Abstract:环境微生物学作为微生物与环境科学相结合的交叉学科，已经在环境污染治理，废弃物资源化利用，生物地球化学循环等方面发挥着重要作用。《微生物学通报》推出的本期“环境微生物主题刊”报道了专论与综述17篇、研究报告19篇，内容涵盖环境污染修复与微生物多样性、环境微生物资源的发掘与利用、环境微生物学研究前沿、环境微生物生理学及生物制剂、环境微生物与环境工程等应用领域，期望该主题刊的出版有助于加强我国环境微生物学研究者间的交流和合作，推动环境微生物学学科的进一步发展。

Abstract:[Background] Antarctic bryophytes harbor highly diverse polar microbes. However, the composition of Antarctic bryophyte bacterial communities is not well understood, which limits the development and application of microbial resources in extreme habitats. [Objective] This study reveals the bacterial community of the Antarctic moss Saniania uncinata sampled randomly around the Antarctic Great Wall Station. [Methods] We used Illumina Hiseq high-throughput sequencing technology to analyse the 16S rRNA gene V4 region of the bacteria. [Results] A total of 273 367 bacterial sequences were obtained from the three moss samples. Totally, 9 759 OTUs (operational taxonomic unit) belonging to 14 phyla, 27 classes, and 50 genera, were grouped based on 97% sequence similarity. The dominant groups were Proteobacteria (30.70%), Bacteroidetes (19.67%), Verrucomicrobia (12.43%), Cyanobacteria (10.55%), and Actinobacteria (9.36%). Particularly, 56.73% of the bacteria in this moss were unclassified at the genus level. [Conclusion] The Antarctic moss Saniania uncinata hosts phylogenetically diverse bacteria. This study provides a basis for the in-depth study of polar microbes.

Abstract:[Background] Fungus-growing termites are a kind of higher termites belonging to the family Macrotermitinae that cultivated monofungus (Termitomyces spp.) in their nest. Fungus-growing termites form a three-dimensional symbiosis system with intestinal microbes and microorganisms in the fungus garden. [Objective] To analyze the microbial diversity of fungus combs and termite feces, and compares with intestinal microbes of fungus-growing termites. [Methods] The bacterial 16S rRNA gene mplicon and fungal ITS rRNA analysis were performed by the Illumina MiSeq high-throughput sequencing method. [Results] The number of filtered sequences and OTU numbers of bacteria and fungi in samples of fungus comb and feces were obtained. The number of bacterial OTU in the five samples was between 90?199, while the fungal OTU was between 10?58. The diversity of bacteria was significantly greater than that of fungi. Both the number of OTU in bacteria and fungi in fecal samples are more than that in fungus comb samples. According to the analysis of taxa classification, the dominant phylum in the fungus comb samples are Proteobacteria, with a relative content of over 82.4%; followed by Bacteroidetes and Firmicutes; the dominant bacteria in fecal samples are Bacteroides, followed by Proteobacteria. The dominant bacteria belong to Alistipes and Dysgonomonas, which is consistent with the diversity of intestinal bacteria in fungus-growing termites. The dominant fungi in termite comb and fecal samples are mainly Basidiomycota and Ascomycota. The dominant fungi genus in fungus comb is Termitomyces, with a relative content of more than 51.83%. Xylaria is also identified in the comb. [Conclusion] This study provides a basis and reference for the future research on the symbiosis of fungus-growing termites with in vivo and in vitro microorganisms and the isolation and culture of microorganisms.

Abstract:[Background] Urban water is facing excessive antibiotic resistance genes (ARGs) contamination. However, few studies have studied the occurrence of ARGs in urban recreational waters. [Objective] To analyze the microbial community and resistance gene composition in urban recreational waters between summer and winter, for the understanding of aquatic ecosystem in recreational waters. [Methods] We determined the summer and winter microbial and ARGs composition of Jiushan Lake, an urban recreational lake, using high-throughput sequencing technology. [Results] The study revealed the existence of 148 and 152 phyla in summer and winter samples, respectively. Proteobacteria and Actinobacteria were the two predominant phyla in both seasons. The dominant genus in summer was Synechococcus, while the dominant genus in winter was Liminohabitans. A total of 449 ARGs were identified (304 shared by both seasons, 66 summer-exclusive, and 79 winter-exclusive). In contrast to the number of ARGs, their abundance was higher in summer samples. MCR-1.2 and BcI were the predominant ARGs in summer and winter water samples, respectively. The resistance mechanisms of the detected ARGs were mainly antibiotic efflux, antibiotic inactivation, or antibiotic target alteration. The results of redundancy analysis and canonical correspondence analysis showed that environmental factors were significantly correlated with the distribution of microbial community and resistance genes. [Conclusion] The microbial community structure and resistance gene composition are significantly different between winter and summer in Jiushan Lake. The results provide useful information toward a more comprehensive understanding of the structure of urban recreational aquatic ecosystems and also highlight the potential health hazards resulting from their ARGs contamination.

Abstract:[Background] The products of denitrification are N2O and N2, thus it causes nitrogen loss and increases greenhouse effect. Sulfide has a significant inhibitory effect on N2O reduction, however, the effect of sulfide on denitrifying bacteria and functional genes of denitrification are unclear. [Objective] To study the effect of sulfide on the accumulation of intermediate products of denitrification (NO and N2O), transcription of functional gene of denitrification (narG, nirS, nirK and nosZ) as well as the structure of the microbial community structure in soil amended with or without carbon source. [Methods] Different levels of sodium sulfide (0 and 150 mg-S/kg-soil) combined different levels of glucose (0 and 1 000 mg-C/kg-soil) were set up in soil microcosms experiment. Robotized incubation system was used to monitor the amount of NO, N2O and N2 accumulated during the incubation, and quantitative reverse transcription PCR (RT-qPCR) was used to quantify the transcriptions of functional gene of denitrification (narG, nirS, nirK and nosZ) as well as the MiSeq technology platform based on 16S rRNA gene high-throughput sequencing was used to analyze microbial community structure. [Results] The addition of sodium sulfide significant inhibited the reduction of N2O, but it had no significant effect on the accumulated N2O. And the addition of sodium sulfide significantly reduced the accumulated NO. Sodium sulfide addition significantly inhibited the activity of N2O reductase at a transcription level in a short time. Sodium sulfide addition inhibited the transcription of Azoarcus, Microvirga, Ensifer, Azohydromonas, Bacillus, Skermanella, Shinella, and Chthoniobacte. According to the query results of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, the addition of sodium sulfide inhibited the growth of N2O reducing denitrifying bacteria that cannot produce N2O. [Conclusion] The increase of soil sulfide caused by compost or other reasons leads to the inhibition of N2O reduction in denitrification process, which is due to the inhibition of nitrous oxide gene transcription and the selection impact of denitrifying bacteria. This study would be helpful to understand the microbial mechanism of the impact of sulfide on nitrogen metabolism.

Abstract:[Background] Recently, frequent haze events affect people’s daily life and economic development adversely. At present, less attention has been paid to airborne microorganisms in such haze events. [Objective] To explain the characteristics of airborne microbes in haze and further clarify the roles of microorganisms in the formation of haze. [Methods] Samples of particulate matter in severe haze in Beijing were collected. The microbial community structure and composition were analyzed by amplicon sequencing of bacterial 16S rRNA genes, and the correlations with pollutants were explored. [Results] Haze events would affect the airborne bacterial community structure significantly, resulted in an obvious increase of Proteobacteria and decrease of Actinobacteria. Particulate matter and the chemical constituents were identified as key factors that affected the α-diversity and community structure of airborne bacteria in severe haze. Meanwhile, compared with gaseous pollutants SO2 and NO2, water-soluble inorganic ions sulfate, nitrate and ammonium had a more obvious effect on airborne bacterial community structure. [Conclusion] This work illuminates the community characteristics of airborne bacteria in severe haze and its correlation with key environmental factors, and provides data references for airborne microbial research, air quality assessment and haze prevention.

Abstract:[Background] Microbial transfer in oilfiled production facilities is closely related to reservoir microbial community compositions and microbiologically improved oil production process. However, it is hard to distinguish the targeted microorganisms from the numerous indigenous microorganisms containing the same specific genes. Therefore, constructing microorganisms with specific gene marks is necessary. [Objective] In order to effectively track microbial transfer in oilfiled production facilities, an engineering strain Pseudomonas aeruginosa SG-rfp containing specific mark gene was constructed. [Methods] The red fluorescent protein gene (rfp) with a constitutive promoter was inserted into amp gene encoding β-lactamase on chromosome of rhamnolipids-producer P. aeruginosa SG isolated from petroleum reservoir by homologous recombination using integration vector pEX18Gm-URD and amp gene. [Results] P. aeruginosa SG-rfp constitutively expressing rfp gene was constructed. Strain SG-rfp is intolerant of ampicillin, kanamycin, streptomycin, and gentamicin. As well as the wild-type strain SG, SG-rfp can produce biosurfactants in aerobic and anaerobic conditions and significantly enhance oil recovery efficiency from oil-bearing core. Using strain SG-rfp, diffusion-limited microbial transfer in oil-bearing porous media was investigated and demonstrated via core-flooding test. [Conclusion] This study provides a powerful tool for in-depth investigation of microbial transfer in oilfiled production facilities and microbiologically improved oil production process.

Abstract:[Background] The industrial wastewater containing Te(IV) has potential toxic effects on organisms. The microbial mediated Te(IV) reduction to Te0 is of great importance. [Objective] Exploring the reducing ability, reductase site and reducing product characteristics of Te(IV) by Bacillus cereus CC-1. [Methods] Te(IV) was reduced by a selenite reducing bacterium Bacillus cereus CC-1. The optimum Te(IV) concentration and pH were confirmed according to the reduction rate within 48 h. The Te(IV) reductase site and the reduction ratio of Te(IV) with the existence of different anions and cations were determined. The composition, crystallinity and morphology of the reduced product of Te(IV) were characterized. [Results] Bacillus cereus CC-1 has the Te(IV) reducing ability. The reduction rate was the highest when the initial concentration of Te(IV) was 0.5 mmol/L and at pH 7.0. The addition of anions and cations in the system has a certain effect on the reduction of Te(IV). Phosphate, sulfate, acetate and molybdate have no obvious effect on the removal rate. Low concentration of nitrate inhibits the remove of Te(IV). Lead and bismuth inhibit the reduction of Te(IV) and copper can increase the removal rate of Te(IV). Te(IV) reductase is active both inside and outside of the cell and on the cell membrane, and the extracellular enzyme activity is higher than the other two sites. The strain CC-1 can partially reduce Te(IV) to tellurium, and the reduction product is encapsulated inside the cell. The reduction product of the intracellular enzyme to Te(IV) is a cluster of flaky structure. [Conclusion] The strain CC-1 has Te(IV) tolerance and reducing ability, and shows a certain pH dependence. There may be multiple transport processes for the reduction of Te(IV) by strain CC-1, and nitrate reductase may play an important role in the process of Te(IV) reduction. Te(IV) reductase is not only present on both inside and outside of the strain CC-1 cells but on the cell membrane as well. The reduction of Te(IV) by intracellular enzyme makes recycling and re-using of Te0 possible.

Abstract:[Background] Cyanophages, the viruses that specifically infect cyanobacteria, are abundant in both marine and fresh waterbodies. They are involved in the regulation of the abundance and population density of cyanobacteria, thus considered as potential agents to prevent and control cyanobacterial bloom. However, previous studies mostly focus on marine cyanophages, rather than on those from freshwater. [Objective] Isolation of as many as possible types of freshwater cyanophages for further studies of the 3-D structures, infection mechanism and co-evolution with the host cyanobacterium, in addition to potential application on prediction and control of cyanobacterial blooms. [Methods] We collected water samples from the surface rich of cyanobacterial blooms in a small pond named Yexihu on the west campus of the University of Science and Technology of China, Hefei, China. In total 17 strains of cyanobacteria were applied to the screening against the collected water samples using liquid culture medium and double-layer plate. Cyanophages in the lysate were purified via NaCl-PEG precipitation followed by CsCl density gradient centrifugation, and further applied to morphology check using transmission electron microscopy. The titer of the lysate was determined by the serial dilution method. [Results] The water samples could specifically infect a strain of Pseudanabaena termed Pan, which was isolated from the Lake Chaohu. The lysate contains four types of cyanophages with different morphology, one type of Podovirus and three types of Siphovirus. Notably, we found an atypical freshwater cyanophage with a prolate head for the first time. [Conclusion] The water sample of Yexihu contains cyanophages that could specifically infect cyanobacteria of the Lake Chaohu, indicating that the pond Yexihu and the Lake Chaohu share a similar pattern of cyanobacteria and cyanophages. Thus, we can use Yexihu as a waterbody to mimic the related molecular ecology studies and cyanobacterial bloom control in the Lake Chaohu.

Abstract:[Background] At present, the physicochemical properties of exopolysaccharide (EPS) produced by microorganisms and their application in heavy metal adsorption have been widely concerned. [Objective] The physicochemical properties of exopolysaccharide produced by Rhodococcus sp. HX-2 was studied and the adsorption of heavy metals by exopolysaccharide was investigated. [Methods] The crude exopolysaccharide was purified by ion exchange and gel chromatography. Sugar content was measured by phenol-sulfuric acid method. Protein content was determined by using the Bradford kit. Lipid content was measured by methanol extraction method. Monosaccharide composition was analyzed by high performance liquid chromatography (HPLC). The surface morphology was observed by scanning electron microscopy (SEM). The adsorption effect of exopolysaccharide on heavy metals was studied by isothermal adsorption model and kinetic model. [Results] The total sugar content, protein content and lipid content of the EPS-G-1 produced by HX-2 were 78.43%, 8.31% and 8.22%, respectively. After purification, the monosaccharide of exopolysaccharide was composed of glucose, mannose, galactose, glucuronic acid and fucose; the mass ratio was 27.31:26.67:24.83:15.85:4.80, respectively. The maximum adsorption capacity of exopolysaccharide produced by HX-2 to Cu2+ was 144.93 mg/g by isothermal adsorption model fitting. [Conclusion] The exopolysaccharide produced by HX-2 has favourable adsorption effect on Cu2+ in water and can be used for the treatment of heavy metal ions in industrial wastewater.

Abstract:[Background] As a highly toxic heavy metal pollutant, the reduction of hexavalent chromium (Cr(VI)) by microbiological methods is not only economical but also environmentally friendly. [ObjectVIe] To explore the proteins or genes related the tolerance or reduction of Cr(VI) in chromium-resistant strain CM01, and to explain the tolerance mechanism of the strain at the molecular level. [Methods] The difference of protein expression in chromium-resistant strain CM01 under the Cr(VI) stress or not was analyzed by isobaric tags for relatVIe and absolute quantitation techniques (iTRAQ). The mRNA expression of 4 up-regulated proteins related to metabolic pathway was verified by RT-qPCR technique. The hydrophobicity of cell surface was determined by UV spectrophotometer. [Results] In this study, 2 570 proteins were identified and 646 were significantly different, of which 343 were up-regulated and 303 were down-regulated. Fe/Mn superoxide dismutase, betaine aldehyde dehydrogenase, pentose phosphate pathway, inositol phosphate pathway and amino acid metabolism in CM01 were involved in the response mechanism to exogenous Cr(VI). The results of RT-qPCR experiments showed that the gene transcription levels and protein level of the four proteins involved in metabolic pathways were consistent. The cell surface hydrophobicity of CM01 in the control group was higher than that in the experimental group. [Conclusion] Cr(VI) response mechanism of chromium-resistant bacteria was preliminarily explored in this study, which provides theoretical support and new research ideas for the use of microorganisms to control environmental pollution.

Abstract:[Background] Forest topsoil transplantation has been widely used in the restoration of degraded ecosystems because it carries a large number of seed banks and microbial communities. However, there are few studies had been carried out on the changes of fungi and bacteria communities after soil transplantation. [Objective] This study compared the composition and diversity of fungi and bacteria of transplanted soil to its mother soil and receptor soil. [Methods] Using Illumina HiSeq high-throughput sequencing technology, the characteristics of fungi and bacteria of mother soil, 15 months of transplanted soil and receptor soil were obtained, and their diversity and richness were compared. [Results] Basidiomycota and Ascomycota were the dominant fungi in the three soil types; Acidobacteria, Proteobacteria, Actinobacteria and Chloroflexi were the dominant bacteria, the relative abundance of dominant fungi and bacteria changed significantly after soil transplantion. PCA analysis showed that there were significant differences in community structure of fungi and bacteria among the three soil types. UPGMA analysis showed that the distance between the transplanted soil and the receptor soil was closer, the species composition of the transplanted soil was more similar to the receptor soil, and there was no significant difference between the dominant genera of fungi and bacteria in the transplanted soil and the receptor soil. After transplantion, the abundance and diversity of fungi and bacteria were significantly different from its mother soil. [Conclusion] The composition and diversity of bacteria and fungi of transplanted soil turned toward the receptor soil after 15 months. The findings provide a theoretical reference for further study of microbial ecosystem on rocky desertification environment, and provide a scientific base for the improvement of soil translocation technology.

Abstract:[Background] Chromium-contaminated soil is a key target for soil pollution remediation in China. In many remediation technologies, microbial method has become a research hotspot because of its simple, economical, and no secondary pollution. It is particularly important to screen strains that can adapt to the polluted site environment and efficiently reduce Cr(VI) in the microbial method. [Objective] Screening strains adapted to the efficient reduction of Cr(VI) in cold and arid regions of Northwest China, enrich the resource pool of chromium reducing bacteria, and lay the foundation for remediation of chromium-contaminated soil. [Methods] Screening bacteria by enrichment, domestication, isolation and purification; the target strain was identified by a combination of morphology and molecular biology; and the reduction mechanism was studied by fourier transform infrared spectroscopy. [Results] G-13 has strong Cr(VI) reducing ability. At pH 9.0 and temperature 30 °C, the reduction rate reached 82.8% in a 100 mg/L Cr(VI) solution within 60 hours. Morphological and molecular biological identification showed that the strain G-13 was Micrococcus luteus. The decrease of Cr(VI) in the reaction was accompanied by the increase of Cr(III), which indicated that the reduction reaction was the main factor, and the reducing ability was dependent on the growth of bacteria. Studies on cell components and denaturation showed that extracellular enzymes play a major role in the reduction reaction. Except for Pd2+ and Cd2+, the other metal ions had no significant inhibitory effect on enzyme activity. Through fourier transform infrared spectroscopy analysis, it was found that the binding sites of G-13 and Cr(VI) were mainly –OH, C=O, ?COOH, ?CH, –CONH2 and so on. [Conclusion] G-13 has strong Cr(VI) reducing ability, and can be used to rich bacterial resources for repairing chromium-contaminated soil in northwestern cold and arid regions.

Abstract:[Background] Organic pollution has a great impact on the microbial diversity of sediment. At present, there are few studies on the fungal community of sediment in polluted water. [Objective] To study the diversity characteristics of fungal community in the sediment of different degrees of organic pollution, and explore the influence of industrial organic pollution on the community structure of fungi. [Methods] Chemical analysis and high-throughput sequencing was adopted to study, and the relationship between environmental factors such as water quality, components of sediment and fungal diversity was analyzed. [Results] With the decrease of pollution degree, the number of fungal sequences, OTU and Shannon index in sediment were all increased. Unclassified Fungi, Ascomycota and Basidiomycota were the dominant species of the fungal community in the sediment. Zopfiella, Westerdykella, Clypeosphaeria, Ilyonectoria, Paracremonium and Aspergillus were the main dominant genera in sediment. Shannon index was significantly correlated with DO of water body, negatively correlated with organic matter and total phosphorus content of sediment. Simpson index was significantly correlated with TN, NH3-N and TP of water body. [Conclusion] Organic pollution leads to the decrease of dissolved oxygen in water and the increase of organic matter in sediment, which finally leads to the significant decrease of fungal diversity in the polluted area. Zopfiella, Penicillium, Emericellopsis, Westerdykella, Jugulospora and Chromelosporium may be mainly involved in the removal of pollutants in the aeration treatment area under facultative condition. Ilyonectria, Mortierella and Epicoccum maybe mainly involved in the decomposition of aquatic organism residues and the adsorption and settlement of pollutants.

Abstract:[Background] Soil heavy metal pollution is serious in the slag heap of mining area. There are some microorganisms in the slag heap of mining area that are resistant to heavy metals. [Objective] To investigate the effects of heavy metal stress on the growth of fungi and pH of fermentation broth. [Methods] The acid-producing ability of two fungi (Aspergillus niger ZJ-I, Penicilium chrysogenum ZJ-V) isolated from the slag heap of mining area as materials and their tolerance to different heavy metal ions Pb2+, Cd2+ and Zn2+ were studied by using traditional microbial culture method. [Results] The results showed that these two strains ZJ-I and ZJ-V were Aspergillus niger and Penicillium chrysogenum respectively by morphological and 18S rRNA gene sequence analysis. When the metal culture was not increased, the pH of the fermentation broth of the above two strains decreased by 0.58 and 0.69, respectively, compared with the control without inoculation of fungi and when the two strains were under heavy metal tolerance, the pH range decreased with the increase of heavy metal concentration, pH of the fermentation broth with different concentrations of Pb2+ decreased by 0.53, 0.39, 0.34 and 0.39 respectively, and by 0.21, 0.23, 0.14 and 0.09 respectively to P. chrysogenum ZJ-V. The pH of the fermentation broth with different concentrations of Cd2+ was decreased by 0.75, 0.43, 0.39 and 0.32 respectively on A. niger ZJ-I and 0.62, 0.46, 0.38 and 0.49 respectively on P. chrysogenum ZJ-V. The pH of the fermentation broth with different concentrations of Zn2+ decreased by 0.87, 0.61, 0.57 and 0.43 respectively, by 1.1, 0.34, 0.44 and 0.49 respectively to P. chrysogenum ZJ-V. The low concentration of Zn2+ promoted the acid production of A. niger ZJ-I and P. Chrysogenum ZJ-V, and the low concentration of Cd2+ promoted the acid production of A. niger ZJ-I. When the concentration of heavy metal ions Cd2+, Zn2+ and Pb2+ was more than 200, 400, 2 000 mg/L respectively, A. niger ZJ-I had significant inhibition rate reached 80%, when the concentration of heavy metal ions Cd2+, Zn2+ and Pb2+ was more than 200, 1 000, 2 000 mg/L respectively, P. chrysogenum ZJ-V had significant inhibition rate reached 80%, [Conclusion] Both fungi have acid production ability and heavy metal tolerance, strain P. chrysogenum ZJ-V is superior to A. niger ZJ-I in acid production and heavy metal tolerance, so strain P. chrysogenum ZJ-V can be used as the dominant strain for bioremediation of heavy metal contaminated soil.

Abstract:[Background] Acinetobacter sp. Tust-DM21 (GenBank: KX390866) is a highly efficient petroleum degrading bacteria isolated early from the water-oil mixed sample collected from the waste oil area of the Bohai Bay offshore oil exploration vessel in this laboratory. It exhibits strong degradability to short, medium and long chain alkanes. [Objective] To investigate the optimal conditions of the strain for degradation at the application level and to investigate the role of degradation genes at the bioinformatics level. [Methods] The strain was incubated at different temperatures and pH for 144 h. Changes in petroleum hydrocarbon components were determined by GC-MS internal standard methods, and the best degradation condition was calculated. Meanwhile, the degrading genes were identified in its genome by bioinformatics analysis, and seven homologous genes were selected for each gene and their protein sequences were compared. Real-time PCR analysis of these two genes at 0?144 h were performed for their transcription expression research. [Results] The optimal degradation conditions were 35 °C and pH 8.5. The relative degradation level of petroleum hydrocarbon under this optimal condition can reach up to 97.5%. The degradation rate was 98.5% for long-chain alkanes, 81% for cycloalkanes and 87% for aromatics. Meanwhile, the common alkane degradation gene alkB (Genbank: MH368539) and the long-chain alkane degradation gene almA (Genbank: MH357335) were found in its genome, the proteins of the two degradation genes are similar to their homologous proteins, and the similarity of the same genus is the highest. Real-time PCR showed that gene relative expression increased gradually over time. [Conclusion] It exhibits strong degradability to short, medium and long chain alkanes under the optimal degradation conditions, especially for long-chain alkanes. Combining with the growth trend in this time period, it was demonstrated that the strain growth and degradation were associated with up-regulated expression of the alkB and almA genes.

Abstract:[Background] Pseudomonas donghuensis HYS is a high-siderophore-yielding strain isolated and identified by our laboratory from the Wuhan East Lake. HYS has strong toxicity to Caenorhabditis elegans. Previous studies have found that insertions in the argS gene in HYS can significantly reduce its toxicity to C. elegans. [Objective] To explore the function of argS gene and how it affects bacterial toxicity, and to provide a theoretical basis for further study on the mechanism of HYS toxicity. [Methods] The biological function of argS gene and the relationship between the arginine succinyltransferase (AST) pathway and bacterial toxicity were investigated with bioinformatics comparison, genetic analysis, physiological assays, and biochemical experiments. [Results] The argS gene in HYS encodes a protein that shares 88% similarity to the arginine succinyltransferase β subunit in Pseudomonas aeruginosa. The deletion of argS prevented the HYS strain from using arginine as the sole carbon source for growth. Deletion strains of key genes in arginine decarboxylase (ADC) pathway, arginine dehydrogenase (ADH) pathway and arginine deiminase (ADI) pathway could normally use arginine as the sole carbon source and had no significantly attenuated effect on the toxicity to C. elegans. Added arginine to these strains significantly attenuates the toxicity, and decreases their ability in producing siderophores. [Conclusion] AST pathway in Pseudomonas donghuensis HYS can affect the toxicity to C. elegans by affecting the synthesis of the siderophores. This study lays the foundation for further studies into the mechanism of arginine metabolism and pathogenicity in Pseudomonas.

Abstract:[Backgroud] The anthrax of Sarcandra glabra was serious, so far there is no research report on the biological control of endophytic bacteria against this pathogen. [Objective] To screen out bacteria that have an antagonistic effect on Colletotrichum dematium, and to study its antibacterial mechanism. [Methods] Endophytic bacteria were isolated and purified from different tissues of healthy plants collected from different regions of Guangxi by the plate dilution method. [Results] The results of the plate confrontation test showed that RJ-4 and JJ-5 from stems had strong antagonistic effects on anthracnose of Sarcandra glabra. Among them, the strain with the strongest antagonistic effect was RJ-4, with an inhibition rate of 84.10%. The results of the antibacterial spectrum showed that RJ-4 and JJ-5 had obvious antagonistic effects on the 14 pathogenic fungi tested. The strongest antagonistic effect was RJ-4, with an average inhibition rate of 95.3%. It shows that the strain can secrete protease and cellulase and chitinase, destroy the mycelium of the pathogen, and inhibit the growth of the pathogen; The fermentation broth containing the antagonistic bacteria obviously inhibits the mycelium of the pathogen, and the mycelium is distorted, broken, and entangled, color deepens and so on. Based on morphological characteristics and 16S rRNA gene identification, strain RJ-4 was Bacillus amyloliquefaciens. [Conclusion] Strain RJ-4 has bacteriostatic and disease-resistant functions and can produce a variety of antibacterial active substances, which can provide resources for new antibacterial substances.

Abstract:Cyanophages are viruses that infect cyanobacteria. They are able to regulate the abundance and diversity of the cyanobacterial populations, and play a critical role in food web dynamics and biogeochemical cycling of many aquatic ecosystems. Cyanophages perform various interactions with the host cells, such as adsorption, invasion and replication, and thereby participate in infection process and complete their life cycle. Based on the relation between cyanophage life cycle and the genome structure, the review mainly introduced several significant cyanophage proteins that interact with cyanobacteria, such as viral attachment proteins, endopeptidases, holins, DNA polymerases, non-bleaching protein A (NblA), virulence factors, virulence factors, anti-CRISPR proteins (Acr), and small heat shock proteins, and thereby analyzed their molecular characteristics and elaborated the molecular mechanisms of cyanophage infection and cyanophage-cyanobacterium interaction. To comprehensively know the driving strategy, infection efficiency and ecological influence of diverse cyanophages with their hosts and aquatic environments, this review not only summarized and discussed the research advances and trends on these significant genes associated with cyanophage infection, but also proposed significant ideas for performing extensive function studies on the related genes with cyanophage infection by using new gene editing technology, and thereby to expand global aquatic virus databases and to enable us to understand more about mechanisms of interaction between cyanophages and the host cyanobacteria.

Abstract:The traditional waste water treatment process with standard discharge as the core goal often requires high energy and material consumption, leading to the situation of reducing pollutants and increasing greenhouse gas emissions, which does not conform to the concept of sustainable development. As a novel membrane treatment technology, the membrane-supported biofilm reactor (MSBR) can utilize bubbleless aeration to provide gaseous electron donor (CH4, H2) or acceptor (O2) for attached biofilm, thereby removing contaminants from water and producing substances of recycling value. Thus, MSBR can achieve the three major goals of contaminants removal, energy saving and resource recovery. This article systematically introduced the mass transfer process of membrane biofilm and the mechanism of removing contaminants, discussed the research prospects of MSBR in resource recovery, and sorted out the typical contaminant removal in water treatment in experimental and pilot scales. Finally, we also summarized the challenges and development trends of the MSBR.

Abstract:Iron, an essential nutrient for the survival of virtually all living organisms, participates in a variety of important biological processes mainly in the form of protein cofactors. For bacteria, iron shortage is a severe challenge to overcome and iron overload imposes an equally critical threat. The dualistic properties of iron prompt bacterial cells to carefully maintain intracellular iron homeostasis. Current mechanic model for iron homeostasis in gram-negative bacteria is mainly derived from the extensive studies of model bacterium Escherichia coli. In recent years, investigations into iron homeostasis in environmental bacteria have revealed surprising diversities in iron-controlling mechanisms among gram-negative bacteria. With respect to iron homeostasis, the biological pathways and their components, major regulators and their physiological impacts, and interactions between iron homeostasis and other physiological activities display a myriad of species-specific characteristics formed by evolution. This review, stemming from the discoveries in Shewanella, summarizes recent advances about the biological processes involved in iron homeostasis, their reciprocal influences, and physiological consequences of imbalanced iron homeostasis due to altered regulation, as well as lists out the questions to be addressed, aiming at facilitate future explorations in the field of iron homeostasis.

Abstract:Methane is a more active greenhouse gas than CO2, and the process of methane anaerobic oxidation (AOM) driven by microorganisms is of great significance in reducing global methane emissions. The final electron acceptors involved in AOM reaction are mainly divided into three categories: sulfate, nitrite/nitrate, and metal ions represented by Fe(III), Mn(IV), etc. Both soluble metal substances and insoluble metal minerals can be used as electron acceptors for AOM, which greatly enhances the ecological value of microorganisms participating in metal-dependent anaerobic oxidation of methane (Metal-AOM). The current research focuses on functional flora, ecological distribution, etc. Some anaerobic methanotrophic archaea (ANME) have the ability to participate in Metal-AOM process directly or indirectly. However, due to the difficulty in purification, enrichment and isolation of functional microorganisms, the study on their physiological, biochemical and ecological characteristics has been limited. Meanwhile, with the discovery of Metal-AOM in different aquatic habitats, its application in the field of pollution control has been widely discussed; but there is a lack of in-depth research of estuarine habitats. Based on the discovery of Metal-AOM, the main microorganisms involved in the process and their ecological distribution in the aquatic environment were described, and the reaction mechanism of Metal-AOM and its opportunities and challenges in practical application were introduced. Finally, based on the existing research results, this paper puts forward the research prospects of functional microflora, mechanisms and environmental applications, including the isolation and purification of microorganisms, the analysis of their metabolic activity and mechanism of action, as well as the design, development and application of new production techniques, in order to provide reference for environmental pollution control and industrial applications in the future.

Abstract:Polyethylene (PE), one of the most widely used general plastics, is usually processed into disposable packaging materials (including plastic bags and containers) and agricultural mulch films. The widespread utilization of PE plastic products has resulted in the accumulation of large amounts of PE waste, posing a serious threat to the ecological environment. Since the 1970s, several studies show that PE plastic could be degraded by a few of microorganisms isolated from a diversity of niches such as soil, marine ecosystem, garbage dump and insect gut. Additionally, a number of oxidoreductases such as monooxygenase, peroxidase and laccase can oxidize PE plastic. These studies have paved the path for the development of bio-treatment of PE waste. This review summarizes the isolation and screening methods of PE-degrading microorganisms, as well as the reported PE-degrading microorganisms and enzymes. Further perspectives and challenges on the research on biodegradation of PE are also highlighted.

Abstract:Aerobic denitrification technology has been widely studied since it was proposed by virtue of many advantages, such as capable of achieving simultaneous nitrification and denitrification, saving investment and operation cost. Here, we summarize the screening and isolation of aerobic denitrifying bacteria in recent years, and the influence of environmental factors on denitrifying efficiency of aerobic denitrifying bacteria, including dissolved oxygen (DO), C/N and temperature. Then, we discuss the theory of aerobic denitrification biological nitrogen removal technology and the key functional genes and enzymes of aerobic denitrification. Meanwhile, the application of molecular biotechnology in the study of aerobic denitrification and the research status on the practical application of aerobic denitrification are reviewed.

Abstract:Microorganisms play an important role in the natural attenuation process of petroleum hydrocarbons removal from the environment. Microorganisms can produce a series of enzymes to utilize and degrade these organic contaminants. The genes encoding the key enzymes in the hydrocarbon biodegradation pathway are called as function genes. Therefore, studying the function genes for petroleum hydrocarbon degradation is an important basis for analyzing the diversity of indigenous microbial communities, evaluating the natural decaying potential and constructing the genetic modified strains. This review introduces the aerobic and anaerobic microorganism for biodegradation of alkanes and aromatic compounds. The major function genes for the degradation are summarized, including genes encoding monooxygenases and dioxygenases.

Abstract:Antibiotics are effective medicines to combat pathogenic microbes. However, the wide use of antibiotic in human medicine and agricultural production has promoted the rapid spread of bacterial resistance in the environment. In particular, the combined use of multiple antibiotics promotes the emergence of multi-drug resistance that seriously threatens human and animal health, food and environmental safety. Therefore, new researches focus on the following aspects: using omics and synthetic biology to discover and synthesize new antibiotics. Using high throughput technology to analyze the new transmission routes of antibiotic resistant bacteria and antibiotic resistance genes and the mechanism of new resistance in the environment. Strategies and related processes are emerging for reducing, replacing and controlling antibiotic resistance genes. Therefore, based on a comprehensive understanding of the transmission of antibiotic resistance genes in the environment, how to block the transmission route in a green and efficient way is still the current research hotspot. In view of this, this review expounds the discovery, development and control strategies of antibiotic from the perspective of bacteria, to provide ideas for further research on control antibiotic resistance development.

Abstract:Lignin is a highly cross-linked aromatic heteropolymer. As it is one of the most abundant carbon reservoirs in the environment, its decomposition plays a key role in the global carbon cycle and biomass utilization. However, lignin degradation remains highly challenge, due to its inherent heterogeneity and recalcitrant chemical structure. Microorganisms from different environments have been found to have the capacities of lignin degradation. Moreover, a variety of oxidoreductases in these microorganisms have been identified to be involved in lignin degradation. However, the lignin degradation mechanisms are not yet well-studied. Thus, exploring the lignin-degrading enzyme system and metabolic network are critical to studying the mechanism of microbial metabolism of lignin. This article reviews the ligninolytic enzymes, including their components and extracellular secretion mechanism, as well as the lignin biodegradation pathways. Moreover, it provides clues to further explore mechanisms of lignin biodegradation and strategies of sustainable biomass utilization.

Abstract:Burkholderia xenovorans LB400 is a strain of polychlorinated biphenyls degrading bacteria PCBs. This organism also cooxidizes chlorinated biphenyl (CB) congeners containing from one to six chlorine substituents. In recent years, LB400 has become a model organism for study of the biochemistry and molecular biology of CB metabolism in prokaryotes, because of excellent degradability and a broad spectrum of chlorinated biphenyl (CB) congeners. At present, the research on strain LB400 is mainly focused on degradation genes, enzymes and enzymes evolution, while its degradation pathway, substrate range and related mechanism of PCBs have been widely discussed; Furthermore, there are few studies on regulatory genes related to degradation of PCBs. This paper focuses on the degradation of polychlorinated biphenyls, and describes its metabolic pathway, related genes and enzyme system and artificial evolution. we hope to provide a reference for the further study of the application of Burkholderia xenovorans LB400 and other polychlorinated biphenyls degradation strains.

Abstract:Hexachlorobutadiene (HCBD), which is a toxic and harmful aliphatic chlorinated hydrocarbon, had been widely used as an important ingredient in industrial chemicals (e.g., pesticides, herbicides, transformer oils, heat transfer fluids). In 2015, HCBD was added to the persistent organic pollutants (POPs) list based on the fact that it met the risk screening criteria (e.g., levels of toxicity, persistence, bioaccumulation, potential for long-range environmental transport). In 2017, HCBD was added in Annex C of the Stockholm Convention to reduce its unintentional production and emission. Environmental transport and fate of HCBD remain a research focus, and a better understanding of the roles and mechanisms of microorganisms in HCBD degradation and transformation is required. Here, we review the microbial biodegradation pathways, rates, and mechanisms of HCBD biotransformation in anoxic environments (e.g., groundwater, sediments). The feasibility of anaerobic biotransformation of HCBD and its degradation products as electron acceptors by calculating the thermodynamic parameters are demonstrated. Finally, future research on the HCBD microbial degradation is discussed, including the use of multi-omics techniques to unravel microbial community structure and their syntrophic mechanisms; isolation of anaerobic microorganisms capable of HCBD reductive dechlorination; development of highly efficient degradation cultures that can be applied for in-situ bioremediation of HCBD contaminated sites.

Abstract:Redox mediators can accelerate anaerobic biotransformation of toxic environmental pollutants. Flavins are the redox mediators synthesized and secreted by bacteria. Their application can effectively avoid the problems of high cost and secondary pollution caused by exogenous mediators. Therefore, they have attracted wide attention. Many studies have shown that the trace amount of flavins synthesized by bacteria can not only be used as coenzyme factors of flavin proteins to participate in the anaerobic biotransformation of azo dyes, chromates and nitroaromatics, but also be secreted to extracellularly transfer electrons to solid electron acceptors such as iron minerals and electrodes for bioremediation. According to the functional roles of flavins, this paper reviews their synthesis and secretion, flavins mediated-intracellular and extracellular electron transfer, and their effects on anaerobic biotransformation of environmental pollutants, so as to promote their application in the treatment of environmental pollutants.

Abstract:Lignocellulose has considerable reserves in nature and is an important source of biofuel production. Consolidated bioprocessing refers to the process that conversion of lignocellulose into a biological product in one step without the addition of hydrolytic enzyme and has important application value in today’s increasingly serious energy crisis. The synthetic microbial consortium is formed by the co-culture of two or more pure cultured microorganisms (wild or engineered strain), and it has the advantages of low complexity and high stability, and can achieve specific functions by coordinating microbial interactions and the stability of the entire ecosystem. In addition, the rapid development of synthetic biology facilitates the development of new methods and tools for the construction and optimization of synthetic microbial communities. This article focuses on the consolidated bioprocessing of lignocellulose, and reviews the research progress of synthetic microbial communities in this field. We first briefly introduce that systems biology provides guidance for the design of synthetic microbial communities, and then detail the design principles, optimization tools, application and challenges in the actual production of synthetic microbial consortium, which provides a reference for consolidated bioprocessing of lignocellulose.

Abstract:Anaerobic digestion process is widely used in the treatment and disposal of various types of wastewater. But in actual operation, the digestion system often suffers from acid inhibition caused by excessive accumulation of volatile fatty acids due to the influence of digestion conditions and material properties. It causes problems such as decreased gas and methane production. In recent years, some researchers have found that the type and concentration of volatile fatty acid, pH and temperature are the main factors affecting acid inhibition. Based on this point, the methods of adding alkaline chemicals, adding trace elements, using bioaugmentation technology and microbial electrochemical technology have been used to relieve acid inhibition. We review here the production process, inhibition mechanism and recovery method of acid inhibition in the anaerobic digestion process, to provide references for solving the acid inhibition problem in anaerobic digestion.

Abstract:Triterpenoids are one of the main active chemical components in Ganoderma. Because of their many important physiological activities, they have become the research focus of domestic and foreign researcher. In this paper, the optimization of triterpenoid fermentation technology and the progress of signal transduction in the biosynthesis of Ganoderma were summarized, and the problems in the research of Ganoderma fermentation were put forward. The aim of this review is to provide reference and inspiration for the regulation of submerged fermentation of triterpenoids and the development of fermentation technology of Ganoderma.

Abstract:The vertical and horizontal transmission of resistance genes in the environment makes antibiotic resistance as a global problem threatening human and animal health. Animal food is an indispensable part of human diet. Due to the overuse and abuse of antibiotics, antibiotic resistance genes in animal farms should be concerned. In this paper, the source, transmission routes and influencing factors of antibiotic resistance genes in animal farms, as well as risk assessment and control techniques are described, and suggestions on the future direction of researches on antibiotic resistance genes are proposed.