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Frontiers of environmental Science & Engineering 2021年第1期15卷 113-123页

作者： Jing Ding Wanyi Seow jizhong zhou Raymond Jianxiong Zeng Jun Gu Yan zhou Advanced environmental Biotechnology Centre Nanyang Environment and Water Research InstituteNanyang Technological UniversitySingapore 637141Singapore School of Civil and environmental Engineering Nanyang Technological UniversitySingapore 639798Singapore Centre of Wastewater Resource Recovery College of Resources and EnvironmentFujian Agriculture and Forestry UniversityFuzhou 350002China institute for environmental genomics and department of microbiology and Plant University of OklahomaNormanOK 73019USA Earth and environmental Sciences Lawrence Berkeley National LaboratoryBerkeleyCA 94720USA School of Environment Tsinghua UniversityBeijing 100084China

Though there are many literatures studying the effects of iron on anammox process,these studies only focus on the reactor performance and/or the microbial community changes,the detailed effects and mechanisms of Fe(II)on anammox bacterial activity and physiology have not been *** this study,four Fe(II)concentrations(0.03,0.09,0.12 and 0.75 mmol/L)were employed into the enriched anammox *** enhancement and inhibition effects of Fe(II)on anammox process and bacterial physiology were *** was discovered that the anammox process and bacterial growth were enhanced by 0.09 and 0.12 mmol/L Fe(II),in which the 0.12 mmol/L Fe(II)had advantage in stimulating the total anammox activity and bacterial abundance,while 0.09 mmol/L Fe(II)enhanced the relative anammox activity *** anammox activity could be inhibited by 0.75 mmol/L Fe(II)immediately,while the inhibition was *** 0.09 and 0.12 mmol/L Fe(II)induced more genes being expressed,while didn’t show a stimulation on the relative expression level of functional *** anammox bacteria showed a stress response to detoxify the Fe inhibition once inhibited by 0.75 mmol/L Fe(II).This study provides more information about physiologic response of anammox bacteria to external influence(enhancement and inhibition),and may also instruct the future application of anammox process in treating various sources of wastewater(containing external disturbances such as heavy metals)and/or different treatment strategies(*** side-stream to main-stream).

关键词： Anaerobic ammonium oxidation(Anammox) Candidatus Kuenenia stuttgartiensis Ferrous iron GeoChip

Development and applications of functional gene microarrays in the analysis of the functional diversity,composition,and structure of microbial communities

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Frontiers of environmental Science & Engineering 2011年第1期5卷 1-20页

作者： Zhili HE Joy DVAN NOSTRAND Ye DENG jizhong zhou institute for environmental genomics Department of Botany and MicrobiologyUniversity of OklahomaNormanOK 73019USA Earth Sciences Division Lawrence Berkeley National LaboratoryBerkeleyCA 94720USA department of environmental Science and Engineering Tsinghua UniversityBeijing 100084China

Functional gene arrays(FGAs)are a special type of microarrays containing probes for key genes involved in microbial functional processes,such as biogeochemical cycling of carbon,nitrogen,sulfur,phosphorus,and metals,biodegradation of environmental contaminants,energy processing,and stress *** are considered as the most comprehensive *** established probe design criteria and a computational pipeline integrating sequence retrieval,probe design and verification,array construction,data analysis,and automatic update are used to develop the GeoChip *** has been systematically evaluated and demonstrated to be a powerful tool for rapid,specific,sensitive,and quantitative analysis of microbial communities in a high-throughput *** generations of GeoChip have been developed and applied to investigate the functional diversity,composition,structure,function,and dynamics of a variety of microbial communities from different habitats,such as water,soil,marine,bioreactor,human microbiome,and extreme *** is able to address fundamental questions related to global change,bioenergy,bioremediation,agricultural operation,land use,human health,environmental restoration,and ecological theories and to link the microbial community structure to environmental factors and ecosystem functioning.

关键词： functional gene arrays(FGAs) GeoChip microbial communities functional diversity/composition/structure environmental factor ecosystem functioning

Functional profiles of soil microbial communities in the alpine and temperate grasslands of China

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Grassland Research 2022年第1期1卷 3-13页

作者： Yunfeng Yang jizhong zhou Xue Guo State Key Joint Laboratory of Environment Simulation and Pollution Control School of EnvironmentTsinghua UniversityBeijingChina institute for environmental genomics and department of microbiology and Plant Biology University of OklahomaNormanOklahomaUSA School of Civil Engineering and environmental Sciences University of OklahomaNormanOklahomaUSA Earth and environmental Sciences Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA

Grassland ecosystems in cold regions are typical of short growing seasons and limited primary productivity,rendering soil microorganisms as major ecosystem engineers in governing biogeochemical *** warming and extensive livestock grazing have dramatically influenced soil microbial diversity and function in grassland worldwide,but it remains elusive how functional microbial communities exist and respond to global ***,we present a review to highlight similarities and differences in soil functional microbial communities between alpine grasslands in the Qinghai-Tibet Plateau and temperate grasslands in the Inner Mongolian Plateau,both of which are major plateaus in China,but differ substantially in *** show that many specialized functional groups thrive under harsh conditions,exhibiting a high functional *** community compositions mirror the heterogeneity and complexity of grassland ***,functional microbial responses to environmental changes have been extremely variable,with few consistent patterns across both *** we identify a lack of technical standardization that prevents in-depth comparative studies for functional microbial communities,we conclude the review by outlining several research gaps that need to be filled in future studies.

关键词： climate changes functional microbial communities grassland soils grazing Inner Mongolian Plateau Qinghai-Tibet Plateau

Lowered water table causes species substitution while nitrogen amendment causes species loss in alpine wetland microbial communities

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Pedosphere 2021年第6期31卷 912-922页

作者： Yuntao LI Jin-Sheng HE Hao WANG jizhong zhou Yunfeng YANG Haiyan CHU State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of Sciences71 East Beijing RoadNanjing 210008(China) university.of Chinese Academy of Sciences Beijing 100049(China) department of Ecology College of Urban and Environmental SciencesPeking UniversityBeijing 100871(China) State Key Laboratory of Grassland Agro-Ecosystems College of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhou 730000(China) State Key Joint Laboratory of Environment Simulation and Pollution Control School of EnvironmentTsinghua UniversityBeijing 100084(China) institute for environmental genomics Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental SciencesUniversity of OklahomaNorman OK 73019(USA) Earth Science Division Lawrence Berkeley National LaboratoryBerkeley CA 94270(USA)

Alpine wetlands are hotspots of carbon(C)storage and methane emission,and they could be key contributors to global *** recent years,rapid warming has lowered the water table in alpine wetlands on the Tibetan Plateau,concurrent with intensified nitrogen(N)deposition via anthropogenic *** carried out a field experiment to investigate the ecological impacts of these two factors on soil bacterial and functional communities,which are essential drivers of greenhouse gas *** amendment alone decreased the phylogenetic alpha-diversity of bacterial communities which could be offset by lowered water *** contrast,microbial functional alpha-diversity,revealed by a high-throughput microarray,remained *** bacterial and functional beta-diversity responded to lowered water table,but only bacterial community responded to N *** alpha-Proteobacteria,beta-Proteobacteria,and Bacteroidetes were the major responsive bacterial lineages,and C degradation,methanogenesis,alkaline shock,and phosphorus oxidation were the major responsive functional *** analysis revealed that N amendment changed bacterial community structure mainly via species loss processes but did not affect bacterial functional communities,with soil pH and ammonium as the key factors influencing changes in bacterial community ***,lowered water table altered bacterial and functional communities through species substitution processes linked to soil pH and soil *** to our results,the response mechanisms of microbial communities to lowered water table and N amendment are fundamentally different in alpine wetlands.

关键词： alpha-diversity bacterial community beta-diversity microbial functional community N amendment water table lowering

GeoChip-based analysis of the microbial community functional structures in simultaneous desulfurization and denitrification process

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Journal of environmental Sciences 2014年第7期26卷 1375-1382页

作者： Hao Yu Chuan Chen Jincai Ma Wenzong Liu jizhong zhou Duu-Jong Lee Nanqi Ren Aijie Wang School of environmental Science and Engineering Liaoning Technical University State Key Laboratory of Urban Water Resource and Environment Harbin Institute of Technology Biosciences and Biotechnology Division Lawrence Livermore National LaboratoryLivermore CA 94550 USA Research Center for Eco-environmental Sciences Chinese Academy of Sciences institute for environmental genomics Department of Botany and Microbiology University of OklahomaNorman OK 73019 USA department of Chemical Engineering National Taiwan University

The elemental sulfur （S^0） recover）, was evaluated in the presence of hi,ate in two development models of simultaneous desulfurization and denitrification （SDD） process. At the loading rates of 0.9 kg S/（m^***） for sulfide and 0.4 kg N/（m^***） for nitrate, SO conversion rate was 91.1% in denitrifying sulfide removal （DSR） model which was higher than in integrated simultaneous desulfurization and denitrification （ISDD） model （25.6%）. A comprehensive analysis of functional diversity, structure and metabolic potential of microbial communities was examined in two models by using functional gene array （GeoChip 2.0）. GeoChip data indicated that diversity indices, community structure, and abundance of functional genes were distinct between two models. Diversity indices （Simpson＇s diversity index （1/D） and Shannon-Weaver index （H′）） of all detected genes showed that with elevated infiuent loading rate, the functional diversity decreased in ISDD model but increased in DSR model. In contrast to ISDD model, the overall abundance of dsr genes was lower in DSR model, while some functional genes targeting from nitrate-reducing sulfide-oxidizingbacteria {NR-SOB）, such as Thiobacillus denitrficans, Sulfurimonas denitrificans, and Paracoccus pantotrophus were more abundant in DSR model which were highly associated with the change of SO conversion rate obtained in two models. The results obtained in this study provide additional insights into the microbial metabolic mechanisms involved in ISDD and DSR models, which in turn will improve the overall performance of SDD process.

关键词： Expanded granular sludge bedElemental sulfur recoveryMicrobial communityFunctional gene array

Community structure and elevational diversity patterns of soil Acidobacteria

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Journal of environmental Sciences 2014年第8期26卷 1717-1724页

作者： Yuguang Zhang Jing Cong Hui Lu Guangliang Li Yuanyuan Qu Xiujiang Su jizhong zhou Diqiang Li institute of Forestry Ecology Environment and ProtectionKey Laboratory of Forest Ecology and Environment of State Forestry AdministrationChinese Academy of Forestry School of Mineral Processing and Bioengineering Central South University institute for environmental genomics Department of Botany and MicrobiologyUniversity of Oklahoma Hunan Baiyunshan National Nature Reserve

Acidobacteria is one of the most dominant and abundant phyla in soil,and was believed to have a wide range of metabolic and genetic functions. Relatively little is known about its community structure and elevational diversity patterns. We selected four elevation gradients from 1000 to 2800 m with typical vegetation types of the northern slope of Shennongjia Mountain in central China. The vegetation types were evergreen broadleaved forest,deciduous broadleaved forest,coniferous forest and sub-alpine shrubs. We analyzed the soil acidobacterial community composition,elevational patterns and the relationship between Acidobacteria subdivisions and soil enzyme activities by using the 16 S rRNA meta-sequencing technique and multivariate statistical analysis. The result found that 19 known subdivisions as well as an unclassified phylotype were presented in these forest sites,and Subdivision 6 has the highest number of detectable operational taxonomic units（OTUs）. A significant single peak distribution pattern（P 〈 0.05） between the OTU number and the elevation was observed. The Jaccard and Bray–Curtis index analysis showed that the soil Acidobacteria compositional similarity significantly decreased（P 〈 0.01） with the increase in elevation distance. Mantel test analysis showed the most of the soil Acidobacteria subdivisions had the significant relationship（P 〈 0.01） with different soil enzymes. Therefore,soil Acidobacteria may be involved in different ecosystem functions in global elemental cycles. Partial Mantel tests and CCA analysis showed that soil pH,soil temperature and plant diversity may be the key factors in shaping the soil Acidobacterial community structure.

关键词： Elevational pattern Potential metabolic activity Acidobacterial subdivision Soil pH Driving factor environmental change

Effects of residual organics in municipal wastewater on hydrogenotrophic denitrifying microbial communities

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Journal of environmental Sciences 2018年第3期30卷 262-270页

作者： Wei Xing Jinlong Li Peng Li Chong Wang Yanan Cao Desheng Li Yunfeng Yang jizhong zhou Jiane Zuo School of Civil Engineering Beijing Jiaotong University Beijing 100044 China State Key Joint Laboratory of environmental Simulation and Pollution Control School of Environment Tsinghua University Beijing 100084 China Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard Beijing 100044 China College of Science Flunan Agricultural University Changsha 410128 China institute for environmental genomics and department of microbiology and Plant Biology University of Oklahoma Norman OK 73019 USA Earth Sciences Division Lawrence Berkeley National Laboratory Berkeley CA 94720 USA

Hydrogenotrophic denitrification is promising for tertiary nitrogen removal from municipal wastewater. To reveal the influence of residual organics in municipal wastewater on hydrogenotrophic denitrifiers, we adopted high-throughput 16 S r RNA gene amplicon sequencing to examine microbial communities in hydrogenotrophic denitrification enrichments. Using effluent from a municipal wastewater treatment plant as water source, COD,nitrate and p H were controlled the same except for a gradient of biodegradable carbon（i.e., primary effluent（PE）, secondary effluent（SE）, or combined primary and secondary effluent（CE））. Inorganic synthetic water（IW） was used as a control. Hydrogenophaga, a major facultative autotroph, accounted for 17.1%, 5.3%, 32.7% and 12.9% of the sequences in PE, CE,SE and IW, respectively, implicating that Hydrogenophaga grew well with or without ***, which contains likely obligate autotrophic denitrifiers, appeared to be the most dominant genera（23.6%） in IW and accounted for 2.5%, 4.6% and 8.9% in PE, CE and SE,respectively. Thermomonas, which is related to heterotrophic denitrification, accounted for 4.2% and 7.9% in PE and CE fed with a higher content of labile organics, *** contrast, Thermomonas was not detected in IW and accounted for only 0.6% in SE. Our results suggest that Thermomonas are more competitive than Thauera in hydrogenotrophic denitrification with biodegradable organics. Moreover, facultative autotrophic denitrifiers,Hydrogenophaga, are accommodating to residual organic in effluent wastewater, thus we propose that hydrogenotrophic denitrification is amenable for tertiary nitrogen removal.

关键词： Tertiary nitrogen removal Hydrogenotrophic denitrification Residual organics High-throughput sequencing Hydrogenophaga

The diversity and ecological significance of microbial traits potentially involved in B_(12) biosynthesis in the global ocean

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mLife 2023年第4期2卷 416-427页

作者： Jiayin zhou Wei Qin Xinda Lu Yunfeng Yang David Stahl Nianzhi Jiao jizhong zhou Jihua Liu Qichao Tu institute of Marine Science and Technology Shandong UniversityQingdaoChina Joint Lab for Ocean Research and Education at Dalhousie university Shandong University and Xiamen UniversityQingdaoChina School of Biological Sciences University of OklahomaNormanOklahomaUSA department of Civil and environmental Engineering Massachusetts Institute of TechnologyCambridgeMassachusettsUSA State Key Joint Laboratory of Environment Simulation and Pollution Control School of EnvironmentTsinghua UniversityBeijingChina department of Civil and environmental Engineering University of WashingtonSeattleWashingtonUSA institute of Marine Microbes and Ecospheres Xiamen UniversityXiamenChina Earth and environmental Sciences Lawrence Berkeley NationalLaboratoryBerkeley CaliforniaUSA institutefr environmental genomics University of OklahomaNormanOklahomaUSA School of Civil Engineering and environmental Sciences University of OklahomaNormanOklahomaUSA School of Computer Sciences University of OklahomaNormanOklahomaUSA DermBiont Inc. BostonMassachusettsUSA

Cobalamin(B_(12)),an essential nutrient and growth cofactor for many living organisms on Earth,can be fully synthesized only by selected prokaryotes in ***,microbial communities related to B_(12) biosynthesis could serve as an example subsystem to disentangle the underlying ecological mechanisms balancing the function and taxonomic make-up of complex functional *** anchoring microbial traits potentially involved in B_(12) biosynthesis,we depict the biogeographic patterns of B_(12) biosynthesis genes and the taxa harboring them in the global ocean,despite the limitations of detecting de novo B_(12) synthesizers via metagenomes *** the taxonomic and functional composition of B_(12) biosynthesis genes were strongly shaped by depth,differentiating the epipelagic zones from the mesopelagic *** genes related to B_(12) biosynthesis were relatively stably distributed across different oceans,but the taxa harboring them varied considerably,showing clear functional redundancy among microbial *** taxa carrying B_(12) biosynthesis genes in the surface water were influenced by environmental factors such as temperature,oxygen,and ***,the composition of functional genes was only weakly associated with these environmental *** model analyses demonstrated that determinism governed the variations in B_(12) biosynthesis genes,whereas a higher degree of stochasticity was associated with taxonomic *** associations were observed between the chlorophyll a concentration and B_(12) biosynthesis,confirming its importance in primary production in the global *** results of this study reveal an essential ecological mechanism governing the assembly of microbes in nature:the environment selects for function rather than taxonomy;functional redundancy underlies stochastic community assembly.

关键词： B_(12)biosynthesis community assembly functional genes functional redundancy ocean primary production

Effects of Fe(Ⅱ) on anammox community activity and physiologic response

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Frontiers of environmental Science & Engineering 2021年第1期15卷 88-98页

作者： Jing Ding Wanyi Seow jizhong zhou Raymond Jianxiong Zeng Jun Gu Yan zhou Advanced environmental Biotechnology Centre Nanyang Environment and Water Research Institute Nanyang Technological University institute for environmental genomics and department of microbiology and Plant University of Oklahoma Earth and environmental Sciences Lawrence Berkeley National Laboratory School of Environment Tsinghua University Centre of Wastewater Resource Recovery College of Resources and Environment Fujian Agriculture and Forestry University School of Civil and environmental Engineering Nanyang Technological University

Though there are many literatures studying the effects of iron on anammox process, these studies only focus on the reactor performance and/or the microbial community changes, the detailed effects and mechanisms of Fe(Ⅱ) on anammox bacterial activity and physiology have not been explored. In this study, four Fe(Ⅱ) concentrations(0.03, 0.09, 0.12 and 0.75 mmol/L) were employed into the enriched anammox culture. The enhancement and inhibition effects of Fe(Ⅱ) on anammox process and bacterial physiology were investigated. It was discovered that the anammox process and bacterial growth were enhanced by 0.09 and 0.12 mmol/L Fe(Ⅱ), in which the 0.12 mmol/L Fe(Ⅱ) had advantage in stimulating the total anammox activity and bacterial abundance, while 0.09 mmol/L Fe(Ⅱ) enhanced the relative anammox activity better. The anammox activity could be inhibited by 0.75mmol/L Fe(Ⅱ) immediately, while the inhibition was recoverable. Both 0.09 and 0.12 mmol/L Fe(Ⅱ)induced more genes being expressed, while didn't show a stimulation on the relative expression level of functional genes. And anammox bacteria showed a stress response to detoxify the Fe inhibition once inhibited by 0.75 mmol/L Fe(Ⅱ). This study provides more information about physiologic response of anammox bacteria to external influence(enhancement and inhibition), and may also instruct the future application of anammox process in treating various sources of wastewater(containing external disturbances such as heavy metals) and/or different treatment strategies(*** side-stream to main-stream).

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