Molecular analysis of the diversity of sulfate-reducing and sulfur-oxidizing prokaryotes in the environment, using aprA as functional marker gene

Co-evolution of early Earth environments and microbial life

Two records of Earth history capture the evolution of life and its co-evolving ecosystems with interpretable fidelity: the geobiological and geochemical traces preserved in rocks and the evolutionary histories captured within genomes. The earliest vestiges of life are recognized mostly in isotopic fingerprints of specific microbial metabolisms, whereas fossils and organic biomarkers become important later. Molecular biology provides lineages that can be overlayed on geologic and geochemical records of evolving life. All these data lie within a framework of biospheric evolution that is primarily characterized by the transition from an oxygen-poor to an oxygen-rich world. In this Review, we explore the history of microbial life on Earth and the degree to which it shaped, and was shaped by, fundamental transitions in the chemical properties of the oceans, continents and atmosphere. We examine the diversity and evolution of early metabolic processes, their couplings with biogeochemical cycles and their links to the oxygenation of the early biosphere. We discuss the distinction between the beginnings of metabolisms and their subsequent proliferation and their capacity to shape surface environments on a planetary scale. The evolution of microbial life and its ecological impacts directly mirror the Earth's chemical and physical evolution through cause-and-effect relationships.

Rumen protozoa are a hub for diverse hydrogenotrophic functions

Ciliate protozoa are an integral part of the rumen microbial community involved in a variety of metabolic processes. These processes are thought to be in part the outcome of interactions with their associated prokaryotic community. For example, methane production is enhanced through interspecies hydrogen transfer between protozoa and archaea. We hypothesize that ciliate protozoa are host to a stable prokaryotic community dictated by specific functions they carry. Here, we modify the microbial community by varying the forage-to-concentrate ratios and show that, despite major changes in the prokaryotic community, several taxa remain stably associated with ciliate protozoa. By quantifying genes belonging to various known reduction pathways in the rumen, we find that the bacterial community associated with protozoa is enriched in genes belonging to hydrogen utilization pathways and that these genes correspond to the same taxonomic affiliations seen enriched in protozoa. Our results show that ciliate protozoa in the rumen may serve as a hub for various hydrogenotrophic functions and a better understanding of the processes driven by different protozoa may unveil the potential role of ciliates in shaping rumen metabolism.

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.

Distribution and Activity of Sulfur-Metabolizing Bacteria along the Temperature Gradient in Phototrophic Mats of the Chilean Hot Spring Porcelana

In terrestrial hot springs, some members of the microbial mat community utilize sulfur chemical species for reduction and oxidization metabolism. In this study, the diversity and activity of sulfur-metabolizing bacteria were evaluated along a temperature gradient (48-69 °C) in non-acidic phototrophic mats of the Porcelana hot spring (Northern Patagonia, Chile) using complementary meta-omic methodologies and specific amplification of the aprA (APS reductase) and soxB (thiosulfohydrolase) genes. Overall, the key players in sulfur metabolism varied mostly in abundance along the temperature gradient, which is relevant for evaluating the possible implications of microorganisms associated with sulfur cycling under the current global climate change scenario. Our results strongly suggest that sulfate reduction occurs throughout the whole temperature gradient, being supported by different taxa depending on temperature. Assimilative sulfate reduction is the most relevant pathway in terms of taxonomic abundance and activity, whereas the sulfur-oxidizing system (Sox) is likely to be more diverse at low rather than at high temperatures. Members of the phylum Chloroflexota showed higher sulfur cycle-related transcriptional activity at 66 °C, with a potential contribution to sulfate reduction and oxidation to thiosulfate. In contrast, at the lowest temperature (48 °C), Burkholderiales and Acetobacterales (both Pseudomonadota, also known as Proteobacteria) showed a higher contribution to dissimilative sulfate reduction/oxidation as well as to thiosulfate metabolism. Cyanobacteriota and Planctomycetota were especially active in assimilatory sulfate reduction. Analysis of the aprA and soxB genes pointed to members of the order Burkholderiales (Gammaproteobacteria) as the most dominant and active along the temperature gradient for these genes. Changes in the diversity and activity of different sulfur-metabolizing bacteria in photoautotrophic microbial mats along a temperature gradient revealed their important role in hot spring environments, especially the main primary producers (Chloroflexota/Cyanobacteriota) and diazotrophs (Cyanobacteriota), showing that carbon, nitrogen, and sulfur cycles are highly linked in these extreme systems.

Sulfur metabolism in subtropical marine mangrove sediments fundamentally differs from other habitats as revealed by SMDB

Shotgun metagenome sequencing provides the opportunity to recover underexplored rare populations and identify difficult-to-elucidate biochemical pathways. However, information on sulfur genes, including their sequences, is scattered in public databases. Here, we introduce SMDB ( https://smdb.gxu.edu.cn/ )-a manually curated database of sulfur genes based on an in-depth review of the scientific literature and orthology database. The SMDB contained a total of 175 genes and covered 11 sulfur metabolism processes with 395,737 representative sequences affiliated with 110 phyla and 2340 genera of bacteria/archaea. The SMDB was applied to characterize the sulfur cycle from five habitats and compared the microbial diversity of mangrove sediments with that of other habitats. The structure and composition of microorganism communities and sulfur genes were significantly different among the five habitats. Our results show that microorganism alpha diversity in mangrove sediments was significantly higher than in other habitats. Genes involved in dissimilatory sulfate reduction were abundant in subtropical marine mangroves and deep-sea sediments. The neutral community model results showed that microbial dispersal was higher in the marine mangrove ecosystem than in others habitats. The Flavilitoribacter of sulfur-metabolizing microorganism becomes a reliable biomarker in the five habitats. SMDB will assist researchers to analyze genes of sulfur cycle from the metagenomic efficiently.

What Controls the Sulfur Isotope Fractionation during Dissimilatory Sulfate Reduction?

Sulfate often behaves conservatively in the oxygenated environments but serves as an electron acceptor for microbial respiration in a wide range of natural and engineered systems where oxygen is depleted. As a ubiquitous anaerobic dissimilatory pathway, therefore, microbial reduction of sulfate to sulfide has been of continuing interest in the field of microbiology, ecology, biochemistry, and geochemistry. Stable isotopes of sulfur are an effective tool for tracking this catabolic process as microorganisms discriminate strongly against heavy isotopes when cleaving the sulfur-oxygen bond. Along with its high preservation potential in environmental archives, a wide variation in the sulfur isotope effects can provide insights into the physiology of sulfate reducing microorganisms across temporal and spatial barriers. A vast array of parameters, including phylogeny, temperature, respiration rate, and availability of sulfate, electron donor, and other essential nutrients, has been explored as a possible determinant of the magnitude of isotope fractionation, and there is now a broad consensus that the relative availability of sulfate and electron donors primarily controls the magnitude of fractionation. As the ratio shifts toward sulfate, the sulfur isotope fractionation increases. The results of conceptual models, centered on the reversibility of each enzymatic step in the dissimilatory sulfate reduction pathway, are in qualitative agreement with the observations, although the underlying intracellular mechanisms that translate the external stimuli into the isotopic phenotype remain largely unexplored experimentally. This minireview offers a snapshot of our current understanding of the sulfur isotope effects during dissimilatory sulfate reduction as well as their potential quantitative applications. It emphasizes the importance of sulfate respiration as a model system for the isotopic investigation of other respiratory pathways that utilize oxyanions as terminal electron acceptors.

The mystery of the ice cold rose-Microbiome of an Arctic winter frost flower

Under very cold conditions, delicate ice-crystal structures called frost flowers emerge on the surface of newly formed sea ice. These understudied, ephemeral structures include saline brine, organic material, inorganic nutrients, and bacterial and archaeal communities in their brine channels. Hitherto, only a few frost flowers have been studied during spring and these have been reported to be dominated by Rhizobia or members of the SAR11 clade. Here we report on the microbiome of frost flowers sampled during the winter and polar night in the Barents Sea. There was a distinct difference in community profile between the extracted DNA and RNA, but both were dominated by members of the SAR11 clade (78% relative abundance and 41.5% relative activity). The data further suggested the abundance and activity of Cand. Nitrosopumilus, Nitrospinia, and Nitrosomonas. Combined with the inference of marker genes based on the 16S rRNA gene data, this indicates that sulfur and nitrogen cycling are likely the major metabolism in these ephemeral structures.

Integration of Microbial Transformation Mechanism of Polyphosphate Accumulation and Sulfur Cycle in Subtropical Marine Mangrove Ecosystems with Spartina alterniflora Invasion

Excessive phosphorus can lead to eutrophication in marine and coastal ecosystems. Sulfur metabolism-associated microorganisms stimulate biological phosphorous removal. However, the integrating co-biotransformation mechanism of phosphorus and sulfur in subtropical marine mangrove ecosystems with Spartina alterniflora invasion is poorly understood. In this study, an ecological model of the coupling biotransformation of sulfur and phosphorus is constructed using metagenomic analysis and quantitative polymerase chain reaction strategies. Phylogenetic analysis profiling, a distinctive microbiome with high frequencies of Gammaproteobacteria and Deltaproteobacteria, appears to be an adaptive characteristic of microbial structures in subtropical mangrove ecosystems. Functional analysis reveals that the levels of sulfate reduction, sulfur oxidation, and poly-phosphate (Poly-P) aggregation decrease with increasing depth. However, at depths of 25-50 cm in the mangrove ecosystems with S. alterniflora invasion, the abundance of sulfate reduction genes, sulfur oxidation genes, and polyphosphate kinase (ppk) significantly increased. A strong positive correlation was found among ppk, sulfate reduction, sulfur oxidation, and sulfur metabolizing microorganisms, and the content of sulfide was significantly and positively correlated with the abundance of ppk. Further microbial identification suggested that Desulfobacterales, Anaerolineales, and Chromatiales potentially drove the coupling biotransformation of phosphorus and sulfur cycling. In particular, Desulfobacterales exhibited dominance in the microbial community structure. Our findings provided insights into the simultaneous co-biotransformation of phosphorus and sulfur bioconversions in subtropical marine mangrove ecosystems with S. alterniflora invasion.

Metagenomic and metatranscriptomic insights into sulfate-reducing bacteria in a revegetated acidic mine wasteland

The widespread occurrence of sulfate-reducing microorganisms (SRMs) in temporarily oxic/hypoxic aquatic environments indicates an intriguing possibility that SRMs can prevail in constantly oxic/hypoxic terrestrial sulfate-rich environments. However, little attention has been given to this possibility, leading to an incomplete understanding of microorganisms driving the terrestrial part of the global sulfur (S) cycle. In this study, genome-centric metagenomics and metatranscriptomics were employed to explore the diversity, metabolic potential, and gene expression profile of SRMs in a revegetated acidic mine wasteland under constantly oxic/hypoxic conditions. We recovered 16 medium- to high-quality metagenome-assembled genomes (MAGs) containing reductive dsrAB. Among them, 12 and four MAGs belonged to Acidobacteria and Deltaproteobacteria, respectively, harboring three new SRM genera. Comparative genomic analysis based on seven high-quality MAGs (completeness >90% and contamination <10%; including six acidobacterial and one deltaproteobacterial) and genomes of three additional cultured model species showed that Acidobacteria-related SRMs had more genes encoding glycoside hydrolases, oxygen-tolerant hydrogenases, and cytochrome c oxidases than Deltaproteobacteria-related SRMs. The opposite pattern was observed for genes encoding superoxide reductases and thioredoxin peroxidases. Using VirSorter, viral genome sequences were found in five of the 16 MAGs and in all three cultured model species. These prophages encoded enzymes involved in glycoside hydrolysis and antioxidation in their hosts. Moreover, metatranscriptomic analysis revealed that 15 of the 16 SRMs reported here were active in situ. An acidobacterial MAG containing a prophage dominated the SRM transcripts, expressing a large number of genes involved in its response to oxidative stress and competition for organic matter.

A Winter-to-Summer Transition of Bacterial and Archaeal Communities in Arctic Sea Ice

The Arctic is warming 2-3 times faster than the global average, leading to a decrease in Arctic sea ice extent, thickness, and associated changes in sea ice structure. These changes impact sea ice habitat properties and the ice-associated ecosystems. Sea-ice algal blooms provide various algal-derived carbon sources for the bacterial and archaeal communities within the sea ice. Here, we detail the transition of these communities from winter through spring to early summer during the Norwegian young sea ICE (N-ICE2015) expedition. The winter community was dominated by the archaeon Candidatus Nitrosopumilus and bacteria belonging to the Gammaproteobacteria (Colwellia, Kangiellaceae, and Nitrinocolaceae), indicating that nitrogen-based metabolisms, particularly ammonia oxidation to nitrite by Cand. Nitrosopumilus was prevalent. At the onset of the vernal sea-ice algae bloom, the community shifted to the dominance of Gammaproteobacteria (Kangiellaceae, Nitrinocolaceae) and Bacteroidia (Polaribacter), while Cand. Nitrosopumilus almost disappeared. The bioinformatically predicted carbohydrate-active enzymes increased during spring and summer, indicating that sea-ice algae-derived carbon sources are a strong driver of bacterial and archaeal community succession in Arctic sea ice during the change of seasons. This implies a succession from a nitrogen metabolism-based winter community to an algal-derived carbon metabolism-based spring/ summer community.

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

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

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

Characteristics of Microbial Community and Function With the Succession of Mangroves

In this study, 16S high-throughput and metagenomic sequencing analyses were employed to explore the changes in microbial community and function with the succession of mangroves (Sonneratia alba, Rhizophora apiculata, and Bruguiera parviflora) along the Merbok river estuary in Malaysia. The sediments of the three mangroves harbored their own unique dominant microbial taxa, whereas R. apiculata exhibited the highest microbial diversity. In general, Gammaproteobacteria, Actinobacteria, Alphaproteobacteria, Deltaproteobacteria, and Anaerolineae were the dominant microbial classes, but their abundances varied significantly among the three mangroves. Principal coordinates and redundancy analyses revealed that the specificity of the microbial community was highly correlated with mangrove populations and environmental factors. The results further showed that R. apiculata exhibited the highest carbon-related metabolism, coinciding with the highest organic carbon and microbial diversity. In addition, specific microbial taxa, such as Desulfobacterales and Rhizobiales, contributed the highest functional activities related to carbon metabolism, prokaryote carbon fixation, and methane metabolism. The present results provide a comprehensive understanding of the adaptations and functions of microbes in relation to environmental transition and mangrove succession in intertidal regions. High microbial diversity and carbon metabolism in R. apiculata might in turn facilitate and maintain the formation of climax mangroves in the middle region of the Merbok river estuary.

Microbes mediating the sulfur cycle in the Atlantic Ocean and their link to chemolithoautotrophy

Only about 10%-30% of the organic matter produced in the epipelagic layers reaches the dark ocean. Under these limiting conditions, reduced inorganic substrates might be used as an energy source to fuel prokaryotic chemoautotrophic and/or mixotrophic activity. The aprA gene encodes the alpha subunit of the adenosine-5'-phosphosulfate (APS) reductase, present in sulfate-reducing (SRP) and sulfur-oxidizing prokaryotes (SOP). The sulfur-oxidizing pathway can be coupled to inorganic carbon fixation via the Calvin-Benson-Bassham cycle. The abundances of aprA and cbbM, encoding RuBisCO form II (the key CO2 fixing enzyme), were determined over the entire water column along a latitudinal transect in the Atlantic from 64°N to 50°S covering six oceanic provinces. The abundance of aprA and cbbM genes significantly increased with depth reaching the highest abundances in meso- and upper bathypelagic layers. The contribution of cells containing these genes also increased from mesotrophic towards oligotrophic provinces, suggesting that under nutrient limiting conditions alternative energy sources are advantageous. However, the aprA/cbbM ratios indicated that only a fraction of the SOP is associated with inorganic carbon fixation. The aprA harbouring prokaryotic community was dominated by Pelagibacterales in surface and mesopelagic waters, while Candidatus Thioglobus, Chromatiales and the Deltaproteobacterium_SCGC dominated the bathypelagic realm. Noticeably, the contribution of the SRP to the prokaryotic community harbouring aprA gene was low, suggesting a major utilization of inorganic sulfur compounds either as an energy source (occasionally coupled with inorganic carbon fixation) or in biosynthesis pathways.

L-Cysteine Synthase Enhanced Sulfide Biotransformation in Subtropical Marine Mangrove Sediments as Revealed by Metagenomics Analysis

High sulfides concentrations can be poisonous to environment because of anthropogenic waste production or natural occurrences. How to elucidate the biological transformation mechanisms of sulfide pollutants in the subtropical marine mangrove ecosystem has gained increased interest. Thus, in the present study, the sulfide biotransformation in subtropical mangroves ecosystem was accurately evaluated using metagenomic sequencing and quantitative polymerase chain reaction analysis. Most abundant genes were related to the organic sulfur transformation. Furthermore, an ecological model of sulfide conversion was constructed. Total phosphorus was the dominant environmental factor that drove the sulfur cycle and microbial communities. We compared mangrove and non-mangrove soils and found that the former enhanced metabolism that was related to sulfate reduction when compared to the latter. Total organic carbon, total organic nitrogen, iron, and available sulfur were the key environmental factors that effectively influenced the dissimilatory sulfate reduction. The taxonomic assignment of dissimilatory sulfate-reducing genes revealed that Desulfobacterales and Chromatiales were mainly responsible for sulfate reduction. Chromatiales were most sensitive to environmental factors. The high abundance of cysE and cysK could contribute to the coping of the microbial community with the toxic sulfide produced by Desulfobacterales. Collectively, these findings provided a theoretical basis for the mechanism of the sulfur cycle in subtropical mangrove ecosystems.

L-Cysteine Synthase Enhanced Sulfide Biotransformation in Subtropical Marine Mangrove Sediments as Revealed by Metagenomics Analysis

High sulfides concentrations can be poisonous to environment because of anthropogenic waste production or natural occurrences. How to elucidate the biological transformation mechanisms of sulfide pollutants in the subtropical marine mangrove ecosystem has gained increased interest. Thus, in the present study, the sulfide biotransformation in subtropical mangroves ecosystem was accurately evaluated using metagenomic sequencing and quantitative polymerase chain reaction analysis. Most abundant genes were related to the organic sulfur transformation. Furthermore, an ecological model of sulfide conversion was constructed. Total phosphorus was the dominant environmental factor that drove the sulfur cycle and microbial communities. We compared mangrove and non-mangrove soils and found that the former enhanced metabolism that was related to sulfate reduction when compared to the latter. Total organic carbon, total organic nitrogen, iron, and available sulfur were the key environmental factors that effectively influenced the dissimilatory sulfate reduction. The taxonomic assignment of dissimilatory sulfate-reducing genes revealed that Desulfobacterales and Chromatiales were mainly responsible for sulfate reduction. Chromatiales were most sensitive to environmental factors. The high abundance of cysE and cysK could contribute to the coping of the microbial community with the toxic sulfide produced by Desulfobacterales. Collectively, these findings provided a theoretical basis for the mechanism of the sulfur cycle in subtropical mangrove ecosystems.

Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene

This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.

Evidence for non-methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales

Recent discoveries of mcr and mcr-like genes in genomes from diverse archaeal lineages suggest that methane metabolism is an ancient pathway with a complicated evolutionary history. One conventional view is that methanogenesis is an ancestral metabolism of the class Thermoplasmata. Through comparative genomic analysis of 12 Thermoplasmata metagenome-assembled genomes (MAGs) basal to the Methanomassiliicoccales, we show that these microorganisms do not encode the genes required for methanogenesis. Further analysis of 770 Ca. Thermoplasmatota genomes/MAGs found no evidence of mcrA homologues outside of the Methanomassiliicoccales. Together, these results suggest that methanogenesis was laterally acquired by an ancestor of the Methanomassiliicoccales. The 12 analysed MAGs include representatives from four orders basal to the Methanomassiliicoccales, including a high-quality MAG that likely represents a new order, Ca. Lunaplasma lacustris ord. nov. sp. nov. These MAGs are predicted to use diverse energy conservation pathways, including heterotrophy, sulfur and hydrogen metabolism, denitrification, and fermentation. Two lineages are widespread among anoxic, sedimentary environments, whereas Ca. Lunaplasma lacustris has thus far only been detected in alpine caves and subarctic lake sediments. These findings advance our understanding of the metabolic potential, ecology, and global distribution of the Thermoplasmata and provide insight into the evolutionary history of methanogenesis within the Ca. Thermoplasmatota.

Functional Seasonality of Free-Living and Particle-Associated Prokaryotic Communities in the Coastal Adriatic Sea

Marine snow is an important habitat for microbes, characterized by chemical and physical properties contrasting those of the ambient water. The higher nutrient concentrations in marine snow lead to compositional differences between the ambient water and the marine snow-associated prokaryotic community. Whether these compositional differences vary due to seasonal environmental changes, however, remains unclear. Thus, we investigated the seasonal patterns of the free-living and marine snow-associated microbial community composition and their functional potential in the northern Adriatic Sea. Our data revealed seasonal patterns in both, the free-living and marine snow-associated prokaryotes. The two assemblages were more similar to each other in spring and fall than in winter and summer. The taxonomic distinctness resulted in a contrasting functional potential. Motility and adaptations to low temperature in winter and partly anaerobic metabolism in summer characterized the marine snow-associated prokaryotes. Free-living prokaryotes were enriched in genes indicative for functions related to phosphorus limitation in winter and in genes tentatively supplementing heterotrophic growth with proteorhodopsins and CO-oxidation in summer. Taken together, the results suggest a strong influence of environmental parameters on both free-living and marine snow-associated prokaryotic communities in spring and fall leading to higher similarity between the communities, while the marine snow habitat in winter and summer leads to a specific prokaryotic community in marine snow in these two seasons.

Diversity of Sulfur-oxidizing Bacteria at the Surface of Cattle Manure Composting Assessed by an Analysis of the Sulfur Oxidation Gene soxB

Sulfur-oxidizing bacterial diversity at the surface of cattle manure was characterized throughout the composting process using a sulfur oxidation gene (soxB) clone library approach. In the mesophilic phase, clones related to the genera Hydrogenophaga and Hydrogenophilus were characteristically detected. In the thermophilic phase, clones related to the genera Hydrogenophaga and Thiohalobacter were predominant. In the cooling phase, the predominant soxB sequences were related to the genus Pseudaminobacter and a new sulfur-oxidizing bacterium belonging to the class Alphaproteobacteria. The present study showed changes in the community composition of sulfur-oxidizing bacteria at the surface of compost throughout the composting process.

The microbiota structure in the cecum of laying hens contributes to dissimilar H2S production

BACKGROUND

Host genotype plays a crucial role in microbial composition of laying hens, which may lead to dissimilar odor gas production. The objective of this study was to investigate the relationship among layer breed, microbial structure and odor production.

RESULTS

Thirty Hy-Line Gray and thirty Lohmann Pink laying hens were used in this study to determine the impact of cecal microbial structure on odor production of laying hens. The hens were managed under the same husbandry and dietary regimes. Results of in vivo experiments showed a lower hydrogen sulfide (H₂S) production from Hy-Line hens and a lower concentration of soluble sulfide (S^2-) but a higher concentration of butyrate in the cecal content of the Hy-Line hens compared to Lohmann Pink hens (P < 0.05), which was consistent with the in vitro experiments (P < 0.05). However, ammonia (NH₃) production was not different between genotypes (P > 0.05). Significant microbial structural differences existed between the two breed groups. The relative abundance of some butyrate producers (including Butyricicoccus, Butyricimonas and Roseburia) and sulfate-reducing bacteria (including Mailhella and Lawsonia) were found to be significantly correlated with odor production and were shown to be different in the 16S rRNA and PCR data between two breed groups. Furthermore, some bacterial metabolism pathways associated with energy extraction and carbohydrate utilization (oxidative phosphorylation, pyruvate metabolism, energy metabolism, two component system and secretion system) were overrepresented in the Hy-Line hens, while several amino acid metabolism-associated pathways (amino acid related enzymes, arginine and proline metabolism, and alanine-aspartate and glutamate metabolism) were more prevalent in the Lohmann hens.

CONCLUSION

The results of this study suggest that genotype of laying hens influence cecal microbiota, which in turn modulates their odor production. Our study provides references for breeding and enteric manipulation for defined microbiota to reduce odor gas emission.

Microbial community structure of soils in Bamenwan mangrove wetland

Microbial community diversity and composition are important for the maintenance of mangrove ecosystem. Bacterial and archaeal community composition of the Bamenwan Mangrove Wetland soil in Hainan, China, was determined using pyrosequencing technique. Bacterial community composition presented differences among the five soil samples. Rhizobiales with higher abundance were observed in inner mangrove forest samples, while Desulfobacterales were in the seaward edge samples, and Frankiales, Gaiellales and Rhodospirillales in the landedge sample. For archaea, Crenarchaeota and Euryarchaeota dominated in five samples, but the proportion in each samples were different. Dominant archaeal community composition at the order level was similar in the seaward edge samples. The dominant archaeal clusters in the two inner mangrove forest samples were different, with Soil Crenarchaeotic Group (SCG) and Halobacteriales in sample inside of Bruguiera sexangula forest and SCG, Methanosarcinales and Marine Benthic Group B (MBGB) in sample inside of Xylocarpus mekongensis forest. The dominant archaeal clusters in land sample were unique, with Terrestrial Group and South African Gold Mine Group 1. The metabolic pathways including metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems and human diseases were all detected for bacterial and archaeal functional profiles, but metabolic potentials among five samples were different.

Chemosynthetic ectosymbionts associated with a shallow-water marine nematode

Prokaryotes and free-living nematodes are both very abundant and co-occur in marine environments, but little is known about their possible association. Our objective was to characterize the microbiome of a neglected but ecologically important group of free-living benthic nematodes of the Oncholaimidae family. We used a multi-approach study based on microscopic observations (Scanning Electron Microscopy and Fluorescence In Situ Hybridization) coupled with an assessment of molecular diversity using metabarcoding based on the 16S rRNA gene. All investigated free-living marine nematode specimens harboured distinct microbial communities (from the surrounding water and sediment and through the seasons) with ectosymbiosis seemed more abundant during summer. Microscopic observations distinguished two main morphotypes of bacteria (rod-shaped and filamentous) on the cuticle of these nematodes, which seemed to be affiliated to Campylobacterota and Gammaproteobacteria, respectively. Both ectosymbionts belonged to clades of bacteria usually associated with invertebrates from deep-sea hydrothermal vents. The presence of the AprA gene involved in sulfur metabolism suggested a potential for chemosynthesis in the nematode microbial community. The discovery of potential symbiotic associations of a shallow-water organism with taxa usually associated with deep-sea hydrothermal vents, is new for Nematoda, opening new avenues for the study of ecology and bacterial relationships with meiofauna.

A combined approach of 16S rRNA and a functional marker gene, soxB to reveal the diversity of sulphur-oxidising bacteria in thermal springs

With the advent of new molecular tools, new taxa of sulphur-oxidising bacteria (SOB) in diverse environments are being discovered. However, there is a significant gap of knowledge about the ecology and diversity of SOB in thermal springs. Here, the species diversity and phylogenetic affiliations of SOB were investigated using 16S rRNA and functional gene marker, soxB in thermal springs of Thane district of Maharashtra, India. Most SOB detected by 16S rDNA sequences belong to different operational taxonomic units (OTU's): Firmicutes, α-, β-, γ-Proteobacteria and Actinobacteria with the dominance of first class. However, the soxB gene clone library sequences had shown affiliation with the β-, γ- and α-Proteobacteria. β-Proteobacteria-related sequences were dominant, with 53.3% clones belonging to genus Hydrogenophaga. The thiosulphate oxidation assay carried out for different isolates having distinct identity showed the mean sulphate-sulphur production from 117.86 ± 0.50 to 218.82 ± 2.56 mg SO₄-S l^-1 after 9 days of incubation. Also, sulphur oxidation by the genus Nitratireductor, Caldimonas, Geobacillus, Paenibacillus, Brevibacillus, Tristrella and Chelatococcus has been reported for the first time that reveals ecological widening over which thiotrophs are distributed.

Gill symbionts of the cold-seep mussel Bathymodiolus platifrons: Composition, environmental dependency and immune control

Deep-sea Bathymodiolus mussels depend on the organic carbon supplied by symbionts inside their gills. In this study, optimized methods of quantitative real-time PCR and fluorescence in situ hybridization targeted to both mRNA and 16S rRNA were used to investigate the gill symbionts of the cold-seep mussel Bathymodiolus platifrons, including species composition, environmental dependency and immune control by the host. Our results showed that methanotrophs were the major symbiotic bacteria in the gills of B. platifrons, while thiotrophs were scarce. In the mussels freshly collected from the deep sea, methanotrophs were housed in bacteriocytes in a unique circular pattern, and a lysosome-related gene (VAMP) encoding a vesicle-associated membrane protein was expressed at a high level and presented exactly where the methanotrophs occurred. After the mussels were reared for three months in aquaria without methane supply, the abundance of methanotrophs decreased significantly and their circle-shaped distribution pattern disappeared; in addition, the expression of VAMP decreased significantly. These results suggest that the symbiosis between B. platifrons and methanotrophs is influenced by the environment and that the lysosomal system plays an important immune role in controlling the abundance of endosymbionts in host. This study provides a reliable method for investigating symbionts in deep-sea mussels and enriches the knowledge about symbionts in B. platifrons.

Molecular biological tools in concrete biodeterioration - a mini review

Concrete structures develop biofilms when exposed to various environments. At a certain stage, the microbial films destroy the concrete structures leading to significant deterioration. Culture-dependent techniques give an incomplete picture of the microbial communities on the concrete surface. Culture-independent techniques or molecular biological tools pave a new way to analyse microbial communities involved in concrete biodeterioration. This study highlights the need to 'build' a database, for Microbiologically Influenced Concrete Corrosion (MICC) involving microbial groups that are being identified using culture-dependent and independent techniques. The role of molecular tools such as 16S rRNA sequencing, denaturing gradient gel electrophoresis (DGGE), Fluorescent in situ hybridization (FISH), Real-time Polymerase Chain Reaction (RT-PCR), microarray analysis, 2-Dimensional gel electrophoresis (2-DE) in analysing microbial communities on the concrete structures have been reviewed in this paper.

Metabolic potential of microbial communities from ferruginous sediments

Ferruginous (Fe-rich, SO₄ -poor) conditions are generally restricted to freshwater sediments on Earth today, but were likely widespread during the Archean and Proterozoic Eons. Lake Towuti, Indonesia, is a large ferruginous lake that likely hosts geochemical processes analogous to those that operated in the ferruginous Archean ocean. The metabolic potential of microbial communities and related biogeochemical cycling under such conditions remain largely unknown. We combined geochemical measurements (pore water chemistry, sulfate reduction rates) with metagenomics to link metabolic potential with geochemical processes in the upper 50 cm of sediment. Microbial diversity and quantities of genes for dissimilatory sulfate reduction (dsrAB) and methanogenesis (mcrA) decrease with increasing depth, as do rates of potential sulfate reduction. The presence of taxa affiliated with known iron- and sulfate-reducers implies potential use of ferric iron and sulfate as electron acceptors. Pore-water concentrations of acetate imply active production through fermentation. Fermentation likely provides substrates for respiration with iron and sulfate as electron donors and for methanogens that were detected throughout the core. The presence of ANME-1 16S and mcrA genes suggests potential for anaerobic methane oxidation. Overall our data suggest that microbial community metabolism in anoxic ferruginous sediments support coupled Fe, S and C biogeochemical cycling.

MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle

The increasing number of metagenomic and genomic sequences has dramatically improved our understanding of microbial diversity, yet our ability to infer metabolic capabilities in such datasets remains challenging. We describe the Multigenomic Entropy Based Score pipeline (MEBS), a software platform designed to evaluate, compare, and infer complex metabolic pathways in large “omic” datasets, including entire biogeochemical cycles. MEBS is open source and available through https://github.com/eead-csic-compbio/metagenome_Pfam_score. To demonstrate its use, we modeled the sulfur cycle by exhaustively curating the molecular and ecological elements involved (compounds, genes, metabolic pathways, and microbial taxa). This information was reduced to a collection of 112 characteristic Pfam protein domains and a list of complete-sequenced sulfur genomes. Using the mathematical framework of relative entropy (H^΄), we quantitatively measured the enrichment of these domains among sulfur genomes. The entropy of each domain was used both to build up a final score that indicates whether a (meta)genomic sample contains the metabolic machinery of interest and to propose marker domains in metagenomic sequences such as DsrC (PF04358). MEBS was benchmarked with a dataset of 2107 non-redundant microbial genomes from RefSeq and 935 metagenomes from MG-RAST. Its performance, reproducibility, and robustness were evaluated using several approaches, including random sampling, linear regression models, receiver operator characteristic plots, and the area under the curve metric (AUC). Our results support the broad applicability of this algorithm to accurately classify (AUC = 0.985) hard-to-culture genomes (e.g., Candidatus Desulforudis audaxviator), previously characterized ones, and metagenomic environments such as hydrothermal vents, or deep-sea sediment. Our benchmark indicates that an entropy-based score can capture the metabolic machinery of interest and can be used to efficiently classify large genomic and metagenomic datasets, including uncultivated/unexplored taxa.

Metagenomic Insights Into the Microbial Community and Nutrient Cycling in the Western Subarctic Pacific Ocean

The composition and metabolic functions of prokaryotic communities in the western subarctic Pacific (WSP), where strong mixing of waters from the Sea of Okhotsk and the East Kamchatka Current result in transfer to the Oyashio Current, were investigated using a shotgun metagenome sequencing approach. Functional metabolic genes related to nutrient cycling of nitrogen, sulfur, carbohydrates, iron and amino acids were differently distributed between the surface and deep waters of the WSP. Genes related to nitrogen metabolism were mainly found in deep waters, where Thaumarchaeaota, Sphingomonadales, and Pseudomonadales were closely associated and performing important roles in ammonia oxidation, assimilatory nitrate reduction, and dissimilatory nitrate reduction processes, respectively. In addition, orders affiliated to Spingobacteria and Alphaproteobacteria were crucial for sulfate reduction and abundant at 3000 m, whereas orders affiliated to Gammaproteobacteria, which harbored the most sulfate reduction genes, were abundant at 1000 m. Additionally, when compared with the East Kamchatka Current, the prokaryotes in the Oyashio Current were likely to consume more energy for synthesizing cellular components. Also, genes encoding iron transport and siderophore biosynthesis proteins were in low abundance, indicating that the iron was not a limiting factor in the Oyashio current. In contrast, in the East Kamchatka Current, prokaryotes were more likely to directly utilize the amino acids and absorb iron from the environment. Overall, our data indicated that the transformation from the East Kamchatka Current to the Oyashio Current reshapes not only the composition of microbial community, but also the function of the metabolic processes. These results extended our knowledge of the microbial composition and potential metabolism in the WSP.

Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea

Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) have been studied extensively in marine sediments because of their vital roles in both sulfur and carbon cycles, but the available information regarding the highly diverse SRB and SOB communities is not comprehensive. High-throughput sequencing of functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we explored the community structure, diversity, and abundance of SRB and SOB simultaneously through 16S rRNA, dsrB and soxB gene high-throughput sequencing and quantitative PCR analyses of core samples from the East China Sea. Overall, high-throughput sequencing of the dsrB and soxB genes achieved almost complete coverage (>99%) and revealed the high diversity, richness, and operational taxonomic unit (OTU) numbers of the SRB and SOB communities, which suggest the existence of an active sulfur cycle in the study area. Further analysis demonstrated that rare species make vital contributions to the high richness, diversity, and OTU numbers obtained. Depth-based distributions of the dsrB, soxB, and 16S rRNA gene abundances indicated that the SRB abundance might be more sensitive to the sedimentary dynamic environment than those of total bacteria and SOB. In addition, the results of unweighted pair group method with arithmetic mean (UPGMA) clustering analysis and redundancy analysis revealed that environmental parameters, such as depth and dissolved inorganic nitrogen concentrations, and the sedimentary dynamic environment, which differed between the two sampling stations, can significantly influence the community structures of total bacteria, SRB, and SOB. This study provided further comprehensive information regarding the characteristics of SRB and SOB communities.

Bacterial and archaeal communities inhabiting mussels, sediment and water in Indonesian anchialine lakes

Anchialine lakes are a globally rare and unique ecosystem consisting of saline lakes surrounded by land and isolated from the surrounding marine environment. These lakes host a unique flora and fauna including numerous endemic species. Relatively few studies have, however, studied the prokaryote communities present in these lakes and compared them with the surrounding 'open water' marine environment. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach to examine prokaryote (Bacteria and Archaea) composition in three distinct biotopes (sediment, water and the mussel Brachidontes sp.) inhabiting four habitats, namely, three marine lakes and the surrounding marine environment of Berau, Indonesia. Biotope and habitat proved significant predictors of variation in bacterial and archaeal composition and higher taxon abundance. Most bacterial sequences belonged to OTUs assigned to the Proteobacteria. Compared to sediment and water, mussels had relatively high abundances of the classes Mollicutes and Epsilonproteobacteria. Most archaeal sequences, in turn, belonged to OTUs assigned to the Crenarchaeota with the relative abundance of crenarchaeotes highest in mussel samples. For both Bacteria and Archaea, the main variation in composition was between water samples on the one hand and sediment and mussel samples on the other. Sediment and mussels also shared much more OTUs than either shared with water. Abundant bacterial OTUs in mussels were related to organisms previously obtained from corals, oysters and the deepsea mussel Bathymodiolus manusensis. Abundant archaeal OTUs in mussels, in contrast, were closely related to organisms previously obtained from sediment.

Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA

This study evaluates the transcriptionally active, dissimilatory sulfur- and arsenic-cycling components of the microbial community in alkaline, hypersaline Mono Lake, CA, USA. We sampled five depths spanning the redox gradient (10, 15, 18, 25 and 31 m) during maximum thermal stratification. We used custom databases to identify transcripts of genes encoding complex iron-sulfur molybdoenzyme (CISM) proteins, with a focus on arsenic (arrA, aioA and arxA) and sulfur cycling (dsrA, aprA and soxB), and assigned them to taxonomic bins. We also report on the distribution of transcripts related to the ars arsenic detoxification pathway. Transcripts from detoxification pathways were not abundant in oxic surface waters (10 m). Arsenic cycling in the suboxic and microaerophilic zones of the water column (15 and 18 m) was dominated by arsenite-oxidizing members of the Gammaproteobacteria most closely affiliated with Thioalkalivibrio and Halomonas, transcribing arxA. We observed a transition to arsenate-reducing bacteria belonging to the Deltaproteobacteria and Firmicutes transcribing arsenate reductase (arrA) in anoxic bottom waters of the lake (25 and 31 m). Sulfur cycling at 15 and 18 m was dominated by Gammaproteobacteria (Thioalkalivibrio and Thioalkalimicrobium) oxidizing reduced S species, with a transition to sulfate-reducing Deltaproteobacteria at 25 and 31 m. Genes related to arsenic and sulfur oxidation from Thioalkalivibrio were more highly transcribed at 15 m relative to other depths. Our data highlight the importance of Thioalkalivibrio to arsenic and sulfur biogeochemistry in Mono Lake and identify new taxa that appear capable of transforming arsenic.

The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle

During the last decades, our knowledge about the activity of sponge-associated microorganisms and their contribution to biogeochemical cycling has gradually increased. Functional groups involved in carbon and nitrogen metabolism are well documented, whereas knowledge about microorganisms involved in the sulfur cycle is still limited. Both sulfate reduction and sulfide oxidation has been detected in the cold water sponge Geodia barretti from Korsfjord in Norway, and with specimens from this site, the present study aims to identify extant versus active sponge-associated microbiota with focus on sulfur metabolism. Comparative analysis of small subunit ribosomal RNA (16S rRNA) gene (DNA) and transcript (complementary DNA (cDNA)) libraries revealed profound differences. The transcript library was predominated by Chloroflexi despite their low abundance in the gene library. An opposite result was found for Acidobacteria. Proteobacteria were detected in both libraries with representatives of the Alpha- and Gammaproteobacteria related to clades with presumably thiotrophic bacteria from sponges and other marine invertebrates. Sequences that clustered with sponge-associated Deltaproteobacteria were remotely related to cultivated sulfate-reducing bacteria. The microbes involved in sulfur cycling were identified by the functional gene aprA (adenosine-5'-phosphosulfate reductase) and its transcript. Of the aprA sequences (DNA and cDNA), 87 % affiliated with sulfur-oxidizing bacteria. They clustered with Alphaproteobacteria and with clades of deep-branching Gammaproteobacteria. The remaining sequences clustered with sulfate-reducing Archaea of the phylum Euryarchaeota. These results indicate an active role of yet uncharacterized Bacteria and Archaea in the sponge's sulfur cycle.

Microbial Character Related Sulfur Cycle under Dynamic Environmental Factors Based on the Microbial Population Analysis in Sewerage System

The undesired sulfur cycle derived by microbial population can ultimately causes the serious problems of sewerage systems. However, the microbial community characters under dynamic environment factors in actual sewerage system is still not enough. This current study aimed to character the distributions and compositions of microbial communities that participate in the sulfur cycle under the dynamic environmental conditions in a local sewerage system. To accomplish this, microbial community compositions were assessed using 454 high-throughput sequencing (16S rDNA) combined with dsrB gene-based denaturing gradient gel electrophoresis. The results indicated that a higher diversity of microbial species was present at locations in sewers with high concentrations of H₂S. Actinobacteria and Proteobacteria were dominant in the sewerage system, while Actinobacteria alone were dominant in regions with high concentrations of H₂S. Specifically, the unique operational taxonomic units could aid to characterize the distinct microbial communities within a sewerage manhole. The proportion of sulfate-reducing bacteria, each sulfur-oxidizing bacteria (SOB) were strongly correlated with the liquid parameters (DO, ORP, COD, Sulfide, NH₃-N), while the Mycobacterium and Acidophilic SOB (M&A) was strongly correlated with gaseous factors within the sewer, such as H₂S, CH₄, and CO. Identifying the distributions and proportions of critical microbial communities within sewerage systems could provide insights into how the microbial sulfur cycle is affected by the dynamic environmental conditions that exist in sewers and might be useful for explaining the potential sewerage problems.

Identity of major sulfur-cycle prokaryotes in freshwater lake ecosystems revealed by a comprehensive phylogenetic study of the dissimilatory adenylylsulfate reductase

Adenylylsulfate reductase is a heterodimeric complex of two subunits, AprB and AprA, and is a key enzyme in dissimilatory sulfate reduction and sulfur oxidation. Common use of aprA as a functional marker gene has revealed the diversity of sulfur-cycle prokaryotes in diverse environments. In this study, we established a comprehensive sequence set of apr genes and employed it to reanalyze apr phylogeny, evaluate the coverage of a widely used primer set (AprA-1-FW/AprA-5-RV), and categorize environmental aprA sequences. Phylogenetic tree construction revealed new members of Apr lineage II and several previously unrecognized lateral gene transfer events. Using the established phylogenetic tree, we classified all previously reported aprA sequences amplified from freshwater lakes with the primer pair AprA-1-FW/AprA-5-RV in addition to the aprA sequences newly retrieved from freshwater lakes; the obtained results were complemented by 16S rRNA clone library analysis. Apr-based classifications of some of operational taxonomic units were supported by 16S rRNA-based analysis. This study updates our knowledge on the phylogeny of aprBA and shows the identities of several sulfur-cycle bacteria, which could not be classified to a known taxa until now. The established apr sequence set is publicly available and can be applied to assign environmental sequences to known lineages.

Abundance and Diversity of Denitrifying and Anammox Bacteria in Seasonally Hypoxic and Sulfidic Sediments of the Saline Lake Grevelingen

Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox, and sulfide-dependent denitrifying bacteria in the sediments of the seasonally hypoxic saline Lake Grevelingen, known to harbor an active microbial community involved in sulfur oxidation pathways. Depth distributions of 16S rRNA gene, nirS gene of denitrifying and anammox bacteria, aprA gene of sulfur-oxidizing and sulfate-reducing bacteria, and ladderane lipids of anammox bacteria were studied in sediments impacted by seasonally hypoxic bottom waters. Samples were collected down to 5 cm depth (1 cm resolution) at three different locations before (March) and during summer hypoxia (August). The abundance of denitrifying bacteria did not vary despite of differences in oxygen and sulfide availability in the sediments, whereas anammox bacteria were more abundant in the summer hypoxia but in those sediments with lower sulfide concentrations. The potential activity of denitrifying and anammox bacteria as well as of sulfur-oxidizing, including sulfide-dependent denitrifiers and sulfate-reducing bacteria, was potentially inhibited by the competition for nitrate and nitrite with cable and/or Beggiatoa-like bacteria in March and by the accumulation of sulfide in the summer hypoxia. The simultaneous presence and activity of organoheterotrophic denitrifying bacteria, sulfide-dependent denitrifiers, and anammox bacteria suggests a tight network of bacteria coupling carbon-, nitrogen-, and sulfur cycling in Lake Grevelingen sediments.

New Dimensions in Microbial Ecology-Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment

During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5'phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane monooxygenase (pmoA) for methane oxidizing bacteria.

Rhizosphere Microbiomes of European + Seagrasses Are Selected by the Plant, But Are Not Species Specific

Seagrasses are marine flowering plants growing in soft-body sediments of intertidal and shallow sub-tidal zones. They play an important role in coastal ecosystems by stabilizing sediments, providing food and shelter for animals, and recycling nutrients. Like other plants, seagrasses live intimately with both beneficial and unfavorable microorganisms. Although much is known about the microbiomes of terrestrial plants, little is known about the microbiomes of seagrasses. Here we present the results of a detailed study on the rhizosphere microbiome of seagrass species across the North-eastern Atlantic Ocean: Zostera marina, Zostera noltii, and Cymodocea nodosa. High-resolution amplicon sequencing of 16S rRNA genes showed that the rhizobiomes were significantly different from the bacterial communities of surrounding bulk sediment and seawater. Although we found no significant differences between the rhizobiomes of different seagrass species within the same region, those of seagrasses in different geographical locations differed strongly. These results strongly suggest that the seagrass rhizobiomes are shaped by plant metabolism, but not coevolved with their host. The core rhizobiome of seagrasses includes mostly bacteria involved in the sulfur cycle, thereby highlighting the importance of sulfur-related processes in seagrass ecosystems.

Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments

Marine sediments are the largest carbon sink on earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70-86% of dark carbon fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with (14)C-bicarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark carbon fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and carbon fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine carbon and sulfur cycles.

Expanding the World of Marine Bacterial and Archaeal Clades

Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 “clades,” at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as our CTU approach breaks down these randomly lumped clades into smaller objectively calculated subgroups. Finally, all taxa were classified and named following standards compatible with the Bacteriological Code rules, enhancing their digitization, and comparability with future microbial ecological and taxonomy studies.

Sulfurifustis variabilis gen. nov., sp. nov., a sulfur oxidizer isolated from a lake, and proposal of Acidiferrobacteraceae fam. nov. and Acidiferrobacterales ord. nov

A novel autotrophic bacterium, strain skN76T, was isolated from sediment of a lake in Japan. As sole electron donor to support chemolithoautotrophic growth, the strain oxidized thiosulfate, tetrathionate and elemental sulfur. For growth, the optimum temperature was 42–45 °C and the optimum pH was 6.8–8.2. The cells were Gram-stain-negative, catalase-positive and oxidase-positive. The strain exhibited changes in morphology depending on growth temperature. Cells grown at the optimum temperature were rod-shaped (0.9–3.0 μm long and 0.3–0.5 μm wide), whereas a filamentous form was observed when the strain was cultured at the lowest permissive growth temperatures. The G+C content of genomic DNA was 69 mol%. The major components in the fatty acid profile were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the closest cultivated relative of strain skN76T was Acidiferrobacter thiooxydans m-1T, with sequence similarity of 93 %. On the basis of its phylogenetic and phenotypic properties, strain skN76T ( = DSM 100313T =  NBRC 110942T) is proposed as the type strain of a novel species of a novel genus, Sulfurifustis variabilis gen. nov., sp. nov. Novel taxa, Acidiferrobacteraceae fam. nov. and Acidiferrobacterales ord. nov., are also proposed to accommodate the genera Acidiferrobacter and Sulfurifustis gen. nov.

Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses

To characterize the activity and interactions of methanotrophic archaea (ANME) and Deltaproteobacteria at a methane-seeping mud volcano, we used two complimentary measures of microbial activity: a community-level analysis of the transcription of four genes (16S rRNA, methyl coenzyme M reductase A (mcrA), adenosine-5′-phosphosulfate reductase α-subunit (aprA), dinitrogenase reductase (nifH)), and a single-cell-level analysis of anabolic activity using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Transcript analysis revealed that members of the deltaproteobacterial groups Desulfosarcina/Desulfococcus (DSS) and Desulfobulbaceae (DSB) exhibit increased rRNA expression in incubations with methane, suggestive of ANME-coupled activity. Direct analysis of anabolic activity in DSS cells in consortia with ANME by FISH-NanoSIMS confirmed their dependence on methanotrophy, with no ¹⁵NH₄⁺ assimilation detected without methane. In contrast, DSS and DSB cells found physically independent of ANME (i.e., single cells) were anabolically active in incubations both with and without methane. These single cells therefore comprise an active ‘free-living' population, and are not dependent on methane or ANME activity. We investigated the possibility of N₂ fixation by seep Deltaproteobacteria and detected nifH transcripts closely related to those of cultured diazotrophic Deltaproteobacteria. However, nifH expression was methane-dependent. ¹⁵N₂ incorporation was not observed in single DSS cells, but was detected in single DSB cells. Interestingly, ¹⁵N₂ incorporation in single DSB cells was methane-dependent, raising the possibility that DSB cells acquired reduced ¹⁵N products from diazotrophic ANME while spatially coupled, and then subsequently dissociated. With this combined data set we address several outstanding questions in methane seep microbial ecosystems and highlight the benefit of measuring microbial activity in the context of spatial associations.

The "Oil-Spill Snorkel": an innovative bioelectrochemical approach to accelerate hydrocarbons biodegradation in marine sediments

This study presents the proof-of-concept of the “Oil-Spill Snorkel”: a novel bioelectrochemical approach to stimulate the oxidative biodegradation of petroleum hydrocarbons in sediments. The “Oil-Spill Snorkel” consists of a single conductive material (the snorkel) positioned suitably to create an electrochemical connection between the anoxic zone (the contaminated sediment) and the oxic zone (the overlying O₂-containing water). The segment of the electrode buried within the sediment plays a role of anode, accepting electrons deriving from the oxidation of contaminants. Electrons flow through the snorkel up to the part exposed to the aerobic environment (the cathode), where they reduce oxygen to form water. Here we report the results of lab-scale microcosms setup with marine sediments and spiked with crude oil. Microcosms containing one or three graphite snorkels and controls (snorkel-free and autoclaved) were monitored for over 400 days. Collectively, the results of this study confirmed that the snorkels accelerate oxidative reactions taking place within the sediment, as documented by a significant 1.7-fold increase (p = 0.023, two-tailed t-test) in the cumulative oxygen uptake and 1.4-fold increase (p = 0.040) in the cumulative CO₂ evolution in the microcosms containing three snorkels compared to snorkel-free controls. Accordingly, the initial rate of total petroleum hydrocarbons (TPH) degradation was also substantially enhanced. Indeed, while after 200 days of incubation a negligible degradation of TPH was noticed in snorkel-free controls, a significant reduction of 12 ± 1% (p = 0.004) and 21 ± 1% (p = 0.001) was observed in microcosms containing one and three snorkels, respectively. Although, the “Oil-Spill Snorkel” potentially represents a groundbreaking alternative to more expensive remediation options, further research efforts are needed to clarify factors and conditions affecting the snorkel-driven biodegradation processes and to identify suitable configurations for field applications.