Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria)

Analyzing bacterial networks and interactions in skin and gills of Sparus aurata with microalgae-based additive feeding

The inclusion of microalgae in functional fish diets has a notable impact on the welfare, metabolism and physiology of the organism. The microbial communities associated with the fish are directly influenced by the host's diet, and further understanding the impact on mucosal microbiota is needed. This study aimed to analyze the microbiota associated with the skin and gills of Sparus aurata fed a diet containing 10% microalgae. Sequencing of the V3-V4 variable region of 16S rDNA molecules was employed to determine the composition of the microbial communities. The study employed bioinformatics tools to explore the taxonomic composition and interactions of the microbiota, emphasizing the integration of taxonomic analysis and abundance correlation networks as crucial for understanding microbial community dynamics and the impact of functional diets. The results indicated that there were not changes in the composition of the skin and gill microbiota. However, notable differences were observed in the bacterial interaction networks. The skin and gill networks exhibited distinct overall patterns influenced by their respective environments and functions. The gill network showed a highly connected and redundant structure, increasing its resilience, while the skin network showed a more fragmented structure, suggesting a potentially greater vulnerability to perturbations. Key taxa, such as Acinetobacter and Polaribacter, were identified as critical for maintaining the stability and functionality of these microbial ecosystems. Polaribacter could demonstrate potential protection against pathogens through negative interactions. These tentative studies open up an additional avenue to consider, such as the interactions among bacterial communities, as well as new proposals to corroborate these findings. These observations underline the importance of understanding the composition and interactions within bacterial groups to fully grasp the dynamics of microbial communities.

Chronic polystyrene microplastics exposure-induced changes in thick-shell mussel (Mytilus coruscus) metaorganism: A holistic perspective

Microplastics have emerged as a significant global concern, particularly in marine ecosystems. While extensive research has focused on the toxicological effects of microplastics on marine animals and/or their associated microorganisms as two separate entities, the holistic perspective of the adaptability and fitness of a marine animal metaorganism-comprising the animal host and its microbiome-remains largely unexplored. In this study, mussel metaorganisms subjected chronic PS-MPs exposure experienced acute mortality but rapidly adapted. We investigated the response of innate immunity, digestive enzymes and their associated microbiomes to chronic PS-MPs exposure. We found that PS-MPs directly and indirectly interacted with the host and microbe within the exposure system. The adaptation was a joint effort between the physiological adjustments of mussel host and genetic adaptation of its microbiome. The mussel hosts exhibited increased antioxidant activity, denser gill filaments and increased immune cells, enhancing their innate immunity. Concurrently, the gill microbiome and the digestive gland microbiome respective selectively enriched for plastic-degrading bacteria and particulate organic matter-utilizing bacteria, facilitating the microbiome's adaptation. The microbial adaptation to chronic PS-MPs exposure altered the ecological roles of mussel microbiome, as evidenced by alterations in microbial interactions and nutrient cycling functions. These findings provided new insights into the ecotoxicological impact of microplastics on marine organisms from a metaorganism perspective.

Digital Microbe: a genome-informed data integration framework for team science on emerging model organisms

The remarkable pace of genomic data generation is rapidly transforming our understanding of life at the micron scale. Yet this data stream also creates challenges for team science. A single microbe can have multiple versions of genome architecture, functional gene annotations, and gene identifiers; additionally, the lack of mechanisms for collating and preserving advances in this knowledge raises barriers to community coalescence around shared datasets. "Digital Microbes" are frameworks for interoperable and reproducible collaborative science through open source, community-curated data packages built on a (pan)genomic foundation. Housed within an integrative software environment, Digital Microbes ensure real-time alignment of research efforts for collaborative teams and facilitate novel scientific insights as new layers of data are added. Here we describe two Digital Microbes: 1) the heterotrophic marine bacterium Ruegeria pomeroyi DSS-3 with > 100 transcriptomic datasets from lab and field studies, and 2) the pangenome of the cosmopolitan marine heterotroph Alteromonas containing 339 genomes. Examples demonstrate how an integrated framework collating public (pan)genome-informed data can generate novel and reproducible findings.

Heterotrophic bacteria trigger transcriptome remodelling in the photosynthetic picoeukaryote Micromonas commoda

Marine biogeochemical cycles are built on interactions between surface ocean microbes, particularly those connecting phytoplankton primary producers to heterotrophic bacteria. Details of these associations are not well understood, especially in the case of direct influences of bacteria on phytoplankton physiology. Here we catalogue how the presence of three marine bacteria (Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14 and Polaribacter dokdonensis MED152) individually and uniquely impact gene expression of the picoeukaryotic alga Micromonas commoda RCC 299. We find a dramatic transcriptomic remodelling by M. commoda after 8 h in co-culture, followed by an increase in cell numbers by 56 h compared with the axenic cultures. Some aspects of the algal transcriptomic response are conserved across all three bacterial co-cultures, including an unexpected reduction in relative expression of photosynthesis and carbon fixation pathways. Expression differences restricted to a single bacterium are also observed, with the Flavobacteriia P. dokdonensis uniquely eliciting changes in relative expression of algal genes involved in biotin biosynthesis and the acquisition and assimilation of nitrogen. This study reveals that M. commoda has rapid and extensive responses to heterotrophic bacteria in ways that are generalizable, as well as in a taxon specific manner, with implications for the diversity of phytoplankton-bacteria interactions ongoing in the surface ocean.

Interplay between autotrophic and heterotrophic prokaryotic metabolism in the bathypelagic realm revealed by metatranscriptomic analyses

BACKGROUND

Heterotrophic microbes inhabiting the dark ocean largely depend on the settling of organic matter from the sunlit ocean. However, this sinking of organic materials is insufficient to cover their demand for energy and alternative sources such as chemoautotrophy have been proposed. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes.

METHODS

Seawater samples were collected from Labrador Sea Water (LSW, ~ 2000 m depth) in the North Atlantic and incubated in the dark at in situ temperature unamended, amended with 1 µM thiosulfate, or with 1 µM thiosulfate plus 10 µM glucose and 10 µM acetate (thiosulfate plus dissolved organic matter, DOM). Inorganic carbon fixation was measured in the different treatments and samples for metatranscriptomic analyses were collected after 1 h and 72 h of incubation.

RESULTS

Amendment of LSW with thiosulfate and thiosulfate plus DOM enhanced prokaryotic inorganic carbon fixation. The energy generated via chemoautotrophy and heterotrophy in the amended prokaryotic communities was used for the biosynthesis of glycogen and phospholipids as storage molecules. The addition of thiosulfate stimulated unclassified bacteria, sulfur-oxidizing Deltaproteobacteria (SAR324 cluster bacteria), Epsilonproteobacteria (Sulfurimonas sp.), and Gammaproteobacteria (SUP05 cluster bacteria), whereas, the amendment with thiosulfate plus DOM stimulated typically copiotrophic Gammaproteobacteria (closely related to Vibrio sp. and Pseudoalteromonas sp.).

CONCLUSIONS

The gene expression pattern of thiosulfate utilizing microbes specifically of genes involved in energy production via sulfur oxidation and coupled to CO2 fixation pathways coincided with the change in the transcriptional profile of the heterotrophic prokaryotic community (genes involved in promoting energy storage), suggesting a fine-tuned metabolic interplay between chemoautotrophic and heterotrophic microbes in the dark ocean. Video Abstract.

Genomic potential for inorganic carbon sequestration and xenobiotic degradation in marine bacterium Youngimonas vesicularis CC-AMW-ET affiliated to family Paracoccaceae

Ecological studies on marine microbial communities largely focus on fundamental biogeochemical processes or the most abundant constituents, while minor biological fractions are frequently neglected. Youngimonas vesicularis CC-AMW-ET, isolated from coastal surface seawater in Taiwan, is an under-represented marine Paracoccaceae (earlier Rhodobacteraceae) member. The CC-AMW-ET genome was sequenced to gain deeper insights into its role in marine carbon and sulfur cycles. The draft genome (3.7 Mb) contained 63.6% GC, 3773 coding sequences and 51 RNAs, and displayed maximum relatedness (79.06%) to Thalassobius litoralis KU5D5T, a Roseobacteraceae member. While phototrophic genes were absent, genes encoding two distinct subunits of carbon monoxide dehydrogenases (CoxL, BMS/Form II and a novel form III; CoxM and CoxS), and proteins involved in HCO3- uptake and interconversion, and anaplerotic HCO3- fixation were found. In addition, a gene coding for ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO, form II), which fixes atmospheric CO2 was found in CC-AMW-ET. Genes for complete assimilatory sulfate reduction, sulfide oxidation (sulfide:quinone oxidoreductase, SqrA type) and dimethylsulfoniopropionate (DMSP) cleavage (DMSP lyase, DddL) were also identified. Furthermore, genes that degrade aromatic hydrocarbons such as quinate, salicylate, salicylate ester, p-hydroxybenzoate, catechol, gentisate, homogentisate, protocatechuate, 4-hydroxyphenylacetic acid, N-heterocyclic aromatic compounds and aromatic amines were present. Thus, Youngimonas vesicularis CC-AMW-ET is a potential chemolithoautotroph equipped with genetic machinery for the metabolism of aromatics, and predicted to play crucial roles in the biogeochemical cycling of marine carbon and sulfur.

Alteration in Community Dynamics of Chaetoceros curvisetus and Bacterioplankton Communities in Response to Surfactin Exposure

The use of surfactin is a promising method to mitigate algal blooms. However, little is known about surfactin toxicity to algae and bacterioplankton. Here, we treated Chaetoceros curvisetus, the dominant species of algal blooms in the East China Sea, with 0, 0.5, 1, 2, 3, and 4 mg/L of surfactin for 96 h to investigate temporal variability. Our results showed that low concentrations of surfactin (<2 mg/L) changed the cell morphology of C. curvisetus, and higher concentrations (>3 mg/L) had lethal effects. Meanwhile, we examined the community dynamics of the free-living (FL, 0.22-5 μm) and particle-attached (PA, >5 μm) bacterioplankton of C. curvisetus in response to different surfactin concentrations and cultivation periods. Both PA and FL bacterioplankton were mainly composed of Proteobacteria, Actinobacteria, and Bacteroidetes, while FL bacterioplankton were more diverse than PA bacterioplankton. The variations of FL and PA bacterioplankton were significantly constrained by the surfactin concentration. Surfactin changed the lifestyle of some bacterioplankton from FL to PA, which mainly belonged to abundant bacterioplankton. Furthermore, we identified some surfactin-sensitive species/taxa. Our study will help enhance the ability to predict marine microbial responses under the effect of surfactin, providing a research foundation for this new harmful algal bloom mitigation method.

Biogeographic Analysis Suggests Two Types of Planktonic Prokaryote Communities in the Barents Sea

The Barents Sea is one of the most rapidly changing Arctic regions, with an unprecedented sea ice decline and increase in water temperature and salinity. We have studied the diversity of prokaryotic communities using 16S metabarcoding in the western and northeastern parts of the Barents Sea along the Kola Section and the section from Novaya Zemlya to Franz Joseph Land. The hypothesis-independent clustering method revealed the existence of two distinct types of communities. The most common prokaryotic taxa were shared between two types of communities, but their relative abundance was different. It was found that the geographic location of the sampling sites explained more than 30% of the difference between communities, while no statistically significant correlation between environmental parameters and community composition was found. The representatives of the Psychrobacter, Sulfitobacter and Polaribacter genera were dominant in samples from both types of communities. The first type of community was also dominated by members of Halomonas, Pseudoalteromonas, Planococcaceae and an unclassified representative of the Alteromonadaceae family. The second type of community also had a significant proportion of Nitrincolaceae, SAR92, SAR11 Clade I, NS9, Cryomorphaceae and SUP05 representatives. The origin of these communities can be explained by the influence of environmental factors or by the different origins of water masses. This research highlights the importance of studying biogeographic patterns in the Barents Sea in comparison with those in the North Atlantic and Arctic Ocean prokaryote communities.

Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation

Traditional culture techniques usually retrieve a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale. We compared 16S rRNA gene sequences from a collection of 2003 cultured heterotrophic marine bacteria with global 16S rRNA metabarcoding datasets (16S TAGs) covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 23 samples used for isolation. These global datasets represent 60 322 unique 16S amplicon sequence variants (ASVs). Our results reveal a significantly higher proportion of isolates identical to ASVs in deeper ocean layers reaching up to 28% of the 16S TAGs of the bathypelagic microbial communities, which included the isolation of 3 of the top 10 most abundant 16S ASVs in the global bathypelagic ocean, related to the genera Sulfitobacter, Halomonas and Erythrobacter. These isolates contributed differently to the prokaryotic communities across different plankton size fractions, recruiting between 38% in the free-living fraction (0.2-0.8 µm) and up to 45% in the largest particles (20-200 µm) in the bathypelagic ocean. Our findings support the hypothesis that sinking particles in the bathypelagic act as resource-rich habitats, suitable for the growth of heterotrophic bacteria with a copiotroph lifestyle that can be cultured, and that these cultivable bacteria can also thrive as free-living bacteria.

Rhodopsin-mediated nutrient uptake by cultivated photoheterotrophic Verrucomicrobiota

Rhodopsin photosystems convert light energy into electrochemical gradients used by the cell to produce ATP, or for other energy-demanding processes. While these photosystems are widespread in the ocean and have been identified in diverse microbial taxonomic groups, their physiological role in vivo has only been studied in few marine bacterial strains. Recent metagenomic studies revealed the presence of rhodopsin genes in the understudied Verrucomicrobiota phylum, yet their distribution within different Verrucomicrobiota lineages, their diversity, and function remain unknown. In this study, we show that more than 7% of Verrucomicrobiota genomes (n = 2916) harbor rhodopsins of different types. Furthermore, we describe the first two cultivated rhodopsin-containing strains, one harboring a proteorhodopsin gene and the other a xanthorhodopsin gene, allowing us to characterize their physiology under laboratory-controlled conditions. The strains were isolated in a previous study from the Eastern Mediterranean Sea and read mapping of 16S rRNA gene amplicons showed the highest abundances of these strains at the deep chlorophyll maximum (source of their inoculum) in winter and spring, with a substantial decrease in summer. Genomic analysis of the isolates suggests that motility and degradation of organic material, both energy demanding functions, may be supported by rhodopsin phototrophy in Verrucomicrobiota. Under culture conditions, we show that rhodopsin phototrophy occurs under carbon starvation, with light-mediated energy generation supporting sugar transport into the cells. Overall, this study suggests that photoheterotrophic Verrucomicrobiota may occupy an ecological niche where energy harvested from light enables bacterial motility toward organic matter and supports nutrient uptake.

Metabolic Versatility of the Family Halieaceae Revealed by the Genomics of Novel Cultured Isolates

The family Halieaceae (OM60/NOR5 clade) is a gammaproteobacterial group abundant and cosmopolitan in coastal seawaters and plays an important role in response to phytoplankton blooms. However, the ecophysiology of this family remains understudied because of the vast gap between phylogenetic diversity and cultured representatives. Here, using six pure cultured strains isolated from coastal seawaters, we performed in-depth genomic analyses to provide an overview of the phylogeny and metabolic capabilities of this family. The combined analyses of 16S rRNA genes, genome sequences, and functional genes relevant to taxonomy demonstrated that each strain represents a novel species. Notably, two strains belonged to the hitherto-uncultured NOR5-4 and NOR5-12 subclades. Metabolic reconstructions revealed that the six strains likely have aerobic chemo- or photoheterotrophic lifestyles; five of them possess genes for proteorhodopsin or aerobic anoxygenic phototrophy. The presence of blue- or green-tuned proteorhodopsin in Halieaceae suggested their ability to adapt to light conditions varying with depth or coastal-to-open ocean transition. In addition to the genes of anaplerotic CO2 fixation, genes encoding a complete reductive glycine pathway for CO2 fixation were found in three strains. Putative polysaccharide utilization loci were detected in three strains, suggesting the association with phytoplankton blooms. Read mapping of various metagenomes and metatranscriptomes showed that the six strains are widely distributed and transcriptionally active in marine environments. Overall, the six strains genomically characterized in this study expand the phylogenetic and metabolic diversity of Halieaceae and likely serve as a culture resource for investigating the ecophysiological features of this environmentally relevant bacterial group. IMPORTANCE Although the family Halieaceae (OM60/NOR5 clade) is an abundant and cosmopolitan clade widely found in coastal seas and involved in interactions with phytoplankton, a limited number of cultured isolates are available. In this study, we isolated six pure cultured Halieaceae strains from coastal seawaters and performed a comparative physiological and genomic analysis to give insights into the phylogeny and metabolic potential of this family. The cultured strains exhibited diverse metabolic potential by harboring genes for anaplerotic CO2 fixation, proteorhodopsin, and aerobic anoxygenic phototrophy. Polysaccharide utilization loci detected in some of these strains also indicated an association with phytoplankton blooms. The cultivation of novel strains of Halieaceae and their genomic characteristics largely expanded the phylogenetic and metabolic diversity, which is important for future ecophysiological studies.

Impacts of microplastics and the associated plastisphere on physiological, biochemical, genetic expression and gut microbiota of the filter-feeder amphioxus

Oceanic plastic pollution is of major concern to marine organisms, especially filter feeders. However, limited is known about the toxic effects of the weathered microplastics instead of the pristine ones. This study evaluates the effects of weathered polystyrene microplastic on a filter-feeder amphioxus under starvation conditions via its exposure to the microplastics previously deployed in the natural seawater allowing for the development of a mature biofilm (so-called plastisphere). The study focused on the integration of physiological, histological, biochemical, molecular, and microbiota impacts on amphioxus. Overall, specific alterations in gene expression of marker genes were observed to be associated with oxidative stresses and immune systems. Negligible impacts were observed on antioxidant biochemical activities and gut microbiota of amphioxus, while we highlighted the potential transfer of 12 bacterial taxa from the plastisphere to the amphioxus gut microbiota. Moreover, the classical perturbation of body shape detected in control animals under starvation conditions (a slim and curved body) but not for amphioxus exposed to microplastic, indicates that the microorganisms colonizing plastics could serve as a nutrient source for this filter-feeder, commitment with the elevated proportions of goblet cell-like structures after the microplastic exposure. The multidisciplinary approach developed in this study underlined the trait of microplastics that acted as vectors for transporting microorganisms from the plastisphere to amphioxus.

Bacterial transcriptional response to labile exometabolites from photosynthetic picoeukaryote Micromonas commoda

Dissolved primary production released into seawater by marine phytoplankton is a major source of carbon fueling heterotrophic bacterial production in the ocean. The composition of the organic compounds released by healthy phytoplankton is poorly known and difficult to assess with existing chemical methods. Here, expression of transporter and catabolic genes by three model marine bacteria (Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, and Polaribacter dokdonensis MED152) was used as a biological sensor of metabolites released from the picoeukaryote Micromonas commoda RCC299. Bacterial expression responses indicated that the three species together recognized 38 picoeukaryote metabolites. This was consistent with the Micromonas expression of genes for starch metabolism and synthesis of peptidoglycan-like intermediates. A comparison of the hypothesized Micromonas exometabolite pool with that of the diatom Thalassiosira pseudonana CCMP1335, analyzed previously with the same biological sensor method, indicated that both phytoplankton released organic acids, nucleosides, and amino acids, but differed in polysaccharide and organic nitrogen release. Future ocean conditions are expected to favor picoeukaryotic phytoplankton over larger-celled microphytoplankton. Results from this study suggest that such a shift could alter the substrate pool available to heterotrophic bacterioplankton.

Colwellia maritima sp. nov. and Polaribacter marinus sp. nov., isolated from seawater

Two Gram-stain-negative, catalase- and oxidase-positive, and aerobic bacteria, strains MSW7^T and MSW13^T, were isolated from seawater. Cells of strains MSW7^T and MSW13^T are motile and non-motile rods, respectively. Strain MSW7^T optimally grew at 25 °C and pH 7.0 and in the presence of 3 % (w/v) NaCl, whereas strain MSW13^T optimally grew at 25 °C and pH 6.0-7.0 and in the presence of 2 % NaCl. As the sole respiratory quinone and the major fatty acids and polar lipids, strain MSW7^T contained ubiquinone-8, C_16 : 0, C_15 : 1  ω8c, C_17 : 1  ω8c and summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), and phosphatidylethanolamine and phosphatidylglycerol, respectively, whereas strain MSW13^T contained menaquinone-6, C_15 : 1  ω6c, iso-C_15 : 0, anteiso-C_15 : 0, and iso-C_15 : 0 3-OH, and phosphatidylethanolamine, respectively. The DNA G+C contents of strains MSW7^T and MSW13^T were 37.3 and 29.9 %, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains MSW7^T and MSW13^T were most closely related to Colwellia echini A3^T and Polaribacter atrinae WP25^T with 98.8 and 98.1 % sequence similarities, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strain MSW7^T and C. echini A3^T and between strain MSW13^T and P. atrinae KACC 17473^T were 73.6 and 22.6 % and 80.4 and 23.8 %, respectively. Based on phenotypic, chemotaxonomic and phylogenetic data, strains MSW7^T and MSW13^T represent novel species of the genera Colwellia and Polaribacter, respectively, for which the names Colwellia maritima sp. nov. and Polaribacter marinus sp. nov. are proposed, respectively. The type strains of C. maritima sp. nov. and P. marinus sp. nov. are MSW7^T (=KACC 22339^T=JCM 35001^T) and MSW13^T (=KACC 22341^T=JCM 35021^T), respectively.

Evaluation and Determinants of the Digital Inclusive Financial Support Efficiency for Marine Carbon Sink Fisheries: Evidence from China

The development of digital inclusive finance has greatly improved the feasibility of financial inclusion. Therefore, in the context of the constrained financing of marine carbon sink fisheries, we try to investigate whether digital inclusive finance exhibits a supportive effect on marine carbon sink fisheries and thus enhances the capacity of marine carbon sinks. Specifically, this paper empirically calculates the grey correlation between the development of digital inclusive finance and marine carbon sinks based on data in nine coastal provinces of China from 2011 to 2019. The empirical results show that the grey relational coefficients between the above two in China are more than 0.5, revealing a significant positive correlation. Then, on this basis, we estimate the digital inclusive financial support efficiency (DIFSE) for marine carbon sink fisheries by applying the Super-EBM model. In addition, the determinants affecting the DIFSE for marine carbon sink fisheries selected based on the grounded theory are explored through the Tobit model. The conclusions are as follows. First, there are time-varying characteristics and regional heterogeneity in DIFSE. Generally, the effect of China's digital inclusive financial support for marine carbon sink fisheries is expanding year by year. Among them, the DIFSE in the northern marine economic circle is currently the highest, followed by that in the south and east. Second, the input of productive factors, promotion of fishery skill, development of fishery technology, and Internet coverage will significantly increase the value of DIFSE, while output structure, income level, fishery disasters, and marine pollution will have significant negative effects on DIFSE. These empirical results can help policymakers better understand the contribution of digital inclusive finance to marine carbon sink fisheries and provide them with valuable information for the formulation of supportive policies.

Structural shifts in sea ice prokaryotic communities across a salinity gradient in the subarctic

Current knowledge of the processes that shape prokaryotic community assembly in sea ice across polar ecosystems is scarce. Here, we coupled culture-dependent (bacterial isolation on R2A medium) and culture-independent (high-throughput 16S rRNA gene sequencing) approaches to provide the first comprehensive assessment of prokaryotic communities in the late winter ice and its underlying water along a natural salinity gradient in coastal Hudson Bay, an iconic cryo-environment that marks the ecological transition between Canadian Subarctic and Arctic biomes. We found that prokaryotic community assembly processes in the ice were less selective at low salinity since typical freshwater taxa such as Frankiales, Burkholderiales, and Chitinophagales dominated both the ice and its underlying water. In contrast, there were sharp shifts in community structure between the ice and underlying water samples at sites with higher salinity, with the orders Alteromonadales and Flavobacteriales dominating the ice, while the abovementioned freshwater taxa dominated the underlying water communities. Moreover, primary producers including Cyanobium (Cyanobacteria, Synechococcales) may play a role in shaping the ice communities and were accompanied by known Planctomycetes and Verrucomicrobiae taxa. Culture-dependent analyses showed that the ice contained pigment-producing psychrotolerant or psychrophilic bacteria from the phyla Proteobacteria, Actinobacteriota, and Bacteroidota, likely favored by the combination of low temperatures and the seasonal increase in sunlight. Our findings suggest that salinity, photosynthesis and dissolved organic matter are the main drivers of prokaryotic community structure in the late winter ice of coastal Hudson Bay, the ecosystem with the fastest sea ice loss rate in the Canadian North.

Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach

Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.

Organic matter availability drives the spatial variation in the community composition and activity of Antarctic marine bacterioplankton

Carbon cycling by Antarctic microbial plankton is poorly understood but it plays a major role in CO₂ sequestration in the Southern Ocean. We investigated the summer bacterioplankton community in the largely understudied Weddell Sea, applying Illumina amplicon sequencing, measurements of bacterial production and chemical analyses of organic matter. The results revealed that the patchy distribution of productive coastal polynyas and less productive, mostly ice-covered sites was the major driver of the spatial changes in the taxonomic composition and activity of bacterioplankton. Gradients in organic matter availability induced by phytoplankton blooms were reflected in the concentrations and composition of dissolved carbohydrates and proteins. Bacterial production at bloom stations was, on average, 2.7 times higher than at less productive sites. Abundant bloom-responsive lineages were predominately affiliated with ubiquitous marine taxa, including Polaribacter, Yoonia-Loktanella, Sulfitobacter, the SAR92 clade, and Ulvibacter, suggesting a widespread genetic potential for adaptation to sub-zero seawater temperatures. A co-occurrence network analysis showed that dominant taxa at stations with low phytoplankton productivity were highly connected, indicating beneficial interactions. Overall, our study demonstrates that heterotrophic bacterial communities along Weddell Sea ice shelves were primarily constrained by the availability of labile organic matter rather than low seawater temperature. This article is protected by copyright. All rights reserved.

Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting

Marine microbes genetically evolved to survive varying salinity, temperature, pH, and other stress factors by producing different bioactive metabolites. These microbial secondary metabolites (SMs) are novel, have high potential, and could be used as lead molecule. Genome sequencing of microbes revealed that they have the capability to produce numerous novel bioactive metabolites than observed under standard in vitro culture conditions. Microbial genome has specific regions responsible for SM assembly, termed biosynthetic gene clusters (BGCs), possessing all the necessary genes to encode different enzymes required to generate SM. In order to augment the microbial chemo diversity and to activate these gene clusters, various tools and techniques are developed. Metagenomics with functional gene expression studies aids in classifying novel peptides and enzymes and also in understanding the biosynthetic pathways. Genome shuffling is a high-throughput screening approach to improve the development of SMs by incorporating genomic recombination. Transcriptionally silent or lower level BGCs can be triggered by artificially knocking promoter of target BGC. Additionally, bioinformatic tools like antiSMASH, ClustScan, NAPDOS, and ClusterFinder are effective in identifying BGCs of existing class for annotation in genomes. This review summarizes the significance of BGCs and the different approaches for detecting and elucidating BGCs from marine microbes.

Microbial Activities and Selection from Surface Ocean to Subseafloor on the Namibian Continental Shelf

Oxygen minimum zones (OMZs) are hot spots for redox-sensitive nitrogen transformations fueled by sinking organic matter. In comparison, the regulating role of sulfur-cycling microbes in marine OMZs, their impact on carbon cycling in pelagic and benthic habitats, and activities below the seafloor remain poorly understood. Using ¹³C DNA stable isotope probing (SIP) and metatranscriptomics, we explored microbial guilds involved in sulfur and carbon cycling from the ocean surface to the subseafloor on the Namibian shelf. There was a clear separation in microbial community structure across the seawater-seafloor boundary, which coincided with a 100-fold-increased concentration of microbial biomass and unique gene expression profiles of the benthic communities. ¹³C-labeled 16S rRNA genes in SIP experiments revealed carbon-assimilating taxa and their distribution across the sediment-water interface. Most of the transcriptionally active taxa among water column communities that assimilated ¹³C from diatom exopolysaccharides (mostly Bacteroidetes, Actinobacteria, Alphaproteobacteria, and Planctomycetes) also assimilated ¹³C-bicarbonate under anoxic conditions in sediment incubations. Moreover, many transcriptionally active taxa from the seafloor community (mostly sulfate-reducing Deltaproteobacteria and sulfide-oxidizing Gammaproteobacteria) that assimilated ¹³C-bicarbonate under sediment anoxic conditions also assimilated ¹³C from diatom exopolysaccharides in the surface ocean and OMZ waters. Despite strong selection at the sediment-water interface, many taxa related to either planktonic or benthic communities were found to be present at low abundance and actively assimilating carbon under both sediment and water column conditions. In austral winter, mixing of shelf waters reduces stratification and suspends sediments from the seafloor into the water column, potentially spreading metabolically versatile microbes across niches.

IMPORTANCE Microbial activities in oxygen minimum zones (OMZs) transform inorganic fixed nitrogen into greenhouse gases, impacting the Earth’s climate and nutrient equilibrium. Coastal OMZs are predicted to expand with global change and increase carbon sedimentation to the seafloor. However, the role of sulfur-cycling microbes in assimilating carbon in marine OMZs and related seabed habitats remain poorly understood. Using ¹³C DNA stable isotope probing and metatranscriptomics, we explore microbial guilds involved in sulfur and carbon cycling from ocean surface to subseafloor on the Namibian shelf. Despite strong selection and differential activities across the sediment-water interface, many active taxa were identified in both planktonic and benthic communities, either fixing inorganic carbon or assimilating organic carbon from algal biomass. Our data show that many planktonic and benthic microbes linked to the sulfur cycle can cross redox boundaries when mixing of the shelf waters reduces stratification and suspends seafloor sediment particles into the water column.

Growth-stage-related shifts in diatom endometabolome composition set the stage for bacterial heterotrophy

Phytoplankton-derived metabolites fuel a large fraction of heterotrophic bacterial production in the global ocean, yet methodological challenges have limited our understanding of the organic molecules transferred between these microbial groups. In an experimental bloom study consisting of three heterotrophic marine bacteria growing together with the diatom Thalassiosira pseudonana, we concurrently measured diatom endometabolites (i.e., potential exometabolite supply) by nuclear magnetic resonance (NMR) spectroscopy and bacterial gene expression (i.e., potential exometabolite uptake) by metatranscriptomic sequencing. Twenty-two diatom endometabolites were annotated, with nine increasing in internal concentration in the late stage of the bloom, eight decreasing, and five showing no variation through the bloom progression. Some metabolite changes could be linked to shifts in diatom gene expression, as well as to shifts in bacterial community composition and their expression of substrate uptake and catabolism genes. Yet an overall low match indicated that endometabolome concentration was not a good predictor of exometabolite availability, and that complex physiological and ecological interactions underlie metabolite exchange. Six diatom endometabolites accumulated to higher concentrations in the bacterial co-cultures compared to axenic cultures, suggesting a bacterial influence on rates of synthesis or release of glutamate, arginine, leucine, 2,3-dihydroxypropane-1-sulfonate, glucose, and glycerol-3-phosphate. Better understanding of phytoplankton metabolite production, release, and transfer to assembled bacterial communities is key to untangling this nearly invisible yet pivotal step in ocean carbon cycling.

Biological recovery of phosphorus from waste activated sludge via alkaline fermentation and struvite biomineralization by Brevibacterium antiquum

Struvite biomineralization is a promising method for phosphorus recovery from wastewater treatment plant streams, and the growth of responsible microorganisms in mixed cultures is one of the most critical points for applying this process in pilot and full-scale. This study aimed to investigate the growth and bio-struvite production of Brevibacterium antiquum in mixed sludge culture. Alkaline fermentation was applied at different pH conditions to enhance the phosphorus content of sludge for an efficient recovery, and pH 8 was determined as the most feasible considering the phosphorus release and sludge characteristics. Growth optimization studies showed that NaCl's presence decreases the growth rate of Brevibacterium antiquum and bio-struvite production. At the same time, pH in the range of 6.8-8.2 did not alter the growth significantly. In addition, studies showed the ability of Brevibacterium antiquum in unsterilized fermented sludge centrate to grow and recover the phosphorus as struvite. Thus, our results indicated the potential of struvite biomineralization in full-scale wastewater treatment plants.

Prochlorococcus extracellular vesicles: molecular composition and adsorption to diverse microbes

Extracellular vesicles are small (~50–200 nm diameter) membrane‐bound structures released by cells from all domains of life. While vesicles are abundant in the oceans, their functions, both for cells themselves and the emergent ecosystem, remain a mystery. To better characterize these particles – a prerequisite for determining function – we analysed the lipid, protein, and metabolite content of vesicles produced by the marine cyanobacterium Prochlorococcus. We show that Prochlorococcus exports a diverse array of cellular compounds into the surrounding seawater enclosed within discrete vesicles. Vesicles produced by two different strains contain some materials in common, but also display numerous strain‐specific differences, reflecting functional complexity within vesicle populations. The vesicles contain active enzymes, indicating that they can mediate extracellular biogeochemical reactions in the ocean. We further demonstrate that vesicles from Prochlorococcus and other bacteria associate with diverse microbes including the most abundant marine bacterium, Pelagibacter. Together, our data point toward hypotheses concerning the functional roles of vesicles in marine ecosystems including, but not limited to, possibly mediating energy and nutrient transfers, catalysing extracellular biochemical reactions, and mitigating toxicity of reactive oxygen species.

Reconstructing large interaction networks from empirical time series data

Reconstructing interactions from observational data is a critical need for investigating natural biological networks, wherein network dimensionality is usually high. However, these pose a challenge to existing methods that can quantify only small interaction networks. Here, we proposed a novel approach to reconstruct high-dimensional interaction Jacobian networks using empirical time series without specific model assumptions. This method, named "multiview distance regularised S-map," generalised the state space reconstruction to accommodate high dimensionality and overcome difficulties in quantifying massive interactions with limited data. When evaluating this method using time series generated from theoretical models involving hundreds of interacting species, estimated strengths of interaction Jacobians were in good agreement with theoretical expectations. Applying this method to a natural bacterial community helped identify important species from the interaction network and revealed mechanisms governing the dynamical stability of a bacterial community. The proposed method overcame the challenge of high dimensionality in large natural dynamical systems.

Cultivable Winogradskyella species are genomically distinct from the sympatric abundant candidate species

Winogradskyella is a genus within the phylum Bacteroidetes with a clear marine origin. Most members of this genus have been found associated with marine animals and algae, but also with inorganic surfaces such as sand. In this study, we analyzed genomes of eleven species recently isolated from surface seawater samples from the North Sea during a single spring algae bloom. Corresponding metagenomes yielded a single Candidatus species for this genus. All species in culture, with the exception of W. ursingii, affiliated with a Winogradskyella lineage characterized by large genomes (~4.3 ± 0.4 Mb), with high complexity in their carbohydrate and protein degradation genes. Specifically, the polysaccharide utilization loci (PULs) were diverse within each individual strain, indicating large substrate versatility. Although present in the North Sea, the abundances of these strains were at, or below, the detection limit of the metagenomes. In contrast, the single species, classified as Candidatus W. atlantica, to which all North Sea MAGs belonged, affiliated with a lineage in which the cultivated representatives showed small genomes of ~3.0-3.5 Mb, with the MAGs having ~2.3 Mb. In Ca. W. atlantica, genome streamlining has apparently resulted in the loss of biosynthesis pathways for several amino acids including arginine, methionine, leucine and valine, and the PUL loci were reduced to a single one for utilizing laminarin. This as-yet uncultivated species seems to capitalize on sporadically abundant substrates that are released by algae blooms, mainly laminarin. We also suggest that this streamlined genome might be responsible for the lack of growth on plates for this Candidatus species, in contrast to growth of the less abundant but coexisting members of the genus.

Characteristics of bacterial community and ARGs profile in engineered goldfish tanks with stresses of sulfanilamide and copper

Abuse of antibiotics in aquaculture have been alarming and might aggravate spread of resistance genes in the environment. Holistic ARGs proliferation checks require deeper analyses of coupled absolute abundances in 16S rRNA bacteria communities at the phylum level to detect biomarkers. Sulfanilamide (sul) and copper II sulfate (CuSO₄ II) were, therefore, designed and added as separate or combined treatments in 9 replicate engineered goldfish tanks comprising 3 individual sul, 3 CuSO₄ II, 3 (sul + CuSO₄ II) combinations, and 3 controls within 180 days. The DNA from water and fish guts was sequenced under qPCR to determine 16S rRNA bacteria biomarkers co-occurring with the correspondent ARGs. Combined chemical addition at 0.8-1.5 mg sul + 0.5-1.0 mg CuSO₄ II/3 L of tank waters reduced sequenced 16S rRNA bacteria absolute abundances in fish gut and water samples while portraying the biomarkers. Absolute abundances of the entire 16S rRNA bacteria was higher in fish guts (3.4 × 10¹⁴-4.9 × 10⁸ copies/g) than water samples (1.5 × 10⁹-2.6 × 10¹⁵ copies/L), respectively. Much as sul 1(log) were dominant over intl 1(log) genes, and their fundamental profiles were also higher in the fish guts than water samples; the Spearman's correlation analyses revealed positive relationship (p < 0.01 and r = 0.873) among the biomarkers of both ARG pairs at the phylum level and the physicochemical parameters. In the fish gut and water samples ratios, Bacteroidetes (10-85:12-85%) > Proteobacteria (10-50:15-65%) > Planktomycetes (10-52:8-25%) featured prominently based on LEfSe use as the hot-spotted biomarkers, hence justifying its higher prospects towards innovative environmental microbiological and biotechnological studies.

Bacterial community structure and functional profiling of high Arctic fjord sediments

Kongsfjorden, an Arctic fjord is significantly affected by the glacier melt and Atlantification, both the processes driven by accelerated warming in the Arctic. This has lead to changes in primary production, carbon pool and microbial communities, especially that in the sediment. In this study, we have examined the bacterial community structure of surface (0-2 cm) and subsurface (3-9 cm) sediments of Kongsfjorden using the high throughput sequencing analysis. Results revealed that bacterial community structure of Kongsfjorden sediments were dominated by phylum Proteobacteria followed by Bacteroidetes and Epsilonbacteraeota. While α- and γ-Proteobacterial class were dominant in surface sediments; δ-Proteobacteria were found to be predominant in subsurface sediments. The bacterial community structure in the surface and subsurface sediments showed significant variations (p ≤ 0.05). Total organic carbon could be one of the major parameters controlling the bacterial diversity in the surface and subsurface sediments. Functional prediction analysis indicated that the bacterial community could be involved in the degradation of complex organic compounds such as glycans, glycosaminoglycans, polycyclic aromatic hydrocarbons and also in the biosynthesis of secondary metabolites.

Growth rate-dependent synthesis of halomethanes in marine heterotrophic bacteria and its implications for the ozone layer recovery

Halomethanes (e.g., CH₃ Cl, CH₃ Br, CH₃ I and CHBr₃ ) are ozone-depleting compounds that, in contrast to the human-made chlorofluorocarbons, marine organisms synthesize naturally. Therefore, their production cannot be totally controlled by human action. However, identifying all their natural sources and understanding their synthesis regulation can help to predict their production rates and their impact on the future recovery of the Earth's ozone layer. Here we show that the synthesis of mono-halogenated halocarbons CH₃ Cl, CH₃ Br, and CH₃ I is a generalized process in representatives of the major marine heterotrophic bacteria groups. Furthermore, halomethane production was growth rate dependent in all the strains we studied, implying uniform synthesis regulation patterns among bacterioplankton. Using these experimental observations and in situ halomethane concentrations, we further evaluated the potential production rates associated with higher bacterial growth rates in response to global warming in a coastal environment within the Southern California Bight. Our estimates show that a 3°C temperature rise would translate into a 35%-84% increase in halomethane production rate by 2100. Overall, these data suggest that marine heterotrophic bacteria are significant producers of these climate-relevant gases and that their contribution to the atmospheric halogen budget could increase in the future, impacting the ozone layer recovery.

Patterns in Benthic Microbial Community Structure Across Environmental Gradients in the Beaufort Sea Shelf and Slope

The paradigm of tight pelagic-benthic coupling in the Arctic suggests that current and future fluctuations in sea ice, primary production, and riverine input resulting from global climate change will have major impacts on benthic ecosystems. To understand how these changes will affect benthic ecosystem function, we must characterize diversity, spatial distribution, and community composition for all faunal components. Bacteria and archaea link the biotic and abiotic realms, playing important roles in organic matter (OM) decomposition, biogeochemical cycling, and contaminant degradation, yet sediment microbial communities have rarely been examined in the North American Arctic. Shifts in microbial community structure and composition occur with shifts in OM inputs and contaminant exposure, with implications for shifts in ecological function. Furthermore, the characterization of benthic microbial communities provides a foundation from which to build focused experimental research. We assessed diversity and community structure of benthic prokaryotes in the upper 1 cm of sediments in the southern Beaufort Sea (United States and Canada), and investigated environmental correlates of prokaryotic community structure over a broad spatial scale (spanning 1,229 km) at depths ranging from 17 to 1,200 m. Based on hierarchical clustering, we identified four prokaryotic assemblages from the 85 samples analyzed. Two were largely delineated by the markedly different environmental conditions in shallow shelf vs. upper continental slope sediments. A third assemblage was mainly comprised of operational taxonomic units (OTUs) shared between the shallow shelf and upper slope assemblages. The fourth assemblage corresponded to sediments receiving heavier OM loading, likely resulting in a shallower anoxic layer. These sites may also harbor microbial mats and/or methane seeps. Substructure within these assemblages generally reflected turnover along a longitudinal gradient, which may be related to the quantity and composition of OM deposited to the seafloor; bathymetry and the Mackenzie River were the two major factors influencing prokaryote distribution on this scale. In a broader geographical context, differences in prokaryotic community structure between the Beaufort Sea and Norwegian Arctic suggest that benthic microbes may reflect regional differences in the hydrography, biogeochemistry, and bathymetry of Arctic shelf systems.

Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities

In this study, we aimed to investigate, through high-resolution metagenomics and metatranscriptomics, the composition and the trajectories of microbial communities originating from a natural sample, fed exclusively with methane, over 14 weeks of laboratory incubation. This study builds on our prior data, suggesting that multiple functional guilds feed on methane, likely through guild-to-guild carbon transfer, and potentially through intraguild and intraspecies interactions. We observed that, under two simulated dioxygen partial pressures—low versus high—community trajectories were different, with considerable variability among the replicates. In all microcosms, four major functional guilds were prominently present, representing Methylococcaceae (the true methanotrophs), Methylophilaceae (the nonmethanotrophic methylotrophs), Burkholderiales, and Bacteroidetes. Additional functional guilds were detected in multiple samples, such as members of Opitutae, as well as the predatory species, suggesting additional complexity for methane-oxidizing communities. Metatranscriptomic analysis suggested simultaneous expression of the two alternative types of methanol dehydrogenases in both Methylococcaceae and Methylophilaceae, while high expression of the oxidative/nitrosative stress response genes suggested competition for dioxygen among the community members. The transcriptomic analysis further suggested that Burkholderiales likely feed on acetate that is produced by Methylococcaceae under hypoxic conditions, while Bacteroidetes likely feed on biopolymers produced by both Methylococcaceae and Methylophilaceae.

Candidatus Abditibacter, a novel genus within the Cryomorphaceae, thriving in the North Sea

Coastal phytoplankton blooms are frequently followed by successive blooms of heterotrophic bacterial clades. The class Flavobacteriia within the Bacteroidetes has been shown to play an important role in the degradation of high molecular weight substrates that become available in the later stages of such blooms. One of the flavobacterial clades repeatedly observed over the course of several years during phytoplankton blooms off the coast of Helgoland, North Sea, is Vis6. This genus-level clade belongs to the family Cryomorphaceae and has been resistant to cultivation to date. Based on metagenome assembled genomes, comparative 16S rRNA gene sequence analyses and fluorescence in situ hybridization, we here propose a novel candidate genus Abditibacter, comprising three novel species Candidatus Abditibacter vernus, Candidatus Abditibacter forsetii and Candidatus Abditibacter autumni. While the small genomes of the three novel photoheterotrophic species encode highly similar gene repertoires, including genes for degradation of proteins and algal storage polysaccharides such as laminarin, two of them - Ca. A. vernus and Ca. A. forsetii - seem to have a preference for spring blooms, while Ca. A. autumni almost exclusively occurs in late summer and autumn.

Light supports cell-integrity and growth rates of taxonomically diverse coastal photoheterotrophs

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

Prokaryotic Response to Phytodetritus-Derived Organic Material in Epi- and Mesopelagic Antarctic Waters

Particulate organic matter (POM) export represents the underlying principle of the biological carbon pump, driving the carbon flux from the sunlit to the dark ocean. The efficiency of this process is tightly linked to the prokaryotic community, as >70% of POM respiration is carried out by particle-associated prokaryotes. In the Ross Sea, one of the most productive areas of the Southern Ocean, up to 50% of the surface primary production is exported to the mesopelagic ocean as POM. Recent evidence suggests that a significant fraction of the POM in this area is composed of intact phytoplankton cells. During austral summer 2017, we set up bottle enrichment experiments in which we amended free-living surface and deep prokaryotic communities with organic matter pools generated from native microplankton, mimicking the particle export that may derive from mild (1 μg of Chlorophyll a L-1) and intense (10 μg of Chlorophyll a L-1) phytoplankton bloom. Over a course of 4 days, we followed free-living and particle-attached prokaryotes' abundance, the degradation rates of polysaccharides, proteins and lipids, heterotrophic production as well as inorganic carbon utilization and prokaryotic community structure dynamics. Our results showed that several rare or undetected taxa in the initial community became dominant during the time course of the incubations and that different phytodetritus-derived organic matter sources induced specific changes in microbial communities, selecting for peculiar degradation and utilization processes spectra. Moreover, the features of the supplied detritus (in terms of microplankton taxa composition) determined different colonization dynamics and organic matter processing modes. Our study provides insights into the mechanisms underlying the prokaryotic utilization of phytodetritus, a significant pool of organic matter in the dark ocean.

Symbiolite formation: a powerful in vitro model to untangle the role of bacterial communities in the photosynthesis-induced formation of microbialites

Microbially induced calcification is an ancient, community-driven mineralisation process that produces different types of microbialites. Symbiolites are photosynthesis-induced microbialites, formed by calcifying co-cultures of dinoflagellates from the family Symbiodiniaceae and bacteria. Symbiolites encase the calcifying community as endolithic cells, pointing at an autoendolithic niche of symbiotic dinoflagellates, and provide a rare opportunity to study the role of bacteria in bacterial-algal calcification, as symbiodiniacean cultures display either distinct symbiolite-producing (SP) or non-symbiolite-producing (NP) phenotypes. Using Illumina sequencing, we found that the bacterial communities of SP and NP cultures differed significantly in the relative abundance of 23 genera, 14 families, and 2 phyla. SP cultures were rich in biofilm digesters from the phylum Planctomycetes and their predicted metagenomes were enriched in orthologs related to biofilm formation. In contrast, NP cultures were dominated by biofilm digesters from the Bacteroidetes, and were inferred as enriched in proteases and nucleases. Functional assays confirmed the potential of co-cultures and bacterial isolates to produce biofilms and point at acidic polysaccharides as key stimulators for mineral precipitation. Hence, bacteria appear to influence symbiolite formation primarily through their biofilm-producing and modifying activity and we anticipate that symbiolite formation, as a low-complexity in vitro model, will significantly advance our understanding of photosynthesis-induced microbial calcification processes.

Ancestral niche separation and evolutionary rate differentiation between sister marine flavobacteria lineages

Marine flavobacteria are specialists for polysaccharide degradation. They dominate in habitats enriched with polysaccharides, but are also prevalent in pelagic environments where polysaccharides are less available. These niches are likely occupied by distinct lineages, but evolutionary processes underlying their niche differentiation remain elusive. Here, genomic analyses and physiological assays indicate that the sister flavobacteria lineages Leeuwenhoekiella and Nonlabens likely explore polysaccharide-rich macroalgae and polysaccharide-poor pelagic niches respectively. Phylogenomic analyses inferred that the niche separation likely occurred anciently and coincided with increased sequence evolutionary rate in Nonlabens compared with Leeuwenhoekiella. Further analyses ruled out the known mechanisms likely driving evolutionary rate acceleration, including reduced selection efficiency, decreased generation time and increased mutation rate. In particular, the mutation rates were determined using an unbiased experimental method, which measures the present-day populations and may not reflect ancestral populations. These data collectively lead to a new hypothesis that an ancestral and transient mutation rate increase resulted in evolutionary rate increase in Nonlabens. This hypothesis was supported by inferring that gains and losses of genes involved in SOS response, a mechanism known to drive transiently increased mutation rate, coincided with evolutionary rate acceleration. Our analyses highlight the evolutionary mechanisms underlying niche differentiation of flavobacteria lineages.

Differential visible spectral influence on carbon metabolism in heterotrophic marine flavobacteria

The visible spectrum of solar radiation is known to stimulate photoheterotrophic bacterial carbon metabolism. However, its impact on 'strictly' heterotrophic bacteria remains less explored. Here, we show that heterotrophic flavobacteria exhibit enhanced uptake and mineralization of dissolved organic carbon with increasing wavelengths of visible light, without employing any 'known' light-harvesting mechanisms. RNA sequencing identified blue light as a major constraint in the extracellular enzymatic hydrolysis of polymeric carbohydrates and acquisition of sugars, despite acting as a stimulus for inorganic carbon sequestration. In contrast, green-red and continuous full-spectrum lights activated diverse hydrolytic enzymes and sugar transporters, but obstructed inorganic carbon fixation. This 'metabolic switching' was apparent through limited nutrient uptake, suppressed light-sensitivity, oxidative stress response and promotion of inorganic carbon sequestration pathways under blue light. The visible light impact on metabolism may be of significant ecological relevance as it appears to promote cell-mediated mineralization of organic carbon in 'green-colored' chlorophyll-rich copiotrophic coastal seawater and inorganic carbon sequestration in 'blue-colored' oligotrophic open ocean. Thus, a novel regulatory role played by light on heterotrophic metabolism and a hidden potential of flavobacteria to sense and respond differentially to monochromatic lights influencing marine carbon cycling were unraveled.

Photochemical characterization of flavobacterial rhodopsin: The importance of the helix E region for heat stability

Although many microbial rhodopsins have been discovered many of organisms in a variety of habitats, little is known about the property and diversity of rhodopsin in flavobacteria. Recent studies discovered that many proteorhodopsin (PR)-like proteins exist in genomes of flavobacteria. Following the isolation of a flavobacterial rhodopsins (FR) from the flavobacteria IMCC1997 from the East Sea of Korea, we characterized its photochemical features. We confirmed that the FR expression is induced by light in the IMCC1997 cell. Upon receiving light energy in vitro, the proton acceptor (D83) and donor (E94) of the FR translocate protons from intracellular to extracellular regions. Compared with proteorhodopsin (PR), the FR from IMCC 1997 cells is very unstable, which may be explained by their primary sequence differences. The ratio of all trans/13-cis retinal conformation does not influence this stability. To measure the stability of FR, we tested heat endurance at 70 °C and found that the heat endurance time of some FR mutants increased. Based upon these results, we found the helix E of this protein to be critical for the unstability of FR.

Ecological and functional capabilities of an uncultured Kordia sp

Cultivable bacteria represent only a fraction of the diversity in microbial communities. However, the official procedures for classification and characterization of a novel prokaryotic species still rely on isolates. Nevertheless, due to single cell genomics, it is possible to retrieve genomes from environmental samples by sequencing them individually, and to assign specific genes to a specific taxon, regardless of their ability to grow in culture. In this study, a complete description was performed for uncultured Kordia sp. TARA_039_SRF, a proposed novel species within the genus Kordia, using culture-independent techniques. The type material was a high-quality draft genome (94.97% complete, 4.65% gene redundancy) co-assembled using ten nearly identical single amplified genomes (SAGs) from surface seawater in the North Indian Ocean during the Tara Oceans Expedition. The assembly process was optimized to obtain the best possible assembly metrics and a less fragmented genome. The closest relative of the species was Kordia periserrulae, which shared 97.56% similarity of the 16S rRNA gene, 75% orthologs and 89.13% average nucleotide identity. The functional potential of the proposed novel species included proteorhodopsin, the ability to incorporate nitrate, cytochrome oxidases with high affinity for oxygen, and CAZymes that were unique features within the genus. Its abundance at different depths and size fractions was also evaluated together with its functional annotation, revealing that its putative ecological niche could be particles of phytoplanktonic origin. It could putatively attach to these particles and consume them while sinking to the deeper and oxygen depleted layers of the North Indian Ocean.

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime

One of the most prominent manifestations of climate change is the changing Arctic sea-ice regime with a reduction in the summer sea-ice extent and a shift from thicker, perennial multiyear ice towards thinner, first-year ice. These changes in the physical environment are likely to impact microbial communities, a key component of Arctic marine food webs and biogeochemical cycles. During the Norwegian young sea ICE expedition (N-ICE2015) north of Svalbard, seawater samples were collected at the surface (5 m), subsurface (20 or 50 m), and mesopelagic (250 m) depths on 9 March, 27 April, and 16 June 2015. In addition, several physical and biogeochemical data were recorded to contextualize the collected microbial communities. Through the massively parallel sequencing of the small subunit ribosomal RNA amplicon and metagenomic data, this work allows studying the Arctic's microbial community structure during the late winter to early summer transition. Results showed that, at compositional level, Alpha- (30.7%) and Gammaproteobacteria (28.6%) are the most frequent taxa across the prokaryotic N-ICE2015 collection, and also the most phylogenetically diverse. Winter to early summer trends were quite evident since there was a high relative abundance of thaumarchaeotes in the under-ice water column in late winter while this group was nearly absent during early summer. Moreover, the emergence of Flavobacteria and the SAR92 clade in early summer might be associated with the degradation of a spring bloom of Phaeocystis. High relative abundance of hydrocarbonoclastic bacteria, particularly Alcanivorax (54.3%) and Marinobacter (6.3%), was also found. Richness showed different patterns along the depth gradient for prokaryotic (highest at mesopelagic depth) and protistan communities (higher at subsurface depths). The microbial N-ICE2015 collection analyzed in the present study provides comprehensive new knowledge about the pelagic microbiota below drifting Arctic sea-ice. The higher microbial diversity found in late winter/early spring communities reinforces the need to continue with further studies to properly characterize the winter microbial communities under the pack-ice.

Isolation, cultivation, and genome analysis of proteorhodopsin-containing SAR116-clade strain Candidatus Puniceispirillum marinum IMCC1322

Strain IMCC1322 was isolated from a surface water sample from the East Sea of Korea. Based on 16S rRNA analysis, IMCC1322 was found to belong to the OCS28 sub-clade of SAR116. The cells appeared as short vibrioids in logarithmic-phase culture, and elongated spirals during incubation with mitomycin or in aged culture. Growth characteristics of strain IMCC1322 were further evaluated based on genomic information; proteorhodopsin (PR), carbon monoxide dehydrogenase, and dimethylsulfoniopropionate (DMSP)-utilizing enzymes. IMCC1322 PR was characterized as a functional retinylidene protein that acts as a light-driven proton pump in the cytoplasmic membrane. However, the PR-dependent phototrophic potential of strain IMCC1322 was only observed under CO-inhibited and nutrient-limited culture conditions. A DMSP-enhanced growth response was observed in addition to cultures grown on C₁ compounds like methanol, formate, and methane sulfonate. Strain IMCC1322 cultivation analysis revealed biogeochemical processes characteristic of the SAR116 group, a dominant member of the microbial community in euphotic regions of the ocean. The polyphasic taxonomy of strain IMCC1322 is given as Candidatus Puniceispirillum marinum, and was confirmed by chemotaxonomic tests, in addition to 16S rRNA phylogeny and cultivation analyses.

Influence of Light on Particulate Organic Matter Utilization by Attached and Free-Living Marine Bacteria

Light plays a central role on primary productivity of aquatic systems. Yet, its potential impact on the degradation of photosynthetically produced biomass is not well understood. We investigated the patterns of light-induced particle breakdown and bacterial assimilation of detrital C and N using ¹³C and ¹⁵N labeled freeze-thawed diatom cells incubated in laboratory microcosms with a marine microbial community freshly collected from the Pacific Ocean. Particles incubated in the dark resulted in increased bacterial counts and dissolved organic carbon concentrations compared to those incubated in the light. Light also influenced the attached and free-living microbial community structure as detected by 16S rRNA gene amplicon sequencing. For example, Sphingobacteriia were enriched on dark-incubated particles and taxa from the family Flavobacteriaceae and the genus Pseudoalteromonas were numerically enriched on particles in the light. Isotope incorporation analysis by phylogenetic microarray and NanoSIMS (a method called Chip-SIP) identified free-living and attached microbial taxa able to incorporate N and C from the particles. Some taxa, including members of the Flavobacteriaceae and Cryomorphaceae, exhibited increased isotope incorporation in the light, suggesting the use of photoheterotrophic metabolisms. In contrast, some members of Oceanospirillales and Rhodospirillales showed decreased isotope incorporation in the light, suggesting that their heterotrophic metabolism, particularly when occurring on particles, might increase at night or may be inhibited by sunlight. These results show that light influences particle degradation and C and N incorporation by attached bacteria, suggesting that the transfer between particulate and free-living phases are likely affected by external factors that change with the light regime, such as time of day, water column depth and season.

Stable-isotope probing of bacterial community for dissolved inorganic carbon utilization in Microcystis aeruginosa-dominated eutrophic water

Dissolved inorganic carbon (DIC) is an important source of carbon in aquatic ecosystems, especially under conditions of increased frequency of cyanobacterial bloom. However, the importance of bacteria in direct or indirect utilization of DIC has been widely overlooked in eutrophic freshwater. To identify the functional bacteria that can actively utilize DIC in eutrophic freshwater during cyanobacterial bloom, stable-isotope probing (SIP) experiments were conducted on eutrophic river water with or without inoculation with cyanobacteria (Microcystis aeruginosa). Our 16S rRNA sequencing results revealed the significance of Betaproteobacteria, with similar relative abundance as Alphaproteobacteria, in the active assimilation of H¹³CO₃^- into their DNA directly or indirectly, which include autotrophic genera Betaproteobacterial ammonia-oxidizing bacteria. Other bacterial groups containing autotrophic members, e.g. Planctomycetes and Nitrospira, also presented higher abundance among free-living bacteria in water without cyanobacteria. Microcystis aggregates showed a preference for some specific bacterial members that may utilize H¹³CO₃^- metabolized by Microcystis as organic matter, e.g. Bacteroidetes (Cytophagales, Sphingobacteriales), and microcystin-degrading bacteria Betaproteobacteria (Paucibacter/Burkholderiaceae). This study provides some valuable information regarding the functional bacteria that can actively utilize DIC in eutrophic freshwater.

Functional Expression of Gloeobacter Rhodopsin in PSI-Less Synechocystis sp. PCC6803

The approach of providing an oxygenic photosynthetic organism with a cyclic electron transfer system, i.e., a far-red light-driven proton pump, is widely proposed to maximize photosynthetic efficiency via expanding the absorption spectrum of photosynthetically active radiation. As a first step in this approach, Gloeobacter rhodopsin was expressed in a PSI-deletion strain of Synechocystis sp. PCC6803. Functional expression of Gloeobacter rhodopsin, in contrast to Proteorhodopsin, did not stimulate the rate of photoheterotrophic growth of this Synechocystis strain, analyzed with growth rate measurements and competition experiments. Nevertheless, analysis of oxygen uptake and—production rates of the Gloeobacter rhodopsin-expressing strains, relative to the ΔPSI control strain, confirm that the proton-pumping Gloeobacter rhodopsin provides the cells with additional capacity to generate proton motive force. Significantly, expression of the Gloeobacter rhodopsin did modulate levels of pigment formation in the transgenic strain.

Microbial community composition in alpine lake sediments from the Hengduan Mountains

Microbial communities in sediments play an important role in alpine lake ecosystems. However, the microbial diversity and community composition of alpine lake sediments from the Hengduan Mountains remain largely unknown. Therefore, based on the Illumina MiSeq platform, high‐throughput sequencing analysis of the 16S rRNA gene was performed on 15 alpine lake sediments collected at different locations in the Hengduan Mountains. The abundance‐based coverage estimate (ACE), Chao1, and Shannon indices indicated that the microbial abundance and diversity of these sediments were high. There are some differences in the composition of microbial communities among sediments. However, in general, Proteobacteria accounted for the largest proportion of all sediments (22.3%–67.6%) and was the dominant phylum. Followed by Bacteroidetes, Acidobacteria, Chloroflexi, and Planctomycetes. In addition, the operational taxonomic unit (OTU) interactions network had modular structures and suggested more cooperation than competition in the microbial community. Besides, we also found that temperature has a significant contribution to the sample–environment relationship. This study revealed the diversity and composition of microbial communities in alpine lake sediments from the Hengduan Mountains, and describe the correlation between microbial community structure and different environmental variables.

Distribution and Diversity of Rhodopsin-Producing Microbes in the Chesapeake Bay

Although sunlight is an abundant source of energy in surface environments, less than 0.5% of the available photons are captured by (bacterio)chlorophyll-dependent photosynthesis in plants and bacteria. Metagenomic data indicate that 30 to 60% of the bacterial genomes in some environments encode rhodopsins, retinal-based photosystems found in heterotrophs, suggesting that sunlight may provide energy for more life than previously suspected. However, quantitative data on the number of cells that produce rhodopsins in environmental systems are limited. Here, we use total internal reflection fluorescence microscopy to show that the number of free-living microbes that produce rhodopsins increases along the salinity gradient in the Chesapeake Bay. We correlate this functional data with environmental data to show that rhodopsin abundance is positively correlated with salinity and with indicators of active heterotrophy during the day. Metagenomic and metatranscriptomic data suggest that the microbial rhodopsins in the low-salinity samples are primarily found in Actinobacteria and Bacteroidetes, while those in the high-salinity samples are associated with SAR-11 type AlphaproteobacteriaIMPORTANCE Microbial rhodopsins are common light-activated ion pumps in heterotrophs, and previous work has proposed that heterotrophic microbes use them to conserve energy when organic carbon is limiting. If this hypothesis is correct, rhodopsin-producing cells should be most abundant where nutrients are most limited. Our results indicate that in the Chesapeake Bay, rhodopsin gene abundance is correlated with salinity, and functional rhodopsin production is correlated with nitrate, bacterial production, and chlorophyll a We propose that in this environment, where carbon and nitrogen are likely not limiting, heterotrophs do not need to use rhodopsins to supplement ATP synthesis. Rather, the light-generated proton motive force in nutrient-rich environments could be used to power energy-dependent membrane-associated processes, such as active transport of organic carbon and cofactors, enabling these organisms to more efficiently utilize exudates from primary producers.

Microbial community networks associated with variations in community respiration rates during upwelling in nearshore Monterey Bay, California

Respiration of organic material is a central process in the global carbon (C) cycle catalysed by diverse microbial communities. In the coastal ocean, upwelling can drive variation in both community respiration (CR) and the microbial community, but linkages between the two are not well-understood. We measured CR rates and analysed microbial dynamics via 16S rRNA gene sequencing, to assess whether CR correlated with upwelling irrespective of changes in the microbial community, or if the particular microbial community present was a factor in explaining variations in CR. CR varied significantly over time as a function of temperature, dissolved oxygen (DO) and chlorophyll-all of which are altered by upwelling-but also varied with a 'subnetwork' (i.e., a group of microbial taxa that covaried with one another) of the whole community. One subnetwork was associated with higher CR and warmer temperatures, while another was associated with lower CR and DO. Our results suggest that CR in the coastal ocean varies with both environmental variables, and a portion of the microbial community that is not directly correlated with upwelling intensity.