How sulphate-reducing microorganisms cope with stress: lessons from systems biology

Inoculum source determines the stress resistance of electroactive functional taxa in biofilms: A metagenomic perspective

The inoculum has a crucial impact on bioreactor initialization and performance. However, there is currently a lack of guidance on selecting appropriate inocula for applications in environmental biotechnology. In this study, we applied microbial electrolysis cells (MECs) as models to investigate the differences in the functional potential of electroactive microorganisms (EAMs) within anodic biofilms developed from four different inocula (natural or artificial), using shotgun metagenomic techniques. We specifically focused on extracellular electron transfer (EET) function and stress resistance, which affect the performance and stability of MECs. Community profiling revealed that the family Geobacteraceae was the key EAM taxon in all biofilms, with Geobacter as the dominant genus. The c-type cytochrome gene imcH showed universal importance for Geobacteraceae EET and was utilized as a marker gene to evaluate the EET potential of EAMs. Additionally, stress response functional genes were used to assess the stress resistance potential of Geobacter species. Comparative analysis of imcH gene abundance revealed that EAMs with comparable overall EET potential could be enriched from artificial and natural inocula (P > 0.05). However, quantification of stress response gene copy numbers in the genomes demonstrated that EAMs originating from natural inocula possessed superior stress resistance potential (196 vs. 163). Overall, this study provides novel perspectives on the inoculum effect in bioreactors and offers theoretical guidance for selecting inoculum in environmental engineering applications.

Cathodic poised potential stimulated the electron-sensitive C-P lyase pathway in glyphosate biodegradation

Glyphosate, the most widely used herbicide globally, is accumulating in the environment and poses significant potential eco- and bio-toxicity risks. While natural attenuation of glyphosate has been reported, the efficacy varies considerably and the dominant metabolite, aminomethylphosphonic acid (AMPA), is potentially more persistent and toxic. This study investigated the bioelectrochemical system (BES) for glyphosate degradation under anaerobic, reductive conditions. Atomistic simulations using density functional theory (DFT) predicted increased thermodynamic favorability for the non-dominant C-P lyase degradation pathway under external charge, which suppressed AMPA production. Experimental results confirmed that cathodic poised potential (-0.4 V vs. Ag/AgCl) enhanced glyphosate degradation (75 % in BES vs. ∼40 % in the control conditions after 37 days), and lowered the AMPA yield (0.52 mol AMPA yield per mol glyphosate removed in BES vs. 0.77-0.86 mol mol-1 in the control conditions). Geobacter lovleyi was likely the active species driving the C-P lyase pathway, as evidenced by the increase of its relative abundance, the upregulation of its extracellular electron transfer genes (most notably mtr) and the up-regulation of its phnJ and hcp genes (encoding C-P layse and hydroxylamine reductase respectively).

Novel Insights on Extracellular Electron Transfer Networks in the Desulfovibrionaceae Family: Unveiling the Potential Significance of Horizontal Gene Transfer

Some sulfate-reducing bacteria (SRB), mainly belonging to the Desulfovibrionaceae family, have evolved the capability to conserve energy through microbial extracellular electron transfer (EET), suggesting that this process may be more widespread than previously believed. While previous evidence has shown that mobile genetic elements drive the plasticity and evolution of SRB and iron-reducing bacteria (FeRB), few have investigated the shared molecular mechanisms related to EET. To address this, we analyzed the prevalence and abundance of EET elements and how they contributed to their differentiation among 42 members of the Desulfovibrionaceae family and 23 and 59 members of Geobacteraceae and Shewanellaceae, respectively. Proteins involved in EET, such as the cytochromes PpcA and CymA, the outer membrane protein OmpJ, and the iron-sulfur cluster-binding CbcT, exhibited widespread distribution within Desulfovibrionaceae. Some of these showed modular diversification. Additional evidence revealed that horizontal gene transfer was involved in the acquiring and losing of critical genes, increasing the diversification and plasticity between the three families. The results suggest that specific EET genes were widely disseminated through horizontal transfer, where some changes reflected environmental adaptations. These findings enhance our comprehension of the evolution and distribution of proteins involved in EET processes, shedding light on their role in iron and sulfur biogeochemical cycling.

Multi-omics analyses provide insights into the sulfur metabolism of a novel deep-sea sulfate-reducing bacterium

Sulfate-reducing bacteria (SRB) are ubiquitously distributed across various biospheres and play key roles in global sulfur and carbon cycles. However, few deep-sea SRB have been cultivated and studied in situ, limiting our understanding of the true metabolism of deep-sea SRB. Here, we firstly clarified the high abundance of SRB in deep-sea sediments and successfully isolated a sulfate-reducing bacterium (zrk46) from a cold seep sediment. Our genomic, physiological, and phylogenetic analyses indicate that strain zrk46 is a novel species, which we propose as Pseudodesulfovibrio serpens. We found that supplementation with sulfate, thiosulfate, or sulfite promoted strain zrk46 growth by facilitating energy production through the dissimilatory sulfate reduction, which was coupled to the oxidation of organic matter in both laboratory and deep-sea conditions. Moreover, in situ metatranscriptomic results confirmed that other deep-sea SRB also performed the dissimilatory sulfate reduction, strongly suggesting that SRB may play undocumented roles in deep-sea sulfur cycling.

Chemical-physical parameters and microbial community changes induced by electrodes polarization inhibit PCB dechlorination in a marine sediment

Microbial reductive dechlorination of organohalogenated pollutants is often limited by the scarcity of electron donors, that can be overcome with microbial electrochemical technologies (METs). In this study, polarized electrodes buried in marine sediment microcosms were investigated to stimulate PCB reductive dechlorination under potentiostatic (-0.7 V vs Ag/AgCl) and galvanostatic conditions (0.025 mA·cm-2-0.05 mA·cm-2), using graphite rod as cathode and iron plate as sacrificial anode. A single circuit and a novel two antiparallel circuits configuration (2AP) were investigated. Single circuit polarization impacted the sediment pH and redox potential (ORP) proportionally to the intensity of the electrical input and inhibited PCB reductive dechlorination. The effects on the sediment's pH and ORP, along with the inhibition of PCB reductive dechlorination, were mitigated in the 2AP system. Electrodes polarization stimulated sulfate-reduction and promoted the enrichment of bacterial clades potentially involved in sulfate-reduction as well as in sulfur oxidation. This suggested the electrons provided were consumed by competitors of organohalide respiring bacteria and specifically sequestered by sulfur cycling, which may represent the main factor limiting the applicability of METs for stimulating PCB reductive dechlorination in marine sediments.

Synergistic effects of chemical additives and mature compost on reducing H2S emission during kitchen waste composting

Additives could improve composting performance and reduce gaseous emission, but few studies have explored the synergistic of additives on H2S emission and compost maturity. This research aims to make an investigation about the effects of chemical additives and mature compost on H2S emission and compost maturity of kitchen waste composting. The results showed that additives increased the germination index value and H2S emission reduction over 15 days and the treatment with both chemical additives and mature compost achieved highest germination index value and H2S emission reduction (85%). Except for the treatment with only chemical additives, the total sulfur content increased during the kitchen waste composting. The proportion of effective sulfur was higher with the addition of chemical additives, compared with other groups. The relative abundance of H2S-formation bacterial (Desulfovibrio) was reduced and the relative abundance of bacterial (Pseudomonas and Paracoccus), which could convert sulfur-containing substances and H2S to sulfate was improved with additives. In the composting process with both chemical additives and mature compost, the relative abundance of Desulfovibrio was lowest, while the relative abundance of Pseudomonas and Paracoccus was highest. Taken together, the chemical additives and mature compost achieved H2S emission reduction by regulating the dynamics of microbial community.

Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments

Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.

Deep-sea in situ and laboratory multi-omics provide insights into the sulfur assimilation of a deep-sea Chloroflexota bacterium

Chloroflexota bacteria are abundant and globally distributed in various deep-sea ecosystems. It has been reported based on metagenomics data that two deep-sea Chloroflexota lineages (the SAR202 group and Dehalococcoidia class) have the potential to drive sulfur cycling. However, the absence of cultured Chloroflexota representatives is a significant bottleneck toward understanding their contribution to the deep-sea sulfur cycling. In this study, we find that Phototrophicus methaneseepsis ZRK33 isolated from deep-sea sediment has a heterotrophic lifestyle and can assimilate sulfate and thiosulfate. Using combined physiological, genomic, proteomic, and in situ transcriptomic methods, we find that strain ZRK33 can perform assimilatory sulfate reduction in both laboratory and deep-sea conditions. Metabolism of sulfate or thiosulfate by strain ZRK33 significantly promotes the transport and degradation of various macromolecules and thereby stimulates the energy production. In addition, metagenomic results show that genes associated with assimilatory and dissimilatory sulfate reduction are ubiquitously distributed in the metagenome-assembled genomes of Chloroflexota members derived from deep-sea sediments. Metatranscriptomic results also show that the expression levels of related genes are upregulated, strongly suggesting that Chloroflexota bacteria may play undocumented roles in deep-sea sulfur cycling.

IMPORTANCE

The cycling of sulfur is one of Earth's major biogeochemical processes and is closely related to the energy metabolism of microorganisms living in the deep-sea cold seep and hydrothermal vents. To date, some of the members of Chloroflexota are proposed to play a previously unrecognized role in sulfur cycling. However, the sulfur metabolic characteristics of deep-sea Chloroflexota bacteria have never been reported, and remain to be verified in cultured deep-sea representatives. Here, we show that the deep-sea Chloroflexota bacterium ZRK33 can perform sulfate assimilation in both laboratory and deep-sea conditions, which expands our knowledge of the sulfur metabolic potential of deep-sea Chloroflexota bacteria. We also show that the genes associated with assimilatory and dissimilatory sulfate reduction ubiquitously distribute in the deep-sea Chloroflexota members, providing hints to the roles of Chloroflexota bacteria in deep-sea sulfur biogeochemical cycling.

Nitrate and oxygen significantly changed the abundance rather than structure of sulphate-reducing and sulphur-oxidising bacteria in water retrieved from petroleum reservoirs

Sulphate-reducing bacteria (SRB) are the main culprits of microbiologically influenced corrosion in water-flooding petroleum reservoirs, but some sulphur-oxidising bacteria (SOB) are stimulated when nitrate and oxygen are injected, which control the growth of SRB. This study aimed to determine the distributions of SRB and SOB communities in injection-production systems and to analyse the responses of these bacteria to different treatments involving nitrate and oxygen. Desulfovibrio, Desulfobacca, Desulfobulbus, Sulfuricurvum and Dechloromonas were commonly detected via 16S rRNA gene sequencing. Still, no significant differences were observed for either the SRB or SOB communities between injection and production wells. Three groups of water samples collected from different sampling sites were incubated. Statistical analysis of functional gene (dsrB and soxB) clone libraries and quantitative polymerase chain reaction showed that the SOB community structures were more strongly affected by the nitrate and oxygen levels than SRB clustered according to the sampling site; moreover, both the SRB and SOB community abundances significantly changed. Additionally, the highest SRB inhibitory effect and the lowest dsrB/soxB ratio were obtained under high concentrations of nitrate and oxygen in the three groups, suggesting that the synergistic effect of nitrate and oxygen level was strong on the inhibition of SRB by potential SOB.

Black soldier fly larvae recruit functional microbiota into the intestines and residues to promote lignocellulosic degradation in domestic biodegradable waste

Lignocellulose is an important component of domestic biodegradable waste (DBW), and its complex structure makes it an obstacle in the biological treatment of DBW. Here, we identify black soldier fly larvae (Hermetia illucens L., BSFL) as a bioreactor for lignocellulose degradation in DBW based on their ability to effectively recruit lignocellulose-degrading bacteria. This study mainly examined the lignocellulose degradation, dynamic succession of the microbial community, gene expression of carbohydrate-active enzymes (CAZymes), and co-occurrence network analysis. Investigation of lignocellulose degradation by BSFL within 14 days indicated that the lignocellulose biodegradation rate in the larvae treatment (LT, 26.5%) group was higher than in natural composting (NC, 4.06%). In order to gain a more comprehensive understanding of microbiota, we conducted metagenomic sequencing of larvae intestines (LI), along with the LT and NC. The relative abundance of lignocellulose-degrading bacteria and CAZymes genes in LT and LI were higher than those in NC based on metagenomics sequencing. Importantly, genes coding cellulase and hemicellulase in LI were 3.36- and 2.79-fold higher, respectively, than that in LT, while the ligninase genes in LT were 1.82-fold higher than in LI. A co-occurrence network analysis identified Enterocluster and Luteimonas as keystone taxa in larvae intestines and residues, respectively, with a synergistic relationship to lignocellulose-degrading bacteria. The mechanism of recruiting functional bacteria through the larvae intestines promoted lignocellulose degradation in DBW, improving the efficiency of BSFL biotechnology and resource regeneration.

The hind information: Exploring the impact of physical damage on mask microbial composition in the aquatic environment

Due to poor management and the lack of environmental awareness, lots of masks (an emerging form of plastic pollution) are discarded into the environment during the COVID-19, thereby jeopardizing the health of humans and the environment. Our study introduces a novel perspective by examining the impact of physical damage on the microbial composition of masks in the water environment. We focus on the variations in biofilm formation on each layer of both damaged and undamaged masks, which allows us to understand more about the biofilm on each layer and the significant changes that occur when masks are physically damaged. Research has shown that the community structure of microorganisms on discarded masks can be altered in just ten days, showing an evolution from undifferentiated pioneer colonizing species ("non-picky") to adaptive dominant species ("picky"). Especially, considering that discarded masks were inevitably damaged, we found that the biomass on the damaged samples is 1.62-2.38 times higher than that of the undamaged samples, respectively. Moreover, the microbial community structure on it was also significantly different. Genes involved in biogeochemical cycles of nutrients are more enriched in damaged masks. When damaged, the colonization process and community structure in the middle layer significantly differ from those in the inner and outer layers and even enrich more pathogenic bacteria. Based on the above, it is evident that the environmental risk of masks cannot be assessed as a whole, and the middle layer carries a higher risk.

Site-specific response of sediment microbial community to supplementation of polyhydroxyalkanoates as biostimulants for PCB reductive dechlorination

The use of biodegradable plastics is constantly raising, increasing the likeliness for these polymers to end up in the environment. Environmental applications foreseeing the intentional release of biodegradable plastics have been also recently proposed, e.g., for polyhydroxyalkanoates (PHAs) acting as slow hydrogen releasing compounds to stimulate microbial reductive dehalogenation processes. However, the effects of their release into the environment on the ecosystems still need to be thoroughly explored. In this work, the use of PHAs to enhance the microbial reductive dechlorination of polychlorobiphenyls (PCBs) and their impact on the metabolic and compositional features of the resident microbial community have been investigated in laboratory microcosms of a polluted marine sediment from Mar Piccolo (Taranto, Italy), and compared with recent findings on a different contaminated marine sediment from Pialassa della Baiona (Ravenna, Italy). A decreased biostimulation efficiency of PHAs on PCBs reductive dechlorination was observed in the sediment from Mar Piccolo, with respect to the sediment from Pialassa della Baiona, suggesting that the sediments' physical-chemical characteristics and/or the biodiversity and composition of its microbial community might play a key role in determining the outcome of this biostimulation strategy. Regardless of the sediment origin, PHAs were found to have a specific and pervasive effect on the sediment microbial community, reducing its biodiversity, defining a newly arranged microbial core of primary degraders and consequently affecting, in a site-specific way, the abundance of subdominant bacteria, possibly cross-feeders. Such potential to dramatically change the structure of autochthonous microbial communities should be carefully considered, since it might have secondary effects, e.g., on the natural biogeochemical cycles.

In situ enrichment of sulphate-reducing microbial communities with different carbon sources stimulating the acid mine drainage sediments

The applications of sulphate-reducing microorganisms (SRMs) in acid mine drainage (AMD) treatment systems have received extensive attention due to their ability to reduce sulphate and stabilize metal(loid)s. Despite great phylogenetic diversity of SRMs, only a few have been used in AMD treatment bioreactors. In situ enrichment could be an efficient approach to select new effective SRMs for AMD treatment. Here, we performed in situ enrichment of SRMs in highly stratified AMD sediment cores using different kinds of carbon source mixture. The dsrAB (dissimilatory sulfite reductase) genes affiliated with nine phyla (two archaeal and seven bacterial phyla) and 26 genera were enriched. Remarkably, those genes affiliated with Aciduliprofundum and Vulcanisaeta were enriched in situ in AMD-related environments for the first time, and their relative abundances were negatively correlated with pH. Furthermore, 107 dsrAB-containing metagenome-assembled genomes (MAGs) were recovered from metagenomic datasets, with 14 phyla (two archaeal and 12 bacterial phyla) and 15 genera. The relative abundances of MAGs were positively correlated with total carbon and sulphate contents. Our findings expanded the diversity of SRMs that can be enriched in AMD sediment, and revealed the physiochemical properties that might affect the growth of SRMs, which provided guidance for AMD treatment bioreators.

Syntrophic entanglements for propionate and acetate oxidation under thermophilic and high-ammonia conditions

Propionate is a key intermediate in anaerobic digestion processes and often accumulates in association with perturbations, such as elevated levels of ammonia. Under such conditions, syntrophic ammonia-tolerant microorganisms play a key role in propionate degradation. Despite their importance, little is known about these syntrophic microorganisms and their cross-species interactions. Here, we present metagenomes and metatranscriptomic data for novel thermophilic and ammonia-tolerant syntrophic bacteria and the partner methanogens enriched in propionate-fed reactors. A metagenome for a novel bacterium for which we propose the provisional name 'Candidatus Thermosyntrophopropionicum ammoniitolerans' was recovered, together with mapping of its highly expressed methylmalonyl-CoA pathway for syntrophic propionate degradation. Acetate was degraded by a novel thermophilic syntrophic acetate-oxidising candidate bacterium. Electron removal associated with syntrophic propionate and acetate oxidation was mediated by the hydrogen/formate-utilising methanogens Methanoculleus sp. and Methanothermobacter sp., with the latter observed to be critical for efficient propionate degradation. Similar dependence on Methanothermobacter was not seen for acetate degradation. Expression-based analyses indicated use of both H2 and formate for electron transfer, including cross-species reciprocation with sulphuric compounds and microbial nanotube-mediated interspecies interactions. Batch cultivation demonstrated degradation rates of up to 0.16 g propionate L-1 day-1 at hydrogen partial pressure 4-30 Pa and available energy was around -20 mol-1 propionate. These observations outline the multiple syntrophic interactions required for propionate oxidation and represent a first step in increasing knowledge of acid accumulation in high-ammonia biogas production systems.

Relating bacterial dynamics and functions to greenhouse gas and odor emissions during facultative heap composting of four kinds of livestock manure

Although facultative heap composting is widely used in small and medium-sized livestock farms in China, there are few studies on greenhouse gas (GHG) and odor emissions from this composting system. This study focused on GHG and odor emissions from facultative heap composting of four types of livestock manure and revealed the relationship between the gaseous emissions and microbial communities. Results showed that pig, sheep, and cow manure reached high compost maturity (germination index (GI) > 70%), whereas chicken manure had higher phytotoxicity (GI = 0.02%) with higher electrical conductivity and a lower carbon/nitrogen ratio. The four manure types significantly differed in the total GHG emission, with the following pattern: pig manure (308 g CO2-eq·kg-1) > cow manure (146 g CO2-eq·kg-1) > chicken manure (136 g CO2-eq·kg-1) > sheep manure (95 g CO2-eq·kg-1). Bacterium with Fermentative, Methanotrophy and Nitrite respiratory functions (e.g. Pseudomonas and Lactobacillus) are enriched within the pile so that more than 90% of the GHGs are produced in the early (days 0-15) and late (days 36-49) composting periods. CO2 contributed more than 90% in the first 35 d, N2O contributed 40-75% in the late composting period, and CH4 contributed less than 8.0%. NH3 and H2S emissions from chicken and pig manure were 4.8 times those from sheep and cow manure. Overall, the gas emissions from facultative heap composting significantly differed among the four manure types due to the significant differences in their physicochemical properties and microbial communities.

Behaviors and mechanisms of microbially-induced corrosion in metal-based water supply pipelines: A review

Microbially-induced corrosion (MIC) is unstoppable and extensively spread throughout drinking water distribution systems (DWDSs) as the cause of pipe leakage and deteriorating water quality. For maintaining drinking water safety and reducing capital inputs in pipe usage, the possible consequences from MIC in DWDSs is still a research hotspot. Although most studies have investigated the effects of changing environmental factors on MIC corrosion, the occurrence of MIC in DWDSs has not been discussed sufficiently. This review aims to fill this gap by proposing that the formation of deposits with microbial capture may be a source of MIC in newly constructed DWDSs. The microbes early attaching to the rough pipe surface, followed by chemically and microbially-induced mineral deposits which confers resistance to disinfectants is ascribed as the first step of MIC occurrence. MIC is then activated in the newly-built, viable, and accessible microenvironment while producing extracellular polymers. With longer pipe service, oligotrophic microbes slowly grow, and metal pipe materials gradually dissolve synchronously with electron release to microbes, resulting in pipe-wall damage. Different corrosive microorganisms using pipe material as a reaction substrate would directly or indirectly cause different types of corrosion. Correspondingly, the formation of scale layers may reflect the distribution of microbial species and possibly biogenic products. It is therefore assumed that the porous and loose layer is an ideal microbial-survival environment, capable of providing diverse and sufficient ecological niches. The usage and chelation of metabolic activities and metabolites, such as acetic, oxalic, citric and glutaric acids, may lead to the formation of a porous scale layer. Therefore, the microbial interactions within the pipe scale reinforce the stability of microbial communities and accelerate MIC. Finally, a schematic model of the MIC process is presented to interpret MIC from its onset to completion.

Bacterial Sulfate Reduction Facilitates Iodine Mobilization in the Deep Confined Aquifer of the North China Plain

Bacterial sulfate reduction plays a crucial role in the mobilization of toxic substances in aquifers. However, the role of bacterial sulfate reduction on iodine mobilization in geogenic high-iodine groundwater systems has been unexplored. In this study, the enrichment of groundwater δ34SSO4 (15.56 to 69.31‰) and its significantly positive correlation with iodide and total iodine concentrations in deep groundwater samples of the North China Plain suggested that bacterial sulfate reduction participates in the mobilization of groundwater iodine. Similar significantly positive correlations were further observed between the concentrations of iodide and total iodine and the relative abundance of the dsrB gene by qPCR, as well as the composition and abundance of sulfate-reducing bacteria (SRB) predicted from 16S rRNA gene high-throughput sequencing data. Subsequent batch culture experiments by the SRB Desulfovibrio sp. B304 demonstrated that SRB could facilitate iodine mobilization through the enzyme-driven biotic and sulfide-driven abiotic reduction of iodate to iodide. In addition, the dehalogenation of organoiodine compounds by SRB and the reductive dissolution of iodine-bearing iron minerals by biogenic sulfide could liberate bound or adsorbed iodine into groundwater. The role of bacterial sulfate reduction in iodine mobilization revealed in this study provides new insights into our understanding of iodide enrichment in iodine-rich aquifers worldwide.

Transcriptome-wide marker gene expression analysis of stress-responsive sulfate-reducing bacteria

Sulfate-reducing bacteria (SRB) are terminal members of any anaerobic food chain. For example, they critically influence the biogeochemical cycling of carbon, nitrogen, sulfur, and metals (natural environment) as well as the corrosion of civil infrastructure (built environment). The United States alone spends nearly $4 billion to address the biocorrosion challenges of SRB. It is important to analyze the genetic mechanisms of these organisms under environmental stresses. The current study uses complementary methodologies, viz., transcriptome-wide marker gene panel mapping and gene clustering analysis to decipher the stress mechanisms in four SRB. Here, the accessible RNA-sequencing data from the public domains were mined to identify the key transcriptional signatures. Crucial transcriptional candidate genes of Desulfovibrio spp. were accomplished and validated the gene cluster prediction. In addition, the unique transcriptional signatures of Oleidesulfovibrio alaskensis (OA-G20) at graphene and copper interfaces were discussed using in-house RNA-sequencing data. Furthermore, the comparative genomic analysis revealed 12,821 genes with translation, among which 10,178 genes were in homolog families and 2643 genes were in singleton families were observed among the 4 genomes studied. The current study paves a path for developing predictive deep learning tools for interpretable and mechanistic learning analysis of the SRB gene regulation.

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.

Intensive management facilitates bacterial invasion on soil microbial community

Intensive management has greatly altered natural forests, especially forests around the world are increasingly being converted into economic plantations. Soil microbiota are critical for community functions in all ecosystems, but the effects of microbial disturbance during economic plantation remain unclear. Here, we used Escherichia coli O157:H7, a model pathogenic species for bacterial invasion, to assess the invasion impacts on the soil microbial community under intensive management. The E. coli invasion was tracked for 135 days to explore the instant and legacy impacts on the resident community. Our results showed that bamboo economic plantations altered soil abiotic and biotic properties, especially increasing pH and community diversity. Higher pH in bamboo soils resulted in longer pathogen survivals than in natural hardwood soils, indicating that pathogen suppression during intensive management should arouse our attention. A longer invasion legacy effect on the resident community (P < 0.05) were found in bamboo soils underlines the need to quantify the soil resilience even when the invasion was unsuccessful. Deterministic processes drove community assembly in bamboo plantations, and this selection acted more strongly during by E. coli invasion than in hardwood soils. We also showed more associated co-occurrence patterns in bamboo plantations, suggesting more complex potential interactions within the microbial community. Apart from community structure, community functions are also strongly related to the resident species associated with invaders. These findings provide new perspectives to understand intensive management facilitates the bacterial invasion, and the impacts would leave potential risks on environmental and human health.

Insight into the metabolic potential and ecological function of a novel Magnetotactic Nitrospirota in coral reef habitat

Magnetotactic bacteria (MTB) within the Nitrospirota phylum play important roles in biogeochemical cycles due to their outstanding ability to biomineralize large amounts of magnetite magnetosomes and intracellular sulfur globules. For several decades, Nitrospirota MTB were believed to only live in freshwater or low-salinity environments. While this group have recently been found in marine sediments, their physiological features and ecological roles have remained unclear. In this study, we combine electron microscopy with genomics to characterize a novel population of Nitrospirota MTB in a coral reef area of the South China Sea. Both phylogenetic and genomic analyses revealed it as representative of a novel genus, named as Candidatus Magnetocorallium paracelense XS-1. The cells of XS-1 are small and vibrioid-shaped, and have bundled chains of bullet-shaped magnetite magnetosomes, sulfur globules, and cytoplasmic vacuole-like structures. Genomic analysis revealed that XS-1 has the potential to respire sulfate and nitrate, and utilize the Wood-Ljungdahl pathway for carbon fixation. XS-1 has versatile metabolic traits that make it different from freshwater Nitrospirota MTB, including Pta-ackA pathway, anaerobic sulfite reduction, and thiosulfate disproportionation. XS-1 also encodes both the cbb₃-type and the aa₃-type cytochrome c oxidases, which may function as respiratory energy-transducing enzymes under high oxygen conditions and anaerobic or microaerophilic conditions, respectively. XS-1 has multiple copies of circadian related genes in response to variability in coral reef habitat. Our results implied that XS-1 has a remarkable plasticity to adapt the environment and can play a beneficial role in coral reef ecosystems.

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.

Biomineralization behavior and mechanism of microbial-mediated removal of arsenate from water

The microbial-mediated removal of arsenate by biomineralization received much attention, but the molecular mechanism of Arsenic (As) removal by mixed microbial populations remains to be elucidated. In this study, a process for the arsenate treatment using sulfate-reducing bacteria (SRB) containing sludge was constructed, and the performance of As removal was investigated at different molar ratios of AsO₄^3- to SO₄^2-. It was found that biomineralization mediated by SRB could achieve the simultaneous removal of arsenate and sulfate from wastewater but only occurred when microbial metabolic processes were involved. The reducing ability of the microorganisms for the sulfate and arsenate was equivalent, so the precipitates produced at the molar ratio of AsO₄^3- to SO₄^2-of 2:3 were most significant. X-ray absorption fine structure (XAFS) spectroscopy was the first time used to determine the molecular structure of the precipitates which were confirmed to be orpiment (As₂S₃). Combined with the metagenomics analysis, the microbial metabolism mechanism of simultaneous removal of sulfate and arsenate by the mixed microbial population containing SRB was revealed, that is, the sulfate and As(V) were reduced by microbial enzymes to produce S^2- and As(III) to further form As₂S₃ precipitates. This research provided a reference and theoretical foundation for the simultaneous removal of sulfate and arsenic mediated by SRB-containing sludge in wastewater treatment.

Sulfur: a neglected driver of the increased abundance of antibiotic resistance genes in agricultural reclaimed subsidence land located in coal mines with high phreatic water levels

Due to the shallow burial of groundwater in coal mines with a high phreatic water level, a large area of subsidence lakes is formed after the mine collapses. Agricultural and fishery reclamation activities have been carried out, which introduced antibiotics and exacerbated the contamination of antibiotic resistance genes (ARGs), but this has received limited attention. This study analyzed ARG occurrence in reclaimed mining areas, the key impact factors, and the underlying mechanism. The results show that sulfur is the most critical factor impacting the abundance of ARGs in reclaimed soil, which is due to changes in the microbial community. The species and abundance of ARGs in the reclaimed soil were higher than those in the controlled soil. The relative abundances of most ARGs increased with the depth of reclaimed soil (from 0 to 80 cm). In addition, the microbial structures of the reclaimed and controlled soils were significantly different. Proteobacteria, was the most dominant microbial phylum in the reclaimed soil. This difference is likely related to the high abundance of sulfur metabolism functional genes in the reclaimed soil. Correlation analysis showed that the differences in ARGs and microorganisms in the two soil types were highly correlated with the sulfur content. High levels of sulfur promoted the proliferation of sulfur-metabolizing microbial populations such as Proteobacteria and Gemmatimonadetes in the reclaimed soils. Remarkably, these microbial phyla were the main antibiotic-resistant bacteria in this study, and their proliferation created conditions for the enrichment of ARGs. Overall, this study underscores the risk of the abundance and spread of ARGs driven by high-level sulfur in reclaimed soils and reveals the mechanisms.

Effect of moisture content, aeration rate, and C/N on maturity and gaseous emissions during kitchen waste rapid composting

To determine factors affecting compost maturity and gaseous emissions during the rapid composting of kitchen waste, an orthogonal test was conducted with three factors: moisture content (MC) (55%, 60%, 65%), aeration rate (AR) (0.3,0.6 and 0.9 L·kg^-1DM·min^-1) and C/N ratio (21, 24, 27). The results showed that the importance of factors affecting compost maturity was: C/N > AR > MC, optimal conditions were: C/N of 24, AR of 0.3 L·kg^-1DM·min^-1and MC of 65%. For gaseous emissions, the sequence of essential factors affecting NH₃ emissions was: C/N > MC > AR, and the optimal parameters for NH₃ reduction were: C/N of 27, MC of 65%, and AR of L·kg^-1DM·min^-1. The important factors affecting N₂O and H₂S emissions are both: MC > C/N > AR, while their best parameters were different. The optimal parameters for N₂O emission reduction were MC of 60%, AR of 0.3 L·kg^-1DM·min^-1 and C/N of 24, while these for H₂S were MC of 55%, AR of 0.3 L·kg^-1DM·min^-1 and C/N of 21. The C/N mainly affected the compost maturity and AR further affected the maturity and pollutant gas emissions by influencing the temperature and O₂ content. Considering comprehensively the maturity and gaseous reduction, the optimal control parameters were: MC of 60%-65%, AR of L·kg^-1DM·min^-1, and C/N of 24-27.

Text-Mining to Identify Gene Sets Involved in Biocorrosion by Sulfate-Reducing Bacteria: A Semi-Automated Workflow

A significant amount of literature is available on biocorrosion, which makes manual extraction of crucial information such as genes and proteins a laborious task. Despite the fast growth of biology related corrosion studies, there is a limited number of gene collections relating to the corrosion process (biocorrosion). Text mining offers a potential solution by automatically extracting the essential information from unstructured text. We present a text mining workflow that extracts biocorrosion associated genes/proteins in sulfate-reducing bacteria (SRB) from literature databases (e.g., PubMed and PMC). This semi-automatic workflow is built with the Named Entity Recognition (NER) method and Convolutional Neural Network (CNN) model. With PubMed and PMCID as inputs, the workflow identified 227 genes belonging to several Desulfovibrio species. To validate their functions, Gene Ontology (GO) enrichment and biological network analysis was performed using UniprotKB and STRING-DB, respectively. The GO analysis showed that metal ion binding, sulfur binding, and electron transport were among the principal molecular functions. Furthermore, the biological network analysis generated three interlinked clusters containing genes involved in metal ion binding, cellular respiration, and electron transfer, which suggests the involvement of the extracted gene set in biocorrosion. Finally, the dataset was validated through manual curation, yielding a similar set of genes as our workflow; among these, hysB and hydA, and sat and dsrB were identified as the metal ion binding and sulfur metabolism genes, respectively. The identified genes were mapped with the pangenome of 63 SRB genomes that yielded the distribution of these genes across 63 SRB based on the amino acid sequence similarity and were further categorized as core and accessory gene families. SRB's role in biocorrosion involves the transfer of electrons from the metal surface via a hydrogen medium to the sulfate reduction pathway. Therefore, genes encoding hydrogenases and cytochromes might be participating in removing hydrogen from the metals through electron transfer. Moreover, the production of corrosive sulfide from the sulfur metabolism indirectly contributes to the localized pitting of the metals. After the corroboration of text mining results with SRB biocorrosion mechanisms, we suggest that the text mining framework could be utilized for genes/proteins extraction and significantly reduce the manual curation time.

Effects of carbon/nitrogen ratio and aeration rate on the sheep manure composting process and associated gaseous emissions

There are several issues such as low maturity degree of compost product and severe pollution gas emissions during the composting process. Carbon/Nitrogen (C/N) ratio and aeration rate (AR) are the most important factors affecting the composting performance. According to the results of previous studies, the proper C/N ratio and AR were 20-30:1 and 0.1-0.4 L kg^-1 DM·min^-1, respectively. Therefore, a lab-scale experiment was conducted to investigate the effects of C/N ratio and AR on sheep manure composting process and associated gaseous emissions. The initial C/N ratio in this experiment were set at 23, 26 and 29 to simulate the C/N ratio at low, medium and high levels. The AR were decided at 0.12, 0.24 and 0.36 L kg^-1 DM·min^-1 to simulate the aeration at low, middle and high levels. The results showed that as the C/N ratio or AR increased, the methane (CH₄) and hydrogen sulfide (H₂S) emissions decreased. The nitrous oxide (N₂O) emission peaked at the low C/N ratio or AR treatments. The total greenhouse gas (GHG) emissions decreased with the increase of C/N ratio or AR, and the maximum value occurred in the treatment with C/N ratio 23 and AR 0.24 L kg^-1 DM·min^-1. In the treatment with C/N ratio 26 and AR 0.36 L kg^-1 DM·min^-1, the GI value of compost product was the highest (about 250%), and the total greenhouse effect was the lowest (2.36 kg CO2-eq·t^-1 DM). Therefore, considering reduction of pollution gas emissions and improvement of the quality of compost products comprehensively, the optimum conditions were initial C/N ratio 26 and AR 0.36 L kg^-1 DM·min^-1 during the co-composting of sheep manure and cornstalks. In addition, the key physicochemical factors and eight key bacterial communities were determined to regulate compost maturity and pollution gas emissions during the sheep manure composting, which could provide scientific support and theoretical reference for controlling pollution gas emissions and obtaining high quality sheep manure compost products.

Gut microbiota involved in desulfation of sulfated progesterone metabolites: A potential regulation pathway of maternal bile acid homeostasis during pregnancy

Abnormally raised circulating bile acids (BA) during pregnancy threat fetal and offspring health. Our previous study has identified sulfated progesterone metabolites (PMSs) in part account for dysregulation of maternal BA homeostasis during pregnancy, however, limited intervention strategies to remedy increased serum BA through PMSs during pregnancy are available. The purpose of this study is to test the feasibility of manipulating BA homeostasis and progesterone metabolism through steering gut microbiota. A total of 19 pregnant sows were randomly treated with standard diet or vancomycin-supplemented diet, to investigate the intercorrelation of PMSs, intestinal microbiota, and maternal BA metabolism from day 60 of gestation (G60) until farrowing (L0). Pregnant mice orally gavaged with epiallopregnanolone sulfate (PM5S) or vehicle and nonpregnant mice were sampled and further analyzed to verify the effect of PM5S on maternal BA metabolism. The present study revealed that oral vancomycin reduced maternal fasting serum total BA (TBA) levels and postprandial serum TBA levels at day 90 of gestation (G90). BA profile analysis showed the decreased TBA after vancomycin treatment was attributed to the decrease of primary BA and secondary BA, especially hyodeoxycholic acid (HDCA). By using newly developed UPLC-MS/MS methods, we found vancomycin increased fecal excretion of allopregnanolone sulfate (PM4S) and PM5S during late gestation and thus maintaining the relative stability of serum PM4S and PM5S, which play an important role in BA metabolism. Further study in mice showed that pregnant mice have higher serum and liver TBA levels compared with nonpregnant mice, and PM5S administration induced higher gallbladder TBA levels and TBA pool in pregnant mice. In addition, after oral vancomycin, the continuously decreased Parabacteroides genus, potentially enriched with genes encoding steroids sulfatase, may explain the increased fecal PMSs excretion in pregnant sows. Taken together, our study provides the evidence that pregnancy-induced elevation of BA levels in sow is likely regulated by manipulation of gut microbiota, which offer new insights into the prevention and treatment of disrupted BA homeostasis during pregnancy by targeting specific microbiota.

Hydrocarbon bioremediation on Arctic shorelines: Historic perspective and roadway to the future

Climate change has become one of the greatest concerns of the past few decades. In particular, global warming is a growing threat to the Canadian high Arctic and other polar regions. By the middle of this century, an increase in the annual mean temperature of 1.8 °C-2.7 °C for the Canadian North is predicted. Rising temperatures lead to a significant decrease of the sea ice area covered in the Northwest Passage. As a consequence, a surge of maritime activity in that region increases the risk of hydrocarbon pollution due to accidental fuel spills. In this review, we focus on bioremediation approaches on Arctic shorelines. We summarize historical experimental spill studies conducted at Svalbard, Baffin Island, and the Kerguelen Archipelago, and review contemporary studies that used modern omics techniques in various environments. We discuss how omics approaches can facilitate our understanding of Arctic shoreline bioremediation and identify promising research areas that should be further explored. We conclude that specific environmental conditions strongly alter bioremediation outcomes in Arctic environments and future studies must therefore focus on correlating these diverse parameters with the efficacy of hydrocarbon biodegradation.

Production of bio-stable fluid sediment from accumulation of cyanobacterial bloom biomass under various water depths

While fluid sediments normally formed through hydrodynamic erosion and transport was well known, the fluid sediments caused by organic matter accumulation and degradation in eutrophic lakes was rarely investigated. Here, the effects of cyanobacterial bloom biomass (CBB) accumulation and water depth on the occurrence of fluid sediments were studied. Within 30 days of experiments, the variation of sediment height firstly increased to the maximum with rising in water depth, then decreased due to the high hydraulic pressure. While the surface sediments density decreased slightly from 1.35 g cm^-3 to around 1.32 g cm^-3 without CBB accumulation, and CBB accumulation led to lower density (around 1.02 g cm^-3) but higher shear stress of sediments. Through analyzing the extracellular polymeric substances (EPS), it was found that CBB accumulation improved the polysaccharide/protein ratios of sediment. The infrared analysis further indicated that the bound-EPS could protect fluid sediments bio-stabilization. Meanwhile, the enriched Acinetobacter, Pseudomonas in sediments with CBB accumulation might play roles in EPS production, which benefited the bio-stabilization of fluid sediments. Furthermore, the stability of fluid sediments increased with increase in water depth, and the resuspension of biological fluid sediments would occur more likely in the low water depth area. Altogether, this study reported the formation and stability of the biological fluid sediments in eutrophic shallow lakes, and could help provide clues against sediment resuspension in lake ecosystems.

Microbial associations for bioremediation. What does "microbial consortia" mean?

Microbial associations arise as useful tools in several biotechnological processes. Among them, bioremediation of contaminated environments usually takes advantage of these microbial associations. Despite being frequently used, these associations are indicated using a variety of expressions, showing a lack of consensus by specialists in the field. The main idea of this work is to analyze the variety of microbial associations referred to as "microbial consortia" (MC) in the context of pollutants biodegradation and bioremediation. To do that, we summarize the origin of the term pointing out the features that an MC is expected to meet, according to the opinion of several authors. An analysis of related bibliography was done seeking criteria to rationalize and classify MC in the context of bioremediation. We identify that the microbe's origin and the level of human intervention are usually considered as a category to classify them as natural microbial consortia (NMC), artificial microbial consortia (AMC), and synthetic microbial consortia (SMC). In this sense, NMC are those associations composed by microorganisms obtained from a single source while AMC members come from different sources. SMC are a class of AMC in which microbial composition is defined to accomplish a certain specific task. We propose that the effective or potential existence of the interaction among MC members in the source material should be considered as a category in the classification as well, in combination with the origin of the source and level of intervention. Cross-kingdom MC and new developments were also considered. Finally, the existence of grey zones in the limits between each proposed microbial consortia category is addressed. KEY POINTS: • Microbial consortia for bioremediation can be obtained through different methods. • The use of the term "microbial consortia" is unclear in the specialized literature. • We propose a simplified classification for microbial consortia for bioremediation.

Extracellular proteins of Desulfovibrio vulgaris as adsorbents and redox shuttles promote biomineralization of antimony

Biomineralization is the key process governing the biogeochemical cycling of multivalent metals in the environment. Although some sulfate-reducing bacteria (SRB) are recently recognized to respire metal ions, the role of their extracellular proteins in the immobilization and redox transformation of antimony (Sb) remains elusive. Here, a model strain Desulfovibrio vulgaris Hildenborough (DvH) was used to study microbial extracellular proteins of functions and possible mechanisms in Sb(V) biomineralization. We found that the functional groups (N-H, CO, O-CO, NH₂-R and RCOH/RCNH₂) of extracellular proteins could adsorb and fix Sb(V) through electrostatic attraction and chelation. DvH could rapidly reduce Sb(V) adsorbed on the cell surface and form amorphous nanometer-sized stibnite and/or antimony trioxide, respectively with sulfur and oxygen. Proteomic analysis indicated that some extracellular proteins involved in electron transfer increased significantly (p < 0.05) at 1.8 mM Sb(V). The upregulated flavoproteins could serve as a redox shuttle to transfer electrons from c-type cytochrome networks to reduce Sb(V). Also, the upregulated extracellular proteins involved in sulfur reduction, amino acid transport and protein synthesis processes, and the downregulated flagellar proteins would contribute to a better adaption under 1.8 mM Sb(V). This study advances our understanding of how microbial extracellular proteins promote Sb biomineralization in DvH.

Engineering of salt-tolerant Shewanella aquimarina XMS-1 for enhanced pollutants transformation and electricity generation

Saline wastewater poses a challenge during bio-treatment process due to salinity affecting the physiological activity of microorganisms and inhibiting their growth and metabolism. Thus, screening and engineering the salt-tolerant strains with stronger performances are urgent. Shewanella aquimarina XMS-1, a salt-tolerant dissimilated metal reducing bacteria (DMRB), was isolated from seawater environment. Its ability for reducing pollutants and generating electricity was enhanced by overexpression of riboflavin synthesis pathway encoding genes from S. oneidensis MR-1 under salt stress. Furthermore, upon contact with graphene oxide (GO), the engineered strain XMS-1/pYYDT-rib with enhanced flavins synthesis could reduce GO and self-assemble to form a three-dimensional (3D) biohybrid system named XMS-1/flavins/rGO. This 3D biohybrid system significantly enhanced the EET efficiency of S. aquimarina XMS-1. Our findings provide a feasible strategy for treatment of salt-containing industrial wastewater contaminated by metal and organic pollutants.

Role of microparticles in membrane fouling from acidogenesis to methanogenesis phases in an anaerobic baffled reactor

Microparticles (0.45-10 μm) have been recognized as key foulants in anaerobic membrane bioreactors (AnMBRs). However, their characteristics and fouling behaviors are often understood in single-stage and completely mixed reactors, failing to elucidate the occurrence of microparticles in the multi-stage anaerobic bioprocess. Here, a lab-scale anaerobic baffled reactor with four compartments (C1-C4) was employed to explore the composition and fouling potential of microparticles in different compartments. Photometric analysis showed that the microparticles had an increasing percentage in the total organics of the top supernatant but a decreasing concentration from C1 to C4. Long-term filtration and dead-end filtration tests revealed that the top supernatant in C1 had much higher fouling potential than those in C2-C4. The supernatant microparticles significantly accumulated in the cake layers for each compartment (68-95% of the total organics), particularly the fraction of 1-5 μm, and the fouling rate was positively correlated with the biomass accumulation rate. Based on reactor performance and 16S rRNA gene sequences, a significant bio-phase separation occurred between C1 (acidogenesis) and C2-C4 (methanogenesis). And hydrolytic and fermentative bacteria in the family Veillonellaceae, Streptococcaceae, and Enterobacteriaceae were dominant in the supernatant microparticles, particularly in C1, which had a positive correlation with the fouling rate and biomass accumulation rate. These above results all revealed that the microparticles in the acidogenesis phase had higher fouling potential. In summary, our results suggest that the tactic of pre-hydrolysis and acidification with feedstocks and constructing AnMBRs by coupling with multi-phase anaerobic bioprocesses and membrane units could be beneficial to fouling control.

Nitrogen removal from ammonium- and sulfate-rich wastewater in an upflow anaerobic sludge bed reactor: performance and microbial community structure

Autotrophic ammonium removal by sulfate-dependent anaerobic ammonium oxidation (S-Anammox) process was studied in an upflow anaerobic sludge bed reactor inoculated with Anammox sludge. Over an operation period of 371 days, the reactor with a hydraulic retention time of 16 h was fed with influent in which NH₄⁺ concentration was fixed at 70 mg N L^-1, and the molar ratio of NO₂^-:NO₃^-:SO₄^2- was 1:0.2:0.2, 0.5:0.1:0.3 and 0:0:0.5 in stages I, II and III, respectively. As the NO₂^- in influent was entirely replaced by SO₄^2-, the NH₄⁺ removal rate was 31.02 mg N L^-1 d^-1, and the conversion rate of SO₄^2- was 8.18 mg S L^-1 d^-1. On grounds of the high NH₄⁺:SO₄^2- removal ratio (8.67:1), the S^2- accumulation and pH drop in effluent, as well as the analysis results of microbial community structure, the S-Anammox process was speculated to play a dominant role in stage III. The NH₄⁺ over-transformation was presumably as a consequence of the cyclic regeneration of SO₄^2-. Concerning the microbial characteristics in the system, the Anammox bacteria (Candidatus Brocadia), sulfate-reducing bacteria (SRB) (Desulfatiglans and Desulfurivibrio) and sulfur-oxidizing bacteria (SOB) (Thiobacillus) in biomass was enriched in the case of without addition of NO₂^- in influent. Sulfate reduction driven ammonium anaerobic oxidation was probably attributed to the coordinated metabolism of nitrogen- and sulfur-utilizing bacteria consortium, in which Anammox bacteria dominates the nitrogen removal, and the SRB and SOB participates in the sulfur cycle as well as accepts required electrons from Anammox bacteria through a direct inter-species electron transfer (DIET) pathway.

Potential oxygen consumption and community composition of sediment bacteria in a seasonally hypoxic enclosed bay

The dynamics of potential oxygen consumption at the sediment surface in a seasonally hypoxic bay were monitored monthly by applying a tetrazolium dye (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl-2H-tetrazolium chloride [INT]) reduction assay to intact sediment core samples for two consecutive years (2012–2013). Based on the empirically determined correlation between INT reduction (INT-formazan formation) and actual oxygen consumption of sediment samples, we inferred the relative contribution of biological and non-biological (chemical) processes to the potential whole oxygen consumption in the collected sediment samples. It was demonstrated that both potentials consistently increased and reached a maximum during summer hypoxia in each year. For samples collected in 2012, amplicon sequence variants (ASVs) of the bacterial 16S rRNA genes derived from the sediment surface revealed a sharp increase in the relative abundance of sulfate reducing bacteria toward hypoxia. In addition, a notable shift in other bacterial compositions was observed before and after the INT assay incubation. It was Arcobacter (Arcobacteraceae, Campylobacteria), a putative sulfur-oxidizing bacterial genus, that increased markedly during the assay period in the summer samples. These findings have implications not only for members of Delta- and Gammaproteobacteria that are consistently responsible for the consumption of dissolved oxygen (DO) year-round in the sediment, but also for those that might grow rapidly in response to episodic DO supply on the sediment surface during midst of seasonal hypoxia.

Haloalkaliphilic denitrifiers-dependent sulfate-reducing bacteria thrive in nitrate-enriched environments

As bridge in global cycles of carbon, nitrogen, and sulfur, sulfate-reducing bacteria (SRB) play more and more important role under various environments, especially the saline-alkali environments with significant increase in area caused by human activities. Sulfate reduction can be inhibited by environmental nitrate. However, how SRB cope with environmental nitrate stress in these extreme environments still remain unclear. Here, after a long-term enrichment of sediment from saline-alkali Qinghai Lake of China using anaerobic filter reactors, nitrate was added to evaluate the response of SRB. With the increase in nitrate concentrations, the inhibition on sulfate reduction was gradually observed. Interestingly, extension of hydraulic retention time can relieve the inhibition caused by high nitrate concentration. Mass balance analysis showed that nitrate reduction is prior to sulfate reduction. Further metatranscriptomic analysis shows that, genes of nitrite reductase (periplasmic cytochrome c nitrite reductase gene) and energy metabolisms (lactate dehydrogenase, formate dehydrogenase, pyruvate:ferredoxin-oxidoreductase, and fumarate reductase genes) in SRB was down-regulated, challenging the long-held opinion that up-regulation of these genes can relieve the nitrate inhibition. Most importantly, the nitrate addition activated the denitrification pathway in denitrifying bacteria (DB) via significantly up-regulating the expression of the corresponding genes (nitrite reductase, nitric oxide reductase c subunit, nitric oxide reductase activation protein and nitrous oxide reductase genes), quickly reducing the environmental nitrate and relieving the nitrate inhibition on SRB. Our findings unravel that in response to environmental nitrate stress, haloalkaliphilic SRB show dependency on DB, and expand our knowledge of microbial relationship during sulfur and nitrogen cycles.

Microbial sulfur metabolism and environmental implications

Sulfur as a macroelement plays an important role in biochemistry in both natural environments and engineering biosystems, which can be further linked to other important element cycles, e.g. carbon, nitrogen and iron. Consequently, the sulfur cycling primarily mediated by sulfur compounds oxidizing microorganisms and sulfur compounds reducing microorganisms has enormous environmental implications, particularly in wastewater treatment and pollution bioremediation. In this review, to connect the knowledge in microbial sulfur metabolism to environmental applications, we first comprehensively review recent advances in understanding microbial sulfur metabolisms at molecular-, cellular- and ecosystem-levels, together with their energetics. We then discuss the environmental implications to fight against soil and water pollution, with four foci: (1) acid mine drainage, (2) water blackening and odorization in urban rivers, (3) SANI® and DS-EBPR processes for sewage treatment, and (4) bioremediation of persistent organic pollutants. In addition, major challenges and further developments toward elucidation of microbial sulfur metabolisms and their environmental applications are identified and discussed.

Combined use of high-resolution dialysis, diffusive gradient in thin films (DGT) technique, and conventional methods to assess trace metals in reservoir sediments

Recently, reservoirs in southern China are witnessing incidents involving black water, which are harmful to the aquatic ecosystem. This study unravels the cause of the black water events by studying the occurrence and the ecological risks of contaminants (Pb, Cu, Cd, Zn, Ni, TFe, Mn, S, P, and DOC) in sediments of Tianbao reservoir. Due to the significantly high concentration of TFe, Mn, and P in the sediments, the study further used the thin film diffusion gradient (DGT) technology and high-resolution dialysis method to investigate the movement of Fe²⁺, Mn²⁺, S^2-, and reactive P within the sediments. The ecological risk assessment (threshold effect level and probable effect level) showed that the sediments had a low concentration of Pb, Cu, Cd, Zn, and Ni. High organic matter from the Eucalyptus plantation surrounding the reservoir, as well as the intense thermal stratification of the reservoir, caused the hypolimnion to be hypoxic (DO < 2 mg/L). The diffusion fluxes at the water-sediment boundary (WSB) demonstrated a significant movement of Fe²⁺, Mn²⁺, and PO₄^3- from the sediments into the overlying water, while the movement of S^2- was in both directions due to hypoxia. A high correlation Fe-DOC (r = 0.9), Fe-S (r = 0.8), and Mn-S (r = 0.7) and the redox interaction of Fe²⁺, Mn²⁺, S^2-, P, and DOC at the hypoxic WSB caused the production of black substances in the hypolimnion contributing to the so-called black water reservoir.

Expression, Purification and Characterization of a ZIP Family Transporter from Desulfovibrio vulgaris

The ZIP family transport zinc ions from the extracellular medium across the plasma membrane or from the intracellular compartments across endomembranes, which play fundamental roles in metal homeostasis and are broadly involved in physiological and pathological processes. Desulfovibrio is the predominant sulphate-reducing bacteria in human colonic microbiota, but also a potential choice for metal bioremediation. while, there are no published studies describing the zinc transporters from Desulfovibrio up to now. In this study, we obtained for the first time a heterologously expressed ZIP homolog from Desulfovibrio vulgaris, termed dvZip. The purified dvZip was reconstituted into proteoliposomes, and confirmed its zinc transport ability in vitro. By combining topology prediction, homology modeling and phylogenetic approaches, we also noticed that dvZip belongs to the GufA and probably have 8 transmembrane α-helical segments (TM 1-8) in which both termini are located on the extracellular, with TM2, 4, 5 and 7 create an inner bundle. We believe that purification and characterization of zinc (probably also cadmium) transporters from Desulfovibrio vulgaris such as dvZip could shed light on understanding of metal homeostasis of Desulfovibrio and provided protein products for future detailed function and structural studies.

Comparative metabolic modeling of multiple sulfate-reducing prokaryotes reveals versatile energy conservation mechanisms

Sulfate-reducing prokaryotes (SRPs) are crucial participants in the cycling of sulfur, carbon, and various metals in the natural environment and in engineered systems. Despite recent advances in genetics and molecular biology bringing a huge amount of information about the energy metabolism of SRPs, little effort has been made to link this important information with their biotechnological studies. This study aims to construct multiple metabolic models of SRPs that systematically compile genomic, genetic, biochemical, and molecular information about SRPs to study their energy metabolism. Pan-genome analysis was conducted to compare the genomes of SRPs, from which a list of orthologous genes related to central and energy metabolism was obtained. Twenty-four SRP metabolic models via the inference of pan-genome analysis were efficiently constructed. The metabolic model of the well-studied model SRP Desulfovibrio vulgaris Hildenborough (DvH) was validated via flux balance analysis (FBA). The DvH model predictions matched reported experimental growth and energy yields, which demonstrated that the core metabolic model worked successfully. Further, steady-state simulation of SRP metabolic models under different growth conditions showed how the use of different electron transfer pathways leads to energy generation. Three energy conservation mechanisms were identified, including menaquinone-based redox loop, hydrogen cycling, and proton pumping. Flavin-based electron bifurcation (FBEB) was also demonstrated to be an essential mechanism for supporting energy conservation. The developed models can be easily extended to other species of SRPs not examined in this study. More importantly, the present work develops an accurate and efficient approach for constructing metabolic models of multiple organisms, which can be applied to other critical microbes in environmental and industrial systems, thereby enabling the quantitative prediction of their metabolic behaviors to benefit relevant applications.

Relating bacterial dynamics and functions to gaseous emissions during composting of kitchen and garden wastes

This study aims to relate bacterial dynamics to gaseous emissions during the composting of kitchen and garden wastes. High-throughput sequencing and Functional Annotation of Prokaryotic Taxa (FAPROTAX) were used to analyse the bacterial community and potential functions during composting, respectively. Results show that the addition of garden waste up to 15% of the total wet weight of composting materials notably mitigated gaseous emissions and improved maturity during kitchen waste composting. Ammonium nitrogen, temperature, oxygen content, and electrical conductivity were identified as critical factors to impact gaseous emissions. The bacterial community analysis indicated that the proliferation of anaerobes during the storage of kitchen waste induced the dramatic emission of methane (CH₄) and nitrous oxide (N₂O) at the beginning of composting. Adding garden waste could effectively amend the physiochemical properties of composting materials to reduce the relative abundance of microbes (e.g. Desulfotomaculum and Caldicoprobacter) that contributed to gaseous emissions, but enrich those (e.g. Bacillus and Pseudoxanthomonas) for organic biodegradation. Further analysis by FAPROTAX corroborated that adding garden waste could effectively inhibit relevant microbial metabolisms (e.g. fermentation, nitrite/nitrate respiration and sulphate respiration) and thus alleviate the emission of greenhouse gases and odours during kitchen waste composting.

ANME-1 archaea may drive methane accumulation and removal in estuarine sediments

ANME-1 archaea subsist on the very low energy of anaerobic oxidation of methane (AOM). Most marine sediments shift from net AOM in the sulfate methane transition zone (SMTZ) to methanogenesis in the methane zone (MZ) below it. In White Oak River estuarine sediments, ANME-1 comprised 99.5% of 16S rRNA genes from amplicons and 100% of 16S rRNA genes from metagenomes of the Methanomicrobia in the SMTZ and 99.9% and 98.3%, respectively, in the MZ. Each of the 16 ANME-1 OTUs (97% similarity) had peaks in the SMTZ that coincided with peaks of putative sulfate-reducing bacteria Desulfatiglans sp. and SEEP-SRB1. In the MZ, ANME-1, but none of the putative sulfate-reducing bacteria or cultured methanogens, increased with depth. Our meta-analysis of public data showed only ANME-1 expressed methanogenic genes during both net AOM and net methanogenesis in an enrichment culture. We conclude that ANME-1 perform AOM in the SMTZ and methanogenesis in the MZ of White Oak River sediments. This metabolic flexibility may expand habitable zones in extraterrestrial environments, since it enables greater energy yields in a fluctuating energetic landscape.

OrpR is a σ54 -dependent activator using an iron-sulfur cluster for redox sensing in Desulfovibrio vulgaris Hildenborough

Enhancer binding proteins (EBPs) are key players of σ⁵⁴ -regulation that control transcription in response to environmental signals. In the anaerobic microorganism Desulfovibrio vulgaris Hildenborough (DvH), orp operons have been previously shown to be coregulated by σ⁵⁴ -RNA polymerase, the integration host factor IHF and a cognate EBP, OrpR. In this study, ChIP-seq experiments indicated that the OrpR regulon consists of only the two divergent orp operons. In vivo data revealed that (i) OrpR is absolutely required for orp operons transcription, (ii) under anaerobic conditions, OrpR binds on the two dedicated DNA binding sites and leads to high expression levels of the orp operons, (iii) increasing the redox potential of the medium leads to a drastic down-regulation of the orp operons expression. Moreover, combining functional and biophysical studies on the anaerobically purified OrpR leads us to propose that OrpR senses redox potential variations via a redox-sensitive [4Fe-4S]²⁺ cluster in the sensory PAS domain. Overall, the study herein presents the first characterization of a new Fe-S redox regulator belonging to the σ⁵⁴ -dependent transcriptional regulator family probably advantageously selected by cells adapted to the anaerobic lifestyle to monitor redox stress conditions.

Natural Radioactive Environments as Sources of Local Disequilibrium for the Emergence of Life

Certain subterranean environments of Earth have naturally accumulated long-lived radionuclides, such as ²³⁸U, ²³²Th, and ⁴⁰K, near the presence of liquid water. In these natural radioactive environments, water radiolysis can produce chemical species of biological importance, such as H₂. Although the proposal of radioactive decay as an alternative source of energy for living systems has existed for >30 years, this hypothesis gained strength after the recent discovery of a peculiar ecosystem in a gold mine in South Africa, whose existence is dependent on chemical species produced by water radiolysis. In this study, we calculate the chemical disequilibrium generated locally by water radiolysis due to gamma radiation. We then analyze the possible contribution of this disequilibrium for the emergence of life, considering conditions of early Earth and having as reference the alkaline hydrothermal vent theory. Results from our kinetic model point out the similarities between the conditions caused by water radiolysis and those found on alkaline hydrothermal systems. Our model produces a steady increase of pH with time, which favors the formation of a natural electrochemical gradient and the precipitation of minerals with catalytic activity for protometabolism in this aqueous environment. We conclude by describing a possible free-energy conversion mechanism based on protometabolism, which could be a requisite for the emergence of life in Hadean Earth.

A study on the occurrence of black water in reservoirs in Eucalyptus Plantation region

Tianbao reservoir in southern China (surrounded by Eucalyptus plantation) serves as a source of drinking water for the inhabitants. However, the reservoir water experiences black water (BW) of which the cause remains unclear. In this study, field observation and simulated laboratory experiment were conducted to understand the cause of the BW. The diffusive gradient in thin-film (DGT) device monitored the spatial changes in concentration of iron (Fe²⁺), manganese (Mn²⁺), sulfide (S^2-), and dissolved organic carbon (DOC) at the SWI. The planar optode (PO) showed that hypoxia contributed immensely to the high positive fluxes Fe²⁺, Mn²⁺, and S^2- measured, which co-precipitated to form black materials (FeS and MnS) at the SWI. The co-precipitation between Fe-S and Mn-S was supported by their significant positive correlation (Fe-S: r > 0.05, p < 0.05, Mn-S: r > 0.2, p < 0.05). Significant reduction (p < 0.05) in tannins concentration from November (strong thermal stratification) to December (weak thermal stratification) indicated that Fe²⁺ and tannins reacted during the mixing of reservoir water in December due to weak stratification. The simulated experiment confirmed that fresh Eucalyptus leaves produces a significant (p < 0.05) amount of tannins during hypoxia and reacts with Fe²⁺ to produce black water. A high positive correlation (r > 0.8) between Fe²⁺ and DOC demonstrated that Fe²⁺ and DOC combined and contributed to the reservoir water blackening. The study provides a better understanding on the impact of Eucalyptus plantation on water quality and provide guidance for scientific planting of Eucalyptus plantation in reservoir basins in southern China to ensure safe drinking water.

Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris

Elevated nitrate in the environment inhibits sulfate reduction by important microorganisms of sulfate-reducing bacteria (SRB). Several SRB may respire nitrate to survive under elevated nitrate, but how SRB that lack nitrate reductase survive to elevated nitrate remains elusive. To understand nitrate adaptation mechanisms, we evolved 12 populations of a model SRB (i.e., Desulfovibrio vulgaris Hildenborough, DvH) under elevated NaNO₃ for 1000 generations, analyzed growth and acquired mutations, and linked their genotypes with phenotypes. Nitrate-evolved (EN) populations significantly (p < 0.05) increased nitrate tolerance, and whole-genome resequencing identified 119 new mutations in 44 genes of 12 EN populations, among which six functional gene groups were discovered with high mutation frequencies at the population level. We observed a high frequency of nonsense or frameshift mutations in nitrosative stress response genes (NSR: DVU2543, DVU2547, and DVU2548), nitrogen regulatory protein C family genes (NRC: DVU2394-2396, DVU2402, and DVU2405), and nitrate cluster (DVU0246-0249 and DVU0251). Mutagenesis analysis confirmed that loss-of-functions of NRC and NSR increased nitrate tolerance. Also, functional gene groups involved in fatty acid synthesis, iron regulation, and two-component system (LytR/LytS) known to be responsive to multiple stresses, had a high frequency of missense mutations. Mutations in those gene groups could increase nitrate tolerance through regulating energy metabolism, barring entry of nitrate into cells, altering cell membrane characteristics, or conferring growth advantages at the stationary phase. This study advances our understanding of nitrate tolerance mechanisms and has important implications for linking genotypes with phenotypes in DvH.

High resolution evidence of iron-phosphorus-sulfur mobility at hypoxic sediment water interface: An insight to phosphorus remobilization using DGT-induced fluxes in sediments model

The deterioration of reservoirs in southern China due to the kinetics of Iron (Fe), Phosphorus (P) and sulphide (S) at the sediment-water interface (SWI) is a major problem that needs urgent attention. Studies on the biogeochemistry of Fe, P, and S using high-resolution profile techniques in reservoirs in this region are limited. The diffusive gradient in thin films (DGT) technique, high-resolution dialysis, DGT-computer imaging densitometry (CID), DGT-induced fluxes in sediments (DIFS) and planar optode (PO) device were used to describe the dynamics Fe-P-S in SWI during hypoxia. The results showed the release of Fe-P-S in SWI was due to sulfate reduction and iron reduction influenced greatly by hypoxia. Positive apparent fluxes were recorded indicating that the sediments release Fe-P-S to the overlying water. High positive correlations (r² > 0.7) for DGT-labile Fe and DGT-labile P in sediments revealed that iron-bound P controlled the release of P at SWI during reductive dissolution. The low correlation between DGT-labile Fe and DGT-labile S (r² < 0.4) disclosed the combative nature between sulfate reduction and iron reduction process. The low correlation occurred because of the co-precipitation between Fe and S, forming black materials such as monosulfide (FeS) and pyrite (FeS₂) in a hypoxic environment. The DIFS model showed the resupply ability (R-values) of P in sediments belonged to the partially sustained case with a steady state case of resupply at TB3 (Tc = 1088s, Kd = 1005.61 cm³/g R = 0.72, K_-1 = 0.19 day^-1) and TB4 (Tc = 712 s, Kd = 712.53 cm³/g, R = 0.78, K_-1 = 0.46 day^-1). The resupply rate belonged to the non-steady state case at TB1 (Tc = 10,990 s, Kd = 396.3 cm³/g, R = 0.35, K_-1 = 0.07 day^-1) and TB2 (Tc = 6097 s, Kd = 578.5 cm³/g, R = 0.45, K_-1 = 0.10 day^-1). The DGT-CID-PO-DIFS provided a deep insight on the mechanism of Fe-P-S and remobilization of P at SWI leading to Blackwater events and eutrophication.

Generation of zero valent sulfur from dissimilatory sulfate reduction under methanogenic conditions

Dissimilatory sulfate reduction mediated by sulfate-reducing microorganisms (SRMs) has a pivotal role in the sulfur cycle, from which the generation of zero valent sulfur (ZVS) represents a novel pathway. Nonetheless, information on ZVS production from the dissimilatory sulfate reduction remains scarce. This study successfully showed the ZVS production from the dissimilatory sulfate reduction both in a bioreactor and batch experiments under the methanogenic condition. The ZVS was produced in the form of polysulfide and largely located at extracellular sites. In the bioreactor, interestingly, ZVS could be generated first from partial sulfide oxidation mediated by sulfide-oxidizing bacteria (e.g., Thiobacillus) and later from the dissimilatory sulfate reduction in SRMs when changing the reactor operation from anoxic to obligate anaerobic and black condition. In batch experiments, increasing sulfate concentration was shown to enhance ZVS production. Based on these results, together with thermodynamic calculations, a scenario was proposed for the ZVS production from dissimilatory sulfate reduction, in which SRMs might utilize sulfate-to-ZVS as an alternative pathway to sulfate-to-sulfide to increase the thermodynamic favorability and alleviate the inhibitive effects of sulfide. This study expands our understanding of the SRMs-mediated dissimilatory sulfate reduction and may have important implications in environmental bioremediation.

Effects of moisture and carbon/nitrogen ratio on gaseous emissions and maturity during direct composting of cornstalks used for filtration of anaerobically digested manure centrate

This study investigated the maturity and gaseous emission during direct composting of cornstalks used as organic media for filtration of anaerobically digested manure centrate. Effects of moisture and carbon/nitrogen (C/N) ratio on composting performance were evaluated. Results show that cornstalks could effectively retain suspended solids and organic matter in digested manure centrate to lower their C/N ratio and attain microbial inoculation. Filtered cornstalks became more compostable when their moisture decreased from 76% to 60% or C/N ratio increased from 12 to 24. Nevertheless, such adjustment aggravated the emission of greenhouse and odours gases during composting. Regardless of composting conditions, the phylum Firmicutes was the most dominant with reduced abundance during composting. Similar reduction also occurred to several abundant phyla, including Atribacteria, Synergistetes and Euryarchaeota. By contrast, the phylum Bacteroidetes, Chloroflexi, Proteobacteria and Actinobacteria enriched as composting progressed. In addition, compost maturity was insignificantly affected by matrix moisture and C/N ratio.