Genomic analysis of Alteromonas sp. M12 isolated from the Mariana Trench reveals its role in dimethylsulfoniopropionate cycling.

Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur molecule in marine environments with important roles in stress tolerance, global carbon and sulfur cycling, and chemotaxis. It is the main precursor of the climate active gas dimethyl sulfide (DMS), which is the greatest natural source of bio­sulfur transferred from ocean to atmosphere. Alteromonas sp. M12, a Gram-negative and aerobic bacterium, was isolated from the seawater samples collected from the Mariana Trench at the depth of 2500 m. Here, we report the complete genome sequence of strain M12 and its genomic characteristics to import and utilize DMSP. The genome of strain M12 contains one circular chromosome (5,012,782 bp) with the GC content of 40.88%. Alteromonas sp. M12 can grow with DMSP as a sole carbon source, and produced DMS with DMSP as a precursor. Genomic analysis showed that strain M12 contained a set of genes involved in the downstream steps of DMSP cleavage, but no known genes encoding DMSP transporters or DMSP lyases. The results indicated that this strain contained novel DMSP transport and cleavage genes in its genome which warrants further investigation. The import of DMSP into cells may be a strategy of strain M12 to adapt the hydrostatic pressure environment in the Mariana Trench, as DMSP can be used as a hydrostatic pressure protectant. This study sheds light on the catabolism of DMSP by deep-sea bacteria.

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.

Nitrogen and sulfur cycling and their coupling mechanisms in eutrophic lake sediment microbiomes.

Microorganisms play important roles in the biogeochemical cycles of lake sediment. However, the integrated metabolic mechanisms governing nitrogen (N) and sulfur (S) cycling in eutrophic lakes remain poorly understood. Here, metagenomic analysis of field and bioreactor enriched sediment samples from a typical eutrophic lake were applied to elucidate the metabolic coupling of N and S cycling. Our results showed significant diverse genes involved in the pathways of dissimilatory sulfur metabolism, denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The N and S associated functional genes and microbial groups generally showed significant correlation with the concentrations of NH4+, NO2- and SO42, while with relatively low effects from other environmental factors. The gene-based co-occurrence network indicated clear cooperative interactions between N and S cycling in the sediment. Additionally, our analysis identified key metabolic processes, including the coupled dissimilatory sulfur oxidation (DSO) and DNRA as well as the association of thiosulfate oxidation complex (SOX systems) with denitrification pathway. However, the enriched N removal microorganisms in the bioreactor ecosystem demonstrated an additional electron donor, incorporating both the SOX systems and DSO processes. Metagenome-assembled genomes-based ecological model indicated that carbohydrate metabolism is the key linking factor for the coupling of N and S cycling. Our findings uncover the coupling mechanisms of microbial N and S metabolism, involving both inorganic and organic respiration pathways in lake sediment. This study will enhance our understanding of coupled biogeochemical cycles in lake ecosystems.

Divide and conquer: Spatial and temporal resource partitioning structures benthic cyanobacterial mats.

Benthic cyanobacterial mats are increasing in abundance worldwide with the potential to degrade ecosystem structure and function. Understanding mat community dynamics is thus critical for predicting mat growth and proliferation and for mitigating any associated negative effects. Carbon, nitrogen, and sulfur cycling are the predominant forms of nutrient cycling discussed within the literature, while metabolic cooperation and viral interactions are understudied. Although many forms of nutrient cycling in mats have been assessed, the links between niche dynamics, microbial interactions, and nutrient cycling are not well described. Here, we present an updated review on how nutrient cycling and microbial community interactions in mats are structured by resource partitioning via spatial and temporal heterogeneity and succession. We assess community interactions and nutrient cycling at both intramat and metacommunity scales. Additionally, we present ideas and recommendations for research in this area, highlighting top-down control, boundary layers, and metabolic cooperation as important future directions.

A Synthetic Microbiome Based on Dominant Microbes in Wild Rice Rhizosphere to Promote Sulfur Utilization.

Sulfur (S) is one of the main components of important biomolecules, which has been paid more attention in the anaerobic environment of rice cultivation. In this study, 12 accessions of rice materials, belonging to two Asian rice domestication systems and one African rice domestication system, were used by shotgun metagenomics sequencing to compare the structure and function involved in S cycle of rhizosphere microbiome between wild and cultivated rice. The sulfur cycle functional genes abundances were significantly different between wild and cultivated rice rhizosphere in the processes of sulfate reduction and other sulfur compounds conversion, implicating that wild rice had a stronger mutually-beneficial relationship with rhizosphere microbiome, enhancing sulfur utilization. To assess the effects of sulfate reduction synthetic microbiomes, Comamonadaceae and Rhodospirillaceae, two families containing the genes of two key steps in the dissimilatory sulfate reduction, aprA and dsrA respectively, were isolated from wild rice rhizosphere. Compared with the control group, the dissimilatory sulfate reduction in cultivated rice rhizosphere was significantly improved in the inoculated with different proportions groups. It confirmed that the synthetic microbiome can promote the S-cycling in rice, and suggested that may be feasible to construct the synthetic microbiome step by step based on functional genes to achieve the target functional pathway. In summary, this study reveals the response of rice rhizosphere microbial community structure and function to domestication, and provides a new idea for the construction of synthetic microbiome.

Groundwater microbial communities reflect geothermal activity on volcanic island.

Studies of the effects of volcanic activity on the Hawaiian Islands are extremely relevant due to the past and current co-eruptions at both Mauna Loa and Kilauea. The Big Island of Hawai'i is one of the most seismically monitored volcanic systems in the world, and recent investigations of the Big Island suggest a widespread subsurface connectivity between volcanoes. Volcanic activity has the potential to add mineral contaminants into groundwater ecosystems, thus affecting water quality, and making inhabitants of volcanic islands particularly vulnerable due to dependence on groundwater aquifers. As part of an interdisciplinary study on groundwater aquifers in Kona, Hawai'i, over 40 groundwater wells were sampled quarterly from August 2017 through March 2019, before and after the destructive eruption of the Kilauea East Rift Zone in May 2018. Sample sites occurred at great distance (~80 km) from Kilauea, allowing us to pose questions of how volcanic groundwater aquifers might be influenced by volcanic subsurface activity. Approximately 400 water samples were analyzed and temporally split by pre-eruption and post-eruption for biogeochemical analysis. While most geochemical constituents did not differ across quarterly sampling, microbial communities varied temporally (pre- and post-eruption). When a salinity threshold amongst samples was set, the greatest microbial community differences were observed in the freshest groundwater samples. Differential analysis indicated bacterial families with sulfur (S) metabolisms (sulfate reducers, sulfide oxidation, and disproportionation of S-intermediates) were enriched post-eruption. The diversity in S-cyclers without a corresponding change in sulfate geochemistry suggests cryptic cycling may occur in groundwater aquifers as a result of distant volcanic subsurface activity. Microbial communities, including taxa that cycle S, may be superior tracers to changes in groundwater quality, especially from direct inputs of subsurface volcanic activity.

Impact of redox fluctuations on microbe-mediated elemental sulfur disproportionation and coupled redox cycling of iron.

Elemental sulfur (S0) plays a vital role in the coupled cycling of sulfur and iron, which in turn affects the transformation of carbon and various pollutants. These processes have been well characterized under static anoxic or oxic conditions, however, how the natural redox fluctuations affect the bio-mediated sulfur cycling and coupled iron cycling remain enigmatic. The present work examined S0 disproportionation as driven by natural microbial communities under fluctuating redox conditions and the contribution of S0 disproportionation to ferrihydrite transformation. Samples were incubated at either neutral or alkaline pH values, applying sequential anaerobic, aerobic and anaerobic conditions over 60 days. Under anaerobic conditions, S0 was found to undergo disproportionation to sulfate and sulfide, which subsequently reduced ferrihydrite at both pH 7.4 and 9.5. Ferrihydrite promoted S0 disproportionation by scavenging biogenic sulfide and maintaining a suitable degree of sulfate formation. After an oxic period, during the subsequent anoxic incubation, bioreduction of sulfate occurred and the biogenic sulfide reduced iron (hydr)oxides at a rate approximately 25 % lower than that observed during the former anoxic period. A 16S rDNA-based microbial community analysis revealed changes in the microbial community in response to the redox fluctuations, implying an intimate association with the coupled cycling of sulfur and iron. Microscopic and spectroscopic analyses confirmed the S0-mediated transformation of ferrihydrite to crystalline iron (hydr)oxide minerals such as lepidocrocite and magnetite and the formation of iron sulfides precipitated under fluctuating redox conditions. Finally, a reaction mechanism based on mass balance was proposed, demonstrating that bio-mediated sulfur transformation maintained a sustainable redox reaction with iron (hydr)oxides under fluctuating anaerobic-aerobic-anaerobic conditions tested in this study. Altogether, the finding of our study is critical for obtaining a more complete understanding of the dynamics of iron redox reactions and pollutant transformation in sulfur-rich aquatic environments.

Tidal dynamics regulates potential coupling of carbon­nitrogen­sulfur cycling microbes in intertidal flats.

Tide-driven hydrodynamic process causes significant geochemical gradients that influence biogeochemical cycling and ecological functioning of estuarine and coastal ecosystems. However, the effects of tidal dynamics on microbial communities, particularly at the functional gene level, remain unclear even though microorganisms play critical roles in biogeochemical carbon (C), nitrogen (N) and sulfur (S) cycling. Here, we used 16S rRNA gene amplicon sequencing and microarray-based approach to reveal the stratification of microorganisms related to C, N and S cycles along vertical redox gradients in intertidal wetlands. Alpha-diversity of bacteria and archaea was generally higher at the deep groundwater-sediment interface. Microbial compositions were markedly altered along the sediment profile, and these shifts were largely due to changes in nutrient availability and redox potential. Furthermore, functional genes exhibited redox partitioning between interfaces and transition layer, with abundant genes involved in C decomposition, methanogenesis, heterotrophic denitrification, sulfite reduction and sulfide oxidation existed in the middle anoxic zone. The influence of tidal dynamics on sediment function was highly associated with redox state, sediment texture, and substrates availability, leading to distinct distribution pattern of metabolic coupling of microbes involved in energy flux and elemental cycling in intertidal wetlands. These results indicate that tidal cycles are critical in determining microbial community and functional structure, and they provide new insights into sediment microbe-mediated biogeochemical cycling in intertidal habitats.

Genomic analysis of Marinomonas algicola SM1966T reveals its role in marine sulfur cycling.

Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur molecule in marine environments with important roles in global sulfur and nutrient cycling, which is mainly produced by marine phytoplankton and macroalgae. Marinomonas algicola SM1966T, a Gram-negative, aerobic and rod-shaped bacterium, was isolated from the surface of Ulva pertusa (Chlorophyta) algal sample collected off the coastal areas of Rongcheng, China. Here, we report the complete genome sequence of strain SM1966T and its genomic characteristics to utilize DMSP, which may be produced by Ulva pertusa. The genome of strain SM1966T contains one circular chromosome (4.3 Mbp) and one circular plasmid (149,271 bp). Genomic analysis showed that strain SM1966T possesses a set of genes involved in DMSP transport, DMSP cleavage and the catabolism of acrylate, one product of DMSP cleavage. The results indicated that strain SM1966T has the capacity to utilize DMSP and produce dimethyl sulfide (DMS), a volatile infochemical with important roles in global sulfur cycling. This study provides genetic insights into DMSP catabolism by algae-associated bacteria.

Metagenomic and metaproteomic insights into the microbiome and the key geobiochemical potentials on the sandstone of rock-hewn Beishiku Temple in Northwest China.

Metagenomics and metaproteomics analyses were used to determine the microbial diversity and taxon composition, as well as the biochemical potentials of the microbiome on the sandstone of Beishiku Temple located in Northwest China. Taxonomic annotation of the metagenomic dataset revealed the predominant taxa of the stone microbiome on this cave temple with characteristics of resistance to harsh environmental conditions. Meanwhile, there were also taxa in the microbiome that showed sensitivity to environmental factors. The taxa distribution and the metabolic functional distribution patterns by the metagenome and metaproteome, respectively, showed clear differences. The high abundance of energy metabolism represented in the metaproteome suggested that there were active geomicrobiological cycles of elements within the microbiome. The taxa responsible for reactions in the nitrogen cycle from both metagenome and metaproteome supported a metabolically active nitrogen cycle, and the high activity of Comammox bacteria indicated the strong metabolic activity of ammonia oxidation to nitrate in the outdoor site. The SOX-related taxa involved in the sulfur cycle showed higher activity outdoors than indoors, and on the outdoor ground than at the outdoor cliff, as detected through metaproteomic analysis. The development of petrochemical industry in the vicinity resulting in the deposition of sulfur/oxidized sulfur via atmosphere may stimulate the physiological activity of SOX. Our findings provide metagenomic and metaproteomic evidence for microbially driven geobiochemical cycles that result in the biodeterioration of stone monuments.

Biogeochemical sulfur cycling of virus auxiliary metabolic genes involved in Napahai plateau wetland.

Virus plays important roles in regulating microbial community structure, horizontal gene transfer, and promoting biological evolution, also augmenting host metabolism during infection via the expression of auxiliary metabolic genes (AMGs), and thus affect biogeochemical cycling in the oceans. As the "kidney of the earth," wetlands have rich biodiversity and abundant resources. Based on metagenomic data, 10 AMGs associated with sulfur cycling, i.e., tusA, moaD, dsrE, soxA, soxB, soxC, soxD, soxX, soxY, and soxZ, were analyzed in Napahai plateau wetland. The phylogenetic trees of AMGs involved in sulfur metabolism from different habitats and host origins were constructed. Combined with principal coordinate analysis, it revealed that most AMGs associated with sulfur metabolism clustered separately, indicating the abundance and uniqueness in this region. The sulfur metabolism pathways involved by AMGs were mainly SOX systems, among which sulfur oxidation was associated with moaD and dsrE genes, while sulfur transport was related to tusA genes. It provides an insight into the biogeochemical sulfur cycling in plateau wetlands and lays the foundation for further study on the co-evolution of virus and host.

Unravelling microbial drivers of the sulfate-reduction process inside landfill using metagenomics.

Hydrogen sulfide (H2S) is one of the common landfill odor. This research demonstrates that the sulfate transformation behavior is significantly enhanced during the landfill process, accompanied by a shift in microbial structure. The relative abundance of dissimilatory sulfate reduction (DSR) and thiosulfate oxidation by SOX (sulfur-oxidation) complex gradually decreases through the landfill processes while the assimilatory sulfate reduction (ASR) demonstrates the opposite behavior. The major module for landfill sulfate reduction is ASR, accounting for 31.72% ± 2.84% of sulfate metabolism. Based on the functional genes for the sulfate pathway, the drivers for sulfate biotransformation in landfills were determined and further identified their contribution in the sulfate metabolism during landfill processes. Pseudomonas, Methylocaldum, Bacillus, Methylocystis and Hyphomicrobium were the top 5 contributors for ASR pathway, and only one genus Pseudomonas was found for DSR pathway. Among the 26 high-quality metagenome-assembled genomes of sulfate functional species, 24 were considered novel species for sulfuric metabolism. Overall, this study provides unique insight into the sulfate transformation process related to the H2S odor control in landfill management.

Phytoplankton Sources and Sinks of Dimethylsulphoniopropionate (DMSP) in Temperate Coastal Waters of Australia.

The ecologically important organic sulfur compound, dimethylsulfoniopropionate (DMSP), is ubiquitous in marine environments. Produced by some species of phytoplankton and bacteria, it plays a key role in cellular responses to environmental change. Recently, uptake of DMSP by non-DMSP-producing phytoplankton species has been demonstrated, highlighting knowledge gaps concerning DMSP distribution through the marine microbial food web. In this study, we traced the uptake and distribution of DMSP through a natural marine microbial community collected from off the eastern coastline Australia. We found a diverse phytoplankton community representing six major taxonomic groups and conducted DMSP-enrichment experiments both on the whole community, and the community separated into large (≥8.0 µm), medium (3.0−8.0 µm), and small (0.2−3.0 µm) size fractions. Our results revealed active uptake of DMSP in all three size fractions of the community, with the largest fraction (>8 µm) forming the major DMSP sink, where enrichment resulted in an increase of DMSPp by 144%. We observed evidence for DMSP catabolism in all size fractions with DMSP enrichment, highlighting loss from the system via MeSH or DMS production. Based on taxonomic diversity, we postulate the sources of DMSP were the dinoflagellates, Phaeocystis sp., and Trichodesmium sp., which were present in a relatively high abundance, and the sinks for DMSP were the diatoms and picoeucaryotes in this temperate community. These findings corroborate the role of hitherto disregarded phytoplankton taxa as potentially important players in the cycling of DMSP in coastal waters of Australia and emphasize the need to better understand the fate of accumulated DMSP and its significance in cellular metabolism of non-DMSP producers.

Sulfur cycling at natural hydrocarbon and sulfur seeps in Santa Paula Creek, CA.

Biogeochemical cycling of sulfur is relatively understudied in terrestrial environments compared to marine environments. However, the comparative ease of access, observation, and sampling of terrestrial settings can expand our understanding of organisms and processes important in the modern sulfur cycle. Furthermore, these sites may allow for the discovery of useful process analogs for ancient sulfur-metabolizing microbial communities at times in Earth's past when atmospheric O2 concentrations were lower and sulfide was more prevalent in Earth surface environments. We identified a new site at Santa Paula Creek (SPC) in Ventura County, CA-a remarkable freshwater, gravel-bedded mountain stream charged with a range of oxidized and reduced sulfur species and heavy hydrocarbons from the emergence of subsurface fluids within the underlying sulfur- and organic-rich Miocene-age Monterey Formation. SPC hosts a suite of morphologically distinct microbial biofacies that form in association with the naturally occurring hydrocarbon seeps and sulfur springs. We characterized the geology, stream geochemistry, and microbial facies and diversity of the Santa Paula Creek ecosystem. Using geochemical analyses and 16S rRNA gene sequencing, we found that SPC supports a dynamic sulfur cycle that is largely driven by sulfide-oxidizing microbial taxa, with contributions from smaller populations of sulfate-reducing and sulfur-disproportionating taxa. This preliminary characterization of SPC revealed an intriguing site in which to study geological and geochemical controls on microbial community composition and to expand our understanding of sulfur cycling in terrestrial environments.

Oceanospirillales containing the DMSP lyase DddD are key utilisers of carbon from DMSP in coastal seawater.

BACKGROUND: Ubiquitous and diverse marine microorganisms utilise the abundant organosulfur molecule dimethylsulfoniopropionate (DMSP), the main precursor of the climate-active gas dimethylsulfide (DMS), as a source of carbon, sulfur and/or signalling molecules. However, it is currently difficult to discern which microbes actively catabolise DMSP in the environment, why they do so and the pathways used. RESULTS: Here, a novel DNA-stable isotope probing (SIP) approach, where only the propionate and not the DMS moiety of DMSP was 13C-labelled, was strategically applied to identify key microorganisms actively using DMSP and also likely DMS as a carbon source, and their catabolic enzymes, in North Sea water. Metagenomic analysis of natural seawater suggested that Rhodobacterales (Roseobacter group) and SAR11 bacteria were the major microorganisms degrading DMSP via demethylation and, to a lesser extent, DddP-driven DMSP lysis pathways. However, neither Rhodobacterales and SAR11 bacteria nor their DMSP catabolic genes were prominently labelled in DNA-SIP experiments, suggesting they use DMSP as a sulfur source and/or in signalling pathways, and not primarily for carbon requirements. Instead, DNA-SIP identified gammaproteobacterial Oceanospirillales, e.g. Amphritea, and their DMSP lyase DddD as the dominant microorganisms/enzymes using DMSP as a carbon source. Supporting this, most gammaproteobacterial (with DddD) but few alphaproteobacterial seawater isolates grew on DMSP as sole carbon source and produced DMS. Furthermore, our DNA-SIP strategy also identified Methylophaga and other Piscirickettsiaceae as key bacteria likely using the DMS, generated from DMSP lysis, as a carbon source. CONCLUSIONS: This is the first study to use DNA-SIP with 13C-labelled DMSP and, in a novel way, it identifies the dominant microbes utilising DMSP and DMS as carbon sources. It highlights that whilst metagenomic analyses of marine environments can predict microorganisms/genes that degrade DMSP and DMS based on their abundance, it cannot disentangle those using these important organosulfur compounds for their carbon requirements. Note, the most abundant DMSP degraders, e.g. Rhodobacterales with DmdA, are not always the key microorganisms using DMSP for carbon and releasing DMS, which in this coastal system were Oceanospirillales containing DddD. Video abstract.

Enrichment of sulfur-oxidizing bacteria using S-doped NiFe2O4 nanosheets as the anode in microbial fuel cell enhances power production and sulfur recovery.

Microbial fuel cells (MFCs) have great promise for power generation by oxidizing organic wastewater, yet the challenge to realize high efficiency in simultaneous energy production and resource recovery remains. In this study, we designed a novel MFC anode by synthesizing S-doped NiFe2O4 nanosheet arrays on carbon cloth (S10-NiFe2O4@CC) to build a three-dimensional (3D) hierarchically porous structure, with the aim to regulate the microbial community of sulfur-cycling microbes in order to enhance power production and elemental sulfur (S0) recovery. The S10-NiFe2O4@CC anode obtained a faster start-up time of 2 d and the highest power density of 4.5 W/m2 in acetate-fed and mixed bacteria-based MFCs. More importantly, sulfide removal efficiency (98.3 %) (initial concentration of 50 mg/L S2-) could be achieved within 3 d and sulfur (S8) could be produced. Microbial community analysis revealed that the S10-NiFe2O4@CC anode markedly enriched sulfur-oxidizing bacteria (SOB) and promoted enrichment of SOB and sulfate-reducing bacteria (SRB) in the bulk solution as well, leading to the enhancement of power generation and S0 recovery. This study shows how carefully designing and optimizing the composition and structure of the anode can lead to the enrichment of a multifunctional microbiota with excellent potential for sulfide removal and resource recovery.

Biochar decreases Cd mobility and rice (Oryza sativa L.) uptake by affecting soil iron and sulfur cycling.

Biochar has been used as an amendment in Cd-contaminated soils. However, the mechanisms of which biochar reduce Cd mobility and rice (Oryza sativa L.) Cd uptake by modifying the iron and sulfur cycling in soil has rarely been addressed in the literature. A pot experiment has been carried out with two Cd-contaminated paddy soils (FG and DBS) from South China. Rice straw biochar (RSB) and rape straw biochar (RASB) pyrolyzed at 450 °C were applied at 0, 0.5, and 1% (w/w), respectively. The results showed that biochar amendment at a rate of 1% reduced grain Cd concentrations by 29.3-35.2%. Furthermore, biochar significantly reduced the Cd concentration of root, while the decline of Cd concentration by RASB treatment was higher than by RSB treatment. Root Cd in RASB0.5 was significantly reduced by 56.4-51.8% compared to than that in RSB0.5 at the maturing stage. Biochar reduced soil acid-soluble Cd by 15.9-25.3% with the increase of pH at the maturing stage in FG soil, and 30.1-59.3% by promoting soil into more reductive condition at the heading stage in DBS soil with higher contents of Fe and S. In addition, biochar impeded Cd transport from soil to rice roots by increasing the formation of iron plaque at the flooding stage. Owing to the influence of RASB1, DCB-Cd concentration increased significantly, with 99.7% at the heading stage in FG soil and 237.9% at the tillering stage in DBS soil, respectively. Furthermore, RASB with a higher sulfur concentration had a more positive effect on Cd immobilization and iron plaque formation compared to RSB. As a conclusion, this study suggested that biochar might be able to promote the Cd immobilization by affecting the cycling of iron and sulfur in soil.

Transformation of sulfidized nanoscale zero-valent iron particles and its effects on microbial communities in soil ecosystems.

Sulfidized nanoscale zero-valent iron (S-nZVI) is a promising material for in situ soil remediation. However, its transformation (i.e., aging) and effects on the microbial community in soil ecosystems are largely unknown. In this study, S-nZVI having low (S-nZVI (L)) and high sulfur-doping (S-nZVI (H)) were incubated in soil microcosms and bare nZVI was used as a control. Their aged products were characterized using microspectroscopic analyses and the changes in the corresponding soil microbial community were determined using high-throughput sequencing analyses. The results indicate that severe corrosion of both bare and S-nZVI occurred over 56 days of aging with significant morphological and mineral changes. Magnetite, lepidocrocite, and goethite were detected as the main aged products. In addition, sulfate ions, pyrite, and iron polysulfide were formed in the aged products of S-nZVI. Cr(VI) removal test results indicated that S-nZVI(L) achieved the best results after aging, likely because of the optimal FeS arrangement on its nanoparticle surfaces. The presence of nZVI and S-nZVI increased the abundance of some magnetotactic microorganisms and altered bacterial and fungal community structures and compositions. Moreover, the addition of S-nZVI enriched some bacterial and fungal genera related to sulfur cycling because of the presence of sulfide-bearing material. The findings reveal the transformation of S-nZVI during aging and its effects on microbial communities in soil ecosystems, thereby helping to the evaluation of S-nZVI application in soil remediation.

Microbial Diversity and Sulfur Cycling in an Early Earth Analogue: From Ancient Novelty to Modern Commonality.

Life emerged and diversified in the absence of molecular oxygen. The prevailing anoxia and unique sulfur chemistry in the Paleo-, Meso-, and Neoarchean and early Proterozoic eras may have supported microbial communities that differ from those currently thriving on the earth's surface. Zodletone spring in southwestern Oklahoma represents a unique habitat where spatial sampling could substitute for geological eras namely, from the anoxic, surficial light-exposed sediments simulating a preoxygenated earth to overlaid water column where air exposure simulates oxygen intrusion during the Neoproterozoic era. We document a remarkably diverse microbial community in the anoxic spring sediments, with 340/516 (65.89%) of genomes recovered in a metagenomic survey belonging to 200 bacterial and archaeal families that were either previously undescribed or that exhibit an extremely rare distribution on the current earth. Such diversity is underpinned by the widespread occurrence of sulfite, thiosulfate, tetrathionate, and sulfur reduction and the paucity of sulfate reduction machineries in these taxa. Hence, these processes greatly expand lineages mediating reductive sulfur-cycling processes in the tree of life. An analysis of the overlaying oxygenated water community demonstrated the development of a significantly less diverse community dominated by well-characterized lineages and a prevalence of oxidative sulfur-cycling processes. Such a transition from ancient novelty to modern commonality underscores the profound impact of the great oxygenation event on the earth's surficial anoxic community. It also suggests that novel and rare lineages encountered in current anaerobic habitats could represent taxa that once thrived in an anoxic earth but have failed to adapt to earth's progressive oxygenation. IMPORTANCE Life on earth evolved in an anoxic setting; however, the identity and fate of microorganisms that thrived in a preoxygenated earth are poorly understood. In Zodletone spring, the prevailing geochemical conditions are remarkably similar to conditions prevailing in surficial earth prior to oxygen buildup in the atmosphere. We identify hundreds of previously unknown microbial lineages in the spring and demonstrate that these lineages possess the metabolic machinery to mediate a wide range of reductive sulfur processes, with the capacity to respire sulfite, thiosulfate, sulfur, and tetrathionate, rather than sulfate, which is a reflection of the differences in sulfur-cycling chemistry in ancient versus modern times. Collectively, such patterns strongly suggest that microbial diversity and sulfur-cycling processes in a preoxygenated earth were drastically different from the currently observed patterns and that the Great Oxygenation Event has precipitated the near extinction of a wide range of oxygen-sensitive lineages and significantly altered the microbial reductive sulfur-cycling community on earth.

Microbial communities in swamps of four mangrove reserves driven by interactions between physicochemical properties and microbe in the North Beibu Gulf, China.

Mangroves are distributed in coastal and estuarine regions and are characterized as a sink for terrestrial pollution. It is believed that complex interactions between environmental factors and microbial communities exist in mangrove swamps. However, little is known about environment-microbe interactions. There is a need to clarify some important environmental factors shaping microbial communities and how environmental factors interact with microbial assemblages in mangrove swamps. In the present study, physicochemical and microbial characteristics in four mangrove reserves (named ZZW, Qin, Bei, and GQ) in the North Beibu Gulf were determined. The interactions between environmental factors and microbial assemblages were analyzed with statistical methods in addition to CCA and RDA. Higher concentrations of sulfate (SO42--S) and Fe but lower concentrations of total phosphorus (TP) and NO3--N were detected in ZZW and Qin. Nutrient elements (NO3--N, NH4+-N, organic matter (OM), SO42--S, Fe, and TP) were more important than heavy metals for determining the microbial assemblages, and NO3--N was the most important factor. NO3--N, SO42--S, TP, and Fe formed a significant co-occurrence network in conjunction with some bacterial taxa, most of which were Proteobacteria. Notably, comparatively elevated amounts of sulfate-reducing bacteria (Desulfatibacillum, Desulfomonile, and Desulfatiglans) and sulfur-oxidizing bacteria (Thioprofundum and Thiohalophilus) were found in ZZW and Qin. The co-occurrence network suggested that some bacteria involved in sulfate reduction and sulfur oxidation drive the transformation of P and N, resulting in the reduction of P and N in mangrove swamps. Through the additional utilization of multivariate regression tree (MRT) and co-occurrence network analysis, our research provides a new perspective for understanding the interactions between environmental factors and microbial communities in mangroves.