Abstract:面对物种数量繁多、生态分布广泛、生态功能强大的微生物资源，微生物生态学的任务一方面在于不断发现和认识这类生命“暗物质”及其存在机制，另一方面要充分挖掘和利用这些微生物资源。微生物生态学的应用从最早的混合发酵发展到极端微生物资源利用、微生物生态制剂开发甚至合成微生物生态等多个领域。2019年10月在湖南省长沙市举行的“中国生态学学会微生物生态专业委员会学术年会”设立了3个与微生物生态学应用相关的分会场，本期《微生物学通报》也开辟了“人工生态系统微生物”栏目，展现了我国微生物生态学在资源、能源和环境等应用领域的成果，让我们看到了其成为社会与经济“绿色高效发展”重要驱动力的希望。

Abstract:微生物是地球上生命的主体之一，拥有丰富多彩的代谢途径，在一定程度上塑造了今天的地球。由于绝大部分环境中的微生物无法被分离和培养，微生物被喻为生命物质中的“暗物质”。近年来，迅猛发展的测序技术有力地推动了微生物“暗物质”的研究。依托2019年10月在湖南省长沙市举行的中国生态学学会微生物生态专业委员会学术年会，《微生物学通报》组织了“微生物生态学主题刊”，展现了我国微生物生态学研究的部分最新进展和成果，揭示了微生物的群落组成、功能的新视角和新技术方法。

Abstract:[Background] The interaction between marine phytoplankton-derived organic matter and heterotrophic bacteria is an important part of biogeochemistry cycle in the upper ocean. [Objective] Studying the responses of microbial communities in oligotrophic environment to Synechococcus-derived organic matter (SOM) could increase our understanding of marine biogeochemistry cycle. [Methods] A SOM-addition incubation experiment was conducted in the South China Sea, and the variations of organic carbon, nutrients, and active microbial communities were monitored during the incubation. [Results] During the short-term incubations, 60%–73% of SOM was utilized by microbes. Gammaproteobacteria was the fastest responder, and the most dominant microbial population over the entire incubations. The addition of SOM changed the in situ microbial community structure, and the succession of microbial community structure was also observed corresponding the consumption of labile organic matter. [Conclusion] Most of the SOM belong to labile organic matter which could be quickly degraded and utilized by heterotrophic bacteria. Microbes could respond positively to phytoplankton-derived fresh organic matter, and their activities drive the biogeochemistry cycle in the ocean.

Abstract:[Background] Most marine microorganisms are uncultivated. In order to excavate the culturable microbial resources in the marine ecosystem, we tried some methods, such as oligotrophic culture. [Objective] To compare the differences in bacterial population, community structure and utilization characteristics of carbon sources of South China Sea under different low-nutrient culture conditions. [Methods] The seawater samples from South China Sea were cultured in the original 2216E medium (group Y), diluted 10 times (group Y-10) and 50 times (group Y-50) in 2216E culture medium. The number of bacteria and the structure of bacterial communities were detected by real-time PCR and 16S rRNA gene. The number of heterotrophic bacteria was also counted by plate counting method, and the culturable bacteria were separated and identified. The utilization characteristics of carbon sources of bacterial communities in different media were analyzed by Biolog EcoPlateTM method. [Results] The total number of bacteria in Y group was higher than that in Y-10 group and Y-50 group (P>0.05), but the number of heterotrophic bacteria was significantly higher than that in Y-10 group and Y-50 group (P<0.05). The sequencing of 16S rRNA gene shows that the bacterial community structure was significantly different under different dilution multiples, in the Y group, 10 phyla and 193 genera were detected, and the dominant groups were Proteobacteria (56.44%) and Bacteroides (37.27%); in the Y-10 group, 15 phyla and 220 genera were detected, and the dominant groups were Proteobacteria (40.30%), Bacteroides (36.91%) and Firmicutes (17.30%); in the Y-50 group, 14 phyla and 226 genera were detected, and the dominant groups were Proteobacteria (45.19%), Bacteroides (25.29%), Planctomycetes (13.58%) and Firmicutes (11.21%). Through plate culture, 14 dominant bacteria of 6 genera were isolated from Y group and Y-10 group, 13 dominant bacteria of 7 genera were isolated from Y-50 group. Among them, Bacillus is the common dominant bacteria. Four dominant bacteria (1 strain of Microbacterium, 1 strain of Vibro, 1 strain of Idiomarina, 1 strain of Halobacillus) screened by diluting 10 times of culture medium and nine dominant bacteria (1 strain of Alcanivorax, 1 strain of Sulfitobacter, 1 strain of Alteromonas, 1 strain of Pseudomonas, 2 strains of Exiguobacterium, 3 strains of Vibro) screened by diluting 50 times of culture medium were different from the original culture medium. Through low-nutrient culture, the metabolic activity and McIntosh index of culturable bacterial communities increased significantly (P<0.05), and its utilization rate of polymers, carboxylic acids, amino acids and carbohydrates also increased significantly (P<0.05). [Conclusion] Low-nutrient culture can increase the richness and diversity of bacterial community, improve the metabolic activity of culturable bacteria and the utilization of carbon sources, especially polymers, carboxylic acids, amino acids and carbohydrates. Therefore, in the collection and recovery of culturable bacteria samples in the pelagic area of South China Sea, more abundant culturable microbial resources can be obtained through low-nutrient culture method.

Abstract:[Background] Some anaerobic bacteria with simultaneous dissimilatory iron reduction and hydrogen production, belonging to fermentative dissimilatory Fe(III)-reducing bacteria, have been paid more and more attention for dual characteristics of energy-saving and environment-friendliness. [Objective] The composition of dissimilatory Fe(III) reduction mixed bacteria in marine sediments was obtained, and the characteristics of dissimilatory Fe(III) reduction and hydrogen production were analyzed. [Methods] The dominant population of Fe(III)-reducing mixed culture was obtained using high-throughput sequencing data, and on this basis the characteristics of microbial Fe(III) reduction coupled to hydrogen production were analyzed under the condition with six different electron donors. [Results] The result of high-throughput sequencing data showed that the dominant population was Clostridium, which was attributed to fermentative-type dissimilatory Fe(III)-reducing bacteria. The mixed culture could reduce Fe(III) and produce hydrogen using sucrose, glucose and sodium pyruvate as electron donor and iron hydroxide as electron acceptor. Among the six electron donors, glucose was the most effective electron donor for double characteristics with high microbial Fe(III) reduction and hydrogen production, with Fe(II) concentration of 59.34±6.73 mg/L and hydrogen production of 629.70±11.42 mL/L. [Conclusion] The results provide evidence for the application of dissimilatory Fe(III)-reducing bacteria for biological hydrogen production, which will widen the germplasm resource of fermentative-type dissimilatory Fe(III)-reducing bacteria.

Abstract:[Background] The Challenger Deep in the Mariana Trench is the deepest known site in the earth’s ocean. Understanding of its microbial community structure and bacterial isolation are important for mining of deep-sea genetic resources. [Objective] Various types of bacteria were isolated from water samples at different depths in the Mariana Trench, and these microbes were compared with high-throughput sequencing results to know microbes that should be further isolated. [Methods] Different media were used to isolate bacteria from water samples, and Illumina Miseq high-throughput sequencing system was used for the diversity analysis of bacteria and archaea. [Results] A total of 783 strains were isolated from 6 water samples at different depths and stations. These isolates belonged to 4 phyla, 6 classes and 28 genera. Among them, Proteobacteria was dominant and 67.8% of total strains belonged to Gammaproteobacteria. The microbes were mainly belonged to Sulfitobacter, Pseudomonas and Pseudoalteromonas. These types of microbes were widely distributed in all samples and detected by high-throughput sequencing. High-throughput sequencing results showed that Cyanobacteria was the major bacteria in samples at shallow depth and Proteobacteria were dominated in other samples. The microbial community structures of samples at different depths were quite different. [Conclusion] Not only bacteria with relatively high abundance in Mariana Trench water were isolated, but also some bacteria with relatively low abundance. The isolated microbes in the Mariana Trench water samples will be helpful for the mining of functional microbes and enzymes.

Abstract:[Background] Anaerobic ammonium oxidation (anammox) bacteria, members of the phylum Planctomycetes, which drive effective N-removal of high concentration ammonia from municipal or industrial wastewater, are designated as eco-friendly microorganisms. However, the structural and functional differentiation of Planctomycetes communities across space and the main environmental drivers have not been paid much attention. [Objective] To elucidate the spatial differentiation of Planctomycetes community structure and the main environmental factors driving associated anammox or denitrification. [Methods] 16S rRNA gene high-throughput sequencing was used to detect the spatial distribution changes of Planctomycetes community structure in sandy or silty sediments/soils of river ecosystem from the temperate semi-arid region. Meanwhile, statistical method was used to analyze the effect of physicochemical factors such as silt particles and water content on the structural differentiation of Planctomycetes communities. [Results] OM190_ub_o_o. o1 population was mainly distributed in oligotrophic sandy sediments, only positively driven by sand particles. OM190_o_o_o. o2 and SM1A02. ub5 populations were mainly distributed in mesotrophic silty-sandy soils, positively driven by water content and pH, etc. AKYG587. ub3, Pla4_lineage_o_o_o. o6, Singulisphaera o7, Singulisphaera ub8 and Planctomycetaceae_u. ub9 populations were mainly distributed in copiotrophic silty soils, positively driven by the clay and silt particles, salinity, organic carbon, total nitrogen, total phosphorus and nitrate nitrogen. Although Phycisphaera ub4 population was preferentially distributed in mesotrophic silty-sandy soils, it displayed a tendency from mesotrophs to copiotrophs, negatively driven by nitrate nitrogen. The entire populations were negatively driven by ammonia nitrogen. Variation partitioning analysis showed that silt particles, ammonia nitrogen, water content contributed to the spatial variation of Planctomycetes communities with 52.7%, 10.4%, 10.3%, respectively. [Conclusion] Planctomycetes communities of river ecosystem in temperate semiarid showed obvious spatial differentiation characteristics, mainly driven by soil/sediment silt particles, ammonia nitrogen and water content. Planctomycetes communities in copiotrophic silty soil might be particle-attached heterotrophic denitrifying bacteria, while Planctomycetes communities in oligotrophic silty soils might be free-living autotrophic ammonia oxidizing or denitrifying bacteria with high affinity for ammonia nitrogen and nitrate nitrogen, respectively. This study provides a scientific basis for the efficient application of ammonia oxidizing bacteria and denitrifying bacteria associated with Planctomycetes to biological removal of high concentration ammonia from polluted systems.

Abstract:[Background] Endophyte is beneficial to host plants for survival and diffusion, and the interaction network of flora provides a basic guarantee for the realization of ecological functions of endophyte. [Objective] To understand the main endophytic microbiota and their interaction network of Oxytropis glacialis that affects the development of animal husbandry in Tibet, so as to provide a reference for the scientific management and utilization of the poisonous plants of locoweed on the Qinghai-Tibet Plateau. [Methods] High-throughput sequencing was used to analyze the endophytic microbiota in the ecotone, to construct the endophytic microbiota correlation network, and to analyze the interaction model of ecotone with the endophytic microbiota related to the metabolism of swainsonine. [Results] A total of 175 791 valid sequences of endophytic bacteria were obtained by sequencing, which annotated to 428 bacterial OTU, belonging to 19 phyla and 267 genera. A total of 757 113 valid sequences of endophytic fungi were obtained, which annotated to 391 fungal OTU, belonging to 7 phylum and 149 genera, Venn diagram analysis showed that the number of endophytic bacteria genus in the core of root and leaf tissues (54, 62) was greater than that of the core endophytic fungi (22, 13), and the core endophytic bacteria species in root tissues were similar to that in leaf tissues (76, 75). Phylogenetic tree analysis showed that Alternaria and Brevundimonas, presenting in Oxytropis glacialis were endophyte that produced and degraded swainsonine. Network analysis showed that the correlation between endogenous bacteria flora was given priority to positive feedback interaction network relationship, the core flora may mainly through indirect interaction modes to affect the microbial community, including Alternaria and Brevundimonas as core species with indirect significant correlation (|r|>0.6, P<0.01) in bacteria interactions within networks. [Conclusion] Oxytropis glacialis core microbiota indirectly participates in the interaction network among endophytes, and the high degree of bacterial connectivity makes it possible to realize the function of endophytes.

Abstract:[Background] Soil microorganism is an important component of soil organisms and participates in key biochemical cycles in soil ecosystem. However, we still poorly understand on soil microorganisms in permafrost soils in cold temperate regions. [Objective] To study the microbial diversity and community structure of the permafrost in the Greater Khingan Mountains. [Methods] high-throughput sequencing technology was employed to analyze the soil bacterial diversity and community structure which were taken from Huzhong National Nature Reserve in the Greater Khingan Mountains of northern Heilongjiang. [Results] The composition of the soil bacterial dominant phyla were basically the same in the Larix gmelinii and Pinus sylvestris forest. At the level of the phylum, the dominant phyla were Verrucomicrobia, Proteobacteria, Acidobacteria, Planctomycetes, Chlorobi, Parcubacteria, Actinobacteria, Bacteroidetes, Firmicutes, Gemmatimonadetes, of which Verrucomicrobia in Pinus sylvestris forest permafrost has relatively high abundance compared with Larix gmelinii forest permafrost. Alpha diversity analysis revealed that the species diversity of the Larix gmelinii permafrost in the frozen soil is higher than that in the Pinus sylvestris permafrost. Moreover, the compositions and structures of soil microorganisms of the two forest types were quite different. [Conclusion] These findings are intended to provide data support for an in-depth understanding of the soil microbial community structure and influencing factors in the permafrost area of the Greater Khingan Mountains.

Abstract:[Background] Arbuscular mycorrhizal fungus (AMF) can form mycorrhizal symbiosis with most of the plants, to play an important role in vegetation succession and ecological restoration process. [Objective] To reveal the influence of land use patterns on AMF communities in the karst graben basin of Yunnan province, China. [Methods] Soils collected from woodland, shrubland and grassland in the karst graben basin of Yunnan province were used to study the influence of land use patterns on AMF communities based on next-generation sequencing. [Results] Total phosphorus, available potassium, exchangeable magnesium, and electrical conductivity in the grassland were significantly higher than those in the woodland and shrubland, yet total nitrogen and soil organic carbon in the woodland were higher than those in the shrubland and grassland. Soil organic carbon, total nitrogen, and available potassium were the most important factors affecting AMF communities. Chao1, ACE, Shannon and observed species indices in the grassland were significantly higher than those in the woodland and shrubland. Simpson index has no significant difference among land use patterns, but it was higher than those in the woodland and shrubland. Among the nine soil samples, AMF belonged to 953 OTUs, 3 classes, 4 orders, 9 families and 13 genera. Glomeromycetes and Paraglomeromycetes were the dominant class. Glomus and Paraglomus were the dominant genus, followed by Claroideoglomus, Acaulospora and Diversispora. Among the nine soil samples, Glomus and Diversispora were mainly distributed in grassland and shrubland, the relative abundance of Glomus and Diversispora population decreased with vegetation succession process, and the relative abundance of Paraglomus increased. [Conclusion] The AMF communities was significant different among land use patterns. The fungi communities were mostly affected by soil physicochemical properties in the karst graben basin of Yunnan province.

Abstract:[Background] Microorganisms in grassland soils are important for ecosystem functioning and stability maintaining. To discover the profile of microbes along the soil vertical depths is essential for our understanding about microbial contributions in grassland ecosystems. [Objective] To comprehensively investigate the vertical patterns of total prokaryotic quantity, diversity and interaction networks in 0?80 cm soil profiles. [Methods] Based on the quantitative PCR and high-throughput sequencing on 16S rRNA gene in a typical agropasture grassland, Inner Mongolia, the total microbial quantity and diversity were cautiously measured. Besides, the molecular ecological network approach (MENA) was used to explore the changes of microbial species interactions. [Results] The quantity and diversity of prokaryotes decreased with depths, as well as the variations of community. Along the soil vertical depths, the close association among microbes would gradually become sparse and the network structures become simpler. In addition, Acidobacteria was one of top abundant phyla, and network analysis revealed that some species in Acidobacteria were the keystone taxa in this grassland ecosystem. These species might play an important role in maintaining the stability of soil ecological functions. [Conclusion] The quantity, diversity and interactions of prokaryotes showed highly consistent with vertical patterns. The quantity and diversity of prokaryotes is negatively correlated with the soil depth, and the variation of community structure will gradually expand at deep soils. Meanwhile the interactions among species in molecular network are decreasingly weakened. These results provide important insights into the dynamic change of microbial community, and are valuable for the ecological protection of grasslands in typical agropasture area.

Abstract:[Background] The members of Anaerolineaceae family (e.g., Anaerolinea genus) from Anaerolineales order of Anaerolineae class are mainly distributed in marine sediments and wetland soils. However, little is known about the spatial heterogeneity of sediments/soils Anaerolineaceae communities and environmental drivers under a specific moisture gradient. [Objective] To elucidate the spatial heterogeneity of Anaerolineaceae communities and core environmental drivers under the moisture gradient along aquatic, hygrophic and xerophytic environments in river system from semiarid region of Mongolian Plateau, and deciphering the early predicting function of Anaerolineaceae communities during the rewetting process of drought-induced shrinking river wetland. [Methods] High-throughput sequencing of 16S rRNA gene, Pearson correlation and variation partitioning analyses were employed to detect the compositions, abundance, spatial distribution of sediment/soil different populations in Anaerolineaceae communities and environmental drivers under the moisture gradient. [Results] The 15 populations of Anaerolineaceae communities were mainly distributed in the aquatic, hygrophic environments, which were positively driven by moisture, pH, sand and ammonia nitrogen, while negatively driven by salinity, total nitrogen and total phosphorus, silt and clay particles. Exceptionally, Uncultured_us15 population was negatively driven by sand and ammonia while positively driven by silt and salinity. Interestingly, 9 and 6 populations in Anaerolineaceae communities showed positive and negative correlation with total organic carbon, respectively. Variation partitioning analysis showed that moisture, ammonia, salinity, organic carbon and pH explained the spatial variation of Anaerolineaceae communities with 64.8%, 8.9%, 7.5%, 2.2% and 1.7%, respectively. [Conclusion] Anaerolineaceae communities demonstrated obvious spatial heterogeneity, which preferred to aquatic and hygrophic environments with high moisture, sand, ammonia and high pH rather than xerophytic environments with relatively rich salinity and nutrition from semiarid region of Mongolia Plateau. The spatial heterogeneity of Anaerolineaceae communities was mainly driven by moisture. Anaerolineaceae communities were key indicators predicting the rewetting process of drought-induced shrinking river wetland, which were probably autotrophic or heterotrophic ammonia-oxidizing bacteria.

Abstract:[Background] Mollisols in Northeast China are rich in organic matter and fertile soil, which become an important food production base in China and a sensitive area affected by climate change. Soil microorganism is sensitive to the changes of environmental factors and closely related to the soil fertility. Therefore, it is helpful to maintain the productivity of mollisols by studying the influence of environmental factors on soil microorganism. [Objective] Explore the effects of organic matter contents and climatic conditions on fungal community structure and diversity in arable mollisols, and provide important basic data and theoretical basis for agricultural sustainable development in mollisols regions under global climate change. [Methods] Long-term soil spatial transplant experiments were used in the present study and the species of fungi in mollisols, and the diversity and community structure of fungi were analyzed by Illumina Miseq sequencing. [Results] Under the two climatic conditions, there were abundant fungal species in arable mollisols with different organic matter contents. The content of soil organic matter had little effect on fungal diversity, while the climate conditions and fertilizer application largely affected the fungal diversity. The dominant fungi phyla in mollisols with five organic matter contents were Ascomycota, Basidiomycota, and Zygomycota, accounting for 92.5% of all the sequences. Under the colder climate, OTU numbers, Chao1, Shannon and Simpson indices all decreased in varying degrees; fertilization also reduced the number and diversity of fungi in arable mollisols, but the decreasing rate decreased as increase of organic matter contents. Climate conditions, organic matter contents, total nitrogen, fertilization and pH were the main factors that driving the changes of fungal community structure in arable mollisols with different organic matter contents. [Conclusion] Organic matter contents, fertilization and climate conditions changed the composition, diversity, and structure of the fungal community in arable mollisols. Climate conditions and fertilization had a greater impact on the fungal community structure of mollisols with different contents, while organic matter contents had a smaller effect on it. However, the effects of the first two factors would weaken with the increase of soil organic matter contents, which was obvious in Ascomycota.

Abstract:[Background] Fertilization is the better strategy to improve crop yield. Fertilization measures can affect soil fertility and microbial community structure. [Objective] The inter-relationship between physicochemical properties and soil culturable bacterial communities will be explored. An optimal fertilization plan will be selected, and the result will provide the basic data for future work. [Methods] Three fertilization treatments of no fertilization, conventional fertilization, conventional fertilization and green manure were carried out on karst paddy soil. Based on the study of soil physical and chemical properties, abundance and diversity of cultivable bacterial communities, the effect of different fertilization measures on karst paddy soil was discussed about influence bacterial community. [Results] Compared with no fertilization treatment, the soil pH value and organic carbon content decreased along conventional fertilization treatment. Combined with a large number of research results, it proved that the long-term excessive application of inorganic fertilizer or nitrogen fertilizer decreased the soil pH value. The accumulation of organic carbon appeared in conventional fertilization plus green manure. A total of 164 strains of bacteria were obtained by separation and purification, which were from Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. At the genus level, the abundance of conventional fertilization combined with green manure was higher than that of the conventional fertilization group of dominant bacteria of Sphingomonas and Lysobacter. The diversity of bacterial communities has increased with the emergence of specific functional bacterial genera such as Paenibacillus, Streptomyces and Pseudomonas. The dominant bacteria Sphingopyxis, Lysobacter, Paenibacillus, Bosea, Streptomyces, Pseudomonas and Bacillus were significantly positively correlated with TN, and they were enriched in soil treated with conventional fertilization and green manure. [Conclusion] Under the treatment of conventional fertilization and green manure, the abundance of functional bacteria relating to nitrogen fixation and phosphorus increased which could increase soil fertility and have an important role in increasing crop production. The effect of conventional fertilization combined with green manure treatment on karst paddy soil is better than those with no fertilizer and conventional fertilization treatment.

Abstract:[Background] Tobacco is one of the most important economic crops in China, and its characteristics of avoiding continuous cropping have seriously affected the development of tobacco industry in China. [Objective] The relationship between tobacco continuous cropping obstacles, soil physical and chemical properties and microbial diversity was studied to provide a theoretical basis for solving tobacco continuous cropping obstacles and formulating effective tobacco production techniques. [Methods] Tobacco fields with serious continuous cropping obstacles and tobacco fields that overcome continuous cropping obstacles were selected as research objects. Based on high-throughput sequencing technology, the relationship between continuous cropping obstacles, physical and chemical properties of tobacco fields and soil microbial diversity was studied. [Results] The contents of pH, total nitrogen and organic matter in tobacco fields overcoming continuous cropping obstacles were significantly higher than those in tobacco fields with serious continuous cropping obstacles. There was no significant difference in soil microbial diversity between tobacco fields overcoming continuous cropping obstacles and serious continuous cropping obstacles, but soil microbial dominant communities changed significantly. pH, organic matter, available phosphorus and total nitrogen in tobacco soil were significantly correlated with microbial community. [Conclusion] The difference of overcoming the obstacle of continuous cropping in tobacco field may be related to the difference of soil physical and chemical properties and microbial composition in tobacco field. This study provides theoretical basis and technical support for solving the problem of continuous cropping obstacles in Xiangxi tobacco area.

Abstract:[Background] The severe continuous cropping obstacles of Panax notoginseng may be related to the microbial community imbalance. Hence, it is important to know whether the microflora could be imbalanced with the change of planting years of Panax notoginseng during the planting process. [Objective] Structure and diversity differences of bacterial and fungal communities in rhizosphere soils of healthy Panax notoginseng with different planting years were studied. Our research can also provide theoretical basis for further reducing Panax notoginseng monocropping obstacle. [Methods] The samples were collected from Panax notoginseng healthy rhizosphere soil planting for one-, two- and three-year in Yanshan county of Wenshan. High-throughput sequencing of 16S rRNA gene and ITS genes were used to compare the diversity and community distribution of bacterial and fungal in rhizosphere soils of healthy Panax notoginseng planting for one-, two- and three-year. [Results] The alpha indices of the one-year healthy rhizosphere bacterial and fungal rhizosphere communities were obviously higher than those of the two- and three-year samples. The results of beta diversity revealed that the bacterial community structures in the one-year Panax notoginseng rhizosphere were different with other treatments. The results of correlation analysis showed that the equitability and shannon indices of fungi showed significant negative correlations with planting years, while the other indices were not significantly correlated. The abundances of Acidobacteria and Aquicella increased with the plantation year, while other top three phylum and genus were all negatively related to the planting years. Among them, the abundance of Bacteroidetes, Proteobacteria, Ascomycota, Basidiomycota and Chytridiomycota phylum decreased with planting years increasing. At the genus level, the abundances of Opitutus of bacteria, Mortierella, Clitopilus and Pholiota of fungi decreased with planting years increasing. The abundances of Alternaria, Cylindrocarpon, Fusarium and Pestalotiopsi genus of two-year rhizosphere soil would be lower than that of one- and three-year treatments, while the abundances of Mucor and Bacillus would show opposite trend. Meanwhile, the richness of the beneficial bacteria like Flavobacterium, beneficial fungi like Myxocephala and Aspergillus decreased with planting years increasing. [Conclusion] With the increase of Panax notoginseng planting years, the microbial community of Panax notoginseng rhizosphere was imbalanced. The abundances of pathogenic fungal genus were enhanced with planting years increasing, while the abundances of beneficial fungal genus were decreased.

Abstract:[Background] The community composition of endophyes changes with species genotypes, different parts and growth environmental, while plant-related microorganisms affect plant growth, metabolism, accumulation and synthesis of chemical components, and the synthesis of active components of medicinal plants. [Objective] By studying the diversity of Paris polyphylla endophytic and soil fungal communities in different growth environments, the differential microbes were found from the garden environment and wild environment, which provided the theoretical basis for the artificial cultivation of wild medicinal plants. [Methods] Physical and chemical indexes in two soil environments were determined, and Illumina HiSeq high-throughput sequencing technique was used to determine the genes of endophytic and soil fungi communities in wild and garden environments. Bioinformatics analysis was carried out on the composition and the differences of fungal communities in different environments. [Results] The results of diversity analysis of soil and endophytic fungi showed that the abundance and diversity of fungi in wild environment were higher than garden environment. Among them, there was significant difference in the abundance of rhizosphere soil and soil fungal in the garden (P<0.05). The results of fungal community annotation showed that there were 8 phyla in the two environments, 82 gena in the wild and 78 gena in the garden. There were 4.04% unique OTU in the wild environment and 4.84% unique in the garden environment. In addition, through the LEfSe analysis, we found the significant difference biomarker from garden environment and the wild environment, Ttracladium marohalianum, Thelephorales, and Thelephoraceae was the biomarker which distinguishes the two environments. [Conclusion] The wild environment than the garden environment has higher water content, higher mineral element content, and its fungal community diversity and abundance is more abundant than the soil conditions of garden environment. The results of this study provide a theoretical basis for the change of quality and effect after introduction and cultivation of Paris polyphylla.

Abstract:[Background] Arbuscular mycorrhizal fungi (AMF) is the most widely distributed mycorrhizal fungus among soil microflora. They can form mycorrhizal symbiosis with more than 90% of the vascular plants, and enhance the plant’s resistance by regulating the plant’s physiological and metabolic processes. [Objective] To reveal the structure and composition of AMF in rhizosphere soil of Chinese herbal medicine Atractylodes lancea (Thunb.) DC. from Chongqing area, and to analyze the influence of soil factors on AMF groups. [Methods] Using rhizosphere soils of A. lancea (Thunb.) DC. collected from Pengshui, Xiushan, Shizhu, Nanchuan and Youyang counties in Chongqing as material, to analyze the differences in the composition and diversity of AMF from different locations and soils via high-throughput sequencing. [Results] The mycorrhizal infection rate of A. lancea (Thunb.) DC. was more than 50%, and the content of soil spores was more than 50 per 10 g of air dried soil, and the highest number was 144. Three classes, 4 orders, 8 families and 9 genera of Glomeromycota including Glomus, Claroideoglomus, Gigaspora, Paraglomus, Archaeospora, Ambispora, Acaulospora, Diversispora and Scutellospora were detected in rhizosphere soil. The first six genera were common to soil samples of five counties. Glomus had the highest relative abundance of 67%, which was the dominant group in all samples. RDA analysis showed that soil pH had the greatest effect on AMF community composition. Soil pH, organic matter, alkaline nitrogen and available potassium were positively correlated with Shannon index, while available phosphorus was negatively correlated. The correlation between each soil factor and Simpson index was opposite. Five soil factors were negatively correlated with Chao1 index. In addition, pH and organic matter were positively correlated with ACE index, while alkaline nitrogen, available potassium and available phosphorus were negatively correlated. [Conclusion] The rhizosphere soil of A. lancea (Thunb.) DC. is rich in AMF resources, and soil factors have significant effects on the composition and abundance of AMF community, which is one of the important reasons for the difference of AMF community structure and geographical distribution pattern.

Abstract:[Background] Acid mine drainage should be treated before discharge. After treatment, its physicochemical properties will be changed significantly, which would affect the whole microbial community structure. [Objective] The changes of bacterial and fungal communities before and after treatment and their relationships with physicochemical parameters were analyzed to provide reference indexes for the treatment of acid mine drainage and theoretical basis for the remediation of mine-contaminated sites. [Methods] Acid mine drainage in Zijinshan copper mine, Fujian province was collected, followed by analysis of physicochemical properties. The microbial community structures of water samples were analyzed by high-throughput sequencing technology based on 16S rRNA gene V4 region of prokaryotes and 18S rRNA gene ITS sequences of fungi. [Results] Compared with the pit water and leachate from the dump-leaching, the back water showed a higher pH and a lower content of heavy metal ions after the neutralization treatment. The diversity of prokaryotes was higher than that of fungi in all samples, and the microbial diversity of back water was higher than that of pit water and leachate. Proteobacteria was the most abundant lineage in the back water, and Euryarchaeota and Nitrospirae were of the highest abundance in the pit water and the leachate, respectively. At the genus level, Hydrogenophaga in the back water was the dominant group, while Leptospirillum was the dominant bacterium in the pit water and leachate, and archaea such as Ferroplasma also accounted for a considerable proportion. The pH, Al, Mn and Zn were significantly correlated with the genera with high relative abundance in the back water, while the high-abundance groups in the pit water and leachate had no significant correlation with the environmental factors. [Conclusion] The study indicated that the neutralization and precipitation treatment of acid mine drainage imposes a great impact on the microbial community, and the changes in microbial community structure could be used as a reference index for acid mine drainage pollution treatment efficiency.

Abstract:[Background] In the past decade, high-throughput sequencing technology on ribosomal RNA amplicons has been widely used to explore the diversity and composition of microbial communities in a variety of ecosystems. [Objective] With the development of sequencing technology and the expanding of reference databases, commonly adopted primers still need to be cautiously verified for different environmental samples. [Methods] We collected several marker gene amplification primers for microbial communities (i.e. bacteria, archaea, fungi and other eukaryotic microorganisms), including 8 universal primer sets and 2 archaea primer sets of 16S rRNA amplification, 9 universal primer sets for internal transcribed spacer (ITS) amplification, 4 universal primer sets and 1 fungal universal primer set for 18S rRNA amplification, which contained two 16S primer sets, one ITS1 primer set and one 18S primer set recommended by the Earth Microbiome Project (EMP). These primers were evaluated for the coverage and specificity using a recently updated standard reference databases. [Results] The EMP recommended primers all still have high coverage in current databases, while other primers have their own advantages in coverage and specificity to specific environments or taxonomic groups. In addition, recent studies have made some improvements on these universal primers. Changes in one single base may lead to changes in evaluation results or amplification products. The single degenerate base added to primers may cover more species, but it may also reduce the species specificity to some extent. [Conclusion] For different environmental samples, the selection of primers and experimental process still need more detailed verification. Our results could be a guide for the selection and improvement of amplified primers in microbial ecological studies.

Abstract:[Background] Smoking has become one of the foremost public health problem, which may affect oral health and even host health by changing the salivary microbiome. [Objective] To study the effects of smoking on the salivary microbiome of healthy Chinese people, and to provide enlightenment for the role of smoking in disease-development. [Methods] We collected saliva samples from 167 healthy volunteers, using high-throughput Hiseq sequencing technology for sequencing 16S rRNA gene sequence in the V3?V4 region of samples to research the salivary microbiome of current smokers and never smokers. [Results] The α diversity of the salivary microbiome did not show a significant difference between current smokers and never smokers. However, the relative abundance of the genera Neisseria, Eikenella and Porphyromonas reduced in current smokers, whereas the genera Prevotella, Veillonella, Atopobium, Actinomyces and Megasphaera were significantly increased. Functional analysis from PICRUSt showed that decreased abundance of aerobic metabolism pathways and increased abundance of oxygen-independent carbohydrate metabolism pathways in current smokers. [Conclusion] smoking is a factor influencing salivary microbiome, and then potentially leading to the shifts in functional pathways with implications for smoking-related diseases.

Abstract:[Background] Due to the low-temperature at maize straw returning time, the straw degradation is slow in the northern part of China. The acceleration of straw decomposition is thus important. [Objective] To isolate strains with high cellulose degradation ability at low temperature from soil sample collected from cold region. [Methods] Dilution and plating method was used to isolate strains from soil sample at low temperature culture. The sodium carboxymethyl cellulose (CMC-Na) hydrolysis circle assay, extracellular enzyme activity assay and straw weight loss method were used to screen fungi with cellulose degradation ability at low cultural temperature. Strains were identified based on method of morphological characteristics and ITS rDNA sequence analysis. Using the reducing sugar method of DNS, the cellulase activity of the strains under different inoculation volumes, initial pH of the medium and culture temperature was studied. The straw degradation ability of the strain was studied by sandbag method. [Results] A cold adapted fungus SDF-25 with higher cellulose activity was screened and identified as Penicillium oxalicum. It could grow from 4 to 37 °C. The optimal cultural condition for cellulase production was determined as follow: inoculation quantity 2%, initial pH 7.0, the optimal temperature 10 °C. The enzyme activity at the optimal cultural condition was 993.3 U/mL. The straw degradation rate of SDF-25 was 39.5% and 44.9% with cultural temperature at 10 °C and 16 °C respectively. [Conclusion] P. oxalicum SDF-25 is a fungus with strong cellulase production ability at low temperature and has a good application prospect in straw returning.

Abstract:[Background] Bacilllus-like species are important microbial inoculants in agriculture to promote plant growth, prevent disease and insect. [Objective] To study Bacillus-like species community of several subtropical plant endophyte and rhizosphere soil, providing scientific foundation for mining Bacillus-like species. [Methods] On the basis of the culturable method, Bacillus-like species were isolated from roots and rhizosphere soil samples of Saccharum officinarum, Hibiscus cannabinus L., Corchorus capsularis L., Abelmoschus esculentus, and Hibiscus sabdariffa. Then, the isolates were identified by 16S rRNA gene and phylogenetic tree was constructed to explore the relationship between isolates and their related type species. [Results] There were 144 isolates obtained, including 82 isolates of endophytic bacteria and 62 isolates of rhizosphere bacteria, which were identified as 37 species of 4 genera, including Bacillus, Brevibacillus, Lysinibacillus, and Paenibacillus through 16S rRNA gene sequencing. The dominant genus was Bacillus, and the second one was Paenibacillus. There was great difference of the species number and colonies content in the root and rhizosphere soil. The colonies content in the rhizosphere was greater than roots. The colonies content range of Bacillus-like species in rhizosphere was (0.2?370.0)×105 CFU/g, but (0.1?81.0)×103 CFU/g in the root. Species number in roots was much larger than rhizosphere, which 19 species were obtained from rhizosphere and 32 were from roots. Bacillus aryabhattai, Bacillus mesonae and Bacillus pseudomycoides were both distributed in the 4 crop’s roots and rhizosphere, other species only occurred in the one crop’s roots or rhizosphere. [Conclusion] there were rich Bacillus-like species number and abundant content in the crop’s rhizosphere and roots, and several culturable potential novel Bacillus species, providing the theoretical base and scientific foundation for interaction of plant-microbe and ecological balance of rhizosphere environment.

Abstract:[Background] Soil microbe is an important part of grassland ecosystems, and it plays an irreplaceable role in regulating plant growth, promoting the formation of soil structure, and maintaining the function and stability of grassland ecosystems. [Objective] To explore the diversity of microbial community metabolic function in rhizosphere soil of five different plants in two different grasslands in Siziwang Banner of Inner Mongolia. [Methods] Biolog-ECO microplate method was used to analyze microbial community diversity in rhizosphere soil of Stipa breviflora, Artemisia frigida, Convolvulus ammannii, Heteropappus altaicus and Allium tenuissimum in the 2 plots of Adege and Gentala in Siziwang Banner. [Results] There are significant differences in the number of culturable microorganisms in the rhizosphere soil of 5 different plants in two different grasslands (P<0.05). The total number of culturable microorganisms in S. brevifolia in Adege grassland is significantly higher than that of other plants. The total number of cultivable microorganisms in the rhizosphere soil of H. altaicus in the Gentala grassland was significantly higher than that of other plants. The average color change rate (AWCD) of rhizosphere soil microbes of different plants in the two grassland showed that the AWCD of rhizosphere soil in Gegentala grassland was higher than that in Adege grassland, and showed “S” type change. After 96 hours of cultivation, the Shannon index and Simpson index of the five plants in the Gentara grassland were higher than those in the Adege grassland, and the microbial diversity index of the rhizosphere soil of C. ammannii was very different in the two grasslands. The utilization of carbon sources by soil microorganisms is mainly amino acids and carbohydrate carbon sources, and it is significantly enriched for functional microorganisms such as L-asparagine, r-hydroxybutyric acid, L-serine and D-galacturonic acid. AWCD of rhizosphere soil microorganisms and diversity index of bacteria, actinomycetes and total number of soil microorganisms have a very significant positive correlation (P<0.01). Evenness index and total number of bacteria, actinomycetes and soil microorganisms have significantly negative correlation (P<0.05). [Conclusion] different plant rhizosphere soil microorganisms had different utilization and preference of carbon source. The number of microorganisms in rhizosphere soil was higher, the microbial carbon metabolism capacity and microbial community diversity was more abundant.

Abstract:As an important component of the biological community, the growth of microorganisms is greatly affected by external physicochemical conditions (such as temperature, salinity, pH, etc.). Hot springs, as one of the extreme aquatic environments, belong to a relatively stable and special ecosystem. Microorganisms growing in hot springs may have special survival physiological mechanisms that are adapted to special environments such as high temperatures. More specifically, diversity and novelty are high in microbial species and their active secondary metabolites. This paper reviews the research progress of microorganisms in Chinese hot springs from January 2015 to August 2020 with a focus on microbial species diversity and enzymatic activity, in order to provide references for the exploitation and protection of microbial resources in hot spring and other extreme environments.

Abstract:Biological soil crusts (BSC), known as “desert ecosystem engineer”, play an important role in the restoration and stability maintenance of desert vegetation. BSC microbial communities are the main components of their functions. They participate in the formation of BSC, the improvement of soil physiochemical properties, the stability of soil aggregates and the development of vegetation. In the early stage, due to the limitation of technical methods, the mechanism of how BSC microbial communities regulate the stability of desert vegetation is unclear. However, with the rapid development of soil microbiome technologies in recent years, the research on the composition and function of BSC microbial communities has made great progress, and the contribution of BSC microbial communities to desert ecosystem has a clearer understanding. In this paper, the compositional structure of bacterial, fungal and archaeal communities and their potential functional changes in the carbon and nitrogen cycles during BSC succession in temperate desert are reviewed. Additionally, the soil environmental factors affecting the structure and function of microbial communities are summarized, and the successional model of interaction between different BSC microbial groups and soil physiochemical properties is explained. These results help us to clarify the mechanism of BSC promoting the improvement of desert soil conditions, and to provide theoretical basis for understanding the restoration process of desert vegetation and the contribution of temperate desert ecosystems to the world.

Abstract:Soil pesticide contamination and bacterial drug resistance are hotspots in the field of environmental study. In recent years, a growing number of studies have shown that the development of bacterial pesticide-antibiotic cross-resistance was related to soil pesticide contamination. Based on the research progress in recent years, the pollution status of pesticides including insecticides, herbicides, and fungicides in the soil at home and abroad were described in this paper. Pesticide degrading bacteria and their resistance to pesticide, and the problem of bacterial antibiotic resistance and pesticide-antibiotic cross-resistance were also introduced. Finally, research priorities in future studies on pesticide-antibiotic cross-resistance were prospected.

Abstract:Salt-tolerant bioleaching microorganism is a kind of microorganism that could survive in the salt-containing environments during bioleaching process. It is found that these species show great application potential in biometallurgy when freshwater resources are scarce. This paper systematically reviews current knowledge and understanding of taxonomic diversity, the salt-adapted mechanisms and the application status of salt-tolerant microorganisms, aiming to provide more information for the research and application of salt-tolerant microorganisms.

Abstract:The performance and stability of the biological wastewater treatment system are closely related to the microbial community structure and dynamics. An in-depth understanding of the microbial community structure in activated sludge and its influencing factors can contribute to improve pollutants removal in the treatment process. In different sewage wastewater treatment systems, the distribution of bacterial communities mainly consists of Proteobacteria, Campylobacter, Actinomycetes, Pachythromycetes and Bacteroides. Most of the fungi living in activated sludge belong to Ascomycota and a small amount of Basidiomycota. Meanwhile, the most widely distributed bacteriophages and pathogenic viruses in the virus are the major concerns. By analyzing and summarizing relevant literatures, this paper reviews the environmental factors such as influent composition, different treatment processes, parameters (physicochemical parameters and operating parameters), geographical location and climatic conditions on bacteria, fungi, archaea and virus in activated sludge, and introduces the diversity of microbial communities in sewage plants and their responses to environmental factors as comprehensively as possible. At the same time, the future research direction is discussed in order to provide theoretical and application basis for regulation of functional microorganisms in activated sludge.

Abstract:Nitrogen cycle is a biogeochemical cycle mediated by both abiotic and biotic processes. The important research hotspot in environmental genomics and microbial ecology is to use gene sequencing technology to study microbial communities, microorganisms and functional genes involved in the nitrogen cycle in the environment. In recent years, various types of databases are developed and applied to functional analysis. Combining with the latest research results, we focus here on the functional genes of six inorganic nitrogen cycle pathways driven by microorganisms, containing assimilation nitrate reduction, dissimilation nitrate reduction, denitrification, nitrogen fixation, nitrification (including complete ammonia oxidation) and anaerobic ammonia oxidation. we compare the design concepts and functional characteristics of databases such as National Center for Biotechnology Information (NCBI), Integrated Microbial Genomes (IMG), Universal Protein (UniProt), Kyoto Encyclopedia of Genes and Genomes (KEGG), Protein Families (Pfam), Functional Gene (FunGene), Clusters of Orthologous Groups (COG) and NCycDB. Also, we statistically analyze the selection and application of the above databases in the annotation of nitrogen cycle functional genes, combining with the influence factors such as environmental media, characteristic genes, analysis methods and comparison methods, and prospected the future development direction of the nitrogen cycle gene databases. It is expected to provide reference for researchers to understand the nitrogen cycle gene family and choose an appropriate data analysis platform.

Abstract:Coupled with nutrient cycling, the biogeochemical cycling of manganese (Mn) has so far been considered as one of the most important contributors to worldwide ecology balance and environmental changes. In nature, the formation of manganese oxides is driven by bacterial oxidation. Manganese oxidizing bacteria live in various ecosystems including marine and soil systems, and recently, they have been discovered in plant micro-ecosystem with an unknown physiological and ecological function. The bacterial-mediated oxidation of manganese is a complex process in which multicopper oxidase, peroxidase and catalase are the main enzymes involved. However, the action mode of the enzymes are not fully studied. Here, we review the achievements and unresolved problems on biological diversity, physiological and ecological functions of manganese oxidizing bacteria, as well as action mode to in bacterial manganese oxidation. The development trend in this research field is also prospected.

Abstract:As a global environmental issue, arsenic pollution has attracted great attentions. Inorganic arsenic compounds can be removed from soil and aqueous system through the co-precipitation by complexing with iron hydroxide. Therefore, Fe(II)-oxidizing bacteria have been expected to depollute the arsenic compounds from environment coupling with the microbial iron oxidation. To date, an increasing number of studies have reported that Fe(II)-oxidizing bacteria were used in the bioremediation of environmental arsenic pollution. The Fe(II)-oxidizing bacteria used for the arsenic removal must have an arsenic tolerance in order to function in the arsenic-containing environment. Whether the microorganisms have arsenic tolerance always depends on its genetic basis. Besides, different bacterial strains have different physiological characteristics and are suitable for remediation of different arsenic-contaminated environments. By summarizing the arsenic tolerance genes of eight representative Fe(II)-oxidizing bacteria, this paper represents their arsenic tolerance mechanism, research overview and application prospect, in an attempt to provide a reference for the technological innovation of applying Fe(II)-oxidizing bacteria to arsenic removal.

Abstract:Epstein-Barr virus (EBV) infects the vast majority of the world’s population. The types of diseases, caused by infection of Epstein-Barr virus, in different subgroups and regions are various. However, the immune mechanism of EBV infection is still unclear. Acute EB virus infection related diseases are usually self-healing. On the other hand, most patients with chronic and latent infections are still lack of effective treatment with a poor prognosis, and risk of cancer. The CRISPR/Cas9 (clustered regular interspaced short palindromic repeats/CRISPR-associated nuclease 9) technology was derived from an acquired immune defense system in bacteria and archaea. As the third-generation genomic editing technology, it can perform targeted editing of specific genomic sequences under the guidance of sgRNA. Because of its characteristics of ease to operation, time saving and high efficiency, it has been widely used in new crop cultivation, animal disease model construction and precise diagnosis and treatment of human diseases. The review describes the progression of CRISPR/Cas9 system in immune research of EB virus infection, including exploration of screening key pathogenic genes and host dependency factors, pathogenic mechanisms, and gene targeted editing to treat EBV-related diseases. It provides implications for studying the pathogenesis of Epstein-Barr virus related diseases and exploring new antiviral treatment strategy.