Woeseia oceani gen. nov., sp. nov., a chemoheterotrophic member of the order Chromatiales, and proposal of Woeseiaceae fam. nov

Bacterial Communities from the Copper Mine of Wettelrode (Germany)

Bacterial communities from three different sampling sites of a copper mine tunnel were characterized by 16S rRNA sequencing (NGS). A high presence of halophilic bacteria was confirmed by comparison with literature data and with reference samples from other highly salt-exposed soils. Among others, high read numbers of Gracilimonas, Kangiella, Limibacillus, Marinobacter, Woseia, and uncultivated strains of Actinomarinales, Gammaproteobacterium AT-s16, Actinobacteria 0319-7L14, and Thiotrichaceae were found. The community in a sample from the surface of the copper seam was significantly different from the community composition of a sample from the mine tunnel floor. The specificity in the appearance and in the abundance of special bacterial types (for example, Thiogranum, Thiohalophilus, Sulfuriflexus, Sedimenticolaceae, Desulfomonile, Desulfosporosinus, and Cand. Thiobios) can be partially explained by the different local conditions for sulfur-related metabolisms at the sampling sites.

Describing five new strains in the family Woeseiaceae and emended description of the order Woeseiales with genomic features related to environmental adaptation

The family Woeseiaceae, also known as the JTB255 bacterial group, are ubiquitous and abundant core members of microbial communities in marine surface sediments. However, to date, only one Woeseiaceae strain isolated from marine sediments has been described, and the phylogeny and environmental adaptation mechanisms of this group have been little explored. Here, we isolated five novel Woeseiaceae strains from the marine solar saltern in Weihai, China. Multiple genomic, physiological, and chemotaxonomic characteristics supported that these five isolates represent three novel species within a novel genus, for which Lentisalinibacter gen. nov. and three species Lentisalinibacter sediminis sp. nov., Lentisalinibacter salinarum sp. nov. and Lentisalinibacter orientalis sp. nov. are proposed. Moreover, phylogenetic analysis based on the 16S rRNA genes and genome sequences revealed that Woeseiaceae is most closely related to Steroidobacterales. Further comparative genomics analysis indicated the separate evolution of Woeseiaceae and Steroidobacterales, supporting the emended description of the order Woeseiales. Woeseiales representitives showed facultatively anaerobic characteristics and small genome sizes in contrast to their phylogenetic relatives. They primarily inhabit surface marine sediment environments using multiple metabolic and ecological strategies to adapt to the changing microenvironments. Our results demonstrate the novel representatives of Woeseiales and their environmental adaptation mechanisms in marine environments.

Importance of eukaryotes in shaping microbial benthic communities in Charente-maritime marshes, France

Marshes are wetlands known for providing major ecosystem services in terms of water quality and human activities. These ecosystem services are mainly provided by marshes' benthic community, composed of prokaryotes (bacteria and archaea) but also of eukaryotes (micro-eukaryotes and meiofauna). The aim of this study is to (1) assess the environmental parameters affecting benthic community composition in marshes, (2) highlight the associations between organisms from the three domains of life, and (3) determine the parameters controlling these associations. Hence, benthic communities of eight different marshes from three typologies (salted, brackish and freshwater) and four seasons (autumn 2020, spring 2021, summer 2021 and autumn 2021) were assessed. This study revealed three main drivers of community composition. First, salinity drives the community composition illustrated by the differences observed between the three typologies of marshes. Relative abundance of Nitrososphaeria, Halobacteria, Bacillariophyceae, Conoidasida and nematodes increased with salinity while methanogenic archaea, Chlorophyceae and copepod's relative abundance decreased. The second driver is the physical-chemistry of the site, particularly nutrients. The season is the last driver of community composition, seasonal pattern varying for each site within a typology. LEfSe analyses defined biomarkers of typology and season, among which many prokaryotes involved in the nitrogen cycle and photosynthetic micro-eukaryotes where present in different co-occurrence networks, highlighting the importance of nitrogen cycle in marshes. Co-occurrence networks revealed several connections between organisms of the three domains of life, particularly between prokaryotes and photosynthetic eukaryotes. This study illustrates thus the importance of holistic approaches in microbial ecology for revealing a comprehensive view of the whole microbial interactions occurring in complex ecosystems.

The marine environmental microbiome mediates physiological outcomes in host nematodes

BACKGROUND

Nematodes are the most abundant metazoans in marine sediments, many of which are bacterivores; however, how habitat bacteria affect physiological outcomes in marine nematodes remains largely unknown.  RESULTS: Here, we used a Litoditis marina inbred line to assess how native bacteria modulate host nematode physiology. We characterized seasonal dynamic bacterial compositions in L. marina habitats and examined the impacts of 448 habitat bacteria isolates on L. marina development, then focused on HQbiome with 73 native bacteria, of which we generated 72 whole genomes sequences. Unexpectedly, we found that the effects of marine native bacteria on the development of L. marina and its terrestrial relative Caenorhabditis elegans were significantly positively correlated. Next, we reconstructed bacterial metabolic networks and identified several bacterial metabolic pathways positively correlated with L. marina development (e.g., ubiquinol and heme b biosynthesis), while pyridoxal 5'-phosphate biosynthesis pathway was negatively associated. Through single metabolite supplementation, we verified CoQ10, heme b, acetyl-CoA, and acetaldehyde promoted L. marina development, while vitamin B6 attenuated growth. Notably, we found that only four development correlated metabolic pathways were shared between L. marina and C. elegans. Furthermore, we identified two bacterial metabolic pathways correlated with L. marina lifespan, while a distinct one in C. elegans. Strikingly, we found that glycerol supplementation significantly extended L. marina but not C. elegans longevity. Moreover, we comparatively demonstrated the distinct gut microbiota characteristics and their effects on L. marina and C. elegans physiology.

CONCLUSIONS

Given that both bacteria and marine nematodes are dominant taxa in sedimentary ecosystems, the resource presented here will provide novel insights to identify mechanisms underpinning how habitat bacteria affect nematode biology in a more natural context. Our integrative approach will provide a microbe-nematodes framework for microbiome mediated effects on host animal fitness.

Assessing the impact of heavy metals on bacterial diversity in coastal regions of Southeastern India

Globally, there is growing concern over the environmental contamination of coastal ecosystems caused by anthropogenic activities. Here,we performed a study to evaluate the degree of heavy metal contamination in 5 different sediment samples collected from five sites along the Southeastern coast of India. Additionally, the research aims to explore the potential ecological implications of heavy metal contamination on the bacterial diversity, a crucial factor in upholding a sustainable ecosystem. A total of  seven heavy metals, i.e., chromium (Cr), copper (Cu), nickel (Ni), lead (Pb), mercury (Hg), cadmium (Cd) and arsenic (As), were assessed and quantified using inductively coupled plasma mass spectrometry. Targeted amplicon sequencing revealed that phylum Proteobacteria (36.9%) was the most dominating followed by Halobacterota (25.5%), Actinobacteriota (15%), Firmicutes (6.7%), Bacteroidota (4.0%), Thermoplasmatota (2.3%), Acidobacteriota (2.0%), Chloroflexi (1.6%), Planctomycetota (1.2%) and Crenarchaeota (1.1%). According to the alpha diversity estimate, lesser bacterial diversity was observed in areas with high pollution levels. Moreover, the physicochemical parameters of the sediments were analyzed. The contamination levels of the sediments were evaluated using the geo-accumulation index (Igeo), contamination factor (CF) and pollution loading index (PLI) to ascertain the comprehensive toxicity status of the sediments. The Igeo values revealed sediment pollution with metals such as Hg and Cd. The sediments obtained from the sampling site PU-01 showed the highest concentration of Hg pollution. Considering the ecotoxicological aspect, the estimated risk index (RI) values indicated a range from low to significant ecological risk.

Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan

BACKGROUND

Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions.

RESULTS

The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation.

CONCLUSION

Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.

Structure of Benthic Microbial Communities in the Northeastern Part of the Barents Sea

The Barents Sea shelf is one of the most economically promising regions in the Arctic in terms of its resources and geographic location. However, benthic microbial communities of the northeastern Barents Sea are still barely studied. Here, we present a detailed systematic description of the structures of microbial communities located in the sediments and bottom water of the northeastern Barents Sea based on 16S rRNA profiling and a qPCR assessment of the total prokaryotic abundance in 177 samples. Beta- and alpha-diversity analyses revealed a clear difference between the microbial communities of diverse sediment layers and bottom-water fractions. We identified 101 microbial taxa whose representatives had statistically reliable distribution patterns between these ecotopes. Analysis of the correlation between microbial community structure and geological data yielded a number of important results-correlations were found between the abundance of individual microbial taxa and bottom relief, thickness of marine sediments, presence of hydrotrolite interlayers, and the values of pH and Eh. We also demonstrated that a relatively high abundance of prokaryotes in sediments can be caused by the proliferation of Deltaproteobacteria representatives, in particular, sulfate and iron reducers.

Seasonality in land-ocean connectivity and local processes control sediment bacterial community structure and function in a High Arctic tidal flat

Climate change is altering patterns of precipitation, cryosphere thaw, and land-ocean influxes, affecting understudied Arctic estuarine tidal flats. These transitional zones between terrestrial and marine systems are hotspots for biogeochemical cycling, often driven by microbial processes. We investigated surface sediment bacterial community composition and function from May to September along a river-intertidal-subtidal-fjord gradient. We paired metabarcoding of in situ communities with in vitro carbon-source utilization assays. Bacterial communities differed in space and time, alongside varying environmental conditions driven by local seasonal processes and riverine inputs, with salinity emerging as the dominant structuring factor. Terrestrial and riverine taxa were found throughout the system, likely transported with runoff. In vitro assays revealed sediment bacteria utilized a broader range of organic matter substrates when incubated in fresh and brackish water compared to marine water. These results highlight the importance of salinity for ecosystem processes in these dynamic tidal flats, with the highest potential for utilization of terrestrially derived organic matter likely limited to tidal flat areas (and times) where sediments are permeated by freshwater. Our results demonstrate that intertidal flats must be included in future studies on impacts of increased riverine discharge and transport of terrestrial organic matter on coastal carbon cycling in a warming Arctic.

Insights into the spatial distributions of bacteria, archaea, ammonia-oxidizing bacteria and archaea communities in sediments of Daya Bay, northern South China Sea

Microbe plays an important role in the biogeochemical cycles of the coastal waters. However, comprehensive information about the microbe in the gulf waters is lacking. This study employed high-throughput sequencing and quantitative PCR (qPCR) to investigate the distribution patterns of bacterial, archaeal, ammonia-oxidizing bacterial (AOB), and archaeal (AOA) communities in Daya Bay. Community compositions and principal coordinates analysis (PCoA) exhibited significant spatial characteristics in the diversity and distributions of bacteria, archaea, AOB, and AOA. Notably, various microbial taxa (bacterial, archaeal, AOB, and AOA) exhibited significant differences in different regions, playing crucial roles in nitrogen, sulfur metabolism, and organic carbon mineralization. Canonical correlation analysis (CCA) or redundancy analysis (RDA) indicated that environmental parameters such as temperature, salinity, nitrate, total nitrogen, silicate, and phosphate strongly influenced the distributions of bacterial, archaeal, AOB, and AOA. This study deepens the understanding of the composition and ecological function of prokaryotes in the bay.

Functional response of microbial communities in lab-controlled oil-contaminated marine sediment

Crude oil contamination is one of the biggest problems in modern society. As oil enters into contact with the environment, especially if the point of contact is a body of water, it begins a weathering process by mixing and spreading. This is dangerous to local living organisms' communities and can impact diversity. However, despite unfavorable conditions, some microorganisms in these environments can survive using hydrocarbons as a nutrient source. Thus, understanding the local community dynamics of contaminated areas is essential. In this work, we analyzed the 16S rRNA amplicon sequencing and metatranscriptomic data of uncontaminated versus contaminated shallow marine sediment from publicly available datasets. We investigated the local population's taxonomic composition, species diversity, and fluctuations over time. Co-expression analysis coupled with functional enrichment showed us a prevalence of hydrocarbon-degrading functionality while keeping a distinct transcriptional profile between the late stages of oil contamination and the uncontaminated control. Processes related to the degradation of aromatic compounds and the metabolism of propanoate and butanoate were coupled with evidence of enhanced activity such as flagellar assembly and two-component system. Many enzymes of the anaerobic toluene degradation pathways were also enriched in our results. Furthermore, our diversity and taxonomical analyses showed a prevalence of the class Desulfobacteria, indicating interesting targets for bioremediation applications on marine sediment.

Cerina litoralis gen. nov., sp. nov., a novel potential polysaccharide degrading bacterium of the family Flavobacteriaceae, isolated from marine sediment

The Gram-strain-negative, facultative anaerobic, chemoheterotrophic, short-rod-shaped, non-motile, forming yellow colonies strain, designated F89T, was isolated from marine sediment of Xiaoshi Island, Weihai. Strain F89T grew at 15-37 °C (optimally at 28 °C), at pH 6.0-8.5 (optimally at pH 7.0) and in the presence of 1-5% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain F89T was related to the family Flavobacteriaceae. F89T had highest 16S rRNA gene sequence similarity to Maribacter cobaltidurans MCCC 1K03318T (93.3%). The predominant cellular fatty acids of F89T were iso-C15:0, iso-C15:0 G and Summed Feature 3. The main respiratory quinone of F89T was menaquinone 6 (MK-6), consistent with that observed for all related strains. The polar lipid profile of strain F89T contained phosphatidylethanolamine, two aminolipids and three unidentified polar lipids. The genomic DNA G + C content of strain F89T was 42.7%. Strain F89T encoded 121 glycoside hydrolases and was a potential polysaccharide degrading bacterium. Differential phenotypic and genotypic characteristics of the strain showed that F89T should be classified as a novel genus in Flavobacteriaceae, for which the name Cerina litoralis is proposed. The type strain is F89T (= MCCC 1H00510T = KCTC 92203T).

Enrichment of Aerobic and Anaerobic Hydrocarbon-Degrading Bacteria from Multicontaminated Marine Sediment in Mar Piccolo Site (Taranto, Italy)

Marine sediments act as a sink for the accumulation of various organic contaminants such as polychlorobiphenyls (PCBs). These contaminants affect the composition and activity of microbial communities, particularly favoring those capable of thriving from their biodegradation and biotransformation under favorable conditions. Hence, contaminated environments represent a valuable biological resource for the exploration and cultivation of microorganisms with bioremediation potential. In this study, we successfully cultivated microbial consortia with the capacity for PCB removal under both aerobic and anaerobic conditions. The source of these consortia was a multicontaminated marine sediment collected from the Mar Piccolo (Taranto, Italy), one of Europe's most heavily polluted sites. High-throughput sequencing was employed to investigate the dynamics of the bacterial community of the marine sediment sample, revealing distinct and divergent selection patterns depending on the imposed reductive or oxidative conditions. The aerobic incubation resulted in the rapid selection of bacteria specialized in oxidative pathways for hydrocarbon transformation, leading to the isolation of Marinobacter salinus and Rhodococcus cerastii species, also known for their involvement in aerobic polycyclic aromatic hydrocarbons (PAHs) transformation. On the other hand, anaerobic incubation facilitated the selection of dechlorinating species, including Dehalococcoides mccartyi, involved in PCB reduction. This study significantly contributes to our understanding of the diversity, dynamics, and adaptation of the bacterial community in the hydrocarbon-contaminated marine sediment from one sampling point of the Mar Piccolo basin, particularly in response to stressful conditions. Furthermore, the establishment of consortia with biodegradation and biotransformation capabilities represents a substantial advancement in addressing the challenge of restoring polluted sites, including marine sediments, thus contributing to expanding the toolkit for effective bioremediation strategies.

Mapping the microbial diversity associated with different geochemical regimes in the shallow-water hydrothermal vents of the Aeolian archipelago, Italy

Shallow-water hydrothermal vents are unique marine environments ubiquitous along the coast of volcanically active regions of the planet. In contrast to their deep-sea counterparts, primary production at shallow-water vents relies on both photoautotrophy and chemoautotrophy. Such processes are supported by a range of geochemical regimes driven by different geological settings. The Aeolian archipelago, located in the southern Tyrrhenian sea, is characterized by intense hydrothermal activity and harbors some of the best sampled shallow-water vents of the Mediterranean Sea. Despite this, the correlation between microbial diversity, geochemical regimes and geological settings of the different volcanic islands of the archipelago is largely unknown. Here, we report the microbial diversity associated with six distinct shallow-water hydrothermal vents of the Aeolian Islands using a combination of 16S rRNA amplicon sequencing along with physicochemical and geochemical measurements. Samples were collected from biofilms, fluids and sediments from shallow vents on the islands of Lipari, Panarea, Salina, and Vulcano. Two new shallow vent locations are described here for the first time. Our results show the presence of diverse microbial communities consistent in their composition with the local geochemical regimes. The shallow water vents of the Aeolian Islands harbor highly diverse microbial community and should be included in future conservation efforts.

Surface structures changes and biofilm communities development of degradable plastics during aging in coastal seawater

Biodegradable plastics (BPs) are a suitable alternative to conventional plastics. Still, their excessive or unplanned use may disrupt the abundance and community structure of the microbial population. To this end, a 58-day experiment in which biodegradable plastic objects, such as bags and boxes, were exposed to near-coastal seawater was conducted. They also assessed how they affected the diversity and organization of bacterial populations in seawater and on the surface of BPs products. It is evident that after the exposure time, both BP's bag and box products deteriorate in the ocean to varying degrees. The results of high-throughput sequencing of bacterial communities in seawater and those colonized on BPs products reveal significant differences in microbial community structures between seawater and BPs plastic samples. These suggest that the degradation of biodegradable plastics is shadowed by microorganisms and exposure time, while BP products influence the structural characteristics of microbial communities.

Diversity of the protease-producing bacteria and their extracellular protease in the coastal mudflat of Jiaozhou Bay, China: in response to clam naturally growing and aquaculture

The booming mudflat aquaculture poses an accumulation of organic matter and a certain environmental threat. Protease-producing bacteria are key players in regulating the nitrogen content in ecosystems. However, knowledge of the diversity of protease-producing bacteria in coastal mudflats is limited. This study investigated the bacterial diversity in the coastal mudflat, especially protease-producing bacteria and their extracellular proteases, by using culture-independent methods and culture-dependent methods. The clam aquaculture area exhibited a higher concentration of carbon, nitrogen, and phosphorus when compared with the non-clam area, and a lower richness and diversity of bacterial community when compared with the clam naturally growing area. The major classes in the coastal mud samples were Bacteroidia, Gammaproteobacteria, and Alphaproteobacteria. The Bacillus-like bacterial community was the dominant cultivated protease-producing group, accounting for 52.94% in the non-clam area, 30.77% in the clam naturally growing area, and 50% in the clam aquaculture area, respectively. Additionally, serine protease and metalloprotease were the principal extracellular protease of the isolated coastal bacteria. These findings shed light on the understanding of the microbes involved in organic nitrogen degradation in coastal mudflats and lays a foundation for the development of novel protease-producing bacterial agents for coastal mudflat purification.

Succession and environmental response of sediment bacterial communities in the Liao River Estuary at the centenary scale

Microbial community succession in turbulent estuarine environments is key to the understanding of microbial community development in estuaries. Centennial-scale sediment core samples collected from the Liao River Estuary (LRE) channel bar and side beaches were studied for geochemistry and 16S rRNA gene-based bacterial analyses. The results showed that bacterial community composition significantly differed between the sediments of the two sides of the channel bar, with Campilobacterota and Bacteroidota being dominant bacterial phyla in the tributary (T1, T2) and mainstream (MS1, MS2) sediment, respectively. Co-occurrence network of the bacterial community at the genus level showed more centralized and compacted topological features in tributary with weaker hydrodynamic, and the keystone taxas were Halioglobus, Luteolibacter, and Lutibacter in the bacterial community. The bacterial network structure had more edges and larger average degree in LRE sediments from the stage of the year 2016-2009 and the stage before 1939, which was possibly related to hydrodynamic conditions and nutrients. Stochastic processes (dispersal limitation) were the key factors driving bacterial community assembly in the LRE sediments. In addition, total organic carbon (TOC), total sulfur (TS), and grain size were the main deterministic factors affecting the change of bacterial community structure. Relative microbial abundance has the potential to indicate geologically historical environmental changes. This study provided a new perspective to reveal the succession and response of bacterial communities under frequent fluctuation environments.

Biodegradation of polystyrene (PS) by marine bacteria in mangrove ecosystem

Plastics pollution poses a new threat to marine ecosystems. Mangrove locating at estuary worldwide is probably the most heavily polluted area trapping various plastics transported from terrestrial and nearby marine aquaculture. Expanded polystyrene (EPS) is one of most common plastic debris therein and even in the plastic garbage. Here we showed the bacterial diversity of the polystyrene-degrading microbial community from EPS waste sites from a subtropical mangrove area. After enrichment with EPS, the degradation consortia were obtained. They shared a similar community structure dominated by bacteria of Sphingomonadaceae, Rhodanobacteraceae, Rhizobiaceae, Dermacoccaceae, Rhodocyclaceae, Hyphomicrobiaceae, and Methyloligellaceae. Diverse bacteria standing for the first member of the genera of Novosphingobium, Gordonia, Stappia, Mesobacillus, Alcanivorax, Flexivirga, Cytobacillus, Thioclava, and Thalassospira showed PS degradation capability as a pure culture. Further, PS biodegradation of Gordonia sp. and Novosphingobium sp. was quantified by weight loss, in addition to obvious morphological and structural changes of the PS films observed by SEM, ATR-FTIR, and contact angle analysis. The formation of new oxygen-containing functional groups implied the degradation pathway of oxidation. Although the degradation rates ranged from 2.7% to 7.7% after one month in lab and possibly lower in situ, their role in EPS removal is unneglectable.

Microbial Communities of Seawater and Coastal Soil of Russian Arctic Region and Their Potential for Bioremediation from Hydrocarbon Pollutants

The development of Arctic regions leads to pollution of marine and coastal environments with oil and petroleum products. The purpose of this work was to determine the diversity of microbial communities in seawater, as well as in littoral and coastal soil, and the potential ability of their members to degrade hydrocarbons degradation and to isolate oil-degrading bacteria. Using high-throughput sequencing of the V4 region of the 16S rRNA gene, the dominance of bacteria in polar communities was shown, the proportion of archaea did not exceed 2% (of the total number of sequences in the libraries). Archaea inhabiting the seawater belonged to the genera Nitrosopumilus and Nitrosoarchaeum and to the Nitrososphaeraceae family. In the polluted samples, members of the Gammaproteobacteria, Alphaproteobacteria, and Actinomycetes classes predominated; bacteria of the classes Bacteroidia, Clostridia, Acidimicrobiia, Planctomycetia, and Deltaproteobacteria were less represented. Using the iVikodak program and KEGG database, the potential functional characteristics of the studied prokaryotic communities were predicted. Bacteria were potentially involved in nitrogen and sulfur cycles, in degradation of benzoate, terephthalate, fatty acids, and alkanes. A total of 19 strains of bacteria of the genera Pseudomonas, Aeromonas, Oceanisphaera, Shewanella, Paeniglutamicibacter, and Rhodococcus were isolated from the studied samples. Among them were psychrotolerant and psychrophilic bacteria growing in seawater and utilizing crude oil, diesel fuel, and motor oils. The data obtained suggest that the studied microbial communities could participate in the removal of hydrocarbons from arctic seawater and coastal soils and suggested the possibility of the application of the isolates for the bioaugmentation of oil-contaminated polar environments.

Comparative Analysis of the Gut Microbiota of Mandarin Fish (Siniperca chuatsi) Feeding on Compound Diets and Live Baits

Siniperca chuatsi feeds on live fry throughout their life. The sustainable development of its farming industry has urgently necessitated the development of artificial diets to substitute live baits. It has been demonstrated that gut microbiota assists in feed adaptation and improves the feed conversion rate in fish. Therefore, this study aimed to understand the potential role of intestinal microorganisms in the domestication of S. chuatsi with a compound diet. Accordingly, we performed 16S rRNA sequencing of the gut microbial communities in S. chuatsi groups that were fed a compound diet (including large and small individuals) and live baits. A total of 2,471 OTUs were identified, and the large individual group possessed the highest number of unique OTUs. The α-diversity index of the gut microbiota in groups that were fed a compound diet was significantly higher (p < 0.05) than that in the live bait group. There were no significant differences in the α-diversity between the large and small individual groups. However, relatively higher numbers of Lactococcus, Klebsiella, and Woeseia were observed in the intestines of the large individual group. Prediction of the metabolic function of the microbiota among these three fish groups by Tax4Fun revealed that most metabolic pathways, such as glycan metabolism and amino acid metabolism, were typically more enriched for the larger individuals. The results indicated that certain taxa mentioned above exist in large individuals and may be closely related to the digestion and absorption of compound diets. The present study provides a basis for understanding the utilization mechanism of artificial feed by S. chuatsi.

Halalkalibacterium roseum gen. nov., sp. nov., a new member of the family Balneolaceae isolated from soil

A Gram-stain-negative, non-motile, moderately halophilic and facultatively anaerobic bacterium, designated YR4-1T, was isolated from a saline-alkali and sorghum-planting soil sample collected in Dongying, Shandong Province, PR China. Growth occurred at 28–45 °C with the presence of 4.0–20.0 % (w/v) NaCl and pH 6.0–9.0. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that YR4-1T shared the highest similarity of 92.1–92.4 % with the valid published species of Aliifodinibius . The isolate formed a separate clade at the genus level in recently described family Balneolaceae . The draft genome of strain YR4-1T is 3.83 Mbp long with 44.0 mol% G+C content. The strain possesses several genes involved in the osmotic stress response mechanism and diverse metabolic pathways, probably for the living in saline environment. This may lead to a better understanding of the underrepresented Balneolaceae lineage. The major menaquinone was MK-7. The main polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipids, aminophosphoglycolipid, one glycolipid, and four unidentified lipids. The predominant cellular fatty acids were iso-C15 : 0 (35.7 %) and anteiso-C15 : 0 (33.5 %). On the basis of its phenotypic, chemotaxonomic and phylogenetic features, strain YR4-1T represents a novel species of a new genus, for which the name Halalkalibacterium roseum gen. nov., sp. nov. is proposed. The type strain is YR4-1T (=CGMCC 1.17777T=KCTC 72795T).

Fulvivirga marina sp. nov. and Fulvivirga sediminis sp. nov., two novel Bacteroidetes isolated from the marine sediment

Two novel, designated strains 29W222T and 2943T, were isolated from the marine sediment from Aoshan Bay, Jimo, PR China. Growth was observed at pH 6.0–8.5 (optimum, pH 7.5) for strain 29W222T, and pH 5.5–8.5 (pH 7.0) for strain 2943T. Both strains displayed growth in 0.5–6 % NaCl with an optimum at 1 % for 29W222T; 0.5 % for 2943T. Both strains grew optimally at 33 °C. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that 29W222T and 2943T represented members of the genus Fulvivirga and strain 29W222T was most closely related to Fulvivirga kasyanovii KMM 6220T (97.9 % sequence similarity) and Fulvivirga imtechensis AK7T (95.0 %), and 2943T to Fulvivirga imtechensis AK7T (95.7 %) and Fulvivirga kasyanovii KMM 6220T (94.8 %). The genomic DNA G+C contents of 29W222T and 2943T were 39.9 and 37.7 mol%, respectively. The results of chemotaxonomic analysis indicated that the sole respiratory quinone was menaquinone 7 (MK-7), and the major fatty acid was iso-C15 : 0 for both strains. Average nucleotide identity and average amino acid identity values between strain 29W222T and Fulvivirga kasyanovii KMM 6220T were 78.9 and 83.6 %, respectively; the corresponding values between 2943T and Fulvivirga imtechensis AK7T were 69.8 and 63.6 %, respectively. Therefore, strains 29W222T and 2943T represent to two novel species of the genus Fulvivirga , for which the names Fulvivirga marina sp. nov. (29W222T=KCTC 62848T=MCCC 1K05194T) and Fulvivirga sediminis sp. nov. (2943T=KCTC 62847T= MCCC 1K05144T) are proposed, respectively.

Salinity Gradient Controls Microbial Community Structure and Assembly in Coastal Solar Salterns

Salinity acts as a critical environmental filter on microbial communities in natural systems, negatively affecting microbial diversity. However, how salinity affects microbial community assembly remains unclear. This study used Wendeng multi-pond saltern as a model to evaluate the prokaryotic community composition and diversity and quantify the relative importance of ecological processes across salinity gradients. The results showed that low-saline salterns (45–80 g/L) exhibited higher bacterial diversity than high-saline salterns (175–265 g/L). The relative abundance of taxa assigned to Halomicrobiaceae, Rhodobacteraceae, Saprospiraceae, and Thiotrichaceae exhibited a hump-shaped dependence on increasing salinity. Salinity and pH were the primary environmental factors that directly or indirectly determined the composition and diversity of prokaryotic communities. Microbial co-occurrence network dynamics were more complex in the sediment than in the water of salterns. An infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis (iCAMP) showed that microbial community assembly in sediment and water differed. Our findings provide more information about microbial community structure and the importance of various ecological processes in controlling microbial community diversity and succession along salinity gradients in water and sediment.

Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations

Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root microbiome under historically arid and humid sites, both in situ and performing a common garden experiment. Plants were grown in soils from sites with different drought levels, using in situ collected soils as the microbial source. We described and analyzed bacterial diversity by 16S rRNA gene sequencing (N = 48) from the soil, rhizosphere, and endosphere. Proteobacteria were the most abundant phylum present in humid and arid samples, while Actinobacteriota abundance was higher in arid ones. The β-diversity analyses showed split microbiomes between arid and humid microbiomes, and aridity and soil pH levels could explain it. These differences between humid and arid microbiomes were maintained in the common garden experiment, showing that it is possible to transplant in situ diversity to the greenhouse. We detected a total of 1009 bacterial genera; 199 exclusively associated with roots under arid conditions. By 16S and shotgun metagenomics, we identified dry-associated taxa such as Cellvibrio, Ensifer adhaerens, and Streptomyces flavovariabilis. With shotgun metagenomic sequencing of rhizospheres (N = 6), we identified 2969 protein families in the squash core metagenome and found an increased number of exclusively protein families from arid (924) than humid samples (158). We found arid conditions enriched genes involved in protein degradation and folding, oxidative stress, compatible solute synthesis, and ion pumps associated with osmotic regulation. Plant phenotyping allowed us to correlate bacterial communities with plant growth. Our study revealed that it is possible to evaluate microbiome diversity ex-situ and identify critical species and genes involved in plant-microbe interactions in historically arid locations.

Hydrocarbon biodegradation potential of microbial communities from high Arctic beaches in Canada's Northwest Passage

Sea ice loss is opening shipping routes in Canada's Northwest Passage, increasing the risk of an oil spill. Harnessing the capabilities of endemic microorganisms to degrade oil may be an effective remediation strategy for contaminated shorelines; however, limited data exists along Canada's Northwest Passage. In this study, hydrocarbon biodegradation potential of microbial communities from eight high Arctic beaches was assessed. Across high Arctic beaches, community composition was distinct, potential hydrocarbon-degrading genera were detected and microbial communities were able to degrade hydrocarbons (hexadecane, naphthalene, and alkanes) at low temperature (4 °C). Hexadecane and naphthalene biodegradation were stimulated by nutrients, but nutrients had little effect on Ultra Low Sulfur Fuel Oil biodegradation. Oiled microcosms showed a significant enrichment of Pseudomonas and Rhodococcus. Nutrient-amended microcosms showed increased abundances of key hydrocarbon biodegradation genes (alkB and CYP153). Ultimately, this work provides insight into hydrocarbon biodegradation on Arctic shorelines and oil-spill remediation in Canada's Northwest Passage.

Microbial Diversity of Deep-Sea Ferromanganese Crust Field in the Rio Grande Rise, Southwestern Atlantic Ocean

Seamounts are often covered with Fe and Mn oxides, known as ferromanganese (Fe-Mn) crusts. Future mining of these crusts is predicted to have significant effects on biodiversity in mined areas. Although microorganisms have been reported on Fe-Mn crusts, little is known about the role of crusts in shaping microbial communities. Here, we investigated microbial communities based on 16S rRNA gene sequences retrieved from Fe-Mn crusts, coral skeleton, calcarenite, and biofilm at crusts of the Rio Grande Rise (RGR). RGR is a prominent topographic feature in the deep southwestern Atlantic Ocean with Fe-Mn crusts. Our results revealed that crust field of the RGR harbors a usual deep-sea microbiome. No differences were observed on microbial community diversity among Fe-Mn substrates. Bacterial and archaeal groups related to oxidation of nitrogen compounds, such as Nitrospirae, Nitrospinae phyla, Candidatus Nitrosopumilus within Thaumarchaeota group, were present on those substrates. Additionally, we detected abundant assemblages belonging to methane oxidation, i.e., Methylomirabilales (NC10) and SAR324 (Deltaproteobacteria). The chemolithoautotrophs associated with ammonia-oxidizing archaea and nitrite-oxidizing bacteria potentially play an important role as primary producers in the Fe-Mn substrates from RGR. These results provide the first insights into the microbial diversity and potential ecological processes in Fe-Mn substrates from the Atlantic Ocean. This may also support draft regulations for deep-sea mining in the region.

A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria From Coastal Sediments

Molecular methods revealed that the majority of microbes in natural environments remains uncultivated. To fully understand the physiological and metabolic characteristics of microbes, however, culturing is still critical for microbial studies. Here, we used bacterial community analysis and four culture media, namely, traditional marine broth 2216 (MB), water extracted matter (WEM), methanol extracted matter (MEM), and starch casein agar (SCA), to investigate the diversity of cultivated bacteria in coastal sediments. A total of 1,036 isolates were obtained in pure culture, and they were classified into five groups, namely, Alphaproteobacteria (52.51%), Gammaproteobacteria (23.26%), Actinobacteria (13.32%), Firmicutes, and Bacteroidetes. Compared to other three media, WEM recovered a high diversity of actinobacteria (42 of 63 genotypes), with Micromonospora and Streptomyces as the most cultivated genera. Amplicon sequencing of the bacterial 16S ribosomal RNA (rRNA) gene V3-V4 fragment revealed eight dominant groups, Alphaproteobacteria (12.81%), Gammaproteobacteria (20.07%), Deltaproteobacteria (12.95%), Chloroflexi (13.09%), Bacteroidetes (8.28%), Actinobacteria (7.34%), Cyanobacteria (6.20%), and Acidobacteria (5.71%). The dominant members affiliated to Actinobacteria belonged to "Candidatus Actinomarinales," "Candidatus Microtrichales," and Nitriliruptorales. The cultivated actinobacteria accounted for a small proportion (<5%) compared to the actinobacterial community, which supported that the majority of actinobacteria are still waiting for cultivation. Our study concluded that WEM could be a useful and simple culture medium that enhanced the recovery of culturable actinobacteria from coastal sediments.

Strategies for culturing active/dormant marine microbes

Microorganisms are ubiquitous in the ocean environment and they play key roles in marine ecosystem function and service. However, many of their functions and phenotypes remain unknown because indigenous marine bacteria are mostly difficult to culture. Although many novel techniques have brought previously uncultured microbes into laboratory culture, there are still many most-wanted or key players that need to be cultured from marine environments. This review discusses possible reasons for 'unculturable microbes' and categorizes uncultured bacteria into three groups: dominant active bacteria, rare active bacteria, and dormant bacteria. This review also summarizes advances in cultivation techniques for culturing each group of unculturable bacteria. Simulating the natural environment is an effective strategy for isolating dominant active bacteria, whereas culturomics and enrichment culture methods are proposed for isolating rare active bacteria. For dormant bacteria, resuscitation culture is an appropriate strategy. Furthermore, the review provides a list of the most-wanted bacteria and proposes potential strategies for culturing these bacteria in marine environments. The review provides new insight into the development of strategies for the cultivation of specific groups of uncultured bacteria and therefore paves the way for the detection of novel microbes and their functions in marine ecosystems.

Diversity of microbial community and its metabolic potential for nitrogen and sulfur cycling in sediments of Phu Quoc island, Gulf of Thailand

Although Phu Quoc island, Gulf of Thailand possesses diverse marine and coastal ecosystems, biodiversity and metabolic capability of microbial communities remain poorly investigated. The aim of our study was to evaluate the biodiversity and metabolic potential of sediment microbial communities in Phu Quoc island. The marine sediments were collected from three different areas and analyzed by using 16S rRNA gene-based amplicon approach. A total of 1,143,939 reads were clustered at a 97% sequence similarity into 8,331 unique operational taxonomic units, representing 52 phyla. Bacteria and archaea occupied averagely around 86% and 14%, respectively, of the total prokaryotic community. Proteobacteria, Planctomycetes, Chloroflexi, and Thaumarchaeota were the dominant phyla in all sediments, which were involved in nitrogen and sulfur metabolism. Sediments harboring of higher nitrogen sources were found to coincide with increased abundance of archaeal phylum Thaumarchaeota. Predictive functional analysis showed high abundance prokaryotic genes associated with nitrogen cycling including nifA-Z, amoABC, nirA, narBIJ, napA, nxrAB, nrfA-K, nirBD, nirS, nirK, norB-Z, nlnA, ald, and ureA-J, based on taxonomic groups detected by 16S rRNA sequencing. Although the key genes involved in sulfur cycling were found to be at low to undetectable levels, the other genes encoding for sulfur-related biological processes were present, suggesting that alternative pathways may be involved in sulfur cycling at our study site. In conclusion, our study for the first time shed light on diversity of microbial communities in Phu Quoc island.

Compositional changes of sedimentary microbes in the Yangtze River Estuary and their roles in the biochemical cycle

Due to the geographical circumstances, the Yangtze River Estuary (YRE) and the adjacent East China Sea are extensively influenced by both anthropogenic activities and environmental factors. To reveal the responses of microbes in surface sediment to environmental factors and their contributions to the biogeochemical cycle in this area, surface sediment and overlying water samples were collected at 21 stations from the estuary to the coastal region. Water and sediment parameters were determined, and 16S rRNA genes of microbes in sediment samples were sequenced using high throughput sequencing technology. The results indicated that ocean currents, sediment density (SD), nutrients, sulfate (SO₄^2-), and salinity were the key factors shaping the microbial communities. Coastal microbes were affected mainly by SD, whereas anthropogenic discharge might have been responsible for a decrease in indigenous microbial diversity in the ocean. Due to the anthropogenic discharge, the most representative bacteria in the nearshore were aerobic and chemoheterotrophic bacteria, including ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, denitrifying bacteria, and polyphosphate accumulating organisms. In the offshore, anaerobic bacteria, thermophilic bacteria, halophilic bacteria, sulfate-reducing bacteria, and sulfide oxidizing bacteria were the dominant bacteria, and these were characterized by strong solidarity and cooperative properties within the malnourished environment. In summary, these results provide a new perspective for revealing the biogeochemical significance of the bacterial lineages in the YRE, as well as constructive guidance for the management of the marginal sea ecosystems in distinct regions.

Psychroflexus aurantiacus sp. nov., isolated from soil in the Yellow River Delta wetlands

A Gram-stain-negative, strictly aerobic, non-motile, orange-coloured bacterium, designated YR1-1^T, was isolated from a soil sample collected from the Yellow River Delta wetlands (PR China). Growth was observed at a salinity of 1.0-15.0 % NaCl, 4-45 °C and pH 6.0-9.0. The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that YR1-1^T represented a member of the genus Psychroflexus, with the highest sequence similarity to Psychroflexus sediminis YIM-C238^T (97.9 %), followed by Psychroflexus aestuariivivens (97.1 %) and Psychroflexus torquis (96.4 %). The average nucleotide identity and digital DNA-DNA hybridization values between YR1-1^T and other closely related type strains of species of the genus Psychroflexus were 68.7-86.3% and 17.8-30.9 %. The genome of the strain was 2 899 374 bp in length with 39.8 % DNA G+C content. The predominant fatty acids (>10 %) were iso-C_15 : 0 and anteiso-C_15 : 0. The major respiratory quinone was menaquinone-6 (MK-6) and the major polar lipids were phosphatidylethanolamine, phospholipid, diphosphatidylglycerol, two unidentified aminolipids and four unidentified lipids. The combined genotypic and phenotypic data indicate that YR1-1^T represents a novel species within the genus Psychroflexus, for which the name Psychroflexus aurantiacus sp. nov., is proposed. The type strain is YR1-1^T (=KCTC 72794^T=CGMCC 1.17458^T).

Defining the sediment prokaryotic communities of the Indian River Lagoon, FL, USA, an Estuary of National Significance

The Indian River Lagoon, located on the east coast of Florida, USA, is an Estuary of National Significance and an important economic and ecological resource. The Indian River Lagoon faces several environmental pressures, including freshwater discharges through the St. Lucie Estuary; accumulation of anoxic, fine-grained, organic-rich sediment; and metal contamination from agriculture and marinas. Although the Indian River Lagoon has been well-studied, little is known about its microbial communities; thus, a two-year 16S amplicon sequencing study was conducted to assess the spatiotemporal changes of the sediment bacterial and archaeal groups. In general, the Indian River Lagoon exhibited a prokaryotic community that was consistent with other estuarine studies. Statistically different communities were found between the Indian River Lagoon and St. Lucie Estuary due to changes in porewater salinity causing microbes that require salts for growth to be higher in the Indian River Lagoon. The St. Lucie Estuary exhibited more obvious prokaryotic seasonality, such as a higher relative abundance of Betaproteobacteriales in wet season and a higher relative abundance of Flavobacteriales in dry season samples. Distance-based linear models revealed these communities were more affected by changes in total organic matter and copper than changes in temperature. Anaerobic prokaryotes, such as Campylobacterales, were more associated with high total organic matter and copper samples while aerobic prokaryotes, such as Nitrosopumilales, were more associated with low total organic matter and copper samples. This initial study fills the knowledge gap on the Indian River Lagoon bacterial and archaeal communities and serves as important data for future studies to compare to determine possible future changes due to human impacts or environmental changes.

Aeromicrobium piscarium sp. nov., isolated from the intestine of Collichthys lucidus

A Gram-stain-positive, rod-shaped, whitesmoke-coloured and aerobic bacterium, designated strain Co35T, was isolated from the intestine of Collichthys lucidus collected from the Jiangmen Guangdong Chinese White Dolphin Provincial Nature Reserve. Strain Co35T was able to grow at 15–35 °C (optimal 28 °C), at pH 7.0–8.5 (optimal 8.0) and with 0–9 % (w/v) NaCl (optimal 0.5–1 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Co35T was a member of the genus Aeromicrobium within the family Nocardioidaceae . The genomic DNA G+C content of strain Co35T was 68.4 mol%. Chemotaxonomic analysis showed that the sole respiratory quinone was menaquinone 9 (MK-9), and the major fatty acids included 10-methyl C18 : 0. The polar lipids were found to consist of phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylinositol (PI), two unidentified phospholipids (PL1–2) and two unidentified glycolipids (GL1–2). On the basis of its phylogenetic, phenotypic, chemotaxonomic, genotypic and genomic characteristics presented in this study, strain Co35T represents a novel species in the genus Aeromicrobium , for which the name Aeromicrobium piscarium sp. nov. is proposed. The type strain is Co35T (=KCTC 49280T=MCCC 1K03754T).

Paucihalobacter ruber gen. nov., sp. nov., isolated from a haloalkaline lake sediment sample

A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped bacterium, designated CWB-1^T, was isolated from a haloalkaline lake sediment sample collected from the bottom of Chaiwopu Lake, Urumchi, Xinjiang Province, PR China. Strain CWB-1^T grew at 4-40 °C (optimum, 30-35 °C), pH 6.5-9.0 (optimum, pH 6.5-7.0) and with 0.5-5.5 % (w/v) NaCl (optimum, 2.5-3.0 %). Phylogenetic analyses based on the 16S rRNA gene sequence and the whole genome sequence both revealed that strain CWB-1^T belonged to the family Flavobacteriaceae. The strain had the highest similarity of the 16S rRNA gene sequence to Psychroserpens jangbogonensis PAMC 27130^T (92.8 %). The genome of strain CWB-1^T was 3 548 011 bp long with 36.3 % DNA G+C content. The predominant fatty acids (>10 %) in the CWB-1^T cells were iso-C_15 : 0, iso-C_17 : 0 3-OH and summed feature 1 (iso-C_15 : 1 H/C_13 : 0 3-OH). The major respiratory quinone was menaquinone-6 and the major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and two unidentified lipids. Based on the phylogenetic analyses, as well as the phenotypic characteristics, a novel genus and species of the family Flavobacteriaceae, Paucihalobacter ruber gen. nov., sp. nov., is proposed. The type strain is CWB-1^T (=KCTC 72450^T=CGMCC 1.17149^T).

Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment

Distinct lineages of Gammaproteobacteria clade Woeseiales are globally distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79°N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.

Metagenomic Profiling and Microbial Metabolic Potential of Perdido Fold Belt (NW) and Campeche Knolls (SE) in the Gulf of Mexico

The Gulf of Mexico (GoM) is a particular environment that is continuously exposed to hydrocarbon compounds that may influence the microbial community composition. We carried out a metagenomic assessment of the bacterial community to get an overall view of this geographical zone. We analyzed both taxonomic and metabolic markers profiles to explain how the indigenous GoM microorganims participate in the biogeochemical cycling. Two geographically distant regions in the GoM, one in the north-west (NW) and one in the south-east (SE) of the GoM were analyzed and showed differences in their microbial composition and metabolic potential. These differences provide evidence the delicate equilibrium that sustains microbial communities and biogeochemical cycles. Based on the taxonomy and gene groups, the NW are more oxic sediments than SE ones, which have anaerobic conditions. Both water and sediments show the expected sulfur, nitrogen, and hydrocarbon metabolism genes, with particularly high diversity of the hydrocarbon-degrading ones. Accordingly, many of the assigned genera were associated with hydrocarbon degradation processes, Nitrospira and Sva0081 were the most abundant in sediments, while Vibrio, Alteromonas, and Alcanivorax were mostly detected in water samples. This basal-state analysis presents the GoM as a potential source of aerobic and anaerobic hydrocarbon degradation genes important for the ecological dynamics of hydrocarbons and the potential use for water and sediment bioremediation processes.

Persicimonas caeni gen. nov., sp. nov., the Representative of a Novel Wide-Ranging Predatory Taxon in Bradymonadales

A novel bacterial strain, designated YN101^T, was isolated from a marine solar saltern in the coast of Weihai, Shandong Province, China. Strain YN101^T was Gram-stain negative, facultatively anaerobic, oxidase and catalase negative bacterium with the ability to prey on other microbes. A cross-streaking culture method was utilized to analyze the predatory activity of strain YN101^T. The results showed strain YN101^T could prey on various bacteria, either Gram-stain negative or Gram-stain positive. According to the predatory assays, different species in the same genus may behave differently when attacked by strain YN101^T. The predatory behavior of strain YN101^T to four typical species was analyzed, and furthermore, predation to Algoriphagus marinus am2^T were quantitatively studied by fluorogenic quantitative PCR, and the gene copies decreased over two magnitudes. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN101^T shared the greatest sequence similarity of 93.9% to Bradymonas sediminis FA350^T. The complete genome sequence of strain YN101^T was 8,047,306 bp in size and the genomic DNA G + C content was 63.8 mol%. The digital DNA-DNA hybridization (dDDH) values and average nucleotide identity (ANI) values between strain YN101^T and B. sediminis FA350^T were 13.9 and 74.0%. The genetic features showed that the biosynthesis of many important compounds was deficient in genome of strain YN101^T, which may lead to its predation. Moreover, its genome encoded many genes affiliated with type IV pili, secretion system, membrane proteins and transduction proteins. Similar with myxobacteria and Bdellovibrio and like organisms (BALOs), these genes should play important roles in motility, adhesion or virulence to attack prey cells during predation. The predominant polar lipid profile of strain YN101^T consisted of phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), and one unidentified aminophospholipid (APL). The major cellular fatty acid of strain YN101^T was iso-C_17:0, and the sole respiratory quinone was MK-7. Based on the chemotaxonomic, physiological and biochemical characteristics, strain YN101^T represents a novel species of a novel genus in the family Bradymonadaceae, for which the name Persicimonas caeni gen. nov., sp. nov. is proposed. The type strain is YN101^T (=KCTC 72083^T = MCCC 1H00374^T).

Long-term decomposition captures key steps in microbial breakdown of seagrass litter

Seagrass biomass represents an important source of organic carbon that can contribute to long-term sediment carbon stocks in coastal ecosystems. There is little empirical data on the long-term microbial decomposition of seagrass detritus, despite this process being one of the key drivers of carbon-cycling in coastal ecosystems, that is, it influences the amount and quality of carbon available for sequestration. Here, our goal was to investigate how litter quality (leaf vs. rhizome/root) and the microbial communities involved in organic matter remineralisation shift over a 2-year field decomposition study north of Sydney, Australia using the temperate seagrass Zostera muelleri. The sites varied in bulk sediment characteristics and the sediment-associated microbial communities, but these variables overall had little influence on long-term seagrass decomposition rates or seagrass-associated microbiomes. The results showed a clear succession of bacterial and archaeal communities for both tissues types from r-strategists such as α- and γ-proteobacteria to K-strategies, including δ-proteobacteria, Bacteroidia and Spirochaetes. We used a new mathematical model to capture how decay rates varied over time and found that two decomposition events occurred for some seagrass leaf samples, possibly due to exudate input from living seagrass roots growing into the litter bag. The new model also indicated that conventional single exponential models overestimate long-term decay rates, and we detected for the first time the refractory, or stable, phase of decomposition for rhizome/root biomass. The stable phase began at approximately 20% mass remaining and after 600 days, and the persistence of rhizome/root biomass was attributed to the anoxic conditions and the preservation of refractory organic matter. While we predict that rhizome/root biomass will contribute more to the long-term sediment carbon stocks, the preservation of leaf carbon may be enhanced at locations were sedimentation is high and burial in anoxic conditions is rapid and constant.

Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities

Surveys of 16S rRNA gene sequences derived from marine sediments have indicated that a widely distributed group of Gammaproteobacteria, named “JTB255-Marine Benthic Group” (now the candidate order Woeseiales), accounts for 1–22% of the retrieved sequences. Despite their ubiquity in seafloor communities, little is known about their distribution and specific ecological niches in the deep sea, which constitutes the largest biome globally. Here, we characterized the phylogeny, environmental distribution patterns, abundance, and metabolic potential of Woeseiales bacteria with a focus on representatives from the deep sea. From a phylogenetic analysis of publicly available 16S rRNA gene sequences (≥1400 bp, n = 994), we identified lineages of Woeseiales with greater prevalence in the deep sea than in coastal environments, a pattern corroborated by the distribution of 16S oligotypes recovered from 28 globally distributed sediment samples. Cell counts revealed that Woeseiales bacteria accounted for 5 ± 2% of all microbial cells in deep-sea surface sediments at 23 globally distributed sites. Comparative analyses of a genome, metagenome bins, and single-cell genomes suggested that members of the corresponding clades are likely to grow on proteinaceous matter, potentially derived from detrital cell membranes, cell walls, and other organic remnants in marine sediments.

Metagenomic Resolution of Functional Diversity in Copper Surface-Associated Marine Biofilms

We used metagenomic sequencing combined with morphological and chemical analyses to investigate microbial taxa and functions related to copper-resistance and microbiologically influenced corrosion in mature copper-associated biofilms in coastal seawater for 44 months. Facultative anaerobic microbes such as Woeseia sp. were found to be the dominant groups on the copper surface. Genes related to stress response and possible heavy metal transport systems, especially RNA polymerase sigma factors (rpoE) and putative ATP-binding cassette (ABC) transport system permease protein (ABC.CD.P) were observed to be highly enriched in copper-associated biofilms, while genes encoding DNA-methyltransferase and RNA polymerase subunit were highly enriched in aluminum-associated biofilms and seawater planktonic cells, respectively. Moreover, copper-associated biofilms harbored abundant copper-resistance genes including cus, cop and pco, as well as abundant genes related to extracellular polymeric substances, indicating the presence of diverse copper-resistance patterns. The proportion of dsr in copper-associated biofilms, key genes related to sulfide production, was as low as that in aluminum biofilm and seawater, which ruled out the possibility of microbial sulfide-induced copper-corrosion under field conditions. These results may fill knowledge gaps about the in situ microbial functions of marine biofilms and their effects on toxic-metal corrosion.

Cumulative impact of long-term intensive mariculture on total and active bacterial communities in the core sediments of the Ailian Bay, North China

The exponential growth of off-shore mariculture worldwide over the last 20 years has had significant impact on coastal sediment biogeochemistry. However, there are no long-term records of the cumulative impacts of mariculture on the benthic bacterial community. Here, total (DNA) and active (RNA) bacterial community compositions were characterized using MiSeq sequencing of 16S rRNA gene in four core sediments of the Ailian Bay, one of the typical intensive mariculture areas in China with more than fifty-year history of kelp and scallop cultivation. The γ-Proteobacteria, δ-Proteobacteria, Acidobacteria and Acitinobacteria were more abundant in the total bacterial communities, while β-Proteobacteria, Anaerolineae, Clostridia, Spirochaetes and Cyanobacteria were enriched in the active bacterial communities. Significant differences were observed between total and active benthic bacterial communities. The influences of different mariculture modes on the total bacterial communities were more significant than those on the active bacterial communities. Only limited groups of the total bacterial communities were significant influenced by the cumulative effects of the long-term mariculture. The bacterial genera with the function in the sulfide cycling and organic consumption were enriched in the total bacterial population of the integrated multi-trophic aquaculture (IMTA) areas. The variations of both total and active bacterial communities were significantly influenced by grain sizes, total organic carbon and nutrients. Both total and active bacterial communities exhibited a slightly stronger response to environmental factors than to spatial (distance) factors. The effects of mutualism might dominate the total and active bacterial networks in the Ailian Bay. The present study demonstrated that the cumulative influences of the long-term and intensive IMTA mariculture on total benthic bacterial communities in the sub-surface sediments of the Ailian Bay were stronger than those on the active benthic bacterial communities, which provided some insights into the potential ecological roles of specific taxa in the sediments of the IMTA ecosystems.

Microbial metabolisms in an abyssal ferromanganese crust from the Takuyo-Daigo Seamount as revealed by metagenomics

Rocky outcrops covered with thick Fe and Mn oxide coatings, which are known as ferromanganese (Fe-Mn) crusts, are commonly found on slopes of aged seamounts in bathyal and abyssal zones. Although the presence of diverse microorganisms on these Fe-Mn crusts has been reported, little is known about their metabolism. Here, we report the metabolic potential of the microbial community in an abyssal crust collected in the Takuyo-Daigo Seamount, in the north-western Pacific. We performed shotgun metagenomic sequencing of the Fe-Mn crust, and detected putative genes involved in dissolution and precipitation of Fe and Mn, nitrification, sulfur oxidation, carbon fixation, and decomposition of organics in the metagenome. In addition, four metagenome-assembled genomes (MAGs) of abundant members in the microbial community were recovered from the metagenome. The MAGs were affiliated with Thaumarchaeota, Alphaproteobacteria, and Gammaproteobacteria, and were distantly related to previously reported genomes/MAGs of cultured and uncultured species. Putative genes involved in the above reactions were also found in the crust MAGs. Our results suggest that crust microbial communities play a role in biogeochemical cycling of C, N, S, Fe, and Mn, and imply that they contribute to the growth of Fe-Mn crusts.

Flavobacterium cerinum sp. nov., isolated from Arctic tundra soil

In the present paper, we describe a new species of the genus Flavobacterium, designated as strain 1E403^T, which was isolated from a soil sample collected from the Arctic. Strain 1E403^T was Gram-stain-negative, yellow-pigmented, rod-shaped, gliding and aerobic. Growth occurred at 4-37 °C (optimum, 28 °C), pH 6.0-9.0 (pH 7.0) and with 0-2 % (w/v) NaCl (0 %) on modified marine agar 2216. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain 1E403^T was affiliated with the genus Flavobacterium and was more closely related to Flavobacterium subsaxonicum DSM 21790^T (96.6 %) than to other species. In silico genomic comparisons, including average nucleotide identity and the digital DNA-DNA hybridization values, showed 73.9 % and 18.8 % identity to the closest relative Flavobacterium subsaxonicum DSM 21790^T, respectively. The average amino acid identity value between strain 1E403^T and Flavobacterium aquatile DSM 1132^T was 63.8 %. The DNA G+C content of the strain was 36.8 %, while the sole respiratory quinone was menaquinone-6. Iso-C_15 : 0 and summed feature 3 (C_16 : 1ω7c and/or C_16 : 1ω6c) were the major fatty acids (>10 %) of strain 1E403^T. The polar lipid profile of strain 1E403^T contained phosphatidylethanolamine, four unidentified aminolipids and two unidentified phospholipids. Based on the phenotypic characteristics, chemotaxonomic characteristics and phylogenetic inference, strain 1E403^T represents a novel species of the genus Flavobacterium, and we propose the name Flavobacterium cerinum sp. nov. The type strain of Flavobacterium cerinum sp. nov. is 1E403^T (=KCTC 62960^T=MCCC 1H00356^T).

Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses

Metal-sulfides are wide-spread in marine benthic habitats. At deep-sea hydrothermal vents, they occur as massive sulfide chimneys formed by mineral precipitation upon mixing of reduced vent fluids with cold oxygenated sea water. Although microorganisms inhabiting actively venting chimneys and utilizing compounds supplied by the venting fluids are well studied, only little is known about microorganisms inhabiting inactive chimneys. In this study, we combined 16S rRNA gene-based community profiling of sulfide chimneys from the Manus Basin (SW Pacific) with radiometric dating, metagenome (n = 4) and metaproteome (n = 1) analyses. Our results shed light on potential lifestyles of yet poorly characterized bacterial clades colonizing inactive chimneys. These include sulfate-reducing Nitrospirae and sulfide-oxidizing Gammaproteobacteria dominating most of the inactive chimney communities. Our phylogenetic analysis attributed the gammaproteobacterial clades to the recently described Woeseiaceae family and the SSr-clade found in marine sediments around the world. Metaproteomic data identified these Gammaproteobacteria as autotrophic sulfide-oxidizers potentially facilitating metal-sulfide dissolution via extracellular electron transfer. Considering the wide distribution of these gammaproteobacterial clades in marine environments such as hydrothermal vents and sediments, microbially accelerated neutrophilic mineral oxidation might be a globally relevant process in benthic element cycling and a considerable energy source for carbon fixation in marine benthic habitats.

Marinilabilia rubra sp. nov., isolated from a marine solar saltern

A novel cherry-red-pigmented, Gram-stain-negative, gliding, facultatively anaerobic and rod-shaped bacterium, designated strain WTE16^T, was isolated from a sediment sample taken from a marine solar saltern of Wendeng, China (36° 59' 56.49'' N 122° 1' 38.84'' E). The novel isolate was able to grow at 20-40 °C (optimum 33 °C), at pH 6.0-9.0 (optimum pH 7.0) and with 1.0-12.0 % (w/v) NaCl (optimum 3.0-5.0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the most closely related validly published species is Marinilabilia salmonicolor JCM 21150^T (96.0 % similarity). Average nucleotide identity, average amino acid identity, percentage of conserved proteins and digital DNA-DNA hybridization values between strain WTE16^T and Marinilabilia salmonicolor JCM 21150^T were 73.8 %, 73.5 %, 63.4 % and 19.5-24.2 %, respectively. The genomic DNA G+C content of strain WTE16^T was 40.8 mol%. Chemotaxonomic analysis showed that the sole respiratory quinone was menaquinone 7 (MK-7), and the major fatty acids included iso-C15 : 0 and anteiso-C15 : 0. The polar lipid profile of strain WTE16^T included phosphatidylethanolamine, three unidentified phospholipids and three unidentified lipids. On the basis of its phylogenetic, phenotypic, chemotaxonomic, genotypic and genomic characteristics, strain WTE16^T is suggested to represent a novel species of the genus Marinilabilia, for which the name Marinilabilia rubra sp. nov. is proposed. The type strain is WTE16^T (=KCTC 62599^T=MCCC 1H00311^T).

Purple Sulfur Bacteria Dominate Microbial Community in Brazilian Limestone Cave

The mineralogical composition of caves makes the environment ideal for inhabitation by microbes. However, the bacterial diversity in the cave ecosystem remains largely unexplored. In this paper, we described the bacterial community in an oxic chamber of the Sopradeira cave, an iron-rich limestone cave, in the semiarid region of Northeast Brazil. The microbial population in the cave samples was studied by 16S rDNA next-generation sequencing. A type of purple sulfur bacteria (PSB), Chromatiales, was found to be the most abundant in the sediment (57%), gravel-like (73%), and rock samples (96%). The predominant PSB detected were Ectothiorhodospiraceae, Chromatiaceae, and Woeseiaceae. We identified the PSB in a permanently aphotic zone, with no sulfur detected by energy-dispersive X-ray (EDX) spectroscopy. The absence of light prompted us to investigate for possible nitrogen fixing (nifH) and ammonia oxidizing (amoA) genes in the microbial samples. The nifH gene was found to be present in higher copy numbers than the bacterial-amoA and archaeal-amoA genes, and archaeal-amoA dominated the ammonia-oxidizing community. Although PSB dominated the bacterial community in the samples and may be related to both nitrogen-fixing and ammonia oxidizing bacteria, nitrogen-fixing associated gene was the most detected in those samples, especially in the rock. The present work demonstrates that this cave is an interesting hotspot for the study of ammonia-oxidizing archaea and aphotic PSB.

Hydrocarbon degradation and response of seafloor sediment bacterial community in the northern Gulf of Mexico to light Louisiana sweet crude oil

The Deepwater Horizon (DWH) blowout resulted in the deposition to the seafloor of up to 4.9% of 200 million gallons of oil released into the Gulf of Mexico. The petroleum hydrocarbon concentrations near the wellhead were high immediately after the spill, but returned to background levels a few years after the spill. Microbial communities in the seafloor are thought to be responsible for the degradation of hydrocarbons, however, our knowledge is primarily based upon gene diversity surveys and hydrocarbon concentration in field sediment samples. Here, we investigated the oil degradation potential and changes in bacterial community by amending seafloor sediment collected near the DWH site with crude oil and both oil and Corexit dispersant. Polycyclic aromatic hydrocarbons were rapidly degraded during the first 30 days of incubation, while alkanes were degraded more slowly. With the degradation of hydrocarbons, the relative abundances of Colwelliaceae, Alteromonadaceae, Methylococales, Alcanivorax, Bacteriovorax, and Phaeobacter increased remarkably. However, the abundances of oil-degrading bacteria changed with oil chemistry. Colwelliaceae decreased with increasing oil degradation, whereas Alcanivorax and Methylococcales increased considerably. We assembled seven genomes from the metagenome, including ones belonging to Colwellia, Alteromonadaceae, Rhodobacteraceae, the newly reported genus Woeseia, and candidate phylum NC10, all of which possess a repertoire of genes for hydrocarbon degradation. Moreover, genes related to hydrocarbon degradation were highly enriched in the oiled treatment, suggesting that the hydrocarbons were biodegraded, and that the indigenous microflora have a remarkable potential for the natural attenuation of spilled oil in the deep-sea surface sediment.

Aquimarina celericrescens sp. nov., isolated from seawater

An orange-coloured, slender rod-shaped, gliding bacterium, designated NS08^T, was isolated from coastal water of Xiaoshi Island, Weihai, China (37° 31' 36'' N 122° 00' 58'' E). Cells were Gram-stain-negative, non-spore-forming, non-flagellated, aerobic, catalase-positive and oxidase-negative. Growth occurred at 10-37 °C (optimum 30 °C), in the presence of 1.0-5.0 % (w/v) NaCl (optimum 2.0-3.0 %) and at pH 6.5-9.0 (optimum pH 7.0-7.5). Carotenoid pigments were produced but flexirubin-type pigments were not. The major fatty acids (>10 %) were iso-C15 : 0 and iso-C17 : 0 3-OH. The sole isoprenoid quinone of strain NS08^T was menaquinone MK-6 and the DNA G+C content was 39.4 mol%. The polar lipid compositions of strain NS08^T and the type strain of the type species of the genus Aquimarina, Aquimarina muelleri KCTC 12285^T, were very similar with phosphatidylethanolamine, an unidentified aminolipid and two unknown polar lipids as the major components. A phylogenetic tree based on 16S rRNA gene sequences showed that strain NS08^T formed an evolutionary lineage within the genus Aquimarina and shared the highest level of similarity to A. versatilis JCM 19528^T (96.0 %) while level to A. muelleri KCTC 12285^T was 95.0 %. Phenotypic characteristics distinguished strain NS08^T from described members of the genus Aquimarina. On the basis of the evidence presented in this study, strain NS08^T represents a novel species of the genus Aquimarina, for which the name Aquimarina celericrescens sp. nov. is proposed. The type strain is NS08^T (=KCTC 52897^T=MCCC 1H00191^T).