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Abstract:Methanogens are one kind of archaea that can use simple compounds to generate methane in anaerobic environments. Thanks to the rapid development of the Next Generation Sequencing, metagenomics has revealed plenty of novel potential methanogens, including Methanomassiliicoccales (RC-Ⅲ), Methanofastidiosa (WSA2), Methanonatronarchaeia, Bathyarchaeota, Verstraetearchaeota and Geoarchaeota. Genomic analysis shows that ubiquitous novel methanogens harbor unique methane metabolism pathway indicating that they might play unrecognized important roles in global carbon cycle. To better understand these novel methanogens, this review summarizes the latest researches on the classification, phylogenetic status, methane metabolic mechanism, ecological distribution, isolation and cultivation of these novel methanogens, highlighting their research directions in the future.

Abstract:Terrestrial hot spring, a typical extreme habitat, is the natural lab for exploring co-evolution of life and geological environment. The progress of molecular biological technology sheds light on decoding the "microbial dark matter" in this special habitat. Some outstanding achievements have been gained, such as expanding thermophilic microbial diversity, exploring new metabolic pathways and addressing their ecological functions, by using the combination of omics-based, probe-based and isotope-based approaches. This comprehensive review summarizes the development of molecular biological methods that were commonly used in the study of geo-microbiology in hot springs and discusses recent application of omics-based, probe-based and isotope-based technologies in revealing the microbial diversity and functional roles in terrestrial hot springs. Finally, we prospected the future research in geo-microbiology of terrestrial geothermal environments.

Abstract:Microalgae play an important role in carbon sequestration in aquatic ecosystems. This review focuses on the proposal of biological carbon pump in aquatic ecosystems at karst areas, the role of microalgae biological carbon pump, the main environmental factors that affect microalgal carbon sequestration, and the research progress in carbon sequestration by microalgae in karst areas. By solving the key scientific problems to be put forward, we can provide the information of in-depth study on biological carbon pump mechanism by microalgae in karst aquatic ecosystems. Besides, the carbon sink potential of karst ecosystems will be scientifically understood and the karst carbon cycle theory also will be enriched.

Abstract:[Objective] The aim of this study was to compare the effect of pressure change styles on cultivable bacteria in deep-sea water sample by controlling the different pressure change process, and discuss the cultivable bacteria abundance and community composition of Mariana trench deep-sea water sample under different depressurization process. [Methods] We sampled the uncontaminated deep-sea water at the depth of 6001 m without depressurization. Then, samples were treated with short-time fast depressurization and long-time slow depressurization. After that, bacteria were enriched in the 2216E or 2216E media added trimethylamine N-oxide (TMAO). The 16S rRNA gene of cultivable bacteria and their abundance were analyzed. [Results] Deep-sea water treated with slow and fast depressurization differed greatly in diversity and abundance of cultivable bacteria. In sample treated with slow depressurization process, the average abundance was approximately 190 CFU/mL and Bacillus was the dominant group (96% of total colonies). However, the average abundance of fast depressurized sample was approximately 437 CFU/mL, and diverse groups including Bacillus (27.8%), Achromobacter (24.4%), Microbacterium (34.4%) and Pseudomonas (13.7%) were observed. Noticeable, addition of TMAO had little effect on abundance of cultivable bacteria of both different depressurization samples, but the diversity of both samples increased and abundance of some species obviously changed.[Conclusion] Depressurization process could change the composition and abundance of cultivable bacteria in deep-sea water sample, addition of TMAO during the enrichment could increase the isolated bacterial species. These results made a solid foundation for further in-depth study of deep-sea bacteria.

Abstract:The unique geological environment in the hydrothermal fields of Okinawa Trough has formed special biological communities. Sulfur-oxidizing bacteria play an important role in the hydrothermal ecosystem as a key participant in the biogeochemical cycle. [Objective] To study the diversity and sulfur oxidation activity of cultivable sulfur-oxidizing bacteria in the hydrothermal fields of the Okinawa Trough. [Methods] Sulfur-oxidizing bacteria in sediment samples from different sites in the hydrothermal fields of Okinawa Trough were enriched, cultured and isolated using different culture media. The 16S rRNA sequence was used to identify sulfur-oxidizing bacteria and to carry out phylogenetic analysis. Sulfur oxidation activity was measured using the iodometric method. [Results] In total 85 strains of sulfur-oxidizing bacteria were isolated and identified, belonging to Alphaproteobacteria, Gammaproteobacteria, Actinobacteria and Firmicutes. The dominant genera of culturable sulfur-oxidizing bacteria were Hydrogenovibrio, Labrenzia, Thalassospira and Marinobacter. Seven typical sulfur-oxidizing strains showed different degradation activity on sodium thiosulfate that ranged from 31% to 100%. Halomonas titanicae SOB56, Marinobacter antarcticus SOB93, Thioclava indica SOB107 and Hydrogenovibrio thermophiles CJG136 could completely degrade sodium thiosulfate.[Conclusion] The sulfur-oxidizing bacteria in the hydrothermal fields of Okinawa Trough are abundant in diversity, providing experimental materials and theoretical basis for studying the sulfur cycle in hydrothermal regions. A variety of sulfur oxidizing strains have greatly enriched the bacterial species resources and laid the foundation for exploring the energy pathways and molecular mechanisms of sulfur cycle.

Abstract:[Objective] The Arctic region has unique environmental characteristics such as high latitude, low temperature and high radiation. There are few human traces in the Arctic Ocean and the surrounding land area, but the number of microorganisms hidden in Arctic region is underestimated. We explored the culturable bacterial diversity and antibacterial activity in Arctic tundra soil. [Methods] We isolated bacteria from 7 soil samples collected from different plant roots near the Yellow River Station in Ny-Ålesund (Svalbard) Arctic. [Results] A total of 721 strains were isolated from samples, 608 strains of which belong to 86 genera and 229 species after 16S rRNA gene sequencing. These 16S rRNA gene sequences mainly grouped into the following 5 phyla:Proteobacteria (54.3%), Actinobacteria (21.2%), Bacteroidetes (12.8%), Firmicutes (10.0%) and Deinococcus-Thermus (1.6%). It was suggested 22 strains could be potential novel species for their low sequence similarity. Furthermore, 16 antibacterial strains which could inhibit the growth of Staphylococcus aureus or Acinetobacter baumannii were screened. [Conclusion] The research obtained special bacteria resource of arctic soil, and solidified the foundation of studying bioactive substances.

Abstract:[Objective] The study was aimed to determine the distribution of Bacillus-like species in volcanic valley of Xiaokong Montain, Tengchong County, Yunnan Province. [Methods] On the basis of culturable method, we isolated Bacillus-like species from soil samples collected in shady-slope, sunny-slope and valley bottom of Xiaokong Mountain. Then the isolates were identified using the 16S rRNA gene and phylogenetic tree was constructed to explore the relation between isolates and related type species. The correlation between environmental factors and community of Bacillus-like species was analyzed by software Cano 5. [Results] We obtained 180 isolates from the soil samples, and identified them as 2 families, 6 genera, 34 species using 16S rRNA gene sequences, including genus Bacillus (11 species), Paenibacillus (13 species), Brevibacillus (3 species), Lysinibacillus (4 species), Psychrobacillus (1 species) and Viridibacillus (2 species). Among them, 7 strains had the lower 16S rRNA similarities with their closest type strain, below the species threshold valus 98.65%, indicating that they were potential novel Bacillus species. The dominant genera were Bacillus and Paenibaciilus, and dominant species were B. mycoides, B. toyonensis, B. cereus, L. xylanilyticus, P. alvei and V. arenosi. Among the Bacillus-like species, we got 16 species from sunny-slope, 29 species from shady-slope and 10 species from valley bottom. The diversity index was showed that the order of Shannon index was shady-slope > sunny-slope > valley bottom. We also found that the correlation between Bacillus-like species community structure, altitude and carbon source was negative, but with S and nitrogen source was positive. [Conclusion] There were rich Bacillus-like species in volcanic valley, Tengchong County, Yunnan Province, and some novel potential Bacillus-like species.

Abstract:[Objective] To study the prokaryotic and eukaryotic community structure and the physicochemical factors influencing their distribution in three mine wastewater lakes from a pyrite mine in Anhui Province. [Methods] Geochemical analysis characteristics of three wastewater lakes were measured, and microbial community compositions of the lakes were studied using high-throughput sequencing. The relationship between microbial community structure and environmental factors was also analyzed based on statistical methods. [Results] Samples from three wastewater lakes included two acidic and one neutral, with significant differences in physicochemical properties. Lake TF, typically acidic, formed about 5 years ago and is characterized by low pH (2.55±0.01), Fe (154.95±0.78 mg/L) and SO₄^2- (3374.86±3.81 mg/L). Lake PT is also acidic, pH (2.9±0.02), however, it formed in the 1970's, and has significantly lower Fe (34.57±4.00 mg/L) and higher SO₄^2- (10398.98±626.70 mg/L) than lake TF. Lake DS is neutral (freshwater), characterized by pH (7.55), high content of SO₄^2- (4162.99 mg/L), while other main metal ions detected were Mg (594.90 mg/L) and Ca (650.10 mg/L). It was observed that the prokaryotic biodiversity of the three wastewater lakes generally increased with increasing pH. The prokaryotic composition of the two acidic wastewater lakes was relatively close. However, lake TF was dominated by autotrophic iron oxidizing bacteria (69.54%±2.89%), while lake PT by heterotrophic bacteria (64.45%±13.81%). The ratio of autotrophic iron oxidizing bacteria Ferrovum in TF was (64.17±1.84)%, and it decreased to (35.39±13.74)% in PT. However, heterotrophic bacteria were abundant in PT as observed by the distribution of Acidicapsa (15.75%±3.99%), Acidiphilium (10.65%±2.05%), and Acidisphaera (6.34%±1.02%). Lake DS had a typically distinct microbial community compared to acid lakes (TF and PT) despite of a high content SO₄^2-. Lake DS had an abundance of Limnohabitans (18.47%) and Rhodobacter (8.42%). The eukaryotic community of three wastewater lakes was mainly composed of algae. The acidic lakes (TF and PT) were mainly populated by Ochromonas and Coccomyxa, accounting for (53.65%±2.02%) in TF and (68.84%±10.4%) in PT respectively. Lake DS was mainly characterized by Cyclotella (49.85%). From our analyses of physicochemical factors, we found that pH was the main factor affecting microbial community composition in acidic wastewater lakes.

Abstract:[Objective] To study the distribution and diversity of sulfur-oxidizing bacteria (SOB) in the surface sediments of Tibetan hot springs. [Methods] We collected 25 hot spring sediments from 5 Tibetan geothermal areas. In the field or laboratory, we measured the physicochemical parameters of water or sediment samples. We constructed soxB gene-based clone libraries and performed phylogenetic analysis to analyze the SOB community diversity. We conducted statistical analysis to assess the influencing factors on the SOB community. [Results] Phylogenetic analysis showed that the SOB mainly consisted of α-Proteobacteria, β-Proteobacteria and γ-Proteobacteria in the Tibetan hot spring sediments. The former were dominant classes. The dominant SOB classes differ among the sampled hot springs in our research:β-Proteobacteria were dominant in most of the studied samples, whereas only a few of them were dominated by α-Proteobacteria or γ-Proteobacteria. Mantel test showed that the SOB community composition of the studied samples significantly (P<0.05) correlated with altitude, conductivity, pH, sulfide, total dissolved solids and temperature. [Conclusion] In Tibetan hot spring sediments, α-Proteobacteria and β-Proteobacteria were the main SOB communities, but γ-Proteobacteria was rare. The SOB community structures differed significantly among the studied hot springs, which is mainly caused by their different physical and chemical properties.

Abstract:[Objective] To elucidate the variation patterns of aerobic methanotrophy under the shrinkage process from sediment to saline land and grassland. [Methods] Lake sediment, saline and grassland soils were collected from the shrinkage gradient of Lake Ganggeng in Inner Mongolia, and incubated under different initial CH₄ concentrations to determine their CH₄ oxidation potentials. We analyzed methanotrophic community composition and their abundance change by real-time quantitative PCR and high-throughput sequencing techniques. [Results] During lake shrinkage, soil properties of lake sediment and saline soil showed similar variation trends with methane oxidation rates, and were significantly different from that of grassland soil. In response to shrinkage, the relative abundance of Methylococcus increased significantly (with the relative abundance of 19.2%, 48.8% and 78.3% in lake sediment, saline and grassland soils, respectively), whereas Crenothrix decreased from 54.7% to 32.1% and 13.9%. Microcosm incubation of these samples under different initial CH₄ concentrations demonstrated the predominant increase of Crenothrix and Methylococcus in lake sediment; While Methylococcus and Methylomonas dominated the increase in saline soil; Crenothrix increased 7.81% in grassland soils (196 folds). [Conclusion] Lake shrinkage significantly decreased methane oxidation potential, and methanotrophic community also changed, with numerically dominant Methylococcus and Crenothrix in sediment and grassland respectively. However, it is noteworthy that under high CH₄ concentration, Crenothrix increased rapidly, most likely playing important roles during methane oxidation in all samples tested.

Abstract:[Objective] The soil methane uptake potential, abundance and community structure of methane-oxidizing bacteria were investigated in three grasslands located in three different ecoregions:Maqu, Linze and Huanxian of Gansu province of China. [Methods] Eight days incubation of soil with elevated concentration of methane was carried out to measure methane uptake capacity. The methane-oxidizing bacteria abundance was quantified by real time quantitive PCR targeting particulate methane monooxygenase coding gene (pmoA) in soils. The methane-oxidizing bacteria community structure was assessed by amplicon MiSeq sequencing. [Results] The potential of methane oxidation of three grassland soils ranged from 108.53±13.12 to 168.87±18.57 mg/(m²·h). The abundance of methane-oxidizing bacteria ranged from 1.76×10⁷ to 6.86×10⁷ pmoA gene copies g/d.w.s. The methane oxidation potential was positively correlated with methane-oxidizing bacteria abundance at day 0 (R²=0.5537). MiSeq sequencing analysis revealed significant spatial heterogeneity of methane-oxidizing bacteria community within the same grassland type. The Upland Soil Cluster gamma belonging to uncultured atmospheric methane oxidizers was the dominant methanotrophic lineage within methane-oxidizing bacteria gene types found in situ grassland soils. However, the conventional methane-oxidizing bacteria increased significantly after incubated these soils under high concentration methane, such as Methylocystis in Maqu soil and Methylosarcina in Linze and Huanxian soils. [Conclusion] Both uncultured atmospheric methane-oxidizing bacteria and the conventional methane-oxidizing bacteria may play an important role in the process of methane oxidation in the typical grassland soils in Gansu province of China. These microbes are very likely to oxidize the trace methane in atmosphere, and may also grow with high concentration of methane that stored in the soil. In the future, advanced techniques should be used to observe the atmospheric methane oxidation process in situ and to isolate the corresponding microbial groups, and finally reveal the geographical differentiation of methane-oxidizing bacteria in grassland soils and the environmental driving mechanism.

Abstract:[Objective] To explore the diversity of nitrogen-fixing microbial community and its response to geochemical parameters in the water of the mainstream and branches in the Three Gorges Reservoir (TGR) [Methods] A total of 18 water samples were collected from the mainstream and branches of the TGR before and after drainage (in March and June). The physical and chemical parameters of the samples were measured, and nifH gene diversity was analyized by using clone library-based phylogenetic analysis. The geochemical parameters of water bodies were correlated with the diversity and community composition of nitrogen-fixing microbial. [Results] The geochemical parameters differed significantly before (in March) and after (in June) drainage. The nitrogen-fixing microbes were dominated by Proteobacteria (50.3%) and Firmicutes (40.0%) the TGR waters in March (before drainage), in contrast with the dominance of Proteobacteria (48.4%), Firmicutes (25.4%) and Cyanobacteria (19.0%) in June (after drainage). Significant temporal and spatial variations were observed among the nitrogen-fixing microbial community composition and diversity as indicated by statistical analysis (Cluster and CCA analyses). The diversity of nitrogen-fixing microbes in the TGR waters after drainage (in June) was higher than before. The diversity of nitrogen-fixing microbes was higher in waters from tributaries than that from the main stream. Mantel test showed that the composition of nitrogen-fixing microbes was significantly correlated with the geochemical parameters of water. Water temperature was the most important factor affecting the community and variety of nitrogen-fixing microbes in the TGR waters.[Conclusion] The nitrogen-fixing microbial community compositions in the TGR waters show significant temporal and spatial variations, which could be ascribed to the different geochemical parameters, especially water temperature.

Abstract:[Objective] Anaerobic ammonium oxidation is a biogeochemical process of oxidizing ammonium and reducing nitrite or nitrate to produce N₂ by anaerobic ammonium-oxidizing bacteria under anaerobic conditions, which is an important process for removing fixed nitrogen from global ecosystem. The objective of this study is to demonstrate the biogeography patterns of ammonium-oxidizing bacteria in diverse habitats.[Methods] Based on the 16S rRNA gene sequences of ammonium-oxidizing bacteria from national center for biotechnology information database, we analyzed the distribution and diversity of ammonium-oxidizing bacteria in different habitat by Mothur Software. [Results] Results showed that Ca. Scalindua dominated in marine environment. Ca. Brocadia had broad distribution in both freshwater and agricultural soils ecosystem, and it was also dominant in engineered reactors, showing the higher concentration inorganic nitrogen may facilitate Ca. Brocadia existence. Wetland and estuary ecosystem had the highest diversity of ammonium-oxidizing bacteria in which Ca. Scalindua, Ca. Brocadia and Ca. Kuenenia all had relative higher abundance. [Conclusion] This study demonstrated the community structure and distribution characteristics of ammonium-oxidizing bacteria in different habitat, suggesting that different environmental factors in different habitat affect the population distribution and phylogenetic evolution of ammonium-oxidizing bacteria.

Abstract:[Background] Microorganisms in water are rich in diversity, and various interspecific relationships occur among different microorganisms, which have an important influence on the composition structure and function of water ecosystem. Phytoplankton (microalgae and cyanobacteria) and some microbes in aquatic environment can interact with each other in various formats. However, the beneficial interactions between bacteria and phytoplankton under stress conditions remain unclear.[Objective] Studying the effects of Cd²⁺ on the microbial community of water samples and possible interactions between bacteria and phytoplankton.[Methods] Based on the high throughput sequencing of 16S rRNA gene, we analyzed the changes of microbial community structure under Cd²⁺ stress. We used the microbial interaction network to analyze the possible interaction between bacteria and phytoplankton.[Results] By isolation and culture, we found that the strain Y9 could interact with Synechocystis sp. PCC6803 and help the algae to resist the toxicity of Cd²⁺. [Conclusion] The results showed that strain Y9 belonged to Phyllobacteriaceae family, which was consistent with the results of microbial community composition and microbial interaction network. This study will provide a new scientific basis for exploring the interactions between microorganisms in aquatic environment and the ecological effects of interactions between bacteria and phytoplankton for cadmium resistance.

Abstract:[Objective] To investigate and confirm the role of Na, K-ATPase (NKA) of Aspergillus niger in the weathering process of wollastonite, a silicate mineral. [Methods] Wild type Aspergillus niger was used as the original strain to construct high Na, K-ATPase α1 (NKA α1) gene-expressing strain oeNKA. We determined the biomass of oeNKA and the wild strain, pH of the culture medium and Ca²⁺ concentration released from wollastonite at different cultivation time (0, 2, 4 and 6 d). Besides, we also analyzed the mineralogy of the wollastonite residue by X-ray diffraction (XRD) to compare the weathering effect of oeNKA and the wild strain on wollastonite. [Results] The relative expression of NKA α1 and enzyme activity of oeNKA strain was 103 and 1.76 times higher than those of the wild strain, respectively. The biomass and pH of oeNKA had the same variation tendency as the wild strain during the 6-day cultivation. The biomass difference between the wild strain and oeNKA decreased significantly on the 2nd day, and then was gradually narrowed down over time and reached the lowest on the 6th day. Furthermore, the concentration of Ca²⁺ (1011.36±47.78 μg/g) released from wollastonite was about 4 times as that from the wild strain (248.30±25.21 μg/g). Moreover, the XRD pattern also showed that oeNKA exhibited intense effect on wollastonite weathering. [Conclusion] The weathering ability of oeNKA to wollastonite was significantly higher than that of the wild strain, and Na, K-ATPase in Aspergillus niger was actively involved in wollastonite weathering.

Abstract:[Objective] The aim of this study was to study microbial community structures and type of methanogenesis associated with biogenic gas in Luling Coalfield, China. [Methods] We detected microbial distribution of the formation water by high-throughput pyrosequencing and bioinformatic analysis. Anaerobic culture was also used to verify the type of methanogenesis. [Results] The composition and stable isotopic ratios of gas samples implied a mixed biogenic and thermogenic methane. Archaeal 16S rRNA gene analysis revealed the survival of the acetoclastic, methylotrophic, and hydrogenotrophic methanogen in the produced water. Most detected bacteria could degrade aromatic and cellulose-derived compounds in coal. The activity and potential of methanogens of the related bacteria were confirmed by the obvious methane production in enrichments supplemented with acetate, formate or H₂+CO₂. [Conclusion] Acetoclastic and methylotrophic as well as hydrogenotrophic methanogenesis was responsible for the methanogenesis in Luling coalfield. These results would provide theoretical basis to improve the coal bed methane production using microbial technology and realize the sustainable exploitation of coal bed methane.

Abstract:Microalgae play a key role in diverse marine ecosystem, and they also naturally coexist with a large variety of other microorganisms. In this symbiosis, O₂ released by algal photosynthesis is utilized by aerobicheterotrophic bacteria to mineralize organic compounds, and bacterial respiration provides CO₂ as a carbon source to algae. The algae-bacteria consortia has been extensively studied for applications in wastewater treatment. The algae-bacteria interactions and the application of microalgae-bacteria symbiosis system in wastewater treatment were summarized. According to previous studies, algae-bacteria interactions are categorized into nutrient exchange, signal transduction and gene transfer. The treatment of wastewater, contaminated by nutrients, heavy metals, crude oil, polycyclic aromatic hydrocarbons, and pharmaceutical contaminants through microalgae-bacteria symbiosis system was reviewed. Assimilation, anaerobic ammonia oxidation, nitrification and denitrification, phosphorylation are key mechanisms during inorganic nitrogen and phosphorus removal. The removal mechanisms of heavy metals, crude oil, polycyclic aromatic hydrocarbons, and pharmaceutical contaminants by microalgae-bacteria symbiosis system include bioadsorption, bioaccumulation, and intracellular and extracellular biodegradation.

Abstract:[Objective] To decrease the swelling of water-sensitive minerals via microorganisms in oil reservoir, one thermophilic bacterial strain was isolated from a high-temperature reservoir in the Zhan 3 block of the Shengli Oilfield. Further experiments were conducted to evaluate the interaction between this isolate and bentonite with smectite as the main mineral.[Results] The isolated strain was thermophilic, facultative anaerobic, Gram-positive, and rod-shaped. It could form spores and was identified as Geobacillus icigianus SL-1 via 16S rRNA sequencing. It could reduce structural Fe(Ⅲ) of smectite under anaerobic conditions. Scanning electron microscopy results showed that smectite was irregularly flaky before the experiments, whereas slab-like particles were observed after the experiments with the presence of SL-1, suggesting the formation of secondary minerals. The energy spectrum analysis showed higher Al/Si ratios were detected in the platy minerals and much stronger peaks for K⁺ than those in thin smectites. The percentage of smectite in biotic systems decreased significantly (47.7%) in comparison of those in abiotic systems (70.4%) at the end of experiments as indicated by the X-Ray Diffraction (XRD) analysis. Collectively XRD and Energy Dispersive Spectrometer (EDS) results confirmed the transformation of smectite to illite in the biotic systems, which reduce the mineral swelling property by 25.9%. [Significance] These results confirm that pristine bacteria in oil reservoir can play an important role in mineral transformation, subsequently decreasing the swelling properties of clay minerals. Therefore, our results offer a promising way to deal with the water-sensitive issues in oil recovery process.