increase in average swimming speed within 6 min of coral mucus exposure. RNA sequencing showed that this bacterial behavior was accompanied by an equally rapid differential expression of 53% of the genes in the V. coralliilyticus genome. Specifically, transcript abundance 10 min after mucus exposure showed upregulation of genes involved in quorum sensing, biofilm formation, and nutrient metabolism, and downregulation of flagella synthesis and chemotaxis genes. After 60 min, we observed upregulation of genes associated with virulence, including zinc metalloproteases responsible for causing coral tissue damage and algal symbiont photoinactivation, and secretion systems that may export toxins. Together, our results suggest that V. coralliilyticus employs a suite of behavioral and transcriptional responses to rapidly shift into a distinct infection mode within minutes of exposure to the coral microenvironment.

Analysis of Community Composition of Bacterioplankton in Changle Seawater in China by Illumina Sequencing Combined with Bacteria Culture

OBJECTIVES

To characterize the abundance and relative composition of seawater bacterioplankton communities in Changle city using Illumina MiSeq sequencing and bacterial culture techniques.

METHODS

Seawater samples and physicochemical factors were collected from the coastal zone of Changle city on 8 September 2019. Nineteen filter membranes were obtained after using a suction filtration system. We randomly selected eight samples for total seawater bacteria (SWDNA group) sequencing and three samples for active seawater bacteria (SWRNA group) sequencing by Illumina MiSeq. The remaining eight samples were used for bacterial culture and identification. Alpha diversity including species coverage (Coverage), species diversity (Shannon-Wiener and Simpson index), richness estimators (Chao1), and abundance-based richness estimation (ACE) were calculated to assess biodiversity of seawater bacterioplankton. Beta diversity was used to evaluate the differences between samples. The species abundance differences were determined using the Wilcoxon rank-sum test. Statistical analyses were performed in R environment.

RESULTS

The Alpha diversity in the SWDNA group in each index was ACE 3206.99, Chao1 2615.12, Shannon 4.64, Simpson 0.05, and coverage 0.97; the corresponding index was ACE 1199.55, Chao1 934.75, Shannon 3.49, Simpson 0.09, and coverage 0.99. The sequencing results of seawater bacterial genes in the coastal waters of Changle city showed that the phyla of high-abundance bacteria of both the SWDNA and SWRNA groups included Cyanobacteria, Proteobacteria, and Bacteroidetes. The main classes included Oxyphotobacteria, Alphaproteobacteria, and Gammaproteobacteria. The main genera included Synechococcus CC9902, Chloroplast, and Cyanobium_PCC-6307. Beta diversity analysis showed a significant difference between the SWDNA and SWRNA groups (P < 0.05). The species abundance differences between SWDNA and SWRNA groups after Wilcoxon rank-sum test showed that, at the phylum level, Actinomycetes was more abundant in SWDNA group (9.17 vs 1.02%, P < 0.05); at the class level, Actinomycetes (δ- Proteus) was more abundant in SWDNA group (9.47% vs 1.01%, P < 0.05); and at the genus level, Chloroplast was more abundant in SWRNA group (13.07% vs 44.57%, P < 0.05). Nine species and 53 colonies were found by bacterial culture: 20 strains of Vibrio (37.74%), 22 strains of Enterobacter (41.51%), and 11 strains of non-fermentative bacteria (20.75%).

CONCLUSION

Illumi MiSeq sequencing of seawater bacteria revealed that the total bacterial community groups and the active bacterial community groups mainly comprised Cyanobacteria, Proteobacteria, and Bacteroides at the phylum level; Oxyphotobacteria, α-Proteobacteria, and γ-Proteobacteria at the class level; with Synechococcus_CC9902, Chloroplast, and Cyanobium_PCC-6307 comprising the predominant genera. Exploring the composition and differences of seawater bacteria assists understanding regarding the biodiversity and the infections related to seawater bacteria along the coast of the Changle, provides information that will aid in the diagnosis and treatment of such infections.

Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits

Blooms of marine phytoplankton fix complex pools of dissolved organic matter (DOM) that are thought to be partitioned among hundreds of heterotrophic microbes at the base of the food web. While the relationship between microbial consumers and phytoplankton DOM is a key component of marine carbon cycling, microbial loop metabolism is largely understood from model organisms and substrates. Here, we took an untargeted approach to measure and analyze partitioning of four distinct phytoplankton-derived DOM pools among heterotrophic populations in a natural microbial community using a combination of ecogenomics, stable isotope probing (SIP), and proteomics. Each 13C-labeled exudate or lysate from a diatom or a picocyanobacterium was preferentially assimilated by different heterotrophic taxa with specialized metabolic and physiological adaptations. Bacteroidetes populations, with their unique high-molecular-weight transporters, were superior competitors for DOM derived from diatom cell lysis, rapidly increasing growth rates and ribosomal protein expression to produce new relatively high C:N biomass. Proteobacteria responses varied, with relatively low levels of assimilation by Gammaproteobacteria populations, while copiotrophic Alphaproteobacteria such as the Roseobacter clade, with their diverse array of ABC- and TRAP-type transporters to scavenge monomers and nitrogen-rich metabolites, accounted for nearly all cyanobacteria exudate assimilation and produced new relatively low C:N biomass. Carbon assimilation rates calculated from SIP data show that exudate and lysate from two common marine phytoplankton are being used by taxonomically distinct sets of heterotrophic populations with unique metabolic adaptations, providing a deeper mechanistic understanding of consumer succession and carbon use during marine bloom events.

Composition of Prokaryotic and Eukaryotic Microbial Communities in Waters around the Florida Reef Tract

The Florida Keys, a delicate archipelago of sub-tropical islands extending from the south-eastern tip of Florida, host the vast majority of the only coral barrier reef in the continental United States. Abiotic as well as microbial components of the surrounding waters are pivotal for the health of reef habitats, and thus could play an important role in understanding the development and transmission of coral diseases in Florida. In this study, we analyzed microbial community structure and abiotic factors in waters around the Florida Reef Tract. Both bacterial and eukaryotic community structure were significantly linked with variations in temperature, dissolved oxygen, and total organic carbon values. High abundances of copiotrophic bacteria as well as several potentially harmful microbes, including coral pathogens, fish parasites and taxa that have been previously associated with Red Tide and shellfish poisoning were present in our datasets and may have a pivotal impact on reef health in this ecosystem.

Exploring the Composition and Functions of Plastic Microbiome Using Whole-Genome Sequencing

Besides the ecotoxicological consequences of microplastics and associated chemicals, the association of microbes on plastics has greater environmental implications as microplastics may select for unique microbiome participating in environmentally significant functions. Despite this, the functional potential of the microbiome associated with different types of plastics is understudied. Here, we investigate the interaction between plastic and marine biofilm-forming microorganisms through a whole-genome sequencing approach on four types of microplastics incubated in the marine environment. Taxonomic analysis suggested that the microplastic surfaces exhibit unique microbial profiles and niche partitioning among the substrates. In particular, the abundance of Vibrio alginolyticus and Vibrio campbellii suggested that microplastic pollution may pose a potential risk to the marine food chain and negatively impact aquaculture industries. Microbial genera involved in xenobiotic compound degradation, carbon cycling, and genes associated with the type IV secretion system, conjugal transfer protein TraG, plant-pathogen interaction, CusA/CzcA family heavy metal efflux transfer proteins, and TolC family proteins were significantly enriched on all the substrates, indicating the variety of processes operated by the plastic-microbiome. The present study gives a detailed characterization of the rapidly altering microbial composition and gene pools on plastics and adds new knowledge surrounding the environmental ramifications of marine plastic pollution.

Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis

Bacteria of Halomonas are widely distributed in various environments and play a substantial role in the nutrient cycle. In this report, 14 strains capable of aerobic denitrification and heterotrophic sulfur oxidation were isolated from different habitats. Based on the phenotypic, genotypic, and chemotaxonomic analyses, these strains were considered to represent six novel species of the genus Halomonas, for which the names Halomonas zhangzhouensis sp. nov. type strain CXT3-11T ( = MCCC 1A11036T = KCTC 72087T), Halomonas aerodenitrificans sp. nov. CYD-9T ( = MCCC 1A11058T = KCTC 72088T), Halomonas sulfidoxydans sp. nov. CYN-1-2T ( = MCCC 1A11059T = KCTC 72089T), Halomonas ethanolica sp. nov. CYT3-1-1T ( = MCCC 1A11081T = KCTC 72090T), Halomonas sulfidivorans sp. nov. NLG_F1ET ( = MCCC 1A13718T = KCTC 72091T), and Halomonas tianxiuensis sp. nov. BC-M4-5T ( = MCCC 1A14433T = KCTC 72092T) are proposed. Intriguingly, they formed a unique group with 11 other species designated as the "H. desiderata group." To better understand their featured metabolisms, genes involved in denitrification and sulfur oxidation were analyzed, along with 193 other available genomes of the whole genus. Consistently, complete denitrification pathways were confirmed in the "H. desiderata group," in which napA, narG, nirS, norB, and nosZ genes coexist. Their nitrite reductase NirS formed a unique evolutionary lineage, distinguished from other denitrifiers in Halomonas. In addition, diverse occurrence patterns of denitrification genes were also observed in different phylogenetic clades of Halomonas. With respect to sulfur oxidation, fccAB genes involved in sulfide oxidation commonly exist in the "H. desiderata group," while sqr genes are diverse and can be found in more species; sqr genes co-occurred with fccAB in eight strains of this study, contributing to more active sulfide oxidation. Besides, the tsdA gene, which encodes an enzyme that oxidizes thiosulfate to tetrathionate, is ubiquitous in the genus Halomonas. The widespread presence of sqr/fccAB, pdo, and tsdA in Halomonas suggests that many Halomonas spp. can act as heterotrophic sulfur oxidizers. These results provide comprehensive insights into the potential of denitrification and sulfur oxidation in the whole genus of Halomonas. With regard to the global distribution of Halomonas, this report implies their unneglectable role in the biogeochemical cycle.

The Biogeochemistry of Marine Polysaccharides: Sources, Inventories, and Bacterial Drivers of the Carbohydrate Cycle

Polysaccharides are major components of macroalgal and phytoplankton biomass and constitute a large fraction of the organic matter produced and degraded in the ocean. Until recently, however, our knowledge of marine polysaccharides was limited due to their great structural complexity, the correspondingly complicated enzymatic machinery used by microbial communities to degrade them, and a lack of readily applied means to isolate andcharacterize polysaccharides in detail. Advances in carbohydrate chemistry, bioinformatics, molecular ecology, and microbiology have led to new insights into the structures of polysaccharides, the means by which they are degraded by bacteria, and the ecology of polysaccharide production and decomposition. Here, we survey current knowledge, discuss recent advances, and present a new conceptual model linking polysaccharide structural complexity and abundance to microbially driven mechanisms of polysaccharide processing. We conclude by highlighting specific future research foci that will shed light on this central but poorly characterized component of the marine carbon cycle.

Extensive Microbial Processing of Polysaccharides in the South Pacific Gyre via Selfish Uptake and Extracellular Hydrolysis

Primary productivity occurs throughout the deep euphotic zone of the oligotrophic South Pacific Gyre (SPG), fueled largely by the regeneration of nutrients and thus recycling of organic matter. We investigated the heterotrophic capabilities of the SPG's bacterial communities by examining their ability to process polysaccharides, an important component of marine organic matter. We focused on the initial step of organic matter degradation by measuring the activities of extracellular enzymes that hydrolyze six different polysaccharides to smaller sizes. This process can occur by two distinct mechanisms: "selfish uptake," in which initial hydrolysis is coupled to transport of large polysaccharide fragments into the periplasmic space of bacteria, with little to no loss of hydrolysis products to the external environment, and "external hydrolysis," in which low molecular weight (LMW) hydrolysis products are produced in the external environment. Given the oligotrophic nature of the SPG, we did not expect high enzymatic activity; however, we found that all six polysaccharides were hydrolyzed externally and taken up selfishly in the central SPG, observations that may be linked to a comparatively high abundance of diatoms at the depth and location sampled (75 m). At the edge of the gyre and close to the center of the gyre, four of six polysaccharides were externally hydrolyzed, and a lower fraction of the bacterial community showed selfish uptake. One polysaccharide (fucoidan) was selfishly taken up without measurable external hydrolysis at two stations. Additional incubations of central gyre water from depths of 1,250 and 2,800 m with laminarin (an abundant polysaccharide in the ocean) led to extreme growth of opportunistic bacteria (Alteromonas), as tracked by cell counts and next generation sequencing of the bacterial communities. These Alteromonas appear to concurrently selfishly take up laminarin and release LMW hydrolysis products. Overall, extracellular enzyme activities in the SPG were similar to activities in non-oligotrophic regions, and a considerable fraction of the community was capable of selfish uptake at all three stations. A diverse set of bacteria responded to and are potentially important for the recycling of organic matter in the SPG.

Stable Isotope Probing Identifies Bacterioplankton Lineages Capable of Utilizing Dissolved Organic Matter Across a Range of Bioavailability

Bacterioplankton consume about half of the dissolved organic matter (DOM) produced by phytoplankton. DOM released from phytoplankton consists of a myriad of compounds that span a range of biological reactivity from labile to recalcitrant. Linking specific bacterioplankton lineages to the incorporation of DOM compounds into biomass is important to understand microbial niche partitioning. We conducted a series of DNA-stable isotope probing (SIP) experiments using ¹³C-labeled substrates of varying lability including amino acids, cyanobacteria lysate, and DOM from diatom and cyanobacteria isolates concentrated on solid phase extraction PPL columns (SPE-DOM). Amendments of substrates into Sargasso Sea bacterioplankton communities were conducted to explore microbial response and DNA-SIP was used to determine which lineages of Bacteria and Archaea were responsible for uptake and incorporation. Greater increases in bacterioplankton abundance and DOC removal were observed in incubations amended with cyanobacteria-derived lysate and amino acids compared to the SPE-DOM, suggesting that the latter retained proportionally more recalcitrant DOM compounds. DOM across a range of bioavailability was utilized by diverse prokaryotic taxa with copiotrophs becoming the most abundant ¹³C-incorporating taxa in the amino acid treatment and oligotrophs becoming the most abundant ¹³C-incorporating taxa in SPE-DOM treatments. The lineages that responded to SPE-DOM amendments were also prevalent in the mesopelagic of the Sargasso Sea, suggesting that PPL extraction of phytoplankton-derived DOM isolates compounds of ecological relevance to oligotrophic heterotrophic bacterioplankton. Our study indicates that DOM quality is an important factor controlling the diversity of the microbial community response, providing insights into the roles of different bacterioplankton in resource exploitation and efficiency of marine carbon cycling.

Rapid screening of marine bacterial symbionts using MALDI-TOF MS

Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) is a rapid, cost-effective and high-throughput method for bacteria characterization. However, most previous studies focused on clinical isolates. In this study, we evaluated the use of MALDI-TOF MS as a rapid screening tool for marine bacterial symbionts. A set of 255 isolates from different marine sources (corals, sponge, fish and seawater) was analyzed using cell lysates to obtain a rapid grouping. Cluster analysis of mass spectra and 16S rRNA showed 18 groups, including Vibrio, Bacillus, Pseudovibrio, Alteromonas and Ruegeria. MALDI-TOF distance similarity scores ≥ 60% and ≥ 70% correspond to ≥ 98.7% 16S rRNA gene sequence similarity and ≥ 95% pyrH gene sequence similarity, respectively. MALDI-TOF MS is a useful tool for Vibrio species groups' identification.

How can microbial population genomics inform community ecology?

Populations are fundamental units of ecology and evolution, but can we define them for bacteria and archaea in a biologically meaningful way? Here, we review why population structure is difficult to recognize in microbes and how recent advances in measuring contemporary gene flow allow us to identify clearly delineated populations among collections of closely related genomes. Such structure can arise from preferential gene flow caused by coexistence and genetic similarity, defining populations based on biological mechanisms. We show that such gene flow units are sufficiently genetically isolated for specific adaptations to spread, making them also ecological units that are differentially adapted compared to their closest relatives. We discuss the implications of these observations for measuring bacterial and archaeal diversity in the environment. We show that operational taxonomic units defined by 16S rRNA gene sequencing have woefully poor resolution for ecologically defined populations and propose monophyletic clusters of nearly identical ribosomal protein genes as an alternative measure for population mapping in community ecological studies employing metagenomics. These population-based approaches have the potential to provide much-needed clarity in interpreting the vast microbial diversity in human and environmental microbiomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

The plastisphere in marine ecosystem hosts potential specific microbial degraders including Alcanivorax borkumensis as a key player for the low-density polyethylene degradation

Most plastics are released to the environment in landfills and around 32% end up in the sea, inducing large ecological and health impacts. The plastics constitute a physical substrate and potential carbon source for microorganisms. The present study compares the structures of bacterial communities from floating plastics, sediment-associated plastics and sediments from the Mediterranean Sea. The 16S rRNA microbiome profiles of surface and sediment plastic-associated microbial biofilms from the same geographic location differ significantly, with the omnipresence of Bacteroidetes and Gammaproteobacteria. Our research confirmed that plastisphere hosts microbial communities were environmental distinct niche. In parallel, this study used environmental samples to investigate the enrichment of potential plastic-degrading bacteria with Low Density PolyEthylene (LDPE), PolyEthylene Terephthalate (PET) and PolyStyrene (PS) plastics as the sole carbon source. In this context, we showed that the bacterial community composition is clearly plastic nature dependent. Hydrocarbon-degrading bacteria such as Alcanivorax, Marinobacter and Arenibacter genera are enriched with LDPE and PET, implying that these bacteria are potential players in plastic degradation. Finally, our data showed for the first time the ability of Alcanivorax borkumensis to form thick biofilms specifically on LDPE and to degrade this petroleum-based plastic.

Genomic and phenotypic insights point to diverse ecological strategies by facultative anaerobes obtained from subsurface coal seams

Microbes in subsurface coal seams are responsible for the conversion of the organic matter in coal to methane, resulting in vast reserves of coal seam gas. This process is important from both environmental and economic perspectives as coal seam gas is rapidly becoming a popular fuel source worldwide and is a less carbon intensive fuel than coal. Despite the importance of this process, little is known about the roles of individual bacterial taxa in the microbial communities carrying out this process. Of particular interest is the role of members of the genus Pseudomonas, a typically aerobic taxa which is ubiquitous in coal seam microbial communities worldwide and which has been shown to be abundant at early time points in studies of ecological succession on coal. The current study performed aerobic isolations of coal seam microbial taxa generating ten facultative anaerobic isolates from three coal seam formation waters across eastern Australia. Subsequent genomic sequencing and phenotypic analysis revealed a range of ecological strategies and roles for these facultative anaerobes in biomass recycling, suggesting that this group of organisms is involved in the degradation of accumulated biomass in coal seams, funnelling nutrients back into the microbial communities degrading coal to methane.

Contributions of single-cell genomics to our understanding of planktonic marine archaea

Single-cell genomics has transformed many fields of biology, marine microbiology included. Here, we consider the impact of single-cell genomics on a specific group of marine microbes-the planktonic marine archaea. Despite single-cell enabled discoveries of novel metabolic function in the marine thaumarchaea, population-level investigations are hindered by an overall lower than expected recovery of thaumarchaea in single-cell studies. Metagenome-assembled genomes have so far been a more useful method for accessing genome-resolved insights into the Marine Group II euryarchaea. Future progress in the application of single-cell genomics to archaeal biology in the ocean would benefit from more targeted sorting approaches, and a more systematic investigation of potential biases against archaea in single-cell workflows including cell lysis, genome amplification and genome screening. This article is part of a discussion meeting issue 'Single cell ecology'.

Microbial functional diversity: From concepts to applications

Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.

Microbial distribution and turnover in Antarctic microbial mats highlight the relevance of heterotrophic bacteria in low-nutrient environments

Maritime Antarctica has shown the highest increase in temperature in the Southern Hemisphere. Under this scenario, biogeochemical cycles may be altered, resulting in rapid environmental change for Antarctic biota. Microbes that drive biogeochemical cycles often form biofilms or microbial mats in continental meltwater environments. Limnetic microbial mats from the Fildes Peninsula were studied using high-throughput 16S rRNA gene sequencing. Mat samples were collected from 15 meltwater stream sites, comprising a natural gradient from ultraoligotrophic glacier flows to meltwater streams exposed to anthropogenic activities. Our analyses show that microbial community structure differences between mats are explained by environmental NH4+, NO3-, DIN, soluble reactive silicon and conductivity. Microbial mats living under ultraoligotrophic meltwater conditions did not exhibit a dominance of cyanobacterial photoautotrophs, as has been documented for other Antarctic limnetic microbial mats. Instead, ultraoligotrophic mat communities were characterized by the presence of microbes recognized as heterotrophs and photoheterotrophs. This suggests that microbial capabilities for recycling organic matter may be a key factor to dwell in ultra-low nutrient conditions. Our analyses show that phylotype level assemblages exhibit coupled distribution patterns in environmental oligotrophic inland waters. The evaluation of these microbes suggests the relevance of reproductive and structural strategies to pioneer these psychrophilic ultraoligotrophic environments.

Culture dependent and independent analysis and appraisal of early stage biofilm-forming bacterial community composition in the Southern coastal seawater of India

Microbial aggregation on artificial surfaces is a fundamental phenomenon in aquatic systems that lead to biofouling, corrosion and influence the buoyancy of plastic materials. Despite the maritime activities and with nearshore large industrial sector, Laccadive Sea in the Indian Ocean has rarely been investigated for characterizing early biofilm-forming bacterial community. The present investigation was aimed to catalogue the primary colonizers on artificial surfaces and their comparison with planktonic community in southern coastal seawater of India. Surface seawater samples and biofilm assembled on three artificial surfaces over a period of 72 h of immersion in the intake area of a nuclear power plant at Kudankulam, India were collected. The structure of surface assemblages and plankton were unveiled by employing culture dependent, DGGE and NGS methods. In static condition, a collection of aerobic heterotrophic bacteria was screened in vitro for their ability to form potent biofilm. Proteobacteria preponderated the communities both in seawater and natural biofilm and Gammaproteobacteria accounted for >85% in the latter. Vibrionaceae, Alteromonadaceae and Pseudoalteromonadaceae dominated the biofilm community and constituted for 41, 25 and 8%, respectively. In contrast to other studies that showed Rhodobacteraceae family of Alphaproteobacteria as predominant component, we found Vibrionaceae of Gammaproteobacteria as dominant group in early stage of biofilm formation. Both DGGE and NGS data indicated that the attached community is noticeably distinct from those suspended in water column and form the basis for the proposed hypothesis of species sorting theory, that is, the local environmental conditions influence bacterial community assembly. Collectively, the data are testament for species sorting process that occur during initial assembly of bacterial community in marine environment and shed light on the structure of marine bacterial biofilm development. The outcome of the present study is of immense importance for designing long-term, efficient and appropriate strategies to control the biofouling phenomenon.

Delineation of ecologically distinct units of marine Bacteroidetes in the Northwestern Mediterranean Sea

Bacteroidetes is one of the dominant phyla of ocean bacterioplankton, yet its diversity and population structure is poorly understood. To advance in the delineation of ecologically meaningful units within this group, we constructed near full-length 16S rRNA gene clone libraries from contrasting marine environments in the NW Mediterranean. Based on phylogeny and the associated ecological variables (depth and season), 24 different Bacteroidetes clades were delineated. By considering their relative abundance (from iTag amplicon sequencing studies), we described the distribution patterns of each of these clades, delimiting them as Ecologically Significant Taxonomic Units (ESTUs). Spatially, there was almost no overlap among ESTUs at different depths. In deep waters there was predominance of Owenweeksia, Leeuwenhoekiella, Muricauda-related genera, and some depth-associated ESTUs within the NS5 and NS2b marine clades. Seasonally, multi-annual dynamics of recurring ESTUs were present with dominance of some ESTUs within the NS4, NS5 and NS2b marine clades along most of the year, but with variable relative frequencies between months. A drastic change towards the predominance of Formosa-related ESTUs and one ESTU from the NS5 marine clade was typically present after the spring bloom. Even though there are no isolates available for these ESTUs to determine their physiology, correlation analyses identified the environmental preference of some of them. Overall, our results suggest that there is a high degree of niche specialisation within these closely related clades. This work constitutes a step forward in disentangling the ecology of marine Bacteroidetes, which are essential players in organic matter processing in the oceans.

The chemical cue tetrabromopyrrole induces rapid cellular stress and mortality in phytoplankton

Eukaryotic phytoplankton contribute to the flow of elements through marine food webs, biogeochemical cycles, and Earth's climate. Therefore, how phytoplankton die is a critical determinate of the flow and fate of nutrients. While heterotroph grazing and viral infection contribute to phytoplankton mortality, recent evidence suggests that bacteria-derived cues also control phytoplankton lysis. Here, we report exposure to nanomolar concentrations of 2,3,4,5-tetrabromopyrrole (TBP), a brominated chemical cue synthesized by marine γ-proteobacteria, resulted in mortality of seven phylogenetically-diverse phytoplankton species. A comparison of nine compounds of marine-origin containing a range of cyclic moieties and halogenation indicated that both a single pyrrole ring and increased bromination were most lethal to the coccolithophore, Emiliania huxleyi. TBP also rapidly induced the production of reactive oxygen species and the release of intracellular calcium stores, both of which can trigger the activation of cellular death pathways. Mining of the Ocean Gene Atlas indicated that TBP biosynthetic machinery is globally distributed throughout the water column in coastal areas. These findings suggest that bacterial cues play multiple functions in regulating phytoplankton communities by inducing biochemical changes associated with cellular death. Chemically-induced lysis by bacterial infochemicals is yet another variable that must be considered when modeling oceanic nutrient dynamics.

Emergence of soil bacterial ecotypes along a climate gradient

The high diversity of soil bacteria is attributed to the spatial complexity of soil systems, where habitat heterogeneity promotes niche partitioning among bacterial taxa. This premise remains challenging to test, however, as it requires quantifying the traits of closely related soil bacteria and relating these traits to bacterial abundances and geographic distributions. Here, we sought to investigate whether the widespread soil taxon Curtobacterium consists of multiple coexisting ecotypes with differential geographic distributions. We isolated Curtobacterium strains from six sites along a climate gradient and assayed four functional traits that may contribute to niche partitioning in leaf litter, the top layer of soil. Our results revealed that cultured isolates separated into fine-scale genetic clusters that reflected distinct suites of phenotypic traits, denoting the existence of multiple ecotypes. We then quantified the distribution of Curtobacterium by analysing metagenomic data collected across the gradient over 18 months. Six abundant ecotypes were observed with differential abundances along the gradient, suggesting fine-scale niche partitioning. However, we could not clearly explain observed geographic distributions of ecotypes by relating their traits to environmental variables. Thus, while we can resolve soil bacterial ecotypes, the traits delineating their distinct niches in the environment remain unclear.

Comparative Genomic Analysis of Vibrio diabolicus and Six Taxonomic Synonyms: A First Look at the Distribution and Diversity of the Expanded Species

Vibrio is a diverse genus of Gammaproteobacteria autochthonous to marine environments worldwide. Vibrio diabolicus and V. antiquarius were originally isolated from deep-sea hydrothermal fields in the East Pacific Rise. These species are closely related to members of the Harveyi clade (e.g., V. alginolyticus and V. parahaemolyticus) that are commonly isolated from coastal systems. This study reports the discovery and draft genome sequence of a novel isolate (Vibrio sp. 939) cultured from Pacific oysters (Crassostrea gigas). Questions surrounding the identity of Vibrio sp. 939 motivated a genome-scale taxonomic analysis of the Harveyi clade. A 49-genome phylogeny based on 1,109 conserved coding sequences and a comparison of average nucleotide identity (ANI) values revealed a clear case of synonymy between Vibrio sp. 939, V. diabolicus Art-Gut C1 and CNCM I-1629, V. antiquarius EX25 and four V. alginolyticus strains (E0666, FF273, TS13, and V2). This discovery expands the V. diabolicus species and makes available six additional genomes for comparative genomic analyses. The distribution of the expanded species is thought to be global given the range of isolation sources (horse mackerel, seawater, sediment, dentex, oyster, artemia and polycheate) and origins (China, India, Greece, United States, East Pacific Rise, and Chile). A subsequent comparative genomic analysis of this new eight-genome subclade revealed a high degree of individual genome plasticity and a large repertoire of genes related to virulence and defense. These findings represent a significant revision to the understanding of V. diabolicus and V. antiquarius as both have long been regarded as distinct species. This first look at the expanded V. diabolicus subclade suggests that the distribution and diversity of this species mirrors that of other Harveyi clade species, which are notable for their ubiquity and diversity.

Patterns of triclosan resistance in Vibrionaceae

The antimicrobial additive triclosan has been used in personal care products widely across the globe for decades. Triclosan resistance has been noted among Vibrio spp., but reports have been anecdotal and the extent of phenotypic triclosan resistance across the Vibrionaceae family has not been established. Here, triclosan resistance was determined for Vibrionaceae strains across nine distinct clades. Minimum inhibitory concentrations (MIC) were determined for 70 isolates from clinical (n = 6) and environmental sources (n = 64); only two were susceptible to triclosan. The mean MIC for all resistant Vibrionaceae was 53 µg mL-1 (range 3.1-550 µg mL-1), but was significantly different between clades (p < 0.001). The highest mean triclosan MIC was observed in the Splendidus clade (200 µg mL-1; n = 3). Triclosan mean MICs were 68.8 µg mL-1 in the Damselae clade and 45.3 µg mL-1 in the Harveyi clade. The lowest mean MIC was observed in the Cholerae clade with 14.4 µg mL-1, which was primarily represented by clinical strains. There were no significant differences in triclosan MIC among individual species or among environmental strains isolated from different locations. Overall, phenotypic triclosan resistance appears to be widespread across multiple clades of Vibrionaceae.

Evolution of a Vegetarian Vibrio: Metabolic Specialization of Vibrio breoganii to Macroalgal Substrates

While most Vibrionaceae are considered generalists that thrive on diverse substrates, including animal-derived material, we show that Vibrio breoganii has specialized for the consumption of marine macroalga-derived substrates. Genomic and physiological comparisons of V. breoganii with other Vibrionaceae isolates revealed the ability to degrade alginate, laminarin, and additional glycans present in algal cell walls. Moreover, the widely conserved ability to hydrolyze animal-derived polymers, including chitin and glycogen, was lost, along with the ability to efficiently grow on a variety of amino acids. Ecological data showing associations with particulate algal material but not zooplankton further support this shift in niche preference, and the loss of motility appears to reflect a sessile macroalga-associated lifestyle. Together, these findings indicate that algal polysaccharides have become a major source of carbon and energy in V. breoganii, and these ecophysiological adaptations may facilitate transient commensal associations with marine invertebrates that feed on algae.IMPORTANCE Vibrios are often considered animal specialists or generalists. Here, we show that Vibrio breoganii has undergone massive genomic changes to become specialized on algal carbohydrates. Accompanying genomic changes include massive gene import and loss. These vibrios may help us better understand how algal biomass is degraded in the environment and may serve as a blueprint on how to optimize the conversion of algae to biofuels.

Eco-evolutionary Dynamics Linked to Horizontal Gene Transfer in Vibrios

Vibrio is a genus of ubiquitous heterotrophic bacteria found in aquatic environments. Although they are a small percentage of the bacteria in these environments, vibrios can predominate during blooms. Vibrios also play important roles in the degradation of polymeric substances, such as chitin, and in other biogeochemical processes. Vibrios can be found as free-living bacteria, attached to particles, or associated with other organisms in a mutualistic, commensal, or pathogenic relationship. This review focuses on vibrio ecology and genome plasticity, which confers an ability to adapt to new niches and is driven, at least in part, by horizontal gene transfer (HGT). The extent of HGT and its role in pathogen emergence are discussed based on genomic studies of environmental and pathogenic vibrios, mobile genetically encoded virulence factors, and mechanistic studies on the different modes of HGT.

The distribution of bacterial doubling times in the wild

Generation time varies widely across organisms and is an important factor in the life cycle, life history and evolution of organisms. Although the doubling time (DT) has been estimated for many bacteria in the laboratory, it is nearly impossible to directly measure it in the natural environment. However, an estimate can be obtained by measuring the rate at which bacteria accumulate mutations per year in the wild and the rate at which they mutate per generation in the laboratory. If we assume the mutation rate per generation is the same in the wild and in the laboratory, and that all mutations in the wild are neutral, an assumption that we show is not very important, then an estimate of the DT can be obtained by dividing the latter by the former. We estimate the DT for five species of bacteria for which we have both an accumulation and a mutation rate estimate. We also infer the distribution of DTs across all bacteria from the distribution of the accumulation and mutation rates. Both analyses suggest that DTs for bacteria in the wild are substantially greater than those in the laboratory, that they vary by orders of magnitude between different species of bacteria and that a substantial fraction of bacteria double very slowly in the wild.

Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter

The extent of genome divergence and the evolutionary events leading to speciation of marine bacteria have mostly been studied for (locally) abundant, free-living groups. The genus Phaeobacter is found on different marine surfaces, seems to occupy geographically disjunct habitats, and is involved in different biotic interactions, and was therefore targeted in the present study. The analysis of the chromosomes of 32 closely related but geographically spread Phaeobacter strains revealed an exceptionally large, highly syntenic core genome. The flexible gene pool is constantly but slightly expanding across all Phaeobacter lineages. The horizontally transferred genes mostly originated from bacteria of the Roseobacter group and horizontal transfer most likely was mediated by gene transfer agents. No evidence for geographic isolation and habitat specificity of the different phylogenomic Phaeobacter clades was detected based on the sources of isolation. In contrast, the functional gene repertoire and physiological traits of different phylogenomic Phaeobacter clades were sufficiently distinct to suggest an adaptation to an associated lifestyle with algae, to additional nutrient sources, or toxic heavy metals. Our study reveals that the evolutionary trajectories of surface-associated marine bacteria can differ significantly from free-living marine bacteria or marine generalists.

Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community

To quantitatively link microbial identity with biogeochemical function, we carried out 14 simultaneous stable isotope probing experiments with organic and inorganic C and N substrates to measure the isotope incorporation by over one hundred co-occurring eukaryotic and prokaryotic populations in a coastal community. We found that nitrate was the most commonly incorporated substrate, and that light-driven carbon fixation was carried out by some bacterial taxa from the Flavobacteriales and OM60 (NOR5) clade, in addition to photoautotrophic phytoplankton. We found that organisms that incorporated starch, maltose, glucose, lactose and bicarbonate were phylogenetically clustered, suggesting that specific bacterial lineages specialized in the incorporation of these substrates. The data further revealed that coastal microorganisms spanned a range of resource utilization strategies from generalists to specialists and demonstrated a high level of substrate partitioning, with two thirds of taxa exhibiting unique substrate incorporation patterns and the remaining third shared by no more than three OTUs each. Specialists exhibited more extreme incorporation levels (high or low), whereas generalists displayed more intermediate activity levels. These results shed valuable insights into the bottom-up ecological strategies enabling the persistence of high microbial diversity in aquatic ecosystems.

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome

Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks.

The human microbiome, the collection of microbial communities that colonize the human body, is a crucial component to health and disease. Two major components of the human microbiome are the bacterial and viral communities. These communities have primarily been studied separately using metrics of community composition and diversity. These approaches have failed to capture the complex dynamics of interacting bacteria and phage communities, which frequently share genetic information and work together to maintain ecosystem homestatsis (e.g. kill-the-winner dynamics). Removal of bacteria or phage can disrupt or even collapse those ecosystems. Relationship-based network approaches allow us to capture this interaction information. Using this network-based approach with three independent human cohorts, we were able to present an initial understanding of how phage-bacteria networks differ throughout the human body, so as to provide a baseline for future studies of how and why microbiome networks differ in disease states.