Abstract:

Abstract:[Objective] The zone influenced by the hydrothermal plume includes the waters within and underneath the hydrothermal plume. The structure of microbial communities in that zone varies with the evolution of the hydrothermal plume. However, due to the difficulty in observing and sampling, the diversity of microbes and how they evolve with time and in space are unclear. [Methods] During China DY49-5 cruise, a sediment trap mooring system was deployed approximately 300 m southeast of the Wocan-1 hydrothermal vent field. Eighteen months later, a total of 42 hydrothermal plume samples were retrieved from the areas 40 m and 300 m above the seafloor, respectively. In this paper, we used Illumina MiSeq combined with in-situ turbidity anomaly data to characterize the diversity and temporal evolution of bacterial communities within and beneath the neutrally buoyant plume, hoping to clarify the factors causing the spatial and temporal heterogeneity. [Results] The samples were dominated by Gammaproteobacteria, Camplylobacteria, Alphaproteobacteria, Bacteroidia, Clostridia, and Desulfobulbia. The relative abundance of Camplylobacteria increased when hydrothermal venting was more active as suggested by the anomaly high turbidity, while the relative abundance of Gammaproteobacteria and Alphaproteobacteria decreased. Spatially, Gammaproteobacteria and Camplylobacteria were more abundant within and beneath the hydrothermal plume, respectively. [Conclusion] The water column studied had been affected by the dynamics of hydrothermal plume from Wocan-1 hydrothermal field. When the hydrothermal influence was stronger, the relative abundance of Camplylobacteria was higher. The samples collected beneath the neutrally buoyant plume contained more Camplylobacteria species than those collected within the plume. It is suggested that the hydrothermal input and abundance of sulfide particles are likely the main factors causing the spatial and temporal heterogeneity of bacterial communities in the hydrothermal plume-influenced zone.

Abstract:[Objective] To study the diversity of microorganisms in sediments of hot springs in Yunnan and Tibet, the existence of arxA in them, and the influencing factors. [Methods] Illumina MiSeq and statistical analysis were employed for geochemical analysis and microbial diversity analysis of the 22 samples in 3 geothermal areas in Yunnan and Tibet and the relationship between the microorganisms and environmental factors was elucidated. [Results] The dominant phyla in the sediments were Chloroflexi (abundance: 21.27%), Deinococcus-Thermus (abundance: 17.25%), Aquificae (abundance: 13.39%), Proteobacteria (abundance: 9.27%), Acetothermia (abundance: 8.3%), Bacteroidetes (abundance: 4.96%), and Crenarchaeota (abundance: 4.57%). arxA gene-harboring phyla were Proteobacteria (abundance: 64.87%), Bipolaricaulota (abundance: 9.55%), Deinococcus-Thermus (abundance: 6.42%), and Crenarchaeota (abundance: 4.05%). The dominant populations were different among the geothermal areas, which was mainly caused by the temperature, pH, arsenic content, total dissolved solids (TDS), and altitude, as manifested by the significant correlation (P<0.001) between the microorganisms and the environmental factors verified by Mantel test. [Conclusion] arxA gene-harboring microorganisms in the sediments of hot springs were dominated by Proteobacteria and were affected by environmental factors and geographical isolation. They exhibited geographical distribution pattern, as indicated by unique dominant microbial groups in different geothermal areas. In contrast, the arxA gene-containing microbial groups showed no correlation with pH, but were mainly influenced by altitude, arsenic content, TDS, and spatial variables. This suggests the unique physiological characteristics of them among the whole microbial communities.

Abstract:[Objective] Global survey on microbial diversity of cold seep ecosystem pointed out that cold seeps had developed specific types of microorganisms, the main groups were microorganisms involved in methane metabolism, and their distribution were closely linked to the biogeochemical characteristics of the certain cold seep. However, different environmental conditions and small-scale habitats may present inside the cold seep, and studies comparing the microbial diversity and distribution between small-scale habitats in cold seep were lacking. The purpose of this study was to analyze the differences in microbial diversity among different habitats in the Formosa cold seep of South China Sea, and to improve and understand the impact of different environmental factors on the microbial community structure inside cold seep. [Methods] Sediment samples were collected from different habitats including microbial mat area and carbonate rock area from the Formosa cold seep of South China Sea. 16S rRNA genes of archaea and bacteria were sequenced and analyzed. Combined with environmental factors, we compared differences in microbial diversity, and analyzed the impact of environment factors on microbial distribution. [Results] We found that in different habitats in the Formosa cold seep, anaerobic methanotrophic archaea (ANME) was the major archaeal group, accounting for more than 70% of the total relative abundance of archaea; ANME-1b and ANME-2a/b became the main ANME subgroups in microbial mat area, ANME-1b was dominant in the carbonate rock area. Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) were the main groups of bacteria in each habitat of cold seep, and they both accounted for more than 20% of the total relative abundance of bacteria. Among them, Desulfosarcinaceaeaccounted for more than 50% of the SRB, and Sulfurovaceaeand Sulfurimonadaceae together accounted for more than 90% of the SOB; other taxa accounting for more than 10% of the bacteria were Gammaproteobacteria and Chloroflexi. The quantitative PCR results of the conserved methane metabolism gene mcrA(methyl coenzyme-M reductase alpha subunit) and the sulfate reduction conserved gene dsrA (dissimilatory sulfite reductase alpha subunit) showed that the copy number of mcrA gene was 10⁹–10¹⁰ copies/g (wet weight), and the copy number of dsrA gene was 10⁸–10⁹ copies/g (wet weight), which were 10–100 times higher than those of the control area located outside the cold seep. The results of community analysis showed that there were significant differences in community structure among different habitats, and the results of multivariate analysis showed that the diversity and distribution of microorganisms in different habitats were significantly associated with the concentration of methane, hydrogen sulfide, sulfate, and dissolved inorganic carbon (DIC). [Conclusion] This research analyzed the microbial diversity of the heterogenous habitats including the microbial mat area and the carbonate rock area in the Formosa cold seep. We found that the main microbial groups were involved in methane (anaerobic methane oxidation) and sulfur (sulfate reduction, sulfur oxidation) metabolism cycle, however, the diversity and distribution of microorganisms in different habitats were significantly different, mainly controlled by environmental factors such as methane, sulfate, hydrogen sulfide and DIC.

Abstract:[Objective] Cold seeps are mainly found along continental margins, which are characterized by the seepage of cold fluids rich in hydrocarbons dominated by methane and hydrogen sulfide. With unique geochemical environment, cold seep boasts unique prokaryotic community structure. However, the relationship between prokaryotic composition and cold seep environment is not clear. [Methods] In this paper, the key geochemical parameters, such as CH₄ in sediments and SO₄^2- and H₂S concentration in pore water, were measured along the depth profile based on the sediment samples from the active cold seep area of Makran continental margin. Through high-throughput sequencing of 16S rRNA gene, the community structure and spatial variation of prokaryotic microorganisms in cold seep sediments were systematically analyzed. [Results] Based on the methane- sulfate concentration, the sediments in the active seepage area of the Makran continental margin were divided into sulfate- reduction zone (SZ), sulfate- methane transition zone (SMTZ), and methanogenesis zone (MZ). It was found that the diversity and abundance of prokaryotic microorganisms decreased with the increase of depth through α diversity analysis and genetic quantification. According to the result of 16S rRNA gene sequencing, Gammaproteobacteria, Alphaproteobacteria, and Epsilonbacteraeota were the dominant prokaryotes in SZ, and the relative abundance of JS1, Chroloflexi, Lokiarchaeia, Bathyarchaeia, and Thermoprofundales which were related to organic matter degradation and used sulfate as electron donor was also high. ANME-1a, ANME-1b, and SEEP-SRB1 accounted for a large proportion in SMTZ, indicating that they might jointly mediate the anaerobic oxidation of methane coupled to sulphate reduction (SR-AOM). In addition, the prevalence of Bathyarchaeia and Chroloflexi indicated the potential of other hydrocarbons besides methane in the sediments. [Conclusion] Through the exploration of the prokaryotic communities in Makran cold seep, it is found that the bacterial and archaeal community compositions are closely related to the unique geochemical environment of the cold seep.

Abstract:[Objective] To isolate and screen out the cold-tolerant and aerobic denitrifying bacteria from activated sludge and river sediment in winter, and optimize the key factors that influence denitrification, so as to improve the effect of denitrification at low temperature. [Methods] Cold-tolerant and aerobic denitrifying bacteria were isolated and screened out by enrichment and purification method. Morphological observation and 16S rRNA gene sequence phylogenetic analyses were used to identify the species of the newly isolated strain. Taking the removal rate of NO₃^–-N as the response target, the key factors affecting denitrification, including carbon-nitrogen ratio, temperature, pH and shaking speed, were optimized by Box-Behnken design and response surface regression analysis to determine the optimal culture conditions. [Results] A cold-tolerant and aerobic denitrifying bacterium Z6 was obtained from the river sediment in the cold area of northeast China in winter. The round colony of the strain was white and translucent, and the cell was short rod-shaped, with the size of (0.8–1.6)μm×(0.6–0.8) μm. Gram staining was negative. The strain Z6 was identified as Aeromonas sp. due to the high homology with the 16S rRNA gene sequences of the genus Aeromonas sp.. Based on the response surface analysis, the optimal denitrification conditions of Aeromonas sp. Z6 were 5.9 of carbon-nitrogen ratio at pH 6.8 and 12 ℃ with 155 r/min shaking table speed. Under the optimum conditions, the removal rate of NO₃^–-N was 89.72%, which was not significantly different from the predicted rate (90.34%). [Conclusion] Aeromonas sp. had high denitrification performance under low-temperature conditions, which provided references for biological denitrification of low-temperature wastewater in cold areas.

Abstract:[Objective] As an important part of lake ecosystem, microorganisms play an essential role in the biogeochemical cycle of carbon, nitrogen, sulfur, and other elements, and the community structure and functions of them are crucial to environmental stability and sustainability. However, the lakes in Xinjiang are degraded and salinized, and how microorganisms respond to the degradation is unclear. [Methods] The 16S rRNA gene amplicon sequencing was performed to analyze the soil microbial community structure of the degraded area of Barkol Lake and the potential ecological functions of the microorganisms were predicted. [Results] Pseudomonadota, Chloroflexota, and Bacteroidota dominated different parts in the degraded area. In addition, the abundance of Desulfobacterota and Campylobacterota was the highest in the mildly degraded part of the lake, but the two drastically decreased and even disappeared as the degradation aggravated. The extremely degraded part was dominated by Acidobacteriota, Planctomycetota,etc. According to the oxygen utilization predicted by BugBase, the aerobic groups were mainly Actinomycetota, Pseudomonadota, and Chloroflexota, and the majority of them were in the severely degraded part. Moreover, the anaerobic groups were Pseudomonadota, Bacteroidota, and Acidobacteriota, which were mainly in the mildly degraded part. FAPROTAX was employed for predicting the ecological relevant functions of microorganisms in different parts of the degraded area and the result suggested the weakened sulfate respiration, fermentation, and hydrocarbon degradation, and the enhanced nitrification of microorganisms with the aggravation of degradation. [Conclusion] Microorganisms show high diversity in the degraded area of Barkol Lake, which dominate multiple biogeochemical cycles. As the degradation becomes serious, the microbial niche changes. This study lays a theoretical basis for the rational development and utilization of microbial resources in Barkol Lake.

Abstract:[Objective] To investigate the functional characteristics of cultivable extreme halophiles by analyzing the differences of community composition of extreme halophiles in salt lakes with different types of salt formation. [Methods] Soil samples were collected from Qijiaojing Salt Lake (sulfate type) and Nanhu Salt Lake (carbonate type) in Xinjiang, and extreme halophiles were isolated by the dilution plating method. By morphological observation and characteristic analysis, the representative strains were screened. The salt-tolerance of the strains was tested and the 16S rRNA gene sequencing was performed. Functional activities of the extreme halophiles were also detected, including protease, amylase, cellulase and lipase activities as well as phenol degradation ability. [Results] A total of 1 679 strains of extreme halophiles were obtained, and 45 representative strains were screened, which belonged to 5 phyla and 14 genera, and the number of archaea (accounting for 70.58%) was significantly more than that of bacteria. The optimal salt concentration for growth was in the range of 18.4%–20.0%. At the genus level, the dominant groups were Haloterrigena (32.94%) and Natrialba (26.03%) in archaea, and Aquisalimonas (9.85%) and Aliifodinibius (8.10%) in bacteria. In the two salt lakes, the species richness of Nanhu Salt Lake with lower salinity was higher than that of Qijiaojing Salt Lake, but the composition of archaea species was similar, mainly Haloterrigena. There were differences in bacterial community composition; specifically, Aquisalimonas was dominant in Nanhu Salt Lake, while Aliifodinibius was dominant in Qijiaojing Salt Lake. Functional diversity screening showed that the total positive rate was 80%, and 42.58% of the strains produced amylase and were classified into Natrialba. Extreme halophiles producing protease, cellulase and lipase accounted for 9.71%, 9.29% and 7.21%, respectively, and phenol degrading strains occupied 11.14%. [Conclusion] This study revealed the diversity of cultivable extreme halophiles in Xinjiang salt lakes. Archaea was the dominant group and there were also diverse bacterial species, displaying significant activity of various functional enzymes. Additionally, the dominant Natrialba, Haloterrigena, Aquisalimonas and Aliifodinibius had great application potential, which could enrich bacterial resources for future research and application, and were worthy mining.

Abstract:[Objective] The purpose of this paper is to explore the distribution of bacterial communities along different water depths in a pit lake affected by acid mine drainage (AMD) and its relationship with environmental factors. [Methods] The 16S rRNA gene high-throughput sequencing technology was used to investigate the bacterial communities along different water depths at 6 sampling sites in the lake. The physicochemical indexes of water quality were measured at the same time. The relationship between bacterial distribution and water physicochemical indexes was analyzed by statistical software. [Results] The physicochemical properties and bacterial distribution showed obvious stratification. Dissolved oxygen (DO) decreased while pH and concentrations of metal ions increased from top to bottom. Meanwhile, the bacterial diversity and the abundance of some species increased from top to bottom. Proteobacteria (Alpha, Gammaproteobacteria) and Acidobacteria were dominated in the surface water, while Firmicutes, Acidobacteria,Actinobacteria, Gammaproteobacteria and Patescibacteria were rich in the middle- and deep-layer water. The total nitrogen (TN), DO, oxidation-reduction potential (ORP), pH, Fe, Mn, Al and Zn were significantly correlated with the abundance of acidophilic bacteria, which were the main factors influencing the spatial distribution of bacteria. [Conclusion] The distribution of bacteria in the pit lake affected by AMD showed an obvious vertical pattern, which was caused by the joint action of various environmental factors. This study has reference value for understanding the microbial distribution in the AMD-influencing pit lake and in situ bioremediation of AMD.

Abstract:[Background] Surface water/ground water flows back to the goaf of sulfur-containing coal mine, forming the acidic goaf water. The water, with high salinity and sulfate content, threatens ecosystem health. Microorganisms, which feature low cost and environmental protection, has promising prospect of application in the treatment of goaf water. However, the currently available sulfate-reducing bacteria (SRB) are only highly active under suitable temperature and neutral pH, and are intolerant to low temperature and acidic conditions in northern China. [Objective] To isolate SRB from goaf water in Shandi River Basin of Yangquan, Shanxi, and to domesticate them so that they can tolerate the low temperature and acidic condition and be used for the treatment of goaf water in northern China. [Methods] Microorganisms in goaf water sample from Shandi River Basin were enriched and SRB were isolated. Then the SRB were characterized by Gram staining and scanning electron microscopy and identified based on 16S rRNA sequence alignment. Their growth characteristics and sulfate-reducing capacity were also investigated. On this basis, temperature and pH were lowered to domesticate the efficient SRB, thereby exploring their potential in the treatment of goaf water. [Results] Two strains of SRB, YQ-1 and YQ-2, were isolated, belonging to the Gram-negative Proteiniclasticum and Desulfovibrio, respectively. At 30 ℃ and pH 7.5, YQ-1 and YQ-2 reduced 96.75% and 75.48% of the 1 100 mg/L sulfate, respectively. The highly efficient strain YQ-1 was selected for domestication at low temperature and pH. The sulfate removal rate of the strain was 91.49% at 15 ℃ and pH 7.5 after low-temperature domestication, 85.69% higher than that before domestication. The removal rate was up to 37.21% at 15 ℃ and pH 4.5 after low-pH domestication, which was 34.30% higher than that before domestication. [Conclusion] The tolerance of YQ-1 to low temperature and low pH was improved, and the efficiency of sulfate reduction was also enhanced after domestication. This work provided strain resources and theoretical basis for the treatment of goaf water in northern China.

Abstract:Iron is one of the main components of deep-sea hydrothermal activity products and an important driving element for the chemoautotrophic microbial ecosystems at hydrothermal vents. The neutrophilic microaerophilic iron-oxidizing bacteria, represented by Zetaproteobacteria, are the main drivers of biomediated Fe²⁺ oxidation in hydrothermal vents and their surroundings. Iron-oxidizing bacteria acquires the energy essential to maintain their metabolism through Fe²⁺ oxidation, while secrete organic matter to precipitate the oxidized insoluble iron (oxides or hydroxides) outside the cells, forming microstructures with twisted stalks, hollow sheaths, branching hollow tubes or other special morphological features. These microstructures accumulate into iron-rich oxides/hydroxides widely distributed on the seafloor. Increasing studies have demonstrated that cyc2, encoding cytochrome-porin, is the key gene of Fe²⁺ oxidation by Zetaproteobacteria, while c-type cytochromes or other periplasmic cytochromes are the main electron transport carriers in Fe²⁺ oxidation. The metagenome-based studies reveal that Zetaproteobacteria generally possess multiple functional genes and metabolic pathways associated with nitrogen, sulfur, hydrogen, and arsenic cycling, suggesting the potential role of Zetaproteobacteria in the cycling of the above elements. In this paper, we systematically summarized the diversity, physiological characteristics, biomineralization-formed microstructure records, and key genes and electron transport pathways that mediated Fe²⁺ oxidation of neutrophilic microaerophilic iron-oxidizing bacteria in hydrothermal environments. This review facilitates the systematical understanding about the role of these microorganisms in the migration and enrichment of key ore-forming elements, the maintenance of ecological balance, and the mineralization by microorganisms in submarine hydrothermal vents.

Abstract:Cryoconite is a kind of granular sediment found on the surface of glacier, and comprises minerals, organic materials and biomaterials. The sources of cryoconite mainly come from dust and aerosol transported from far sources, and coarse moraine from local sources and plant debris from surrounding ecosystems. With high absorption of solar radiation, cryoconite can reduce the surface albedo of glacier and promote glacier melting. Cryoconite is also the most diverse microbial habitat on the surface of glacier, where bacteria, fungi, and algae live in. Microbes in cryoconite are the main drivers of the geochemical cycling on the glacial surface, which decompose and transform the organic matter in cryoconite, decrease the albedo, and affect the material balance process of the glacier. In view of this, this paper reviewed the physical and chemical characteristics, potentially influencing factors of which, the microbial community structure, and the biogeochemical cycling of carbon and nitrogen driven by cryoconite microbes in glaciers of Antarctica, Arctic and the third pole (TP). In addition, we also put forward research directions on cryoconite microbes.

Abstract:Psychrophilic microorganisms are a major life form in cold environments of the Earth and drive critical global biogeochemical cycles. The survival strategies of these microorganisms have demonstrated great potential in overcoming the extreme environmental factors. Deciphering their adaptation and evolutionary mechanisms will improve our understanding of the interaction between microorganisms and the environment and facilitate the effective use of microbial resources from extreme environments. With the rapid development of molecular biology and genome sequencing in recent years, researchers have made great breakthroughs in research on the adaptation mechanisms of microorganisms to cold environments and application of these psychrophiles in climate change prediction, industry, and agriculture. In this review, we summarize the progress of research on microbial adaptation to cold environment in terms of genomic GC content, protein stability, transcriptional and translational regulation, cell membrane fluidity, osmotic pressure regulation, oxidation resistance, and genome adaptive evolution.

Abstract:The liquid water under the ice sheet of Antarctic continent consists of subglacial lakes, subglacial rivers/streams, ice-covered lakes, and water bodies under ice shelf. The subglacial aquatic ecosystems are featured with low temperature, darkness, and oligotrophy, and are dominated by microbes characteristic of complex community composition, diverse functions, and unique adaptation mechanisms. These microbes play important roles in biogeochemical cycling of elements. Hence, it is of great significance to clarify the microbial characteristics and their roles in biogeochemical cycles of elements in the subglacial aquatic ecosystems of Antarctic, which avails to reveal the evolution of life on the early Earth and explore life in the extraterrestrial planets. This review summarized the extreme environment conditions, microbial diversity, adaptation mechanisms, and microbial functions related to biogeochemical cycles of elements in subglacial aquatic ecosystems of the Antarctic. Moreover, we summed up the future research trends on Antarctic subglacial microbes.

Abstract:Attributing to the water-carbon dioxide-carbonatite-organism interaction, carbon cycle in karst area is active and 8.24×108 t C/a of karst carbon sink has been formed all over the world, which accounts for 29.4% of the global missing sink. Some karst carbon sinks are stored in the form of soil organic carbon. Therefore, alkaline soil carbon sequestration is expected to be the main way of carbon neutralization. Microorganisms, the important drivers of soil carbon cycle, play an important role in mediating the balance of plant compounds and microbial necromass in soil. This paper reviewed the reserves, composition, and sources of karst soil organic carbon pool, microbial factors affecting the dynamics of karst soil organic carbon pool, and the microbial mechanism on renewal of karst soil organic carbon pool. Moreover, the effects of microorganisms on plant compounds and microbial necromass in karst soil were discussed and the key problems were put forward. This review is expected to help understand the microbial mechanism on the distribution, renewal and maintenance of karst soil organic carbon pool and deepen the understanding of karst soil carbon cycle and its microbial mechanism. In addition, it provides strategies for China to cope with the challenges on Four Per Mille Initiative: Soils for Food Security and Climate.

Abstract:[Objective] Micro-nano flake hydrogen-autunite can be rapidly formed on the surface of biological cells. [Methods] Through simulated calculation, we investigated the interaction between uranyl and the biological macromolecules containing phosphorus (BCP) of phospholipid (ubiquitous in organisms), lipopolysaccharide (unique to Gram-negative bacteria), teichoic acid (unique to Gram-positive bacteria), and phytic acid (unique to plants), the interaction energy, and the distance between related atoms. [Results] According to the Monte Carlo analysis, the adsorption energy of teichoic acid, lipopolysaccharide, phospholipid and phytic acid fell between –109 kcal/mol and –114 kcal/mol in the pure uranyl system and the uranyl-carbonate system, and the energy was mainly relaxation deformation adsorption energy (E_deformation). Considering the adsorption ability and adsorption probability, lipopolysaccharide showed the best ability, followed by phospholipid, phytic acid and teichoic acid. The molecular dynamics relaxation showed that U atom mainly interacted with the group containing P in BPC in the case of uranyl interacting with BCP. In the pure uranyl system, U-P distance was the shortest in the presence of lipopolysaccharide and phytic acid (6.662 Å and 6.539 Å, respectively). In the uranyl-carbonate system, the U-P distance was the shortest in the presence of teichoic acid and phospholipid (5.225 Å and 12.472 Å, respectively). This can be explained with the structure of BCP and the acting force on uranyl. To be specific, in both systems, the dominant force of lipopolysaccharide acting on uranyl was electrostatic force, and that of teichoic acid and phytic acid was van der Waals force. As for the forces of phospholipid acting on uranyl, the van der Waals force was comparable to the electrostatic force. [Conclusion] To sum up, the phosphorus atoms in the phosphate groups have affinity for uranium atoms in uranyl in the process of interaction between the four biological macromolecules containing phosphorus and uranyl ions.

Abstract:Via chemoautotrophic bacteria which are featured by slow growth and high sensitivity to heavy metals, nitrification has been one of the most prevalent biological processes for removing nitrogen species from wastewater. Arsenic, generally existing in two oxidation states of arsenite [AsO₂⁻, As(Ⅲ)] and arsenate [AsO₄³⁻, As(Ⅴ)], is highly toxic, particularly the As(Ⅲ). However, high concentration of As(Ⅲ) (about 400 mg/L) shows no obvious toxicity to nitrifying bacteria in the nitrification system. Through in-depth analysis, we found that the microbial oxidation of As(Ⅲ) was in close relationship with the nitrification. Chemoautotrophic As(III)-oxidizing bacteria can not only directly oxidize As(Ⅲ) under aerobic conditions, but also use NO₂⁻ or NO₃⁻ as electron acceptors to oxidize As(Ⅲ) under anoxic conditions. As typical chemoautotrophic bacteria, nitrifying bacteria may oxidize As(Ⅲ) with O₂, NO₂⁻, and NO₃⁻ as electron acceptors in the nitrification system. In this review, we summarized the detoxification mechanisms of As(Ⅲ) in the nitrification system, such as the EPS adsorption, As(Ⅲ) oxidation, As(Ⅴ) reduction and efflux, arsenic methylation and antioxidant defense. These detoxification mechanisms enhance the resistance to As(Ⅲ) in nitrifying bacteria and play an important role in arsenic biotransformation and geochemical cycling.

Abstract:Organohalide-respiring bacteria (OHRB) are key players involved in the bioremediation of the soil and groundwater contaminated with halogenated compounds. Substrate competition, growth inhibition, cross-feeding interaction (dynamic exchange of nutrients, such as carbon source, nitrogen source, amino acids, vitamins, nucleotides, electron donors, electron acceptors, and other growth factors), horizontal gene transfer, and other interaction mechanisms are contributing to the stability and balance of microbial community structure, which is critical to maintaining the optimal dechlorination efficiency of halogenated contaminants. This review summarized the interaction mechanisms (e.g., cross-feeding, competition, inhibition) in microbial communities harboring OHRB and non-dechlorinating populations. In addition, we highlighted and discussed key scientific questions arising from the current state of OHRB-driven microbial ecology. This review aimed to provide scientific theory and technical reference for enhanced bioremediation at halogenated compounds-contaminated sites.

Abstract:The redox processes of iron significantly influence secondary mineral formation, nutrient transformation, and the fate of contaminants. As a novel process of global iron cycle first discovered in anaerobic environment, microbes-mediated coupling of ammonium oxidation and Fe(Ⅲ) reduction (Feammox) accounts for up to 10% of ammonium oxidation in natural and agricultural ecosystems. Thus, it is of great significance for environmental protection and agricultural production. This review summarized the research on microbial Feammox in recent years, including its research history, related microbes, underlying mechanisms, influencing factors, and environmental significances. In Feammox, Acidimicrobiaceae sp. A6 and dissimilatory Fe-reducing bacteria (DIRB) are potential functional organisms, and pH, Fe(Ⅲ) concentration and speciation, carbon sources, and Mn(Ⅳ) oxides are the main environmental factors. Feammox might be driven by biological process alone, or by the biological-chemical coupling processes. As for the environmental significances, Feammox can reduce the greenhouse gas emission and influence heavy metal transformation, but it causes alternative N loss. Further investigations could focus on the cultivation of related microorganisms and the development of new research methods to further disclose the Feammox mechanism.

Abstract:[Objective] Although Shewanella oneidensis MR-1 is a typical electroactive model bacterium, its biofilm morphology remains to be systematically studied. This work aims to improve the understanding of biofilm morphology of S. oneidensis MR-1, thus providing basic data to support its role as a model strain. [Methods] Culture conditions such as medium type, buffer concentration, vitamins, trace elements, inorganic salts, electron shuttles, donors, and acceptors were taken as the variables to be studied. The biofilm was cultured under potentiostatic conditions and examined by scanning electron microscopy. [Results] The cells were mostly straight and short in low-concentration (30 mmol/L and 100 mmol/L) buffer solutions while became curled and elongated in high-concentration (200 mmol/L and 300 mmol/L) buffer solutions. The shortage of vitamins, trace elements, and inorganic salts made the biofilm become compact and attach closely to the electrode. The addition of an electron shuttle substantially thickened the biofilm, while a lack of an electron acceptor led to serious cell lysis within one day. In addition, a cable-like structure as long as 100 μm was observed in the biofilm, which indicated a long-distance electron transfer survival strategy of S. oneidensis MR-1. [Conclusion] Changing the medium type, buffer concentration, electron shuttles, donors, and acceptors can regulate the biofilm and cell morphology of S. oneidensis MR-1.

Abstract:The strictly anaerobic Gram-negative Geobacter (Geobacteraceae, Deltaproteobacteria) members, the dissimilatory iron-reducing bacteria, are ubiquitous in aquatic sediment, soil, and various underground anaerobic environments. Geobacter is versatile as it participates in the biogeochemical cycles of carbon, nitrogen, iron, and other elements in anaerobic environments through a variety of pathways. To be specific, in the biogeochemical cycle of carbon, it decomposes small organic acids such as acetic acid or aromatic compounds through carbon catabolism, utilizes one-carbon compounds such as formic acid and carbon monoxide by carbon fixation, and drives methane production of methanogens through extracellular electron transfer. It contributes to nitrogen cycle by dissimilatory reduction of nitrate to ammonia (DNRA), nitrogen fixation, and establishing direct interspecies electron interaction with denitrifying bacteria. It expresses quinone dehydrogenases (ImcH, CbcL and CbcAB) in inner membrane and cytochrome C and conductive nanowires in outer membrane to reduce various extracellular Fe(Ⅲ) oxides by direct contact or with the assistance of electron shuttles and chelators, thereby facilitating iron cycle. As a result, the versatile Geobacter survives in a variety of environments and occupies an important niche in anaerobic environments by driving the biogeochemical cycles. This paper introduces the metabolic characteristics and distribution of Geobacter, elucidates the roles in biogeochemical cycles of carbon, nitrogen, and iron, and summarizes the versatile feature of this genus. The result is expected to deepen the understanding of the biogeochemical cycles of key elements driven by Geobacter, lay a solid theoretical basis for understanding the environmental effect of Geobacter in the natural environment, and pave the way for application of Geobacter in maintaining ecological balance and pollution control.

Abstract:[Objective] This study aimed to reveal the composition of endogenous microbial community degrading the polymers for oil displacement in the reservoir and analyze the influence of bio-competitive exclusion on the microbial degradation of polymers. [Methods] Through indoor culture experiments, we observed the influence of bio-competitive exclusion on the viscosity of the polymers, and used high-throughput sequencing technology to analyze the microbial strains related to polymer degradation in Bohai J-oilfield. We then mined the genes (encoding amidase, oxygenase, hydrogen sulfide-generating enzyme) with high abundance and involved in polymer degradation in the samples. After that, we employed the real-time fluorescence PCR to compare the abundance of the above-mentioned functional genes between samples, and finally annotated the microbial taxa carrying the above-mentioned functional genes. [Results] Bio-competitive exclusion mitigated the viscosity loss of the polymers for oil displacement. Nine taxa of microorganisms related to the degradation of polymers were identified, including Acetomicrobium, Tepidiphilus, Thermoanaerobacter, Fervidobacterium, Ralstonia, Halomonas, Roseovarius,Deferribacteraceae, and Comamonadaceae. High-throughput sequencing revealed that bio-competitive exclusion significantly down-regulated the abundance of 7 genes involved in the polymer degradation in the samples. The measurement of abundance in samples showed that the abundance of the amidase gene ansB and the oxygenase gene ssuD was down-regulated by bio-competitive exclusion, which was consistent with the sequencing results. The community composition annotation indicated that bio-competitive exclusion significantly inhibited Delftia, a highly efficient bacterial taxa for polymer degradation in Bohai J-oilfield. [Conclusion] We revealed the endogenous microbial taxa related to the degradation of polymers for oil displacement in the oilfield and discovered the inhibitory effect of bio-competitive exclusion on the degradation, confirming that bio-competitive exclusion can help to stabilize the viscosity of polymers for oil displacement in offshore oilfield.

Abstract:[Objective] The competitive exclusion principle has been adopted to treat the production of hydrogen sulfide in offshore S oilfield, and some achievements have been made. The study aimed to reveal the influence of competitive exclusion on reservoir microbial community structure and to investigate the factors producing differences in hydrogen sulfide treatment. [Methods] High-throughput sequencing was used to analyze the changes of different microbial community structures in low-effective wells, high-effective wells and untreated wells after the addition of nitrate and nitrite. [Results] Compared with the conditions in low-effective wells and untreated wells, the species and abundance of denitrifying bacteria and oil-degrading bacteria in high-effective wells increased by 5.23% and 24.14%, respectively. Moreover, metal ions such as Fe²⁺and Zn²⁺ were found to influence the treatment effects among different wells and the changes of microbial communities. [Conclusion] In offshore oilfields, competitive exclusion could significantly reduce the production of hydrogen sulfide, and impact the microbial community environment of the reservoir. Analysis of the microbial community structure could be used as an important indicator for evaluating the effect of hydrogen sulfide treatment, which provided technical support for treating hydrogen sulfide in offshore oilfields.

Abstract:Estuaries are the transition zones between land and sea, and the health of the ecosystem is essential to the surrounding residents and the sustainable economic development. In recent years, amid the rapid development of the cities nearby, a large number of the permanent polycyclic aromatic hydrocarbons (PAHs) have accumulated in the sediments of estuaries, posing a threat to the health of the aquatic ecosystems. As a result, the degradation and transformation of PAHs have attracted the interest of scholars. According to previous studies, Pseudomonadota, Actinobacteria, and Bacillota dominate the PAHs-degrading bacteria in sediments of main estuaries (Pearl River Estuary, Yangtze River Estuary, Liaohe River Esturay, and Haihe River Estuary) in China, among which Klebsiella, Bacillus, and Pseudomonas have been frequently reported. Bacteria degrade PAHs in estuarine sediments mainly through the anaerobic pathway which is characterized by low efficiency. Low oxygen and high salinity in estuarine sediments are unfavorable for the bacterial degradation of PAHs, and the changeable temperature and pH result in uncertain efficiency of bioremediation. The addition of surfactants, nutrients, and exogenous electron receptors and the co-metabolism can promote the bacterial degradation of PAHs in sediments. At the moment, most studies have been carried out in laboratory, but the environmental conditions of estuarine sediments are complex. Therefore, it is suggested to screen PAHs-degrading strains according to the environmental characteristics of estuarine sediments in the future, and flexibly formulate strategies to enhance the degradation according to the actual situation. This review is expected to serve as a reference for further screening and utilization of indigenous PAHs-degrading bacteria in the sediments of major estuaries in China.

Abstract:Under the goals of carbon peaking and carbon neutrality, traditional fossil energy will be gradually replaced. China’s coal resources feature huge reserves and wide distribution. The biological gasification of untapped coal resources can provide additional natural gas resources. Therefore, it is of great theoretical and practical significance to study the mechanism of biological coalbed methane stimulation. Biological coal gasification is promising, but the difficulty lies in its slow dynamic characteristics. To reveal the generation potential and internal factors of biological coalbed methane, we discussed the influence of physicochemical characteristics of coal on biological gasification, the response of coal physicochemical properties to biological action, and the improvement of coal utilization by pretreatment. The internal factors and environmental conditions of biodegradable coal had been identified through indoor research. It was found that low-rank coal had a higher potential for biological coalbed methane production than high-rank coal. The biotransformation of coal by methanogenic microorganisms is bound to cause changes in the physicochemical properties of coal. It is a challenge to continuously provide available substrates for methanogens, which thus limits the biological coal gasification. Chemical pretreatment of coal is mostly used to improve the efficiency and methane yield of biological gasification, while supercritical CO₂ extraction physically dissolves small molecular organics in a macromolecule network for gasification. The production of biological coalbed methane can be further increased, but the in-situ increase needs to be further studied in light of the obvious differences between indoor experimental conditions and reservoir environments. The microbiological research on the biotransformation of organic matter in coal seams should be improved. The study of the main factors controlling the influence of different coal ranks and different reservoir environments on biological gasification is the key to the commercialization of biological gasification.

Abstract:[Objective] MG I (marine group I archaea) are the main microbial group in the ocean, which have the ability to use ammonia nitrogen to carry out ammonia oxidation autotrophic and are one of the main participant ammonia oxidation processes in the marine environment. The study of the diurnal variation of MG I archaea is of great significance for revealing the process of ammonia oxidation and carbon and nitrogen cycling in the ocean. [Methods] Samples for this study were collected from the waters near Dong’ao Island in the Pearl River Estuary, and 22-hour continuous time series of seawater samples were obtained with 2-hour intervals using a drone sampling technology. This study focused on the following scientific issues at the diurnal scale in the Pearl River Estuary: (1) Changes in the community and abundance of MG I archaea and algae. (2) The impacts of light, temperature and algae on the distribution of MG I archaea. DNA extraction, qPCR, second-generation gene sequencing, and other means, combined with environmental parameter tests (temperature, salinity, nutrient concentration, etc.), were used to explore the potential relationship between algae and MG I archaea in seawater. [Results] The abundance of MG I archaea was (9.1±3.2)×10⁷ copies/L and that of algae was (3.7±0.7)×10⁸ copies/L. High throughput sequencing of archaea showed that MG I were the most dominant archaeal group (36.2%–50.0%) in this region. At the diurnal scale, there was a negative correlation between the abundance of MG I archaea and algae. [Conclusion] Based on previous studies, we hypothesize that, temperature and algae might be the important factors that regulate the MG I archaea in estuarine marine water at the diurnal scale. This study highlights the diurnal variation of MG I archaea, which enhances our understanding of the fine-scale nitrification process in the ocean, especially in the nearshore water.

Abstract:[Objective] This study aimed to elucidate the landward differentiation characteristics of potential anoxygenic photosynthetic bacteria (AnPB) and their influencing factors in Xilin River Basin. [Methods] Soil samples were collected along a landward gradient from the turbulent flow zone with no plant (Np), sluggish flow zone with Juncellus serotinus (Js) and stagnant flow zone with bacterioplankton (Pb) in riverbed, the riparian zones including semi-aquatic (hygrophytic) Juncus effusus (Je) and semi-xerophytic (hygrophytic) Potentilla anserina (Pa) to terrace zones including xerophytic Leymus chinensis (Lc) and Stipa grandis (Sg). The database for AnPB at family level wasestablished based on literature informatics. In addition, landward differentiation of potential AnPB populations at family level and their relative abundance was analyzed by 16S rRNA gene high-throughput sequencing. Furthermore, the environmental influence of physicochemical factors on landward differentiation of potential AnPB was studied based on Pearson correlation analysis, redundancy analysis (RDA), multivariate regression tree (MRT) and structural equation modeling (SEM). [Results]Purple sulfur bacteria (Ectothiorhodospiraceae) and purple non-sulfur bacteria (Rhodobacteraceae, Rhodocyclaceae,Acetobacteraceae, Comamonadaceae and Holophagaceae) populations were mainly distributed in aquatic and semi-aquatic (hygrophytic) habitats, whereas purple non-sulfur bacteria (Rhodospirillaceae, Bradyrhizobiaceae, Hyphomicrobiaceae and Rhodobiaceae), Gemmatimonadaceae, Acidobacteriaceae and green non-sulfur bacteria (Roseiflexaceae) populations were mainly distributed in semi-xerophytic (hygrophytic) and xerophytic habitats. Herein, the relative abundance of the potential AnPB populations in aquatic and semi-aquatic (hygrophytic) habitats showed positive correlation with moisture content (P<0.05 or P<0.01), while that in semi-xerophytic (hygrophytic) and xerophytic habitats was positively correlated with salinity and total nitrogen content (P<0.05 or P<0.01). MRT analysis indicated that the total explanation of salinity, moisture and total nitrogen for the landward differentiation of the potential AnPB populations was 62.39%, 14.01%, and 12.68%, respectively. SEM revealed the positively direct links between salinity and Rhodocyclaceae as well as between moisture/TN and Rhodobacteraceae. [Conclusion] The landward differentiation of potential AnPB populations in Xilin River Basin is clear. Salinity, moisture and total nitrogen are main environmental factors directly or indirectly co-driving the landward differentiation. This study contributes to a better understanding of the biodiversity and ecosystem function of AnPB community in Xilin River Basin, and also underpins the implementation of an innovative strategy for reducing atmospheric carbon dioxide concentration and increasing soil carbon sequestration.

Abstract:[Objective] To investigate the relative abundance, community composition and diversity of sulfate-reducing bacteria in high arsenic groundwater of different depths, and to reveal the main geochemical factors (e.g., δ³⁴S-SO₄^2–) affecting the distribution characteristics of sulfate-reducing bacterial community in high arsenic groundwater and the environmental significance. [Methods] High arsenic groundwater samples from both shallow and deep aquifers were collected from Hetao Plain, a typical high arsenic groundwater-distributed area in China. Various geochemical parameters were measured and the relative abundance of 16S rRNA gene and dsrB gene of the samples was quantified by qPCR. High-throughput sequencing of dsrB gene was conducted to reveal the community composition of sulfate-reducing bacteria. Statistical analysis was further performed to analyze the correlations between geochemical variables and sulfate-reducing bacterial community characteristics. [Results] The relative abundance of dsrB gene in shallow samples was higher than that in deep samples. In shallow high arsenic groundwater, the relative abundance of dsrB gene and the δ³⁴S-SO₄^2– were both significantly positively correlated with the concentration of CH₄. In contrast, the relative abundance of dsrB gene showed positive correlations with the concentrations of SO₄^2– and DOC in deep high arsenic groundwater. The high-throughput sequencing of dsrB gene displayed that the α-diversity of sulfate-reducing bacteria in deep groundwater was remarkably higher than that in shallow groundwater. Sulfate-reducing bacteria in the study area were divided into 264 operational taxonomic units (OTUs), including ten predominant orders such as Desulfobacterales, Nitrospirales, Rhodospirillales and Syntrophobacterales. The relative abundance of each order and the environmental factors affecting their abundance were different in shallow or deep groundwater. Specifically, the relative abundance of Nitrospirales in shallow groundwater was positively correlated with the concentrations of As_T and δ³⁴S-SO₄^2–, indicating the key role of Nitrospirales in arsenic migration and transformation in shallow groundwater. The redundancy analysis (RDA) found that As_T, CH₄ and Fe²⁺ were the key environmental factors controlling the distribution of sulfate-reducing bacterial community in groundwater of the study area. [Conclusion] The relative abundance, community composition and diversity of sulfate-reducing bacteria in deep and shallow high arsenic groundwater varied, and were affected by geochemical parameters.

Abstract:[Objective] To explore the landward distribution and association of the soil stable organic carbon (SOC) fractions and dominant bacterial phyla. [Methods] Along the gradient from the long-term flow with no plant (Np) or Juncellus serotinus (Js), seasonal flow with Juncus effusus (Je) and Potentilla anserina (Pa) to long-term no-flow with Leymus chinensis (Lc) and Stipa grandis (Sg), we collected soil samples in wetland and dryland from Xilin River Basin. We detected the content of SOC fractions [fulvic acid (FA), humic acid (HA), and humin (HM)] in different vegetation zones with the method recommended by International Humic Substances Society (IHSS). Meanwhile, we checked the relative abundance of dominant bacterial phyla by high-throughput sequencing of 16S rRNA gene. Furthermore, we analyzed the association between SOC fractions and dominant bacterial phyla based on Pearson’s correlation analysis, redundancy analysis (RDA), variation partitioning analysis (VPA), and structural equation modeling (SEM). [Results] The SOC fractions (FA, HA, HM), Acidobacteria, Actinobacteria, and Gemmatimonadetes demonstrated the landward distribution with an increasing trend, and peaked in the dryland zone from the long-term no-flow area, whereas Bacteroidetes showed the landward distribution with a decreasing trend. As the dominant bacterial phyla in dryland zone from the long-term no-flow area, Gemmatimonadetes, Acidobacteria, and Actinobacteria showed significantly (P<0.05 or P<0.01) positive correlation with HA and HM. As the dominant bacterial phyla in wetland zone from long-term flow and seasonal flow areas, Bacteroidetes had a significantly (P<0.01) negative correlation with FA, HA, and HM. SEM revealed the direct and indirect links between SOC fractions and dominant bacterial phyla. [Conclusion] SOC fractions and dominant bacterial phyla exhibit obvious landward distribution in Xilin River Basin. The increase of soil SOC fractions is associated with the increase of Gemmatimonadetes, Acidobacteria, and Actinobacteria, and the decrease of Bacteroidetes.

Abstract:[Objective] To explore the relationship of soil bacterial community structure and molecular ecological network with soil environment in farmland with long-term continuous cropping. [Methods] In this study, high-throughput sequencing of 16S rRNA gene was performed to reveal the correlation of soil microbial community structure and topological properties of molecular ecological network with soil physicochemical properties of two 12-year continuous cropping fields (GD with continuous cropping obstacle and healthy YA) in Liuyang, Hunan province. [Results] The content of total nitrogen and available phosphorus in GD soil was significantly higher than that in YA soil, while the content of nitrate nitrogen and available potassium was significantly lower than that in YA soil (P<0.05). The bacterial diversity of GD soil was higher than that in YA soil, and the soil bacterial community structure was significantly different between GD and YA (P<0.01), which was related to soil pH and available phosphorus content. Soil bacterial community in GD had a more complex ecological network than that in YA, as manifested in the functional modules of energy metabolism, carbon cycle, and nitrogen cycle. [Conclusion] Continuous cropping can cause changes in soil bacterial community diversity, structure, and ecological network, which may be closely related to the deterioration of soil physicochemical properties and soil fertility, and affects crop growth and development.

Abstract:Application of green manure is an effective measure to improve soil fertility and crop yield, which is very important to the structure and diversity of soil microbial community. [Objective] To study the effect of green fertilizer combined with nitrogen fertilizer on microbial community structure in karst paddy soil, clarify the interaction among microorganisms, soil environmental factors, and crop yield, and thereby provide theoretical basis and evidence for the replacement of nitrogen fertilizer with green manure in karst area. [Methods] A three-year experiment was carried out on the typical karst paddy soil with the following four treatments: winter fallow + no nitrogen fertilizer (CK), winter fallow + nitrogen fertilizer (N), green manure + no nitrogen fertilizer (M), and green fertilizer + nitrogen fertilizer (MN). Soil microorganisms were sequenced with high throughput sequencing technology to analyze the effect of different fertilization treatments on bacterial and fungal communities. [Results] Compared with CK, MN significantly increased the early rice yield, and the content of soil organic matter (SOM), total nitrogen (TN), available nitrogen (AN), and available potassium (AK), and decreased the content of available phosphorus (AP). Compared with other treatments, MN significantly raised soil bacterial richness and diversity, while the richness and diversity of fungal community decreased in MN. Chloroflexi, Proteobacteria, and Acidobacteria dominated the bacteria, and Ascomycota, Basidiomycota, and Zygomycota were dominant fungal taxa in the karst paddy soil. Redundancy analysis (RDA) revealed that soil AK was the key factor affecting the composition of soil bacterial community. Co-occurrence network analysis indicated that there were mostly synergistic and reciprocal relationships among microorganisms. The main bacterial groups were from Chloroflexi and Proteobacteria, and the main fungal groups were Ascomycota and Basidiomycota. [Conclusion] The combined use of green manure and nitrogen fertilizer can help increase soil nutrient content, and the effect is better than that of the application of chemical green alone or nitrogen fertilizer alone. Moreover, the combination can improve soil microbiological properties. This study provides evidence for the substitution of green fertilizer for nitrogen fertilizer in karst area.