Comprehensive profiles of sulfur cycling microbial communities along a mangrove sediment depth

The sulfur (S) cycle is an important biogeochemical cycle with profound implications for both cellular- and ecosystem-level processes by diverse microorganisms. Mangrove sediments are a hotspot of biogeochemical cycling, especially for the S cycle with high concentrations of S compounds. Previous studies have mainly focused on some specific inorganic S cycling processes without paying specific attention to the overall S-cycling communities and processes as well as organic S metabolism. In this study, we comprehensively analyzed the distribution, ecological network and assembly mechanisms of S cycling microbial communities and their changes with sediment depths using metagenome sequencing data. The results showed that the abundance of gene families involved in sulfur oxidation, assimilatory sulfate reduction, and dimethylsulfoniopropionate (DMSP) cleavage and demethylation decreased with sediment depths, while those involved in S reduction and dimethyl sulfide (DMS) transformation showed an opposite trend. Specifically, glpE, responsible for converting S2O32- to SO32-, showed the highest abundance in the surface sediment and decreased with sediment depths; in contrast, high abundances of dmsA, responsible for converting dimethyl sulfoxide (DMSO) to DMS, were identified and increased with sediment depths. We identified Pseudomonas and Streptomyces as the main S-cycling microorganisms, while Thermococcus could play an import role in microbial network connections in the S-cycling microbial community. Our statistical analysis showed that both taxonomical and functional compositions were generally shaped by stochastic processes, while the functional composition of organic S metabolism showed a transition from stochastic to deterministic processes. This study provides a novel perspective of diversity distribution of S-cycling functions and taxa as well as their potential assembly mechanisms, which has important implications for maintaining mangrove ecosystem functions.

A global metagenomics-based analysis of BPA degradation and its coupling with nitrogen, sulfur, and methane metabolism in landfill leachates

Microbial metabolism in landfill leachate systems is critically important in driving the degradation reactions of organic pollutants, including the emerging pollutant bisphenol A (BPA). However, little research has addressed the microbial degradation of BPA in landfill leachate and its interactions with nitrogen (N), sulfur (S), and methane (CH4) metabolism on a global scale. To this end, in this study on a global scale, an extremely high concentration of BPA was detected throughout the global landfill leachates. Subsequent reconstructive analyses of metagenomic datasets from 113 sites worldwide revealed that the predominant BPA-degrading microflora included Proteobacteria, Firmicutes, and Bacteroidota. Further metabolic analyses revealed that all four biochemical pathways involved in the degradation of BPA were achieved through biochemical cooperation between different bacterial members of the community. In addition, BPA degraders have also been found to actively collaborate synergistically with non-BPA degraders in the N and S removal as well as CH4 catabolism in landfill leachates. Collectively, this study not only provides insights into the dominant microbial communities and specific types of BPA-degrading microbial members in the community of landfill leachates worldwide, but also reveals the synergistic interactions between BPA mineralization and N, S, and CH4 metabolism. These findings offer valuable and important insights for future comprehensive and in-depth investigations into BPA metabolism in different environments.

A comprehensive catalog encompassing 1376 species-level genomes reveals the core community and functional diversity of anammox microbiota

Research on the microbial community and function of the anammox process for environmentally friendly wastewater treatment has achieved certain success, which may mean more universal insights are needed. However, the comprehensive understanding of the anammox process is constrained by the limited taxonomic assignment and functional characterization of anammox microbiota, primarily due to the scarcity of high-quality genomes for most organisms. This study reported a global genome catalog of anammox microbiotas based on numerous metagenomes obtained from both lab- and full-scale systems. A total of 1376 candidate species from 7474 metagenome-assembled genomes were used to construct the genome catalog, providing extensive microbial coverage (averaged of 92.40 %) of anammox microbiota. Moreover, a total of 64 core genera and 44 core species were identified, accounting for approximately 64.25 % and 43.97 %, respectively, of anammox microbiota. The strict core genera encompassed not only functional bacteria (e.g., Brocadia, Desulfobacillus, Zeimonas, and Nitrosomonas) but also two candidate genera (UBA12294 and OLB14) affiliated with the order Anaerolineales. In particular, core denitrifying bacteria with observably taxonomic diversity exhibited diverse functional profiles; for instance, the potential of carbohydrate metabolism in Desulfobacillus and Zeimonas likely improves the mixotrophic lifestyle of anammox microbiota. Besides, a noteworthy association was detected between anammox microbiota and system type. Microbiota in coupling system exhibited complex diversity and interspecies interactions by limiting numerous core denitrifying bacteria. In summary, the constructed catalog substantially expands our understanding of the core community and their functions of anammox microbiota, providing a valuable resource for future studies on anammox systems.

Priestia aryabhattai MBM3-Mediated Enhancement of Sulphur Metabolism in Brassica campestris

Sulphur, an essential element for plant growth, is vital for synthesizing various crucial components such as amino acids and enzymes. Its limited availability in acidic soil inhibits crop development and yield. Our research identified low pH tolerance sulphur-metabolizing bacterial isolate Priestia aryabhattai MBM3, with plant growth-promoting traits. Key sulphur-metabolizing genes viz., cysK, cysE, luxS, and a hypothetical gene, BG04-4883 were increasingly upregulated during the lag phase in acidic environments, indicating to the isolates ability to accumulate sulphur through increased activity of these essential genes. Microcosm experiment revealed bioprimed Brassica campestris L seeds with Priestia aryabhattai MBM3 had improved performance in acidic conditions, as demonstrated by agronomic and physiological, and no metabolic demand for sulphur, unlike control untreated plants which showed requirement for sulphur with significant expression of sulfate transporters, as revealed by molecular studies.

Deciphering the functional assembly of microbial communities driven by heavy metals in the tidal soils of Hangzhou Bay

Understanding the interaction between heavy metals and soil microbiomes is essential for maintaining ecosystem health and functionality in the face of persistent human-induced challenges. This study investigated the complex relationships between heavy metal contamination and the functional characteristics of soil microbial communities in the tidal soils of Hangzhou Bay, a region experiencing substantial environmental pressure due to its proximity to densely populated and industrialized regions. The north-shore sampling site showed moderate contaminations (mg/kg) of total arsenic (16.61 ± 1.13), cadmium (0.3 ± 0.05), copper (31.28 ± 1.23), nickel (37.44 ± 2.74), lead (34.29 ± 5.99), and zinc (120.8 ± 5.96), which are 1.29-2.94 times higher than the geochemical background values in Hangzhou Bay and adjacent areas. In contrast, the south-shore sampling site showed slightly higher levels of total arsenic (13.76 ± 1.35) and cadmium (0.13 ± 0.02) than the background values. Utilizing metagenomic sequencing, we decoded microbial functional genes essential for nitrogen, phosphorus, sulfur, and methane biogeochemical cycles. Although soil available nickel content was relatively low at 1 mg/kg, it exhibited strong associations with diverse microbial genes and biogeochemical pathways. Four key genes-hxlB, glpX, opd, and phny-emerged as pivotal players in the interactions with available nickel, suggesting the adaptability of microbial metabolic responses to heavy metal. Additionally, microbial genera such as Gemmatimonas and Ilumatobacter, which harbored diverse functional genes, demonstrated potential interactions with soil nickel. These findings highlight the importance of understanding heavy metal-soil microbiome dynamics for effective environmental management strategies in the tidal soils of Hangzhou Bay, with the goal of preserving ecosystem health and functionality amidst ongoing anthropogenic challenges.

Thallium spill shifts the structural and functional characteristics of viral communities with different lifestyles in river sediments

Thallium (Tl), a highly toxic heavy metal, can affect microbial community, while little is known about its effect on viral community. The present study investigated the variation of viral communities, as well as their interactions with microbial hosts under Tl stress. Tl in sediments significantly altered the composition and diversity of the viral communities, but showed no significant links with the prokaryotic communities, which may reveal a potential discrepancy in the sensitivity of the viral and prokaryotic communities to heavy metal stress. Auxiliary metabolic genes (AMGs) involved in denitrification, methane oxidation and organic sulfur transformation were enriched at T1-contaminated sites, while the abundance of AMGs related to methanogenesis and sulfate reduction were higher at pristine sites. Specially, the enrichment of AMGs involved in assimilatory sulfate reduction in Tl-contaminated sites could possibly reduce Tl bioavailability by enhancing the microbially-driven sulfur cycling to generate sulfides that could be complexed with Tl. Moreover, there was a significantly positive correlation between virus-carrying metal resistant genes and the sedimentary Tl concentration, implying that Tl contamination might enhance the metal resistant potential of the viruses. Serving as the functional gene reservoir, the response of viral AMGs to Tl stress could represent a potential pathway for microorganisms to be adapted to the metal-polluted environments. Our study provided novel insights into the impact of Tl spill on viral communities, shedding light on functional characteristics and the links of virus-host interaction with Tl level.

Mesobacterium hydrothermale sp. nov., isolated from shallow-sea hydrothermal systems off Kueishantao Island

A Gram-negative, rod-shaped, non-motile, aerobic bacterium, designated as strain TK19101T, was isolated from the intermediate seawater of yellow vent in the shallow-sea hydrothermal system located near Kueishantao Island. The strain was found to grow at 10-40 °C (optimum, 35 °C), at pH 6.0-8.0 (optimum, 7.0), and in 0-5% (w/v) NaCl (optimum, 1%). Strain TK19101T was catalase-positive and oxidase-positive. The predominant fatty acids (> 10%) in strain TK19101T cells were C16:0, summed feature 8 (C18:1 ω6c and/or C18:1 ω7c), and C18:0. The predominant isoprenoid quinone of strain TK19101T was ubiquinone-10. The polar lipids of strain TK19101T comprised phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phospholipid, and unknown polar lipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TK19101T belonged to the genus Mesobacterium. Strain TK19101T exhibited highest 16S rRNA gene sequence similarity value to Mesobacterium pallidum MCCC M24557T (97.48%). The estimated average nucleotide identity and digital DNA-DNA hybridization values between strain TK19101T and the closest related species Mesobacterium pallidum MCCC M24557T were 74.88% and 20.30%, respectively. The DNA G + C content was 63.49 mol%. On the basis of the analysis of 16S rRNA gene sequences, genotypic and phylogenetic data, strain TK19101T has a unique phylogenetic status and represents a novel species of genus Mesobacterium, for which the name Mesobacterium hydrothermale sp. nov. is proposed. The type strain is TK19101T (= MCCC 1K08936T = KCTC 8354T).

Habitat- and lifestyle-dependent structural and functional characteristics of viruses in mangrove wetlands of different functional zonings

Mangrove wetlands, as one of the natural ecosystems with the most ecological services, have garnered widespread attention about their microbial driven biogeochemical cycling. Urbanization have led to different spatial patterns of environmental conditions and microbial communities in mangroves. However, viruses, as the pivotal drivers of biogeochemical cycling in mangroves, remain inadequately explored in terms of how their ecological potential and complex interactions with host respond to functional zonings. To address this knowledge gap, we conducted a comprehensive investigation on the structural and functional properties of temperate and lytic viruses in mangrove wetlands from different functional zonings by jointly using high-throughput sequencing, prokaryotic and viral metagenomics. Multiple environmental factors were found to significantly influence the taxonomic and functional composition, as well as lysogen-lysis decision-making of mangrove viruses. Furthermore, enriched auxiliary metabolic genes (AMGs) involved in methane, nitrogen and sulfur metabolism, and heavy metal resistance were unveiled in mangrove viruses, whose community composition was closely related to lifestyle and host. The virus-host pairs with different lifestyles were also discovered to react to environmental changes in different ways, which provided an empirical evidence for how virus and bacteria dynamics were specific to viral lifestyles in nature. This study expands our comprehension of the intricate interactions among virus, prokaryotic host and the environment in mangrove wetlands from multiple perspectives, including viral lifestyles, virus-host interactions, and habitat dependence. Importantly, it provides a new ecological perspective on how mangrove viruses are adapted to the stress posed by urbanization.

Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland

The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.

How redox gradient potentially influences nitrate reduction coupled with sulfur cycling: A new insight into nitrogen cycling in the hyporheic zone of effluent-dominated rivers

The coupled N and S cycling in variable redox gradients in the hyporheic zone (HZ) of the rivers receiving effluents from wastewater treatment plants is unclear. Using two representative effluent-dominated rivers as model systems, a metagenome approach was employed to explore the spatiotemporal redox zonation of the HZ and the N/S cycling processes within the system. The results manifested that nitrate reduction represented the fundamental nitrogen pathway in the HZ. Interestingly, DNRA coupled with sulfur reduction, and denitrification coupled with sulfur oxidation were respectively abundant in the oxic and anoxic zone. Lower nitrate concentration (0-2.72 mg-N/L) and more abundant genes involved in denitrification (napB, NarGHI) and sulfur oxidation (sseA, glpE) were detected in the anoxic zone. Contrarily, the nitrate concentration (0.07-4.87 mg-N/L) and the abundance of genes involved in sulfur reduction (ttrB, sudA) and DNRA (nirBD) were observed more abundant in the oxic zone. Therefore, the results verified the oxygen-limited condition did not suppress but rather facilitated the denitrification process in the presence of active S cycling. The high relative abundances of nosZ gene encoding sequence (3-5 % relative to all nitrogen-cycling processes) in both the effluent-discharging area and downstream area highly confirmed that HZ was capable of alleviating the N2O emission in the region. The functional keystone taxa were revealed through co-occurrence network analysis. The structural equation model shows that the genes of N/S cycling were positively impacted by functional keystone taxa, especially the N cycling genes. Functional keystone taxa were proven driven by the redox gradient, demonstrating their positive roles in mediating N/S cycling processes. The promoting effect on nitrate reduction coupled with sulfur cycling was clarified when redox conditions oscillated, providing a new perspective on mitigating nitrogen pollution and greenhouse gas emissions in effluent-receiving rivers.

Farmland Microhabitat Mediated by a Residual Microplastic Film: Microbial Communities and Function

How the plastisphere mediated by the residual microplastic film in farmlands affects microhabitat systems is unclear. Here, microbial structure, assembly, and biogeochemical cycling in the plastisphere and soil in 33 typical farmland sites were analyzed by amplicon sequencing of 16S rRNA genes and ITS and metagenome analysis. The results indicated that residual microplastic film was colonized by microbes, forming a unique niche called the plastisphere. Notable differences in the microbial community structure and function were observed between soil and plastisphere. Residual microplastic film altered the microbial symbiosis and assembly processes. Stochastic processes significantly dominated the assembly of the bacterial community in the plastisphere and soil but only in the plastisphere for the fungal community. Deterministic processes significantly dominated the assembly of fungal communities only in soil. Moreover, the plastisphere mediated by the residual microplastic film acted as a preferred vector for pathogens and microorganisms associated with plastic degradation and the nitrogen and sulfur cycle. The abundance of genes associated with denitrification and sulfate reduction activity in the plastisphere was pronouncedly higher than that of soil, which increase the potential risk of nitrogen and sulfur loss. The results will offer a scientific understanding of the harm caused by the residual microplastic film in farmlands.

Metatranscriptomic insights into the microbial metabolic activities during an Ulva prolifera green tide in coastal Qingdao areas

Green tide, a typical marine environmental disaster that profoundly influenced the coastal areas, has been occurred consecutively in the South Yellow Sea of China since 2007. Herein, the active microbial community structure and metabolic pathways in Qingdao offshore during an Ulva prolifera green tide were investigated by using metatranscriptomic approach. The dominant active microbial taxa at the outbreak phase were primarily a functional group that can utilize organic matters derived from U. prolifera, such as Lentibacter, Polaribacter and Planktomarina. While the taxa involved in biogeochemical cycles, including Phaeobacter, Pseudomonas and Marinobacterium, dominated the active microbial communities at the decline phase. The expression level of enzymes involved in U. prolifera polysaccharides degradation was significantly higher at the outbreak phase compared to the decline phase. At the same time, the main players Glaciecola and Polarbacter showed similar trends, suggesting that the low competitiveness for nutrients of related microorganisms at this phase made them degrade more U. prolifera polysaccharides to meet their own nutrient needs, thereby accelerating the degradation of U. prolifera. According to KEGG annotation, the biogeochemical pathways including nitrogen cycle, sulfur cycle and methane oxidation altered during the green tide, with thiosulfate oxidation and methane oxidation probably being the crucial pathways at the outbreak and the decline phase respectively. The coupling of sulfide oxidation and denitrification was also observed in this study. Furthermore, the green tide in Qingdao offshore might impact the greenhouse effects induced by CH4 and N2O through influencing the related microbial processes.

Exploring virus-host-environment interactions in a chemotrophic-based underground estuary

BACKGROUND

Viruses play important roles in modulating microbial communities and influencing global biogeochemistry. There is now growing interest in characterising their ecological roles across diverse biomes. However, little is known about viral ecology in low-nutrient, chemotrophic-based environments. In such ecosystems, virus-driven manipulation of nutrient cycles might have profound impacts across trophic levels. In particular, anchialine environments, which are low-energy underground estuaries sustained by chemotrophic processes, represent ideal model systems to study novel virus-host-environment interactions.

RESULTS

Here, we employ metagenomic sequencing to investigate the viral community in Bundera Sinkhole, an anchialine ecosystem rich in endemic species supported by microbial chemosynthesis. We find that the viruses are highly novel, with less than 2% representing described viruses, and are hugely abundant, making up as much as 12% of microbial intracellular DNA. These highly abundant viruses largely infect important prokaryotic taxa that drive key metabolic processes in the sinkhole. Further, the abundance of viral auxiliary metabolic genes (AMGs) involved in nucleotide and protein synthesis was strongly correlated with declines in environmental phosphate and sulphate concentrations. These AMGs encoded key enzymes needed to produce sulphur-containing amino acids, and phosphorus metabolic enzymes involved in purine and pyrimidine nucleotide synthesis. We hypothesise that this correlation is either due to selection of these AMGs under low phosphate and sulphate concentrations, highlighting the dynamic interactions between viruses, their hosts, and the environment; or, that these AMGs are driving increased viral nucleotide and protein synthesis via manipulation of host phosphorus and sulphur metabolism, consequently driving nutrient depletion in the surrounding water.

CONCLUSION

This study represents the first metagenomic investigation of viruses in anchialine ecosystems, and provides new hypotheses and insights into virus-host-environment interactions in such 'dark', low-energy environments. This is particularly important since anchialine ecosystems are characterised by diverse endemic species, both in their microbial and faunal assemblages, which are primarily supported by microbial chemosynthesis. Thus, virus-host-environment interactions could have profound effects cascading through all trophic levels.

Light Intensity Modulates the Functional Composition of Leaf Metabolite Groups and Phyllosphere Prokaryotic Community in Garden Lettuce (Lactuca sativa L.) Plants at the Vegetative Stage

Light intensity primarily drives plant growth and morphogenesis, whereas the ecological impact of light intensity on the phyllosphere (leaf surface and endosphere) microbiome is poorly understood. In this study, garden lettuce (Lactuca sativa L.) plants were grown under low, medium, and high light intensities. High light intensity remarkably induced the leaf contents of soluble proteins and chlorophylls, whereas it reduced the contents of leaf nitrate. In comparison, medium light intensity exhibited the highest contents of soluble sugar, cellulose, and free amino acids. Meanwhile, light intensity resulted in significant changes in the composition of functional genes but not in the taxonomic compositions of the prokaryotic community (bacteria and archaea) in the phyllosphere. Notably, garden lettuce plants under high light intensity treatment harbored more sulfur-cycling mdh and carbon-cycling glyA genes than under low light intensity, both of which were among the 20 most abundant prokaryotic genes in the leaf phyllosphere. Furthermore, the correlations between prokaryotic functional genes and lettuce leaf metabolite groups were examined to disclose their interactions under varying light intensities. The relative abundance of the mdh gene was positively correlated with leaf total chlorophyll content but negatively correlated with leaf nitrate content. In comparison, the relative abundance of the glyA gene was positively correlated with leaf total chlorophyll and carotenoids. Overall, this study revealed that the functional composition of the phyllosphere prokaryotic community and leaf metabolite groups were tightly linked in response to changing light intensities. These findings provided novel insights into the interactions between plants and prokaryotic microbes in indoor farming systems, which will help optimize environmental management in indoor farms and harness beneficial plant-microbe relationships for crop production.

Global biogeography and ecological implications of cobamide-producing prokaryotes

Cobamides, a class of essential coenzymes synthesized only by a subset of prokaryotes, are model nutrients in microbial interaction studies and play significant roles in global ecosystems. Yet, their spatial patterns and functional roles remain poorly understood. Herein, we present an in-depth examination of cobamide-producing microorganisms, drawn from a comprehensive analysis of 2862 marine and 2979 soil metagenomic samples. A total of 1934 nonredundant metagenome-assembled genomes (MAGs) potentially capable of producing cobamides de novo were identified. The cobamide-producing MAGs are taxonomically diverse but habitat specific. They constituted only a fraction of all the recovered MAGs, with the majority of MAGs being potential cobamide users. By mapping the distribution of cobamide producers in marine and soil environments, distinct latitudinal gradients were observed: the marine environment showed peak abundance at the equator, whereas soil environments peaked at mid-latitudes. Importantly, significant and positive links between the abundance of cobamide producers and the diversity and functions of microbial communities were observed, as well as their promotional roles in essential biogeochemical cycles. These associations were more pronounced in marine samples than in soil samples, which suggests a heightened propensity for microorganisms to engage in cobamide sharing in fluid environments relative to the more spatially restricted soil environment. These findings shed light on the global patterns and potential ecological roles of cobamide-producing microorganisms in marine and soil ecosystems, enhancing our understanding of large-scale microbial interactions.

Soil redox status governs within-field spatial variation in microbial arsenic methylation and rice straighthead disease

Microbial arsenic (As) methylation in paddy soil produces mainly dimethylarsenate (DMA), which can cause physiological straighthead disease in rice. The disease is often highly patchy in the field, but the reasons remain unknown. We investigated within-field spatial variations in straighthead disease severity, As species in rice husks and in soil porewater, microbial composition and abundance of arsM gene encoding arsenite S-adenosylmethionine methyltransferase in two paddy fields. The spatial pattern of disease severity matched those of soil redox potential, arsM gene abundance, porewater DMA concentration, and husk DMA concentration in both fields. Structural equation modelling identified soil redox potential as the key factor affecting arsM gene abundance, consequently impacting porewater DMA and husk DMA concentrations. Core amplicon variants that correlated positively with husk DMA concentration belonged mainly to the phyla of Chloroflexi, Bacillota, Acidobacteriota, Actinobacteriota, and Myxococcota. Meta-omics analyses of soil samples from the disease and non-disease patches identified 5129 arsM gene sequences, with 71% being transcribed. The arsM-carrying hosts were diverse and dominated by anaerobic bacteria. Between 96 and 115 arsM sequences were significantly more expressed in the soil samples from the disease than from the non-disease patch, which were distributed across 18 phyla, especially Acidobacteriota, Bacteroidota, Verrucomicrobiota, Chloroflexota, Pseudomonadota, and Actinomycetota. This study demonstrates that even a small variation in soil redox potential within the anoxic range can cause a large variation in the abundance of As-methylating microorganisms, thus resulting in within-field variation in rice straighthead disease. Raising soil redox potential could be an effective way to prevent straighthead disease.

Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics

BACKGROUND

Leakages of cold, methane-rich fluids from subsurface reservoirs to the sea floor are termed cold seeps. Recent exploration of the deep sea has shed new light on the microbial communities in cold seeps. However, conventional metagenomic methods largely rely on reference databases and neglect the phylogeny of functional genes.

RESULTS

In this study, we developed the REMIRGE program to retrieve the full-length functional genes from shotgun metagenomic reads and fully explored the phylogenetic diversity in cold seep sediments. The abundance and diversity of functional genes involved in the methane, sulfur, and nitrogen cycles differed in the non-seep site and five cold seep sites. In one Haima cold seep site, the divergence of functional groups was observed at the centimeter scale of sediment depths, with the surface layer potentially acting as a reservoir of microbial species and functions. Additionally, positive correlations were found between specific gene sequence clusters of relevant genes, indicating coupling occurred within specific functional groups.

CONCLUSION

REMIRGE revealed divergent phylogenetic diversity of functional groups and functional pathway preferences in a deep-sea cold seep at finer scales, which could not be detected by conventional methods. Our work highlights that phylogenetic information is conducive to more comprehensive functional profiles, and REMIRGE has the potential to uncover more new insights from shotgun metagenomic data. Video Abstract.

Phylogenetic and ecophysiological novelty of subsurface mercury methylators in mangrove sediments

Mangrove sediment is a crucial component in the global mercury (Hg) cycling and acts as a hotspot for methylmercury (MeHg) production. Early evidence has documented the ubiquity of well-studied Hg methylators in mangrove superficial sediments; however, their diversity and metabolic adaptation in the more anoxic and highly reduced subsurface sediments are lacking. Through MeHg biogeochemical assay and metagenomic sequencing, we found that mangrove subsurface sediments (20-100 cm) showed a less hgcA gene abundance but higher diversity of Hg methylators than superficial sediments (0-20 cm). Regional-scale investigation of mangrove subsurface sediments spanning over 1500 km demonstrated a prevalence and family-level novelty of Hg-methylating microbial lineages (i.e., those affiliated to Anaerolineae, Phycisphaerae, and Desulfobacterales). We proposed the candidate phylum Zixibacteria lineage with sulfate-reducing capacity as a currently understudied Hg methylator across anoxic environments. Unlike other Hg methylators, the Zixibacteria lineage does not use the Wood-Ljungdahl pathway but has unique capabilities of performing methionine synthesis to donate methyl groups. The absence of cobalamin biosynthesis pathway suggests that this Hg-methylating lineage may depend on its syntrophic partners (i.e., Syntrophobacterales members) for energy in subsurface sediments. Our results expand the diversity of subsurface Hg methylators and uncover their unique ecophysiological adaptations in mangrove sediments.

Nitrogen fixation and diazotroph diversity in groundwater systems

Biological nitrogen fixation (BNF), the conversion of N2 into bioavailable nitrogen (N), is the main process for replenishing N loss in the biosphere. However, BNF in groundwater systems remains poorly understood. In this study, we examined the activity, abundance, and community composition of diazotrophs in groundwater in the Hetao Plain of Inner Mongolia using 15N tracing methods, reverse transcription qPCR (RT-qPCR), and metagenomic/metatranscriptomic analyses. 15N2 tracing incubation of near in situ groundwater (9.5-585.4 nmol N L-1 h-1) and N2-fixer enrichment and isolates (13.2-1728.4 nmol N g-1 h-1, as directly verified by single-cell resonance Raman spectroscopy), suggested that BNF is a non-negligible source of N in groundwater in this region. The expression of nifH genes ranged from 3.4 × 103 to 1.2 × 106 copies L-1 and was tightly correlated with dissolved oxygen (DO), Fe(II), and NH4+. Diazotrophs in groundwater were chiefly aerobes or facultative anaerobes, dominated by Stutzerimonas, Pseudomonas, Paraburkholderia, Klebsiella, Rhodopseudomonas, Azoarcus, and additional uncultured populations. Active diazotrophs, which prefer reducing conditions, were more metabolically diverse and potentially associated with nitrification, sulfur/arsenic mobilization, Fe(II) transport, and CH4 oxidation. Our results highlight the importance of diazotrophs in subsurface geochemical cycles.

Global diversity and biogeography of DNA viral communities in activated sludge systems

BACKGROUND

Activated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses that regulate microbial metabolism and nutrient cycling, significantly influencing the stability of AS systems. However, our knowledge about the diversity of viral taxonomic groups and functional traits in global AS systems is still limited. To address this gap, we investigated the global diversity and biogeography of DNA viral communities in AS systems using 85,114 viral operational taxonomic units (vOTUs) recovered from 144 AS samples collected across 54 WWTPs from 13 different countries.

RESULTS

AS viral communities and their functional traits exhibited distance-decay relationship (DDR) at the global scale and latitudinal diversity gradient (LDG) from equator to mid-latitude. Furthermore, it was observed that AS viral community and functional gene structures were largely driven by the geographic factors and wastewater types, of which the geographic factors were more important. Carrying and disseminating auxiliary metabolic genes (AMGs) associated with the degradation of polysaccharides, sulfate reduction, denitrification, and organic phosphoester hydrolysis, as well as the lysis of crucial functional microbes that govern biogeochemical cycles were two major ways by which viruses could regulate AS functions. It was worth noting that our study revealed a high abundance of antibiotic resistance genes (ARGs) in viral genomes, suggesting that viruses were key reservoirs of ARGs in AS systems.

CONCLUSIONS

Our results demonstrated the highly diverse taxonomic groups and functional traits of viruses in AS systems. Viral lysis of host microbes and virus-mediated HGT can regulate the biogeochemical and nutrient cycles, thus affecting the performance of AS systems. These findings provide important insights into the viral diversity, function, and ecology in AS systems on a global scale. Video Abstract.

Micro-pressure promotes endogenous phosphorus release in a deep reservoir by favouring microbial phosphate mineralisation and solubilisation coupled with sulphate reduction

Deep reservoirs vary in their hydrostatic pressure owing to artificial water level control. The potential migration of phosphorus (P) in reservoir sediments raises the risk of harmful algal blooms. To ascertain the mechanisms of endogenous P release in reservoirs, we characterised aquatic microbial communities associated with coupled iron (Fe), P and sulphur (S) cycling at the sediment-water interface. The responses of microbial communities to hydrostatic pressures of 0.2-0.7 mega pascals (MPa; that is, micro-pressures) were investigated through a 30-day simulation experiment. Our findings unravelled a potential mechanism that micro-pressure enhanced the solubilisation of Fe/aluminium (Al)-bound P caused by microbially-driven sulphate reduction, leading to endogenous P release in the deep reservoir. Although the vertical distribution of labile Fe was not affected by pressure changes, we did observe Fe resupply at sediment depths of 2-5 cm. Metagenomic analysis revealed increased abundances of functional genes for P mineralisation (phoD, phoA), P solubilisation (pqqC, ppx-gppA) and sulphate reduction (cysD, cysC) in sediments subjected to micro-pressure, which contrasted with the pattern of S oxidation gene (soxB). There was a tight connection between P and S cycling-related microbial communities, based on significant positive correlations between labile element (P and S) concentrations and functional gene (phoD, cysD) abundances. This provided strong support that Fe-P-S coupling processes were governed by micro-pressure through modulation of P and S cycling-related microbial functions. Key taxa involved in P and S cycling (for example, Bradyrhizobium, Methyloceanibacter) positively responded to micro-pressure and as such, indirectly drove P release from sediments by facilitating P mineralisation and solubilisation coupled with sulphate reduction.

Soil depth exerts a stronger impact on microbial communities and the sulfur biological cycle than salinity in salinized soils

The distribution of microbial communities along salinity gradients in the surface layer of salinized soils has been widely studied. However, it is unknown whether microbial communities exhibit similar distribution patterns in surface and deep soils. Additionally, the relationship between soil depth, salinity, and sulfur metabolism remains unclear. Herein, bulk soils in the surface (S, 5-10 cm) and deep (D, 20-25 cm) layers from high- and low-salinity soils were analyzed using metagenomic and physicochemical analyses. Soil depth was significantly correlated to the concentration of sulfur compounds in the soil and exerted a stronger effect than salinity. Non-metric multidimensional scaling analysis revealed significant differences in microbial community structure with varying soil depths and salinities. However, soil depth clearly influenced microbial community abundance, homogeneity, and diversity, while salinity had a limited effect on microbial abundance. Archaea and bacteria were enriched in the surface and deep soils, respectively. Gene abundance analysis revealed significant differences in the abundance of sulfur-related genes at different soil depths. The abundance of sulfur oxidation genes was lower in deep soil than in surface soil, whereas the abundance of other sulfur-related genes showed the opposite trend. Redundancy analysis (RDA) showed that environmental factors and sulfur compounds have a significant impact on sulfur metabolism genes, with sulfide significantly affecting low-salinity soils in the surface and deep layers, whereas salinity and sulfane sulfur had a greater correlation with high-salinity soils. Correlation analysis further showed that Euryarchaeota clustered with Bacteroidetes and Balneolaeota, while Proteobacteria clustered with many phyla, such as Acidobacteria. Various sulfur metabolism genes were widely distributed in both clusters. Our results indicate that microorganisms actively participate in the sulfur cycle in saline soils and that soil depth can affect these processes and the structure of microbial communities to a greater extent than soil salinity.

Environmental selection and evolutionary process jointly shape genomic and functional profiles of mangrove rhizosphere microbiomes

Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning. However, how such activities affect microbially driven methane (CH4), nitrogen (N), and sulfur (S) cycling of rhizosphere microbiomes remains unclear. To understand the effect of environmental selection and the evolutionary process on microbially driven biogeochemical cycles in native and introduced mangrove rhizospheres, we analyzed key genomic and functional profiles of rhizosphere microbiomes from native and introduced mangrove species by metagenome sequencing technologies. Compared with the native mangrove (Kandelia obovata, KO), the introduced mangrove (Sonneratia apetala, SA) rhizosphere microbiome had significantly (p < 0.05) higher average genome size (AGS) (5.8 vs. 5.5 Mb), average 16S ribosomal RNA gene copy number (3.5 vs. 3.1), relative abundances of mobile genetic elements, and functional diversity in terms of the Shannon index (7.88 vs. 7.84) but lower functional potentials involved in CH4 cycling (e.g., mcrABCDG and pmoABC), N2 fixation (nifHDK), and inorganic S cycling (dsrAB, dsrC, dsrMKJOP, soxB, sqr, and fccAB). Similar results were also observed from the recovered Proteobacterial metagenome-assembled genomes with a higher AGS and distinct functions in the introduced mangrove rhizosphere. Additionally, salinity and ammonium were identified as the main environmental drivers of functional profiles of mangrove rhizosphere microbiomes through deterministic processes. This study advances our understanding of microbially mediated biogeochemical cycling of CH4, N, and S in the mangrove rhizosphere and provides novel insights into the influence of environmental selection and evolutionary processes on ecosystem functions, which has important implications for future mangrove reforestation.

Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole

The Sansha Yongle Blue Hole (SYBH), the deepest blue hole in the world, is an excellent habitat for revealing biogeochemical cycles in the anaerobic environment. However, how sulfur cycling is mediated by microorganisms in the SYBH hasn't been fully understood. In this study, the water layers of the SYBH were divided into oxic zone, hypoxic zone, anoxic zone I and II, and microbial-mediated sulfur cycling in the SYBH was comprehensively interpreted. The 16S rRNA genes/transcripts analyses showed that the microbial community structures associated with the sulfur cycling in each zone had distinctive features. Sulfur-oxidizing bacteria were mostly constituted by Gammaproteobacteria, Alphaproteobacteria, Campylobacterota, and Chlorobia above the anoxic zone I and sulfate-reducing bacteria were dominated by Desulfobacterota in anoxic zones. Metagenomic analyses showed that the sulfide-oxidation-related gene sqr and genes encoding the Sox system were mainly distributed in the anoxic zone I, while genes related to dissimilatory sulfate reduction and sulfur intermediate metabolite reduction were mainly distributed in the anoxic zone II, indicating different sulfur metabolic processes between these two zones. Moreover, sulfur-metabolism-related genes were identified in 81 metagenome-assembled genomes (MAGs), indicating a high diversity of microbial communities involved in sulfur cycling. Among them, three MAGs from the candidate phyla JdFR-76 and AABM5-125-24 with genes related to dissimilatory sulfate reduction exhibited distinctive metabolic features. Our results showed unique and novel microbial populations in the SYBH sulfur cycle correlated to the sharp redox gradients, revealing complex biogeochemical processes in this extreme environment. IMPORTANCE Oxygen-deficient regions in the global ocean are expanding rapidly and affect the growth, reproduction and ecological processes of marine organisms. The anaerobic water body of about 150 m in the Sansha Yongle Blue Hole (SYBH) provided a suitable environment to study the specific microbial metabolism in anaerobic seawater. Here, we found that the vertical distributions of the total and active communities of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) were different in each water layer of the SYBH according to the dissolved oxygen content. Genes related to sulfur metabolism also showed distinct stratification characteristics. Furthermore, we have obtained diverse metagenome-assembled genomes, some of which exhibit special sulfur metabolic characteristics, especially candidate phyla JdFR-76 and AABM5-125-24 were identified as potential novel SRB. The results of this study will promote further understanding of the sulfur cycle in extreme environments, as well as the environmental adaptability of microorganisms in blue holes.

Microbe-driven elemental cycling enables microbial adaptation to deep-sea ferromanganese nodule sediment fields

BACKGROUND

Ferromanganese nodule-bearing deep-sea sediments cover vast areas of the ocean floor, representing a distinctive habitat in the abyss. These sediments harbor unique conditions characterized by high iron concentration and low degradable nutrient levels, which pose challenges to the survival and growth of most microorganisms. While the microbial diversity in ferromanganese nodule-associated sediments has been surveyed several times, little is known about the functional capacities of the communities adapted to these unique habitats.

RESULTS

Seven sediment samples collected adjacent to ferromanganese nodules from the Clarion-Clipperton Fracture Zone (CCFZ) in the eastern Pacific Ocean were subjected to metagenomic analysis. As a result, 179 high-quality metagenome-assembled genomes (MAGs) were reconstructed and assigned to 21 bacterial phyla and 1 archaeal phylum, with 88.8% of the MAGs remaining unclassified at the species level. The main mechanisms of resistance to heavy metals for microorganisms in sediments included oxidation (Mn), reduction (Cr and Hg), efflux (Pb), synergy of reduction and efflux (As), and synergy of oxidation and efflux (Cu). Iron, which had the highest content among all metallic elements, may occur mainly as Fe(III) that potentially functioned as an electron acceptor. We found that microorganisms with a diverse array of CAZymes did not exhibit higher community abundance. Instead, microorganisms mainly obtained energy from oxidation of metal (e.g., Mn(II)) and sulfur compounds using oxygen or nitrate as an electron acceptor. Chemolithoautotrophic organisms (Thaumarchaeota and Nitrospirota phyla) were found to be potential manganese oxidizers. The functional profile analysis of the dominant microorganisms further indicated that utilization of inorganic nutrients by redox reactions (rather than organic nutrient metabolism) is a major adaptive strategy used by microorganisms to support their survival in the ferromanganese nodule sediments.

CONCLUSIONS

This study provides a comprehensive metagenomic analysis of microbes inhabiting metal-rich ferromanganese nodule sediments. Our results reveal extensive redundancy across taxa for pathways of metal resistance and transformation, the highly diverse mechanisms used by microbes to obtain nutrition, and their participation in various element cycles in these unique environments. Video Abstract.

Arbuscular mycorrhizal fungi enhance phosphate uptake and alter bacterial communities in maize rhizosphere soil

Arbuscular mycorrhizal fungi (AMF) can symbiose with many plants and improve nutrient uptake for their host plant. Rhizosphere microorganisms have been pointed to play important roles in helping AMF to mobilize soil insoluble nutrients, especially phosphorus. Whether the change in phosphate transport under AMF colonization will affect rhizosphere microorganisms is still unknown. Here, we evaluated the links of interactions among AMF and the rhizosphere bacterial community of maize (Zea mays L.) by using a maize mycorrhizal defective mutant. Loss of mycorrhizal symbiosis function reduced the phosphorus concentration, biomass, and shoot length of maize colonized by AMF. Using 16S rRNA gene amplicon high-throughput sequencing, we found that the mutant material shifted the bacterial community in the rhizosphere under AMF colonization. Further functional prediction based on amplicon sequencing indicated that rhizosphere bacteria involved in sulfur reduction were recruited by the AMF colonized mutant but reduced in the AMF- colonized wild type. These bacteria harbored much abundance of sulfur metabolism-related genes and negatively correlated with biomass and phosphorus concentrations of maize. Collectively, this study shows that AMF symbiosis recruited rhizosphere bacterial communities to improve soil phosphate mobilization, which may also play a potential role in regulating sulfur uptake. This study provides a theoretical basis for improving crop adaptation to nutrient deficiency through soil microbial management practices.

Microbial biogeochemical cycling reveals the sustainability of the rice-crayfish co-culture model

Aquaculture has great potential in nourishing the global growing population, while such staggering yields are coupled with environmental pollution. Rice-crayfish co-culture models (RCFP) have been widely adopted in China due to their eco-friendliness. However, little is known about RCFP's microbiome pattern, which hinders our understanding of its sustainability. This study has conducted metagenomic analysis across aquaculture models and habitats, which revealed aquaculture model-specific biogeochemical cycling pattern (e.g., nitrogen (N), sulfur (S), and carbon (C)): RCFP is advantageous in N-assimilation, N-contamination, and S-pollutants removal, while non-RCFP features N denitrification process and higher S metabolism ability, producing several hazardous pollutants in non-RCFP (e.g., nitric oxide, nitrogen monoxide, and sulfide). Moreover, RCFP has greater capacity for carbohydrate enzyme metabolism compared with non-RCFP in environmental habitats, but not in crayfish gut. Collectively, RCFP plays an indispensable role in balancing aquaculture productivity and environmental protection, which might be applied to the blue transformation of aquaculture.

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.

Generation of zero-valent sulfur from dissimilatory sulfate reduction in sulfate-reducing microorganisms

Dissimilatory sulfate reduction (DSR) mediated by sulfate-reducing microorganisms (SRMs) plays a pivotal role in global sulfur, carbon, oxygen, and iron cycles since at least 3.5 billion y ago. The canonical DSR pathway is believed to be sulfate reduction to sulfide. Herein, we report a DSR pathway in phylogenetically diverse SRMs through which zero-valent sulfur (ZVS) is directly generated. We identified that approximately 9% of sulfate reduction was directed toward ZVS with S8 as a predominant product, and the ratio of sulfate-to-ZVS could be changed with SRMs' growth conditions, particularly the medium salinity. Further coculturing experiments and metadata analyses revealed that DSR-derived ZVS supported the growth of various ZVS-metabolizing microorganisms, highlighting this pathway as an essential component of the sulfur biogeochemical cycle.

Linking microbial biogeochemical cycling genes to the rhizosphere of pioneering plants in a glacier foreland

Glacier retreat raises global concerns but brings about the moment to study soil and ecosystem development. In nutrient-limited glacier forelands, the adaptability of pioneering plant and microbial species is facilitated by their interactions, including rhizosphere effects, but the details of this adaptability are not yet understood. In the rhizosphere of five pioneering plants, we comprehensively deciphered the microbial taxonomic and functional compositions. Two nitrogen-fixing microbial genera, Bradyrhizobium and Mesorhizobium, were among the most abundant taxa in the rhizomicrobiome. Moreover, several rhizobial genera, including Rhizobium, Pararhizobium, Allohrizobium, and Sinorhizobium, head the list of major modules in microbial co-occurrence networks, highlighting the vital roles of nitrogen-cycling taxa in the rhizomicrobiome of pioneering plants. Microbial genes involved in nitrogen, sulfur, phosphorus, and methane cycles were simultaneously correlated with microbial community dissimilarity, and 12 functional pathways were detected with distinct relative abundances among soils. Zooming in on the nitrogen-cycling genes, nifW, narC, nasA, nasB, and nirA were mainly responsible for the significant differences between soils. Furthermore, soil pH and the carbon/nitrogen ratio were among the topsoil properties interacting with nitrogen and sulfur cycling gene dissimilarity. These results explicitly linked biogeochemical cycling genes to the rhizomicrobiome and soil properties, revealing the roles of these genes as microbial drivers in mediating rhizosphere soil-plant-microbiome interactions.

Synergistic between autotrophic and heterotrophic microorganisms for denitrification using bio-S as electron donor

In recent years, biological sulfur (bio-S) was employed in sulfur autotrophic denitrification (SAD) in which autotrophic Thiobacillus denitrificans and heterotrophic Stenotrophomonas maltophilia played a key role. The growth pattern of T.denitrificans and S.maltophilia exhibited a linear relationship between OD₆₀₀ and CFU when OD₆₀₀ < 0.06 and <0.1, respectively. When S.maltophilia has applied alone, the NorBC and NosZ were undetected, and denitrification was incomplete. The DsrA of S.maltophilia could produce sulfide as an alternative electron donor for T.denitrificans. Even though T.denitrificans had complete denitrification genes, its efficiency was low when used alone. The interaction of T.denitrificans and S.maltophilia reduced nitrite accumulation, leading to complete denitrification. A sufficient quantity of S.maltophilia may trigger the autotrophic denitrification activity of T.denitrificans. When the colony-forming units (CFU) ratio of S.maltophilia to T.denitrificans was reached at 2:1, the highest denitrification performance was achieved at 2.56 and 12.59 times higher than applied alone. This research provides a good understanding of the optimal microbial matching for the future application of bio-S.

Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes

BACKGROUND

Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH₄), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches.

RESULTS

Our results showed that the metabolic pathways involved in CH₄, N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly (P < 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0-15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N₂O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly (P < 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH₄ oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments.

CONCLUSIONS

In addition to offering a perspective on the vertical distribution of microbially driven CH₄, N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N₂O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change. Video Abstract.

Tritium and Carbon-14 Contamination Reshaping the Microbial Community Structure, Metabolic Network, and Element Cycle in the Seawater Environment

The potential ecological risks caused by entering radioactive wastewater containing tritium and carbon-14 into the sea require careful evaluation. This study simulated seawater's tritium and carbon-14 pollution and analyzed the effects on the seawater and sediment microenvironments. Tritium and carbon-14 pollution primarily altered nitrogen and phosphorus metabolism in the seawater environment. Analysis by 16S rRNA sequencing showed changes in the relative abundance of microorganisms involved in carbon, nitrogen, and phosphorus metabolism and organic matter degradation in response to tritium and carbon-14 exposure. Metabonomics and metagenomic analysis showed that tritium and carbon-14 exposure interfered with gene expression involving nucleotide and amino acid metabolites, in agreement with the results seen for microbial community structure. Tritium and carbon-14 exposure also modulated the abundance of functional genes involved in carbohydrate, phosphorus, sulfur, and nitrogen metabolic pathways in sediments. Tritium and carbon-14 pollution in seawater adversely affected microbial diversity, metabolic processes, and the abundance of nutrient-cycling genes. These results provide valuable information for further evaluating the risks of tritium and carbon-14 in marine environments.

The link between increased Desulfovibrio and disease severity in Parkinson's disease

Parkinson's disease (PD), a progressive and incurable neurodegenerative disease, has taken a huge economic toll and medical burden on our society. Increasing evidence has shown a strong link between PD and the gut microbiome, but studies on the relationship between the gut microbiome and the severity of PD are limited. In this study, 90 fecal samples were collected from newly diagnosed and untreated patients with PD (n = 47) and matched healthy control subjects (n = 43). The 16S rRNA amplicon and shotgun metagenomic sequencing was performed, aiming to uncover the connection between the gut microbiome and disease severity in PD. The results showed that Desulfovibrio was significantly increased in PD compared to healthy controls and positively correlated with disease severity. The increase in Desulfovibrio was mainly driven by enhanced homogeneous selection and weakened drift. Moreover, through metagenome-assembled genomes (MAGs) analysis, a Desulfovibrio MAG (MAG58) was obtained which was also positively correlated with disease severity. MAG58 possesses a complete assimilatory sulfate reduction pathway and a near-complete dissimilatory sulfate reduction pathway to produce hydrogen sulfide which may influence the development of PD. Based on these results, a potential pathogenic mechanism was presented to illustrate how the increased Desulfovibrio accelerates the development of PD by producing excessive hydrogen sulfide. The present study highlighted the vital role of Desulfovibrio in the development of PD, which may provide a new target for the diagnosis and treatment of PD. KEY POINTS: • The evidence for the link between increased Desulfovibrio and disease severity in PD • A Desulfovibrio MAG was obtained which was correlated with PD • A model was presented to illustrate how increased Desulfovibrio causes PD.

The Early Microbial Colonizers of a Short-Lived Volcanic Island in the Kingdom of Tonga

The island of Hunga Tonga Hunga Ha'apai (HTHH) in the Kingdom of Tonga was formed by Surtseyan eruptions and persisted for 7 years before being obliterated by a massive volcanic eruption on 15 January 2022. Before it was destroyed, HTHH was an unparalleled natural laboratory to study primary succession on a newly formed landmass. We characterized the microbial communities found on the surface sediments of HTHH using a combination of quantitative PCR, marker gene sequencing, and shotgun metagenomic analyses. Contrary to expectations, photosynthetic cyanobacteria were not detected in these sediments, even though they are typically dominant in the earliest stages of primary succession in other terrestrial environments. Instead, our results suggest that the early sediment communities were composed of a diverse array of bacterial taxa, including trace gas oxidizers, anoxygenic photosynthesizers, and chemolithotrophs capable of metabolizing inorganic sulfur, with these bacteria likely sourced from nearby active geothermal environments. While the destruction of HTHH makes it impossible to revisit the site to conduct in situ metabolic measurements or observe how the microbial communities might have continued to change over time, our results do suggest that the early microbial colonizers have unique origins and metabolic capabilities. IMPORTANCE The volcanic island of Hunga Tonga Hunga Ha'apai in the Kingdom of Tonga represents a very rare example of new island formation and thus a unique opportunity to study how organisms colonize a new landmass. We found that the island was colonized by diverse microbial communities shortly after its formation in 2015, with these microbes likely originating from nearby geothermal environments. Primary succession in this system was distinct from that typically observed in other terrestrial environments, with the early microbial colonizers relying on unique metabolic strategies to survive on the surface of this newly formed island, including the capacity to generate energy via sulfur and trace gas metabolism.

Microbial Diversity, Community Turnover, and Putative Functions in Submarine Canyon Sediments under the Action of Sedimentary Geology

Sampling challenges in deep-sea ecosystems lead to a lack of knowledge about the distribution of microbes in different submarine canyons. To study microbial diversity and community turnover under different ecological processes, we performed 16S/18S rRNA gene amplicon sequencing for sediment samples from a submarine canyon in the South China Sea. Bacteria, archaea, and eukaryotes made up 57.94% (62 phyla), 41.04% (12 phyla), and 1.02% (4 phyla) of the sequences, respectively. Thaumarchaeota, Planctomycetota, Proteobacteria, Nanoarchaeota, and Patescibacteria are the five most abundant phyla. Heterogeneous community composition was mainly observed in vertical profiles rather than horizontal geographic locations, and microbial diversity in the surface layer was much lower than that in deep layers. According to the null model tests, homogeneous selection dominated community assembly within each sediment layer, whereas heterogeneous selection and dispersal limitation dominated community assembly between distant layers. Different sedimentation processes of sediments, i.e., rapid deposition caused by turbidity currents or slow sedimentation, seem to be primarily responsible for these vertical variations. Finally, functional annotation through shotgun-metagenomic sequencing found that glycosyl transferases and glycoside hydrolases are the most abundant carbohydrate-active enzyme categories. The most likely expressed sulfur cycling pathways include assimilatory sulfate reduction, the link between inorganic and organic sulfur transformation, and organic sulfur transformation, while the potentially activated methane cycling pathways include aceticlastic methanogenesis and aerobic and anaerobic oxidation of methane. Overall, our study revealed high levels of microbial diversity and putative functions in canyon sediments and the important influence of sedimentary geology on microbial community turnover between vertical sediment layers. IMPORTANCE Deep-sea microbes have received growing attention due to their contribution to biogeochemical cycles and climate change. However, related research lags due to the difficulty of collecting samples. Based on our previous study, which revealed the formation of sediments under the dual action of turbidity currents and seafloor obstacles in a submarine canyon in the South China Sea, this interdisciplinary research provides new insights into how sedimentary geology influences microbial community assembly in sediments. We proposed some uncommon or new findings, including the following: (i) microbial diversity was much lower on the surface than in deeper layers (ii) archaea and bacteria dominated the surface and deep layers, respectively; (iii) sedimentary geology played key roles in vertical community turnover; and (iv) the microbes have great potential to catalyze sulfur, carbon, and methane cycling. This study may lead to extensive discussion of the assembly and function of deep-sea microbial communities in the context of geology.

Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming

The rise of global temperature causes the degradation of the substantial reserves of carbon (C) stored in tundra soils, in which microbial processes play critical roles. Viruses are known to influence the soil C cycle by encoding auxiliary metabolic genes and infecting key microorganisms, but their regulation of microbial communities under climate warming remains unexplored. In this study, we evaluated the responses of viral communities for about 5 years of experimental warming at two depths (15 to 25 cm and 45 to 55 cm) in the Alaskan permafrost region. Our results showed that the viral community and functional gene composition and abundances (including viral functional genes related to replication, structure, infection, and lysis) were significantly influenced by environmental conditions such as total nitrogen (N), total C, and soil thawing duration. Although long-term warming did not impact the viral community composition at the two depths, some glycoside hydrolases encoded by viruses were more abundant at both depths of the warmed plots. With the continuous reduction of total C, viruses may alleviate methane release by altering infection strategies on methanogens. Importantly, viruses can adopt lysogenic and lytic lifestyles to manipulate microbial communities at different soil depths, respectively, which could be one of the major factors causing the differences in microbial responses to warming. This study provides a new ecological perspective on how viruses regulate the responses of microbes to warming at community and functional scales. IMPORTANCE Permafrost thawing causes microbial release of greenhouse gases, exacerbating climate warming. Some previous studies examined the responses of the microbial communities and functions to warming in permafrost region, but the roles of viruses in mediating the responses of microbial communities to warming are poorly understood. This study revealed that warming induced changes in some viral functional classes and in the virus/microbe ratios for specific lineages, which might influence the entire microbial community. Furthermore, differences in viral communities and functions, along with soil depths, are important factors influencing microbial responses to warming. Collectively, our study revealed the regulation of microbial communities by viruses and demonstrated the importance of viruses in the microbial ecology research.

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress

Introduction

Soil salinization is a serious abiotic stress for grapevines. The rhizosphere microbiota of plants can help counter the negative effects caused by salt stress, but the distinction between rhizosphere microbes of salt-tolerant and salt-sensitive varieties remains unclear.

Methods

This study employed metagenomic sequencing to explore the rhizosphere microbial community of grapevine rootstocks 101-14 (salt tolerant) and 5BB (salt sensitive) with or without salt stress.

Results and Discussion

Compared to the control (treated with ddH₂O), salt stress induced greater changes in the rhizosphere microbiota of 101-14 than in that of 5BB. The relative abundances of more plant growth-promoting bacteria, including Planctomycetes, Bacteroidetes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes, Chloroflexi, and Firmicutes, were increased in 101-14 under salt stress, whereas only the relative abundances of four phyla (Actinobacteria, Gemmatimonadetes, Chloroflexi, and Cyanobacteria) were increased in 5BB under salt stress while those of three phyla (Acidobacteria, Verrucomicrobia, and Firmicutes) were depleted. The differentially enriched functions (KEGG level 2) in 101-14 were mainly associated with pathways related to cell motility; folding, sorting, and degradation functions; glycan biosynthesis and metabolism; xenobiotics biodegradation and metabolism; and metabolism of cofactors and vitamins, whereas only the translation function was differentially enriched in 5BB. Under salt stress, the rhizosphere microbiota functions of 101-14 and 5BB differed greatly, especially pathways related to metabolism. Further analysis revealed that pathways associated with sulfur and glutathione metabolism as well as bacterial chemotaxis were uniquely enriched in 101-14 under salt stress and therefore might play vital roles in the mitigation of salt stress on grapevines. In addition, the abundance of various sulfur cycle-related genes, including genes involved in assimilatory sulfate reduction (cysNC, cysQ, sat, and sir), sulfur reduction (fsr), SOX systems (soxB), sulfur oxidation (sqr), organic sulfur transformation (tpa, mdh, gdh, and betC), increased significantly in 101-14 after treatment with NaCl; these genes might mitigate the harmful effects of salt on grapevine. In short, the study findings indicate that both the composition and functions of the rhizosphere microbial community contribute to the enhanced tolerance of some grapevines to salt stress.

Influence of salinity on the diversity and composition of carbohydrate metabolism, nitrogen and sulfur cycling genes in lake surface sediments

Exploring functional gene composition is essential for understanding the biogeochemical functions of lakes. However, little is known about the diversity and composition of biogeochemical cycling genes and their influencing factors in saline lakes. In this study, metagenomic analysis was employed to characterize the diversity and composition of microbial functions predicted from genes involved in carbohydrate metabolisms, nitrogen, and sulfur cycles in 17 surface sediments of Qinghai-Tibetan lakes with salinity ranging from 0.7 to 31.5 g L-1. The results showed that relative abundances of carbohydrate-active enzyme (CAZy), nitrogen, and sulfur cycling genes were 92.7-116.5, 15.1-18.7, 50.8-63.9 per 1,000 amino acid coding reads, respectively. The Shannon diversity indices of CAZy and sulfur cycling genes decreased with increasing salinity, whereas nitrogen cycling gene diversity showed an opposite trend. Relative abundances of many CAZy (i.e., carbohydrate-binding module and carbohydrate esterase), nitrogen (i.e., anammox and organic degradation and synthesis) and sulfur (i.e., dissimilatory sulfur reduction and oxidation, link between inorganic and organic sulfur transformation, sulfur disproportionation and reduction) cycling gene categories decreased with increasing salinity, whereas some CAZy (i.e., auxiliary activity), nitrogen (i.e., denitrification) and sulfur (i.e., assimilatory sulfate reduction and sulfur oxidation) gene categories showed an increasing trend. The compositions of CAZy, nitrogen, and sulfur cycling genes in the studied lake sediments were significantly (p < 0.05) affected by environmental factors such as salinity, total organic carbon, total nitrogen, and total phosphorus, with salinity having the greatest influence. Together, our results suggest that salinity may regulate the biogeochemical functions of carbohydrate metabolisms, nitrogen, and sulfur cycles in lakes through changing the diversity and composition of microbial functional genes. This finding has great implications for understanding the impact of environmental change on microbial functions in lacustrine ecosystems.

AsgeneDB: a curated orthology arsenic metabolism gene database and computational tool for metagenome annotation

Arsenic (As) is the most ubiquitous toxic metalloid in nature. Microbe-mediated As metabolism plays an important role in global As biogeochemical processes, greatly changing its toxicity and bioavailability. While metagenomic sequencing may advance our understanding of the As metabolism capacity of microbial communities in different environments, accurate metagenomic profiling of As metabolism remains challenging due to low coverage and inaccurate definitions of As metabolism gene families in public orthology databases. Here we developed a manually curated As metabolism gene database (AsgeneDB) comprising 400 242 representative sequences from 59 As metabolism gene families, which are affiliated with 1653 microbial genera from 46 phyla. AsgeneDB achieved 100% annotation sensitivity and 99.96% annotation accuracy for an artificial gene dataset. We then applied AsgeneDB for functional and taxonomic profiling of As metabolism in metagenomes from various habitats (freshwater, hot spring, marine sediment and soil). The results showed that AsgeneDB substantially improved the mapping ratio of short reads in metagenomes from various environments. Compared with other databases, AsgeneDB provides more accurate, more comprehensive and faster analysis of As metabolic genes. In addition, we developed an R package, Asgene, to facilitate the analysis of metagenome sequencing data. Therefore, AsgeneDB and the associated Asgene package will greatly promote the study of As metabolism in microbial communities in various environments.

PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes

BACKGROUND

Phosphorus (P) is one of the most essential macronutrients on the planet, and microorganisms (including bacteria and archaea) play a key role in P cycling in all living things and ecosystems. However, our comprehensive understanding of key P cycling genes (PCGs) and microorganisms (PCMs) as well as their ecological functions remains elusive even with the rapid advancement of metagenome sequencing technologies. One of major challenges is a lack of a comprehensive and accurately annotated P cycling functional gene database.

RESULTS

In this study, we constructed a well-curated P cycling database (PCycDB) covering 139 gene families and 10 P metabolic processes, including several previously ignored PCGs such as pafA encoding phosphate-insensitive phosphatase, ptxABCD (phosphite-related genes), and novel aepXVWPS genes for 2-aminoethylphosphonate transporters. We achieved an annotation accuracy, positive predictive value (PPV), sensitivity, specificity, and negative predictive value (NPV) of 99.8%, 96.1%, 99.9%, 99.8%, and 99.9%, respectively, for simulated gene datasets. Compared to other orthology databases, PCycDB is more accurate, more comprehensive, and faster to profile the PCGs. We used PCycDB to analyze P cycling microbial communities from representative natural and engineered environments and showed that PCycDB could apply to different environments.

CONCLUSIONS

We demonstrate that PCycDB is a powerful tool for advancing our understanding of microbially driven P cycling in the environment with high coverage, high accuracy, and rapid analysis of metagenome sequencing data. The PCycDB is available at https://github.com/ZengJiaxiong/Phosphorus-cycling-database . Video Abstract.

Assessment of global health risk of antibiotic resistance genes

Antibiotic resistance genes (ARGs) have accelerated microbial threats to human health in the last decade. Many genes can confer resistance, but evaluating the relative health risks of ARGs is complex. Factors such as the abundance, propensity for lateral transmission and ability of ARGs to be expressed in pathogens are all important. Here, an analysis at the metagenomic level from various habitats (6 types of habitats, 4572 samples) detects 2561 ARGs that collectively conferred resistance to 24 classes of antibiotics. We quantitatively evaluate the health risk to humans, defined as the risk that ARGs will confound the clinical treatment for pathogens, of these 2561 ARGs by integrating human accessibility, mobility, pathogenicity and clinical availability. Our results demonstrate that 23.78% of the ARGs pose a health risk, especially those which confer multidrug resistance. We also calculate the antibiotic resistance risks of all samples in four main habitats, and with machine learning, successfully map the antibiotic resistance threats in global marine habitats with over 75% accuracy. Our novel method for quantitatively surveilling the health risk of ARGs will help to manage one of the most important threats to human and animal health.

Antibiotic resistance genes (ARGs) have accelerated microbial threats to human health. Here, Zhang et al. analyze 4572 metagenomic samples to illustrate the global patterns of ARG distribution in diverse habitats. They quantitatively evaluate the health risk to humans of 2561 ARGs by integrating human accessibility, mobility, pathogenicity and clinical availability. With the machine learning, they map the antibiotic resistance threats in global marine habitats.

Rapid start of high-concentration denitrification and desulfurization reactors by heterotrophic denitrification sulphur-oxidising bacteria

High sulphide concentrations can be toxic to denitrifying and desulphurising microorganisms. In this study, bioaugmentation was used to solve this problem. Pseudomonas sp. gs1 can tolerate 400 mg/L sulphide and converts most of the sulphide into elemental sulphur after 4 h. A solid inoculum of Pseudomonas sp. h1 was prepared. Two reactors, that is, one with and one without inoculum, were simultaneously run for 60 days. Bioreactor II to which bacterial inoculum was added reached a good treatment performance on day 3. The elemental sulphur concentration of the effluent was 342.6 mg/L. It was maintained at 245.3-333.8 mg/L during the subsequent operation. In contrast, reactor I without inoculants achieved the same performance on day 50. High-throughput sequencing shows that Pseudomonas and Azoarcus are the dominant genera. The abundance of the genus Pseudomonas and related denitrifying sulphur-oxidising bacteria in reactor I increases with the operation time. This phenomenon was confirmed by testing the sqr and gltA genes. The quantitative fluorescence PCR test also proves that the addition of bacteria leads to a rapid increase in the sulphur oxidation and carbon metabolism of the activated sludge in the reactor.

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.

Metagenomic insights into the effects of submerged plants on functional potential of microbial communities in wetland sediments

Submerged plants in wetlands play important roles as ecosystem engineers to improve self-purification and promote elemental cycling. However, their effects on the functional capacity of microbial communities in wetland sediments remain poorly understood. Here, we provide detailed metagenomic insights into the biogeochemical potential of microbial communities in wetland sediments with and without submerged plants (i.e., Vallisneria natans). A large number of functional genes involved in carbon (C), nitrogen (N) and sulfur (S) cycling were detected in the wetland sediments. However, most functional genes showed higher abundance in sediments with submerged plants than in those without plants. Based on the comparison of annotated functional genes in the N and S cycling databases (i.e., NCycDB and SCycDB), we found that genes involved in nitrogen fixation (e.g., nifD/H/K/W), assimilatory nitrate reduction (e.g., nasA and nirA), denitrification (e.g., nirK/S and nosZ), assimilatory sulfate reduction (e.g., cysD/H/J/N/Q and sir), and sulfur oxidation (e.g., glpE, soeA, sqr and sseA) were significantly higher (corrected p < 0.05) in vegetated vs. unvegetated sediments. This could be mainly driven by environmental factors including total phosphorus, total nitrogen, and C:N ratio. The binning of metagenomes further revealed that some archaeal taxa could have the potential of methane metabolism including hydrogenotrophic, acetoclastic, and methylotrophic methanogenesis, which are crucial to the wetland methane budget and carbon cycling. This study opens a new avenue for linking submerged plants with microbial functions, and has further implications for understanding global carbon, nitrogen and sulfur cycling in wetland ecosystems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-021-00100-3.

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.

DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data

Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms and processes driving biogeochemical cycling in natural ecosystems. Databases dedicated to depicting biogeochemical pathways (for example, metabolism of dimethylsulfoniopropionate (DMSP), which is an abundant organosulfur compound) from metagenomic/metatranscriptomic data are rarely seen. Additionally, a recognized normalization model to estimate the relative abundance and environmental importance of pathways from metagenomic and metatranscriptomic data has not been organized to date. These limitations impact the ability to accurately relate key microbial-driven biogeochemical processes to differences in environmental conditions. Thus, an easy-to-use, specialized tool that infers and visually compares the potential for biogeochemical processes, including DMSP cycling, is urgently required. To solve these issues, we developed DiTing, a tool wrapper to infer and compare biogeochemical pathways among a set of given metagenomic or metatranscriptomic reads in one step, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) and a manually created DMSP cycling gene database. Accurate and specific formulae for over 100 pathways were developed to calculate their relative abundance. Output reports detail the relative abundance of biogeochemical pathways in both text and graphical format. DiTing was applied to simulated metagenomic data and resulted in consistent genetic features of simulated benchmark genomic data. Subsequently, when applied to natural metagenomic and metatranscriptomic data from hydrothermal vents and the Tara Ocean project, the functional profiles predicted by DiTing were correlated with environmental condition changes. DiTing can now be confidently applied to wider metagenomic and metatranscriptomic datasets, and it is available at https://github.com/xuechunxu/DiTing.