Marine Microbial Communities Research Articles

Lipid biomarkers recording marine microbial community structure changes through the Frasnian-Famennian mass extinction event.

Studying the response and recovery of marine microbial communities during mass extinction events provides an evolutionary window through which to understand the adaptation and resilience of the marine ecosystem in the face of significant environmental disturbances. The goal of this study is to reconstruct changes in the marine microbial community structure through the Late Devonian Frasnian-Famennian (F-F) transition. We performed a multiproxy investigation on a drill core of the Upper Devonian New Albany Shale from the Illinois Basin (western Kentucky, USA). Aryl isoprenoids show green sulfur bacteria expansion and associated photic zone euxinia (PZE) enhancement during the F-F interval. These changes can be attributed to augmented terrigenous influxes, as recorded collectively by the long-chain/short-chain normal alkane ratio, carbon preference index, C30 moretane/C30 hopane, and diahopane index. Hopane/sterane ratios reveal a more pronounced dominance of eukaryotic over prokaryotic production during the mass extinction interval. Sterane distributions indicate that the microalgal community was primarily composed of green algae clades, and their dominance became more pronounced during the F-F interval and continued to rise in the subsequent periods. The 2α-methylhopane index values do not show an evident shift during the mass extinction interval, whereas the 3β-methylhopane index values record a greater abundance of methanotrophic bacteria during the extinction interval, suggesting enhanced methane cycling due to intensified oxygen depletion. Overall, the Illinois Basin during the F-F extinction experienced heightened algal productivity due to intensified terrigenous influxes, exhibiting similarities to contemporary coastal oceans that are currently undergoing globalized cultural eutrophication. The observed microbial community shifts associated with the F-F environmental disturbances were largely restricted to the extinction interval, which suggests a relatively stable, resilient marine microbial ecosystem during the Late Devonian.

Frequent pulse disturbances shape resistance and resilience in tropical marine microbial communities

The Johor Strait separates the island of Singapore from Peninsular Malaysia. A 1-kilometer causeway built in the early 1920s in the middle of the strait effectively blocks water flowing to/from either side, resulting in low water turnover rates and build-up of nutrients in the inner Strait. We have previously shown that short-term rather than seasonal environmental changes influence microbial community composition in the Johor Strait. Here, we present a temporally-intensive study that uncovers the factors keeping the microbial populations in check. We sampled the surface water at four sites in the inner Eastern Johor Strait every other day for two months, while measuring various water quality parameters, and analysed 16S amplicon sequences and flow-cytometric counts. We discovered that microbial community succession revolves around a common stable state resulting from frequent pulse disturbances. Among these, sporadic riverine freshwater input and regular tidal currents influence bottom-up controls including the availability of the limiting nutrient nitrogen and its biological release in readily available forms. From the top-down, marine viruses and predatory bacteria limit the proliferation of microbes in the water. Harmful algal blooms, which have been observed historically in these waters, may occur only when there are simultaneous gaps in the top-down and bottom-up controls. This study gains insight into complex interactions between multiple factors contributing to a low-resistance but high-resilience microbial community and speculate about rare events that could lead to the occurrence of an algal bloom.

The patterns of marine microbial communities in composts with high lignocellulose content

More eco-efficient and high-performance disposal or conversion approaches for practical biomass applications have become a sought-after craze. In this study, microbial communities derived from deep-sea sediments were used in organic compost consisting of more than 50% lignocellulose. The results showed that deep-sea microorganisms did possess the ability to dissolve lignocellulose, and their patterns in composting exhibited specificity. The temperature of the system quickly exceeded 40 °C from the 5th day and the peak was over 60 °C, and then went through the whole period within 17 days. The pH of the system increased from 5 to 9, along with a reduction in moisture content to around 19%. Bacterial diversity increased with composting, while fungal diversity showed a downward trend. Significant temperature-driven variability in bacterial communities was observed, while differences in fungal communities at high-temperature stages and later stages were not pronounced. The system ended up with a 47% reduction in cellulose and an almost 30% reduction in hemicellulose. This study demonstrated the different digestion pathways of bacteria and fungi in response to high lignocellulose environments and the great potential of microbial communities from marine as important candidates for lignocellulose treatment.

Functional annotation and importance of marine bacterial transporters of plankton exometabolites

Metabolite exchange within marine microbial communities transfers carbon and other major elements through global cycles and forms the basis of microbial interactions. Yet lack of gene annotations and concern about the quality of existing ones remain major impediments to revealing currencies of carbon flux. We employed an arrayed mutant library of the marine bacterium Ruegeria pomeroyi DSS-3 to experimentally annotate substrates of organic compound transporter systems, using mutant growth and compound drawdown analyses to link transporters to their cognate substrates. Mutant experiments verified substrates for thirteen R. pomeroyi transporters. Four were previously hypothesized based on gene expression data (taurine, glucose/xylose, isethionate, and cadaverine/putrescine/spermidine); five were previously hypothesized based on homology to experimentally annotated transporters in other bacteria (citrate, glycerol, N-acetylglucosamine, fumarate/malate/succinate, and dimethylsulfoniopropionate); and four had no previous annotations (thymidine, carnitine, cysteate, and 3-hydroxybutyrate). These bring the total number of experimentally-verified organic carbon influx transporters to 18 of 126 in the R. pomeroyi genome. In a longitudinal study of a coastal phytoplankton bloom, expression patterns of the experimentally annotated transporters linked them to different stages of the bloom, and also led to the hypothesis that citrate and 3-hydroxybutyrate were among the most highly available bacterial substrates. Improved functional annotation of the gatekeepers of organic carbon uptake is critical for deciphering carbon flux and fate in microbial ecosystems.

Exploring the plankton bacteria diversity and distribution patterns in the surface water of northwest pacific ocean by metagenomic methods

The study of marine microbial communities is crucial for comprehending the distribution patterns, adaptations to the environment, and the functioning of marine microorganisms. Despite being one of the largest biomes on Earth, the bacterioplankton communities in the Northwest Pacific Ocean (NWPO) remain understudied. In this research, we aimed to investigate the structure of the surface bacterioplankton communities in different water masses of the NWPO. We utilized metagenomic sequencing techniques and cited previous 16S rRNA data to explore the distribution patterns of bacterioplankton in different seasons. Our results revealed that Cyanobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria dominated the microbial communities, accounting for over 95% of the total. During spring, we observed significant differentiation in community structure between the different water masses. For instance, Prochlorococcus and Pseudoalteromonas were primarily distributed in the nutrient-deficient subtropical countercurrent zone, while Flavobacteriaceae and Rhodobacteraceae were found in the Kuroshio-Oyashio mixing zone. During summer, the surface planktonic bacteria communities became homogenized across regions, with Cyanobacteria becoming the dominant group (68.6% to 84.9% relative abundance). The metabolic processes of the microorganisms were dominated by carbohydrate metabolism, followed by amino acid transport and metabolism. However, there was a low relative abundance of functional genes involved in carbohydrate metabolism in the Kuroshio-Oyashio mixing zone. The metagenomic data had assembled 37 metagenomic-assembled genomes (MAGs), which belong to Proteobacteria, Bacteroidetes, and Euryarchaeota. In conclusion, our findings highlight the diversity of the surface bacterioplankton community composition in the NWPO, and its distinct geographic distribution characteristics and seasonal variations.

Cobalamin producers and prokaryotic consumers in the Northwest Atlantic.

Cobalamin availability can influence primary productivity and ecological interactions in marine microbial communities. The characterization of cobalamin sources and sinks is a first step in investigating cobalamin dynamics and its impact on productivity. Here, we identify potential cobalamin sources and sinks on the Scotian Shelf and Slope in the Northwest Atlantic Ocean. Functional and taxonomic annotation of bulk metagenomic reads, combined with analysis of genome bins, were used to identify potential cobalamin sources and sinks. Cobalamin synthesis potential was mainly attributed to Rhodobacteraceae, Thaumarchaeota, and cyanobacteria (Synechococcus and Prochlorococcus). Cobalamin remodelling potential was mainly attributed to Alteromonadales, Pseudomonadales, Rhizobiales, Oceanospirilalles, Rhodobacteraceae, and Verrucomicrobia, while potential cobalamin consumers include Flavobacteriaceae, Actinobacteria, Porticoccaceae, Methylophiliaceae, and Thermoplasmatota. These complementary approaches identified taxa with the potential to be involved in cobalamin cycling on the Scotian Shelf and revealed genomic information required for further characterization. The Cob operon of Rhodobacterales bacterium HTCC2255, a strain with known importance in cobalamin cycling, was similar to a major cobalamin producer bin, suggesting that a related strain may represent a critical cobalamin source in this region. These results enable future inquiries that will enhance our understanding of how cobalamin shapes microbial interdependencies and productivity in this region.

Trophic level and proteobacteria abundance drive antibiotic resistance levels in fish from coastal New England

BackgroundThe natural marine environment represents a vast reservoir of antimicrobial resistant bacteria. The wildlife that inhabits this environment plays an important role as the host to these bacteria and in the dissemination of resistance. The relationship between host diet, phylogeny, and trophic level and the microbiome/resistome in marine fish is not fully understood. To further explore this relationship, we utilize shotgun metagenomic sequencing to define the gastrointestinal tract microbiomes of seven different marine vertebrates collected in coastal New England waters.ResultsWe identify inter and intraspecies differences in the gut microbiota of these wild marine fish populations. Furthermore, we find an association between antibiotic resistance genes and host dietary guild, which suggests that higher trophic level organisms have a greater abundance of resistance genes. Additionally, we demonstrate that antibiotic resistance gene burden is positively correlated with Proteobacteria abundance in the microbiome. Lastly, we identify dietary signatures within the gut of these fish and find evidence of possible dietary selection for bacteria with specific carbohydrate utilization potential.ConclusionsThis work establishes a link between host lifestyle/dietary guild, and microbiome composition and the abundance of antibiotic resistance genes within the gastrointestinal tract of marine organisms. We expand the current understanding of marine organism-associated microbial communities and their role as reservoirs of antimicrobial resistance genes.

Effects of ethoxyquin on metabolism and composition of active marine microbial communities

Salmon culture has the potential to generate environmental impacts due to the release of organic matter and chemical products into the water column. Ethoxyquin (EQ) is a food additive widely used as an antioxidant in fish feed, but due to the scarce evidence on its safety for the environment it has been banned by the European Food Safety Authority. To evaluate and compare responses of marine microbial communities to EQ additions (10, 100 and 1000 μg L−1), we carried out 20 L seawater microcosm experiments in two distinct areas, Achao and Coliumo Bay, where the first is influenced by salmon farming. We estimated metabolic response (respiration, extracellular enzymatic activity and ECOplates) for two size fractions (< 1 μm and < 63 μm) and changes in the active microbial community diversity. The results revealed different responses associated with study sites and size fractions. For the < 1 μm fraction (bacterioplankton), the addition of EQ increased both oxygen consumption and the degradation of proteinaceus compounds, while for the entire community (< 63 μm), the addition of EQ decrease respiration and the capacity to degrade carbohydrates and lipids. The carbon substrates utilization was variable, decreasing in the 100 and 1000 μg EQ. L−1 treatments, suggesting that high EQ concentrations may limit the capacity to process different carbon sources, producing a preference for amino acids and carboxylic acids in the first hours of exposition in Achao. In the area without salmon farming (Coliumo Bay) substrates utilization, mainly carbohydrates and carboxylic acids, was stimulated by the addition of EQ. A shift was observed in the active microbial community between treatments at different taxonomic levels, especially associated with Alphaproteobacteria, which presented lower activity when exposed to EQ. Gammaproteobacteria (KI89A), Bacteroidea (NS10, NS3b clade) and MGII showed higher activity associated with EQ additions. Overall, our study indicates that EQ may generate both changes in the metabolism (respiration, enzymatic extracellular activity, carbon sources preferences) and composition of the active microbial community in the water column altering the degradation of organic matter.

Molecular hydrogen in seawater supports growth of diverse marine bacteria

Molecular hydrogen (H2) is an abundant and readily accessible energy source in marine systems, but it remains unknown whether marine microbial communities consume this gas. Here we use a suite of approaches to show that marine bacteria consume H2 to support growth. Genes for H2-uptake hydrogenases are prevalent in global ocean metagenomes, highly expressed in metatranscriptomes and found across eight bacterial phyla. Capacity for H2 oxidation increases with depth and decreases with oxygen concentration, suggesting that H2 is important in environments with low primary production. Biogeochemical measurements of tropical, temperate and subantarctic waters, and axenic cultures show that marine microbes consume H2 supplied at environmentally relevant concentrations, yielding enough cell-specific power to support growth in bacteria with low energy requirements. Conversely, our results indicate that oxidation of carbon monoxide (CO) primarily supports survival. Altogether, H2 is a notable energy source for marine bacteria and may influence oceanic ecology and biogeochemistry.

Cryo-electron microscopy of extracellular vesicles associated with the marine toxic dinoflagellate Alexandrium minutum

Extracellular Vesicles (EVs) are likely an important strategy of transport and communication in marine microbial community. Their isolation and characterization from axenic culture of microbial eukaryotes represents a technological challenge not fully solved. Here, for the first time, we isolated EVs from a near-axenic culture of the toxic dinoflagellate Alexandrium minutum. Pictures of the isolated vesicles were done with Cryo TEM (Cryogenic Transmission Electron Microscopy). Based on their morphotype the EVs were clustered in five major groups (rounded, rounded electron-dense, lumen electron-dense, double and irregular) and each EV was measured resulting in an average size of 0.36 µm of diameter. Taking in account that in prokaryotes it has been demonstrated that EVs play an important role in the mechanism of toxicity, this descriptive work aims to be the first step to study the possible role of EVs in the toxicity of dinoflagellates.

Spatial co-occurrence patterns of benthic microbial assemblage in response to trace metals in the Atacama Desert Coastline.

Taxonomic and functional microbial communities may respond differently to anthropogenic coastal impacts, but ecological quality monitoring assessments using environmental DNA and RNA (eDNA/eRNA) in response to pollution are poorly understood. In the present study, we investigated the utility of the co-occurrence network approach's to comprehensively explore both structure and potential functions of benthic marine microbial communities and their responses to Cu and Fe fractioning from two sediment deposition coastal zones of northern Chile via 16S rRNA gene metabarcoding. The results revealed substantial differences in the microbial communities, with the predominance of two distinct module hubs based on study zone. This indicates that habitat influences microbial co-occurrence networks. Indeed, the discriminant analysis allowed us to identify keystone taxa with significant differences in eDNA and eRNA comparison between sampled zones, revealing that Beggiatoaceae, Carnobacteriaceae, and Nitrosococcaceae were the primary representatives from Off Loa, whereas Enterobacteriaceae, Corynebacteriaceae, Latescibacteraceae, and Clostridiaceae were the families responsible for the observed changes in Mejillones Bay. The quantitative evidence from the multivariate analyses supports that the benthic microbial assemblages' features were linked to specific environments associated with Cu and Fe fractions, mainly in the Bay. Furthermore, the predicted functional microbial structure suggested that transporters and DNA repair allow the communities to respond to metals and endure the interacting variable environmental factors like dissolved oxygen, temperature, and salinity. Moreover, some active taxa recovered are associated with anthropogenic impact, potentially harboring antibiotic resistance and other threats in the coastal zone. Overall, the method of scoping eRNA in parallel with eDNA applied here has the capacity to significantly enhance the spatial and functional understanding of real-time microbial assemblages and, in turn, would have the potential to increase the acuity of biomonitoring programs key to responding to immediate management needs for the marine environment.

Tracking nitrogen allocation to proteome biosynthesis in a marine microbial community.

Microbial growth in many environments is limited by nitrogen availability, yet there is limited understanding of how complex communities compete for and allocate this resource. Here we develop a broadly applicable approach to track biosynthetic incorporation of 15N-labelled nitrogen substrates into microbial community proteomes, enabling quantification of protein turnover and N allocation to specific cellular functions in individual taxa. Application to oligotrophic ocean surface water identifies taxa-specific substrate preferences and a distinct subset of protein functions undergoing active biosynthesis. The cyanobacterium Prochlorococcus is the most effective competitor for acquisition of ammonium and urea and shifts its proteomic allocation of N over the day/night cycle. Our approach reveals that infrastructure and protein-turnover functions comprise substantial biosynthetic demand for N in Prochlorococcus and a range of other microbial taxa. The direct interrogation of the proteomic underpinnings of N limitation with 15N-tracking proteomics illuminates how nutrient stress differentially influences metabolism in co-existing microbes.

Changes in interactions over ecological time scales influence single-cell growth dynamics in a metabolically coupled marine microbial community

Microbial communities thrive in almost all habitats on earth. Within these communities, cells interact through the release and uptake of metabolites. These interactions can have synergistic or antagonistic effects on individual community members. The collective metabolic activity of microbial communities leads to changes in their local environment. As the environment changes over time, the nature of the interactions between cells can change. We currently lack understanding of how such dynamic feedbacks affect the growth dynamics of individual microbes and of the community as a whole. Here we study how interactions mediated by the exchange of metabolites through the environment change over time within a simple marine microbial community. We used a microfluidic-based approach that allows us to disentangle the effect cells have on their environment from how they respond to their environment. We found that the interactions between two species—a degrader of chitin and a cross-feeder that consumes metabolic by-products—changes dynamically over time as cells modify their environment. Cells initially interact positively and then start to compete at later stages of growth. Our results demonstrate that interactions between microorganisms are not static and depend on the state of the environment, emphasizing the importance of disentangling how modifications of the environment affects species interactions. This experimental approach can shed new light on how interspecies interactions scale up to community level processes in natural environments.

Correction to “Glycine betaine uptake and metabolism in marine microbial communities”

Correction to “Glycine betaine uptake and metabolism in marine microbial communities”

Effect of polyhydroxyalkanoates on the microbial reductive dechlorination of polychlorinated biphenyls and competing anaerobic respirations in a marine microbial culture

The effect of polyhydroxyalkanoates (PHAs) with different composition on the reductive dechlorination activity of a polychlorinated biphenyls (PCBs) dechlorinating marine microbial community and on the activity of sulfate-reducing (SRB) and methanogenic bacteria (MB), were investigated in marine sediment microcosms and compared with the main monomer, 3-hydroxybutyric acid (3HB). Despite PHAs were fermented more slowly than 3HB, all electron donors stimulated constantly sulfate-reduction, methanogenesis and, only transiently, PCB reductive dechlorination. No relevant differences were observed with different compositions of PHAs. According to electron balances, the majority of the supplied electrons (50 %) were consumed by SRB and to less extent by MB (9–31 %), while a small percentage (0.01 %) was delivered to OHRB. In the studied conditions PHAs were confirmed as potential slow‑hydrogen releasing compounds in marine environment but their fermentation rate was sufficiently high to mainly stimulate the competitors of organohalide respring bacteria for electron donors.

Self-assembly of ammonium assimilation microbiomes regulated by COD/N ratio

Marine microorganisms have an inherent advantage in the treatment of saline wastewater due to their halophilic properties. Ammonium assimilation is the most important and common nitrogen conversion pathway in the ocean, which means that it may be a suitable nitrogen removal strategy under high salinity conditions. However, the targeted construction of engineering microbiomes with ammonium assimilation function for nitrogen recovery has not been realized. Here, we constructed four halophilic ammonium assimilation microbiomes from marine microbial community under varying chemical oxygen demand (COD) to nitrogen (COD/N) ratios. The regulation of COD/N ratio on microbial self-assembly was explored at the phenotypic, genetic, and microbial levels. The results of nitrogen balance tests, functional genes abundance and microbial community structure confirmed that the microbiomes regulated by different COD/N ratios all performed obligate ammonium assimilation functions. >93% of ammonium, 90% of TN, 98% of COD, and 82% of phosphorus were simultaneously removed by microbial assimilation under the COD/N ratio of 20. COD/N ratios significantly affected the self-assembly of microbiomes by selectively enriching heterotrophic microorganisms with different preference for organic carbon load. Additionally, the increase of COD/N ratio intensified the competition among species within the microbiome (the proportion of negative connections of microbial network increased from 5.0% to 24.4%), which may enhance the stability of community structure. Taken together, these findings can provide theoretical guidance for the construction and optimization of engineering microbiomes for synergistic nitrogen removal and recovery.

Water mass-driven multiple ecological effects determine the biodiversity and community assembly of microbial flagellates in subtropic-tropic marginal seas of China

Marine microbial flagellates form an important part of marine ecosystems, and play an essential role in maintaining ecosystem functions. However, the underlying biogeographic processes and ecological effects that shape marine microbial flagellate communities (MFCs) on the geographical scale (∼2000 km) remain unclear, especially how their composition is related to movements of water masses. In this study, high-throughput sequencing of 18S rRNA genes was conducted to survey two size-fractioned groups (0.8–2.0 μm for pico-sized and 2.0–20 μm for nano-sized groups) of MFCs in three subtropic-tropic marginal seas of China. In addition, the impacts of environmental factors, spatial factors, and water masses on MFCs were explored and compared across different spatiotemporal conditions. The results demonstrate non-random biogeographic distributions of MFCs in the studied area. These distributions were affected by several ecological processes, such as environmental selection, dispersal limitation, neutral process, and interactions within communities. These processes were driven by complex water masses that formed on a geographical scale. Notably, environmental heterogeneity was identified as the principal determinant of MFCs in each sea area. However, the importance of spatial factors increased with the spatial scale, which weakened biotic interactions within the community on a geographical scale. This effect was more apparent in nano-sized MFCs, indicating stronger dispersal limitation because of their larger cells and weaker dispersal ability. In summary, this study expands the available knowledge on the dynamic biogeographic patterns of MFCs associated with water masses on a geographical scale where strong spatial and environmental gradients exist.

Plastic leachates impair picophytoplankton and dramatically reshape the marine microbiome

BackgroundEach year, approximately 9.5 million metric tons of plastic waste enter the ocean with the potential to adversely impact all trophic levels. Until now, our understanding of the impact of plastic pollution on marine microorganisms has been largely restricted to the microbial assemblages that colonize plastic particles. However, plastic debris also leaches considerable amounts of chemical additives into the water, and this has the potential to impact key groups of planktonic marine microbes, not just those organisms attached to plastic surfaces.ResultsTo investigate this, we explored the population and genetic level responses of a marine microbial community following exposure to leachate from a common plastic (polyvinyl chloride) or zinc, a specific plastic additive. Both the full mix of substances leached from polyvinyl chloride (PVC) and zinc alone had profound impacts on the taxonomic and functional diversity of our natural planktonic community. Microbial primary producers, both prokaryotic and eukaryotic, which comprise the base of the marine food web, were strongly impaired by exposure to plastic leachates, showing significant declines in photosynthetic efficiency, diversity, and abundance. Key heterotrophic taxa, such as SAR11, which are the most abundant planktonic organisms in the ocean, also exhibited significant declines in relative abundance when exposed to higher levels of PVC leachate. In contrast, many copiotrophic bacteria, including members of the Alteromonadales, dramatically increased in relative abundance under both exposure treatments. Moreover, functional gene and genome analyses, derived from metagenomes, revealed that PVC leachate exposure selects for fast-adapting, motile organisms, along with enrichment in genes usually associated with pathogenicity and an increased capacity to metabolize organic compounds leached from PVC.ConclusionsThis study shows that substances leached from plastics can restructure marine microbial communities with the potential for significant impacts on trophodynamics and biogeochemical cycling. These findings substantially expand our understanding of the ways by which plastic pollution impact life in our oceans, knowledge which is particularly important given that the burden of plastic pollution in the marine environment is predicted to continue to rise.DubVoHjQQ1D-hWwEoHQrx7Video

MetaLP: An integrative linear programming method for protein inference in metaproteomics.

Metaproteomics based on high-throughput tandem mass spectrometry (MS/MS) plays a crucial role in characterizing microbiome functions. The acquired MS/MS data is searched against a protein sequence database to identify peptides, which are then used to infer a list of proteins present in a metaproteome sample. While the problem of protein inference has been well-studied for proteomics of single organisms, it remains a major challenge for metaproteomics of complex microbial communities because of the large number of degenerate peptides shared among homologous proteins in different organisms. This challenge calls for improved discrimination of true protein identifications from false protein identifications given a set of unique and degenerate peptides identified in metaproteomics. MetaLP was developed here for protein inference in metaproteomics using an integrative linear programming method. Taxonomic abundance information extracted from metagenomics shotgun sequencing or 16s rRNA gene amplicon sequencing, was incorporated as prior information in MetaLP. Benchmarking with mock, human gut, soil, and marine microbial communities demonstrated significantly higher numbers of protein identifications by MetaLP than ProteinLP, PeptideProphet, DeepPep, PIPQ, and Sipros Ensemble. In conclusion, MetaLP could substantially improve protein inference for complex metaproteomes by incorporating taxonomic abundance information in a linear programming model.

Quorum Sensing and Antimicrobial Production Orchestrate Biofilm Dynamics in Multispecies Bacterial Communities.

Microbial interactions are often mediated by diffusible small molecules, including secondary metabolites, that play roles in cell-to-cell signaling and inhibition of competitors. Biofilms are often "hot spots" for high concentrations of bacteria and their secondary metabolites, which make them ideal systems for the study of small-molecule contributions to microbial interactions. Here, we use a five-member synthetic community consisting of Roseobacteraceae representatives to investigate the role of secondary metabolites on microbial biofilm dynamics. One synthetic community member, Rhodobacterales strain Y4I, possesses two acylated homoserine lactone (AHL)-based cell-to-cell signaling systems (pgaRI and phaRI) as well as a nonribosomal peptide synthase gene (igi) cluster that encodes the antimicrobial indigoidine. Through serial substitution of Y4I with mutants deficient in single signaling molecule pathways, the contribution of these small-molecule systems could be assessed. As secondary metabolite production is dependent upon central metabolites, the influence of growth substrate (i.e., complex medium versus defined medium with a single carbon substrate) on these dynamics was also considered. Depending on the Y4I mutant genotype included, community dynamics ranged from competitive to cooperative. The observed interactions were mostly competitive in nature. However, the community harboring a Y4I variant that was both impaired in quorum sensing (QS) pathways and unable to produce indigoidine (pgaR variant) shifted toward more cooperative interactions over time. These cooperative interactions were enhanced in the defined growth medium. The results presented provide a framework for deciphering complex, small-molecule-mediated interactions that have broad application to microbial biology. IMPORTANCE Microbial biofilms play critical roles in marine ecosystems and are hot spots for microbial interactions that play a role in the development and function of these communities. Roseobacteraceae are an abundant and active family of marine heterotrophic bacteria forming close associations with phytoplankton and carrying out key transformations in biogeochemical cycles. Group members are aggressive primary colonizers of surfaces, where they set the stage for the development of multispecies biofilm communities. Few studies have examined the impact of secondary metabolites, such as cell-to-cell signaling and antimicrobial production, on marine microbial biofilm community structure. Here, we assessed the impact of secondary metabolites on microbial interactions using a synthetic, five-member Roseobacteraceae community by measuring species composition and biomass production during biofilm growth. We present evidence that secondary metabolites influence social behaviors within these multispecies microbial biofilms, thereby improving understanding of bacterial secondary metabolite production influence on social behaviors within marine microbial biofilm communities.