Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing

Spatial and temporal dynamics of prokaryotes in the Eastern Arabian sea

This study resolves the spatial and seasonal variations in prokaryotic abundance (PA) and biomass concerning physicochemical parameters during Spring Inter-Monsoon (April-May), Summer Monsoon (June-September), and Winter Monsoon (November-February) in the Eastern Arabian Sea. PA and biomass distribution estimated using microscopic techniques revealed their peak abundance during Spring Inter-Monsoon, ranging from 2.29-4.41 × 106 Cells mL-1 to 8.39-21.82 μgL-1, respectively. Similarly, high PA and biomass were observed in late Summer Monsoon (September), ranging from 2.01-3.96 × 106 Cells mL-1 to 8.74-16.70 μgL-1, respectively, which was preceded by a higher phytoplankton abundance (chlorophyll a- 14.57 mgm-3) during the peak Summer Monsoon (August). The Winter Monsoon, started with a low PA and phytoplankton abundance. As Winter Monsoon progressed, convective mixing promoted phytoplankton growth in the latter half until March. The decay released dissolved organic carbon (DOC), leading to a rise in PA from January to February, peaking during Spring Inter-Monsoon (first peak). With the advent of Summer Monsoon, upwelling enriched surface layers with nutrients to promote phytoplankton growth in August. The subsequent decaying phase generated higher DOC which enhanced PA by the end of Summer Monsoon (second peak). However, PA declined to its lowest levels by November. Distance-based linear model analysis indicated that temperature and chlorophyll a were the most influential factors affecting PA in the upper photic-zone, while ammonia, dissolved oxygen, and DOC were associated factors. In contrast, nutrients were the major determining factors in disphotic waters (200-2000 m). This study highlights the intricate interplay between physicochemical and biological variables in shaping prokaryotic populations during various physical forcings through intense sampling efforts in the Arabian Sea.

Diversity patterns and ecological assembly mechanisms of bacterial communities in the northeastern Indian Ocean epipelagic waters during the northeast monsoon

Disentangling microbial community diversity patterns and assembly mechanisms is critical for understanding ecological processes and evaluating biogeochemical cycling in ecosystems. However, the diversity patterns and assembly mechanism of the microbial communities in the epipelagic waters in the northeastern Indian Ocean (NEIO) on the spatial scale are still unclear. In this study, we investigated the spatial dynamics, geographic distribution pattern, and assembly process of the bacterial community using 532 samples collected from the epipelagic waters in the NEIO during the northeast monsoon. The results indicate that the bacterial richness and Bray-Curtis dissimilarity exhibited the strongest correlations with depth compared to the latitudinal and longitudinal scales. The dissolved oxygen was identified as the most important environmental factor affecting the bacterial richness and Bray-Curtis dissimilarity compared to temperature and salinity. The distance-decay relationship (DDR) of the bacterial community strengthened with increasing water depth. Turnover was the predominant β-diversity component influencing the spatial changes in the whole bacterial community. The dispersal limitation of the stochastic process and homogeneous selection of the deterministic process governed the bacterial ecological assembly process of the whole bacterial community. Abundant and rare subcommunities differed in terms of the niche breath, composition changes. The abundant subcommunities exhibited a much wider niche breath than the rare subcommunities. Regarding the abundant subcommunity species changes, the contributions of the turnover and nestedness varied with the water depth and oceanic region. In contrast, turnover was the major β-diversity component regarding the changes in the rare species. These data improve our understanding of the ecological processes of bacterial community assemblages in the NEIO.

Metagenomic analysis of pathogenic bacteria and virulence factor genes in coastal sediments from highly urbanized cities of India

A metagenomic approach was employed to investigate the diversity and distribution of Virulence Factors Genes (VFGs) and Pathogenic Bacteria (PB) in sediment samples collected from highly urbanized cities along the Indian coastline. Among the study locations, Mumbai, Veraval and Paradeep showed a higher abundance of PB, with Vibrio and Pseudomonas as dominant at the genus level, and Escherichia coli and Pseudomonas aeruginosa at the species level. In total, 295 VFGs were detected across all sediment samples, of which 40 VFGs showed a similarity of ≥90 % with the Virulence Database (VFDB) and were focused in this study. Among the virulent proteins, twitching motility protein and flagellar P-ring were found to be prevalent and significantly associated with Vibrio spp., and Pseudomonas spp., indicating potential bacterial pathogenicity. This investigation serves as the basis for future studies and provides insights into the comprehensive taxonomic profiles of PB, VFGs and their associated PB in the coastal sediments of India.

Unveiling the microbial diversity across the northern Ninety East Ridge in the Indian Ocean

Prokaryotes play a crucial role in marine ecosystem health and drive biogeochemical processes. The northern Ninety East Ridge (NER) of the Indian Ocean, a pivotal yet understudied area for these cycles, has been the focus of our study. We employed high-throughput 16S rRNA gene sequencing to analyze 35 water samples from five stations along the ridge, categorized into three depth- and dissolved oxygen-level-based groups. Our approach uncovered a clear stratification of microbial communities, with key bioindicators such as Prochlorococcus MIT9313, Sva0996 marine group, and Candidatus Actinomarina in the upper layer; Ketobacter, Pseudophaeobacter, Nitrospina, and SAR324 clade in the middle layer; and Methylobacterium-Methylorubrum, Sphingomonas, Sphingobium, and Erythrobacter in the deep layer. Methylobacterium-Methylorubrum emerged as the most abundant bacterial genus, while Nitrosopumilaceae predominated among archaeal communities. The spatial and depth-wise distribution patterns revealed that Ketobacter was unique to the northern NER, whereas Methylobacterium-Methylorubrum, UBA10353, SAR324 clade, SAR406, Sva0996_marine_group, Candidatus Actinomarina were ubiquitous across various marine regions, exhibiting niche differentiation at the OTU level. Environmental factors, especially dissolved oxygen (DO), silicate, nitrate, and salinity, significantly influence community structure. These findings not only reveal the novelty and adaptability of the microbial ecosystem in the northern NER but also contribute to the broader understanding of marine microbial diversity and its response to environmental heterogeneity.

Size fractionation informs microbial community composition and interactions in the eastern tropical North Pacific Ocean

Marine microorganisms are drivers of biogeochemical cycles in the world's oceans, including oxygen minimum zones (OMZs). Using a metabarcoding survey of the 16S rRNA gene, we investigated prokaryotic communities, as well as their potential interactions with fungi, at the coastal, offshore, and peripheral OMZ of the eastern tropical North Pacific. Water samples were collected along a vertical oxygen gradient, and large volumes were filtered through three size fractions, 0.22, 2, and 22 µm. The changes in community composition along the oxygen gradient were driven by Planctomycetota, Bacteroidota, Verrucomicrobiota, and Gammaproteobacteria; most are known degraders of marine polysaccharides and usually associated with the large particle-associated (LPA) community. The relative abundance of Nitrososphaerota, Alphaproteobacteria, Actinomycetota, and Nitrospinota was high in free-living and small particle-associated (SPA) communities. Network analyses identified putative interactions between fungi and prokaryotes in the particle-associated fractions, which have been largely overlooked in the ocean. In the SPAnetwork analysis, fungal amplicon sequence variants (ASVs) had exclusively negative connections with SAR11 nodes. In the LPA network analysis, fungal ASVs displayed both negative and positive connections with Pseudomonadota, SAR324, and Thermoplasmatota. Our findings demonstrate the utility of three-stage size-fractioned filtration in providing novel insights into marine microbial ecology.

Oxygen levels differentially attenuate the structure and diversity of microbial communities in the oceanic oxygen minimal zones

Global change mediated shifts in ocean temperature and circulation patterns, compounded by human activities, are leading to the expansion of marine oxygen minimum zones (OMZs) with concomitant alterations in nutrient and climate-active trace gas cycling. While many studies have reported distinct bacterial communities within OMZs, much of this research compares across depths rather with oxygen status and does not include eukayrotic microbes. Here, we investigated the Bay of Bengal (BoB) OMZ, where low oxygen conditions are persistent, but trace levels of oxygen remain (< 20 μM from 200 to 500 m). As other environmental variables are similar between OMZ and non-OMZ (NOZ) stations, we compared the abundance, diversity, and community composition of several microbial groups (bacterioplankton, Labyrinthulomycetes, and fungi) across oxygen levels. While prokaryote abundance decreased with depth, no significant differences existed across oxygen groups. In contrast, Labyrinthulomycetes abundance was significantly higher in non-OMZ stations but did not change significantly with depth, while fungal abundance was patchy without clear depth or oxygen-related trends. Bacterial and fungal diversity was lower in OMZ stations at 500 m, while Labyrinthulomycetes diversity only showed a depth-related profile, decreasing below the euphotic zone. Surprisingly, previously reported OMZ-associated bacterial taxa were not significantly more abundant at OMZ stations. Furthermore, compared to the bacterioplankton, fewer Labyrinthulomycetes and fungi taxa showed responses to oxygen status. Thus, this research identifies stronger oxygen-level linkages within the bacterioplankton than in the examined microeukaryotes.

Comparative analysis of microbiome inhabiting oxygenated and deoxygenated habitats using V3 and V6 metabarcoding of 16S rRNA gene

We examine how oxygen levels and the choice of 16S ribosomal RNA (rRNA) tags impact marine bacterial communities using Next-Generation amplicon sequencing. Analyzing V3 and V6 regions, we assess microbial composition in both Oxygen minimum zones (OMZ) and non-OMZ (NOMZ) areas in the Arabian Sea (AS) and the Central Indian Ocean basin (CIOB) respectively. Operational taxonomic units (OTUs) at 97% similarity showed slightly higher richness and diversity with V6 compared to V3. Vertical diversity patterns were consistent across both regions. NOMZ showed greater richness and diversity than OMZ. AS and CIOB exhibited significant differences in bacterial community, diversity, and relative abundance at the order and family levels. Alteromonadaceae dominated the OMZ, while Pelagibacteraceae dominated the NOMZ. Synechococcaceae were found exclusively at 250 m in OMZ. Bacteria putatively involved in nitrification, denitrification, and sulfurylation were detected at both sites. Dissolved oxygen significantly influenced microbial diversity at both sites, while seasonal environmental parameters affected diversity consistently, with no observed temporal variation.

Response of sediment microbial communities to the flow effect of the triangular artificial reef: A simulation-based experimental study

Artificial reefs (ARs), as an important tool for habitat restoration, play significant impacts on benthic microbial ecosystems. This study utilized 16S rRNA gene sequencing technology and computational fluid dynamics (CFD) flow simulation to investigate the effects of flow field distribution around ARs on microbial community structure. The results revealed distinct regional distribution patterns of microbial communities affected by different hydrodynamic conditions. Flow velocity and flow regime of water in sediment-water interface shaped the microbial community structure. The diversity and richness in R-HF were significantly decreased compared to other five regions (p < 0.05). At the phyla and OUT levels, most abundant taxa (1>%) showed an enrichment trend in R-HB. However, more than half of differentially abundant taxa were enriched in R-HB, which was significantly correlated with organic matter (OM). Bugbase phenotypic predictions indicated a low abundance of the anaerobic phenotype in R-HF and a high abundance of the biofilm-forming phenotype in R-HB.

Metagenomic exploration of Andaman region of the Indian Ocean

Ocean microbiome is crucial for global biogeochemical cycles and primary productivity. Despite numerous studies investigating the global ocean microbiomes, the microbiome composition of the Andaman region of the Indian Ocean remains largely unexplored. While this region harbors pristine biological diversity, the escalating anthropogenic activities along coastal habitats exert an influence on the microbial ecology and impact the aquatic ecosystems. We investigated the microbiome composition in the coastal waters of the Andaman Islands by 16S rRNA gene amplicon and metagenomic shotgun sequencing approaches and compared it with the Tara Oceans Consortium. In the coastal waters of the Andaman Islands, a significantly higher abundance and diversity of Synechococcus species was observed with a higher abundance of photosynthesis pigment-related genes to adapt to variable light conditions and nutrition. In contrast, Prochlorococcus species showed higher abundance in open ocean water samples of the Indian Ocean region, with a relatively limited functional diversity. A higher abundance of antibiotic-resistance genes was also noted in the coastal waters region. We also updated the ocean microbiome gene catalog with 93,172 unique genes from the Andaman coastal water microbiome. This study provides valuable insights into the Indian Ocean microbiome and supplements the global marine microbial ecosystem studies.

Depth-dependent microbial metagenomes sampled in the northeastern Indian Ocean

The northeastern Indian Ocean exhibits distinct hydrographic characteristics influenced by various local and remote forces. Variations in these driving factors may alter the physiochemical properties of seawater, such as dissolved oxygen levels, and affect the diversity and function of microbial communities. How the microbial communities change across water depths spanning a dissolved oxygen gradient has not been well understood. Here we employed both 16S rDNA amplicon and metagenomic sequencing approaches to study the microbial communities collected from different water depths along the E87 transect in the northeastern Indian Ocean. Samples were collected from the surface, Deep Chlorophyll Maximum (DCM), Oxygen Minimum Zone (OMZ), and bathypelagic layers. Proteobacteria were prevalent throughout the water columns, while Thermoproteota were found to be abundant in the aphotic layers. A total of 675 non-redundant metagenome-assembled genomes (MAGs) were constructed, spanning 21 bacterial and 5 archaeal phyla. The community structure and genomic information provided by this dataset offer valuable resources for the analysis of microbial biogeography and metabolism in the northeastern Indian Ocean.

Unraveling prokaryotic diversity distribution and functional pattern on nitrogen and methane cycling in the subtropical Western North Pacific Ocean

Prokaryotes play an important role in marine nitrogen and methane cycles. However, their community changes and metabolic modifications to the concurrent impact of ocean warming (OW), acidification (OA), deoxygenation (OD), and anthropogenic‑nitrogen-deposition (AND) from the surface to the deep ocean remains unknown. We examined here the amplicon sequencing approach across the surface (0-200 m; SL), intermediate (200-1000 m; IL), and deep layers (1000-2200 m; DL), and characterized the simultaneous impacts of OW, OA, OD, and AND on the Western North Pacific Ocean prokaryotic changes and their functional pattern in nitrogen and methane cycles. Results showed that SL possesses higher ammonium oxidation community/metabolic composition assumably the reason for excess nitrogen input from AND and modification of their kinetic properties to OW adaptation. Expanding OD at IL showed hypoxic conditions in the oxygen minimum layer, inducing higher microbial respiration that elevates the dimerization of nitrification genes for higher nitrous oxide production. The aerobic methane-oxidation composition was dominant in SL presumably the reason for adjustment in prokaryotic optimal temperature to OW, while anaerobic oxidation composition was dominant at IL due to the evolutionary changes coupling with higher nitrification. Our findings refocus on climate-change impacts on the open ocean ecosystem from the surface to the deep-environment integrating climate-drivers as key factors for higher nitrous-oxide and methane emissions.

The Impact of Anti-Inflammatory Drugs on the Prokaryotic Community Composition and Selected Bacterial Strains Based on Microcosm Experiments

Non-steroidal anti-inflammatory drugs (NSAIDs) are increasingly recognized as potential environmental contaminants that may induce toxicity in aquatic ecosystems. This 3-week microcosm experiment explores the acute impacts of NSAIDs, including diclofenac (DCF), ibuprofen (IBU), and acetylsalicylic acid (ASA), on bacterial communities using a wide range of these substances (200-6000 ppm). The results showed that the NSAID-treated microcosms had higher cell count values than control samples, though the diversity of microbial communities decreased. The isolated heterotrophic bacteria mostly belonged to Proteobacteria, particularly Klebsiella. Next-generation sequencing (NGS) revealed that NSAIDs altered the structure of the bacterial community composition, with the proportion of Proteobacteria aligning with the selective cultivation results. Bacteria had higher resistance to IBU/ASA than to DCF. In DCF-treated microcosms, there has been a high reduction of the number of Bacteroidetes, whereas in the microcosms treated with IBU/ASA, they have remained abundant. The numbers of Patescibacteria and Actinobacteria have decreased across all NSAID-treated microcosms. Verrucomicrobia and Planctomycetes have tolerated all NSAIDs, even DCF. Cyanobacteria have also demonstrated tolerance to IBU/ASA treatment in the microcosms. The archaeal community structure was also impacted by the NSAID treatments, with Thaumarchaeota abundant in all microcosms, especially DCF-treated microcosms, while Nanoarchaeota is more typical of IBU/ASA-treated microcosms with lower NSAID concentrations. These results indicate that the presence of NSAIDs in aquatic environments could lead to changes in the composition of microbial communities.

Bacterial diversity in the aquatic system in India based on metagenome analysis-a critical review

Microbial analysis has become one of the most critical areas in aquatic ecology and a crucial component for assessing the contribution of microbes in food web dynamics and biogeochemical processes. Initial research was focused on estimating the abundance and distribution of the microbes using microscopy and culture-based analysis, which are undoubtedly complex tasks. Over the past few decades, microbiologists have endeavored to apply and extend molecular techniques to address pertinent questions related to the function and metabolism of microbes in aquatic ecology. Metagenomics analysis has revolutionized aquatic ecology studies involving the investigation of the genome of a mixed community of organisms in an ecosystem to identify microorganisms, their functionality, and the discovery of novel proteins. This review discusses the metagenomics analysis of bacterial diversity in and around different aquatic systems in India.

Vertical Microbial Profiling of Arabian Sea Oxygen Minimal Zone Reveals Complex Bacterial Communities and Distinct Functional Implications

Arabian Sea harbours one of the largest oxygen minimal zones (OMZs) among the global oceans wherein biogeochemical cycles are regulated through dominant and complex microbial processes. The present study investigated the bacterial communities at various depths of the Arabian Sea OMZ using high-throughput sequencing of the v3-v4 hyper variable region of 16S rRNA gene. A total of 10 samples which included water samples from 8 different depths and 2 sediment samples were analyzed in this study. About 2.7 million sequences were obtained from all the samples. The sequence analysis revealed high bacterial diversity at deep waters and sediment samples and comparatively less species richness at the core OMZ depths. Number of OTUs ranged from 114 to 14441.Taxonomic assignments of the obtained OTUs showed dominant presence of Proteobacteria, Bacteriodetes, and Chloroflexi across all the samples. The identified OTUs were further affiliated to the phyla Marinimicrobia, Colwellia, Nitrospina, Tepidicaulis, Shewanella, Pseudoalteromonas, Woeseia at various depths along the water column. Correlation with abiotic factors suggested distinct variation in bacterial community composition with change in depth and dissolved oxygen (DO) levels. Predictive functional annotation based on bacterial phylotypes suggested presence of active nitrogen, sulphur, carbon, and methane metabolic cycles along the vertical transect of the studied region. Presence of nitrogen reduction bacterial group below the core OMZ depths may potentially provide insight into the expansion of OMZ region in Arabian Sea. Functional profiling further revealed presence of genes related to xenobiotic degradation in the water and sediment samples indicating a potential hotspot for bio-prospection.

Ontology-driven analysis of marine metagenomics: what more can we learn from our data?

BACKGROUND

The proliferation of metagenomic sequencing technologies has enabled novel insights into the functional genomic potentials and taxonomic structure of microbial communities. However, cyberinfrastructure efforts to manage and enable the reproducible analysis of sequence data have not kept pace. Thus, there is increasing recognition of the need to make metagenomic data discoverable within machine-searchable frameworks compliant with the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for data stewardship. Although a variety of metagenomic web services exist, none currently leverage the hierarchically structured terminology encoded within common life science ontologies to programmatically discover data.

RESULTS

Here, we integrate large-scale marine metagenomic datasets with community-driven life science ontologies into a novel FAIR web service. This approach enables the retrieval of data discovered by intersecting the knowledge represented within ontologies against the functional genomic potential and taxonomic structure computed from marine sequencing data. Our findings highlight various microbial functional and taxonomic patterns relevant to the ecology of prokaryotes in various aquatic environments.

CONCLUSIONS

In this work, we present and evaluate a novel Semantic Web architecture that can be used to ask novel biological questions of existing marine metagenomic datasets. Finally, the FAIR ontology searchable data products provided by our API can be leveraged by future research efforts.

Diversity, structure, and distribution of bacterioplankton and diazotroph communities in the Bay of Bengal during the winter monsoon

The Bay of Bengal (BoB) is conventionally believed to be a low productive, oligotrophic marine ecosystem, where the diazotroph communities presumed to play a vital role in adding "new" nitrogen through the nitrogen fixation process. However, the diazotroph communities in the oceanic region of the BoB are still poorly understood though it represents most of the seawater volume. The present study investigated a detailed account of the bacterioplankton community structure and distribution in the oceanic BoB during the winter monsoon using high throughput sequencing targeting the 16S rRNA and nifH genes. Our study observed diverse groups of bacterioplankton communities in the BoB including both cyanobacterial and non-cyanobacterial phylotypes. Cyanobacteria (Prochlorococcus spp. and Synechococcus spp.) and Proteobacteria (mainly α-, γ-, and δ-Proteobacteria) were the most abundant groups within the bacterial communities, possessing differential vertical distribution patterns. Cyanobacteria were more abundant in the surface waters, whereas Proteobacteria dominated the deeper layers (75 m). However, within the diazotroph communities, Proteobacteria (mainly γ-Proteobacteria) were the most dominant groups than Cyanobacteria. Function prediction based on PICRUSt revealed that nitrogen fixation might more active to add fixed nitrogen in the surface waters, while nitrogen removal pathways (denitrification and anammox) might stronger in deeper layers. Canonical correspondence analysis (CCA) indicated that temperature, salinity, and silicate were major environmental factors driving the distribution of bacterial communities. Additionally, phosphate was also an important factor in regulating the diazotroph communities in the surface water. Overall, this study provided detailed information on bacterial communities and their vital role in the nitrogen cycles in oligotrophic ecosystems.

Deep-sea sediment metagenome from Bay of Bengal reveals distinct microbial diversity and functional significance

Bay of Bengal (BoB) has immense significance with respect to ecological diversity and natural resources. Studies on microbial profiling and their functional significance at sediment level of BoB remain poorly represented. Herein, we describe the microbial diversity and metabolic potentials of BOB deep-sea sediment samples by subjecting the metagenomes to Nanopore sequencing. Taxonomic diversity ascertained at various levels revealed that bacteria belonging to phylum Proteobacteria predominantly represented in sediment samples NIOT_S7 and NIOT_S9. A comparative study with 16S datasets from similar ecological sites revealed depth as a crucial factor in determining taxonomic diversity. KEGG annotation indicated that bacterial communities possess sequence reads corresponding to carbon dioxide fixation, sulfur, nitrogen metabolism, but at varying levels. Additionally, gene sequences related to bioremediation of dyes, plastics, hydrocarbon, antibiotic resistance, secondary metabolite synthesis and metal resistance from both the samples as studied indicate BoB to represent a highly diverse environmental niche for further exploration.

Contrasting sea ice conditions shape microbial food webs in Hudson Bay (Canadian Arctic)

The transition from ice-covered to open water is a recurring feature of the Arctic and sub-Arctic, but microbial diversity and cascading effects on the microbial food webs is poorly known. Here, we investigated microbial eukaryote, bacterial and archaeal communities in Hudson Bay (sub-Arctic, Canada) under sea-ice cover and open waters conditions. Co-occurrence networks revealed a <3 µm pico‒phytoplankton-based food web under the ice and a >3 µm nano‒microphytoplankton-based food web in the open waters. The ice-edge communities were characteristic of post-bloom conditions with high proportions of the picophytoplankton Micromonas and Bathycoccus. Nano‒ to micro‒phytoplankton and ice associated diatoms were detected throughout the water column, with the sympagic Melosira arctica exclusive to ice-covered central Hudson Bay and Thalassiosira in open northwestern Hudson Bay. Heterotrophic microbial eukaryotes and prokaryotes also differed by ice-state, suggesting a linkage between microbes at depth and surface phytoplankton bloom state. The findings suggest that a longer open water season may favor the establishment of a large phytoplankton-based food web at the subsurface chlorophyll maxima (SCM), increasing carbon export from pelagic diatoms to deeper waters and affect higher trophic levels in the deep Hudson Bay.

First insights into the prokaryotic community structure of Lake Cote, Costa Rica: Influence on nutrient cycling

Prokaryotic diversity in lakes has been studied for many years mainly focusing on community structure and how the bacterial assemblages are driven by physicochemical conditions such as temperature, oxygen, and nutrients. However, little is known about how the composition and function of the prokaryotic community changes upon lake stratification. To elucidate this, we studied Lake Cote in Costa Rica determining prokaryotic diversity and community structure in conjunction with physicochemistry along vertical gradients during stratification and mixing periods. Of the parameters measured, ammonium, oxygen, and temperature, in that order, were the main determinants driving the variability in the prokaryotic community structure of the lake. Distinct stratification of Lake Cote occurred (March 2018) and the community diversity was compared to a period of complete mixing (March 2019). The microbial community analysis indicated that stratification significantly altered the bacterial composition in the epi-meta- and hypolimnion. During stratification, the Deltaproteobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, and Euryarchaeota were dominant in the hypolimnion yet largely absent in surface layers. Among these taxa, strict or facultative anaerobic bacteria were likely contributing to the lake nitrogen biogeochemical cycling, consistent with measurements of inorganic nitrogen measurements and microbial functional abundance predictions. In general, during both sampling events, a higher abundance of Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and Cyanobacteria was found in the oxygenated layers. Lake Cote had a unique bacterial diversity, with 80% of Amplicon Sequence Variant (ASV) recovered similar to unclassified/uncultured strains and exhibits archetypal shallow lake physicochemical but not microbial fluctuations worthy of further investigation. This study provides an example of lake hydrodynamics impacts to microbial community and their function in Central American lakes with implications for other shallow, upland, and oligotrophic lake systems.

Microbiome composition of the marine sponge Cliona varians at the Neotropical Southern Caribbean Sea displays a predominant core of Rhizobiales and Nitrosopumilaceae

AIMS

This work aims to characterize the microbial diversity of the encrusting sponge Cliona varians, a pore-forming and coral reef bioeroding marine sponge of emerging spread related to ocean acidification.

METHODS AND RESULTS

We analyzed the microbiome composition by 16S V4 amplicon next-generation sequencing in a community of the bioeroding coral-reef encrusting/excavating marine sponge Cliona varians thriving at the Southern Caribbean Sea. 87.21% and 6.76% of the sequences retrieved were assigned to the domain Bacteria and Archaea. The most predominant operational taxonomic units were classified as members of the order Rhizobiales and family Nitrosopumilaceae, representing members of not yet characterized genera. Features found strictly conserved in the strain/genomic representatives reported in those microbial taxa are nitrogen fixation and transformation.

CONCLUSION

Our results suggest, in accordance with recent results, that these microbiome members and associated functions could be contributing to the biological fitness of the sponge to be able to colonize and bioerode in environments with low access and scarce availability of nitrogen source.

SIGNIFICANCE AND IMPACT OF STUDY

Coral reefs bioresources such as sponge holobionts are intriguing and complex ecosystems units. This study contributes to the knowledge of how C. varians microbiota is composed or shaped, which is crucial to understand its ecological functions.

Salinity Influences Endophytic Bacterial Communities in Rice Roots from the Indian Sundarban Area

In "Sundarbans", the coastal regions of the West Bengal, soil salinity has always been one of the major causes of reduction in yield in these regions. The use of endophytic is a well-demanded strategy to mitigate the problems of salt stress and rice productivity. The present study attempted to analyze rice root endogenous microbial diversity and their relationship with soil salinity and physicochemical factors in the salt stressed region of Sundarbans, India using amplicon metagenomics approaches. Our investigation indicates, that the unique microbiome slightly acidic nutrient enriched non-saline zone is characterized by microbial genera that reported either having plant growth promotion (Flavobacterium, Novosphingobium, and Kocuria) or biocontrol abilities (Leptotrichia), whereas high ionic alkaline saline stressed zone dominated with either salt-tolerant microbes or less characterized endophytes (Arcobacter and Vogesella). The number of genera represented by significantly abundant OTUs was higher in the non-saline zone compared to that of the saline stressed zone probably due to higher nutrient concentrations and the absence of abiotic stress factors including salinity. Physicochemical parameters like nitrogen, phosphorus, and potassium were found significantly positively correlated with Muribaculaceae highly enriched in the non-saline zone. However, relative dissolved oxygen was found significantly negatively correlated with Rikenellaceae and Desulfovibrionaceae, enriched in the non-saline soil. This study first provides the detailed characterizations of rice root endophytic bacterial communities as well as their diversity contributed by measured environmental parameters in salinity Sundarbans areas. Since this study deals with two gradients of salinity, connecting the microbial diversity with the salinity range could be targeted for the use as "bioindicator" taxa and bio-fertilizer formulation in salt-affected regions.

Determinism governs the succession of disturbed bacterioplankton communities in a coastal maricultural ecosystem

Bacterioplankton community is the major engine that drives the biogeochemical cycling of various nutrient and essential elements in the coastal ecosystem. Unraveling the mechanisms governing the succession of such complex bacterioplankton communities in dynamic environment is a challenging issue in environmental science. In this study, we investigated the diversity patterns and succession mechanisms of both free-living and particle-attached bacterioplankton communities that have been exposed to low oxygen and typhoon Lekima. The community evenness was the lowest in August when the temperature was high and dissolved oxygen was low. Similar patterns in community succession were observed for free-living and particle-attached bacterioplankton community after the passing through of typhoon Lekima. Both the free-living and particle-attached bacterioplankton communities in the surface and bottom water columns were strongly affected by geo-environmental factors, among which temperature was the common factor, suggesting that the metabolic theory of ecology also underlie the dynamic patterns of bacterioplankton communities. Although the surface and bottom bacterioplankton compositions were initially different taxonomically and shaped by different environmental conditions, they followed a similar succession pattern over the sampling months. Temperature, dissolved inorganic carbon and dissolved inorganic phosphorus were the major factors associated with the variations of surface bacterioplankton ASVs. Time-decay relationship, in which community similarity decreases with increasing time interval, was clearly observed. Such pattern shall be attributed to the combined effects of time and the changing environmental factors over the sampling months, rather than time alone. Integrating multiple lines of evidences, we demonstrated that determinism governed the succession of both free-living and particle-attached bacterioplankton communities in the coastal maricultural ecosystem, with higher stochastic ratio in habitable months (i.e. fall). This study is expected to provide valuable mechanistic insights into the succession of disturbed complex bacterioplankton communities.

Diversity and ecological footprint of Global Ocean RNA viruses

DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global marine RNA virus diversity, ecology, and ecosystem roles. In this study, we uncover patterns and predictors of marine RNA virus community- and "species"-level diversity and contextualize their ecological impacts from pole to pole. Our analyses revealed four ecological zones, latitudinal and depth diversity patterns, and environmental correlates for RNA viruses. Our findings only partially parallel those of cosampled plankton and show unexpectedly high polar ecological interactions. The influence of RNA viruses on ecosystems appears to be large, as predicted hosts are ecologically important. Moreover, the occurrence of auxiliary metabolic genes indicates that RNA viruses cause reprogramming of diverse host metabolisms, including photosynthesis and carbon cycling, and that RNA virus abundances predict ocean carbon export.

Insights into Prokaryotic Community and Its Potential Functions in Nitrogen Metabolism in the Bay of Bengal, a Pronounced Oxygen Minimum Zone

Ocean oxygen minimum zones (OMZs) around the global ocean are expanding both horizontally and vertically. Multiple studies have identified the significant influence of anoxic conditions (≤1 μM O₂) on marine prokaryotic communities and biogeochemical cycling of elements. However, little attention has been paid to the expanding low-oxygen zones where the oxygen level is still above the anoxic level. Here, we studied the abundance and taxonomic and functional profiles of prokaryotic communities in the Bay of Bengal (BoB), where the oxygen concentration is barely above suboxic level (5 μM O₂). We found the sinking of Trichodesmium into deep water was far more efficient than that of Prochlorococcus, suggesting Trichodesmium blooms might be an essential carbon and nitrogen source for the maintenance of the BoB OMZ. In addition to the shift in the prokaryotic community composition, the abundance of some functional genes also changed with the change of oxygen concentration. Compared to oxic (>60 μM O₂) Tara Ocean and high-hypoxic (>20 to ≤60 μM O₂) BoB samples, we found more SAR11-nar sequences (responsible for reducing nitrate to nitrite) in low-hypoxic (>5 to ≤20 μM O₂) BoB waters. This suggested SAR11-nar genes would be more widespread due to the expansion of OMZs. It seems that the nitrite-N was not further reduced to nitrogen through denitrification but likely oxidized to nitrate by Nitrospinae in the BoB OMZ and then accumulated in the form of nitrate-N. However, the lack of N₂ production in the BoB would change if the BoB OMZ became anoxic. Together, these results suggested that reduction of oxygen concentration and OMZ expansion may increase the use of nitrate by SAR11 and N₂ production in the BoB.

IMPORTANCE Recognizing the prokaryotic community and its functions in hypoxic (>5 to ≤60 μM O₂) environments before further expansion of OMZs is critical. We demonstrate the prokaryotic community and its potential functions in nitrogen metabolism in the Bay of Bengal (BoB), where oxygen concentration is barely above suboxic level. This study highlighted that Trichodesmium might be an essential carbon and nitrogen source in the maintenance of the BoB OMZ. Additionally, we suggest that the lack of N₂ production in the BoB would change if the BoB OMZ became anoxic, and the expansion of OMZs in the global ocean may potentially increase the use of nitrate by SAR11.

Microbial community structures and important taxa across oxygen gradients in the Andaman Sea and eastern Bay of Bengal epipelagic waters

In oceanic oxygen minimum zones (OMZs), the abundances of aerobic organisms significantly decrease and energy shifts from higher trophic levels to microorganisms, while the microbial communities become critical drivers of marine biogeochemical cycling activities. However, little is known of the microbial ecology of the Andaman Sea and eastern Bay of Bengal (BoB) OMZs. In the present study, a total of 131 samples which from the Andaman Sea and eastern BoB epipelagic waters were analyzed. The microbial community distribution patterns across oxygen gradients, including oxygenic zones (OZs, dissolved oxygen [DO] ≥ 2 mg/L), oxygen limited zones (OLZs, 0.7 mg/L < DO < 2 mg/L), and OMZs (DO ≤ 0.7 mg/L), were investigated. Mantel tests and Spearman's correlation analysis revealed that DO was the most important driver of microbial community structures among several environmental factors. Microbial diversity, richness, and evenness were highest in the OLZs and lowest in the OZs. The microbial community compositions of OZ and OMZ waters were significantly different. Random forest analysis revealed 24 bioindicator taxa that differentiated OZ, OLZ, and OMZ water communities. These bioindicator taxa included Burkholderiaceae, HOC36, SAR11 Clade IV, Thioglobaceae, Nitrospinaceae, SAR86, and UBA10353. Further, co-occurrence network analysis revealed that SAR202, AEGEAN-169, UBA10353, SAR406, and Rhodobacteraceae were keystone taxa among the entire interaction network of the microbial communities. Functional prediction further indicated that the relative abundances of microbial populations involved in nitrogen and sulfur cycling were higher in OMZs. Several microbial taxa, including the Thioglobaceae, Nitrospinaceae, SAR202, SAR406, WPS-2, UBA10353, and Woeseiaceae, may be involved in nitrogen and/or sulfur cycling, while also contributing to oxygen consumption in these waters. This study consequently provides new insights into the microbial community structures and potentially important taxa that contribute to oxygen consumption in the Andaman Sea and eastern BoB OMZ.

Diversity pattern of marine culturable heterotrophic bacteria in a region with coexisting upwelling and mud banks in the southeastern Arabian Sea

Mud banks and upwelling are two important oceanographic features occurring along the southwest coast of India during the southwest monsoon period. The study region, Alappuzha lying on the southwest coast of India, is unique due to the co-existence of upwelling and mud banks during the monsoon (MON) season. Water samples were collected from three stations, M1, M2, and M3, from April to September 2014, at weekly/biweekly intervals to determine the total bacterial abundance, viable prokaryotic counts, and total plate counts, along with measurements on physico-chemical parameters. For determining the heterotrophic culturable bacterial diversity, water samples were collected during two seasons, monsoon and pre-monsoon (PRM), from three stations. Water samples were inoculated into two non-selective broths for enrichment, DNA was extracted, and next-generation sequencing analysis was performed using Illumina Miseq sequencing. The sequence analysis revealed that dominant communities were Proteobacteria, followed by Firmicutes and Fusobacteria. Proportions of Fusobacteria increased during monsoon and proportions of Firmicutes were high in premonsoon season. Among Proteobacteria, Gammaproteobacteri is presented more than 99% of all the classes, irrespective of seasons. Vibrio was the most dominant genus during both seasons. The presence of anaerobic genera such as Propionigenium and Cetobacterium at all the stations during MON indicated the presence of upwelled waters. The genus Stenotrophomonas was observed in the M2 station alone. This study provides an overview of the culturable heterotrophic bacterial communities in a region in the southeastern Arabian Sea with coexisting mud banks and upwelling. The results of this study were compared with a published report on culture-independent bacterial diversity (from environmental DNA) from the same region. The study demonstrates that the use of culture media underrepresented the phylogenetic diversity and selectively enriched the class Gammaproteobacteria alone.

Microbial Ecology of Oxygen Minimum Zones Amidst Ocean Deoxygenation

Oxygen minimum zones (OMZs) have substantial effects on the global ecology and biogeochemical processes of marine microbes. However, the diversity and activity of OMZ microbes and their trophic interactions are only starting to be documented, especially in regard to the potential roles of viruses and protists. OMZs have expanded over the past 60 years and are predicted to expand due to anthropogenic climate change, furthering the need to understand these regions. This review summarizes the current knowledge of OMZ formation, the biotic and abiotic factors involved in OMZ expansion, and the microbial ecology of OMZs, emphasizing the importance of bacteria, archaea, viruses, and protists. We describe the recognized roles of OMZ microbes in carbon, nitrogen, and sulfur cycling, the potential of viruses in altering host metabolisms involved in these cycles, and the control of microbial populations by grazers and viruses. Further, we highlight the microbial community composition and roles of these organisms in oxic and anoxic depths within the water column and how these differences potentially inform how microbial communities will respond to deoxygenation. Additionally, the current literature on the alteration of microbial communities by other key climate change parameters such as temperature and pH are considered regarding how OMZ microbes might respond to these pressures. Finally, we discuss what knowledge gaps are present in understanding OMZ microbial communities and propose directions that will begin to close these gaps.

Diversity and structure of soil bacterial community in intertidal zone of Daliao River estuary, Northeast China

Soil samples from the intertidal zone of Daliao River, Northeast China, were collected in three seasons (autumn, L1; winter, L2; and spring, L3) to evaluate the diversity and structure of bacterial community using high-throughput sequencing. Soil physicochemical characteristics varied greatly with seasons, and the potential nitrification rates were detected in the range of 1.04-2.71 μg NO₃^--N·g^-1 dry soil·h^-1 with the highest rate in spring (L3). Soil bacterial communities also differed seasonally, and nitrogen nutrients were the important variables affecting the bacterial communities as demonstrated by distance-based redundancy analysis and Mantel tests. Proteobacteria was the predominant phylum in soils showing a descending trend from L1 to L3. Woeseia and Ignatzschineria, both affiliating with Gammaproteobacteria, were the two most dominant genera, but they exerted different seasonal variations. The predicted functional profiles revealed 6 major nitrogen cycling processes, and the functional genes in relation to denitrification process were dominant in intertidal soils.