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,b...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 responses.GeoChips are considered as the most comprehensive FGAs.Experimentally 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 technology.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 manner.Several 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 ecosystems.GeoChip 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.展开更多
A new method designated cDNA array was developed by hybridization of quantitatively arrayed DNA samples isolated randomly from a cDNA library with probes reverse-transcribed from mRNAs of different sources or treatmen...A new method designated cDNA array was developed by hybridization of quantitatively arrayed DNA samples isolated randomly from a cDNA library with probes reverse-transcribed from mRNAs of different sources or treatments. The gene expression patterns of 1 000 randomly chosen clones from an Arabidopsis library were analyzed with green seedlings versus suspension cells and seedlings irradiated under UV light. Northern blot and sequence analysis of some differentially expressed clones confirmed the results revealed by cDNA array, indicating that this method is efficient and reliable to monitor gene expression.展开更多
Limited oxygen supply to anaerobic wastewater treatment systems had been demonstrated as an effective strategy to improve elemental sulfur （So） recovery, coupling sulfate reduction and sulfide oxidation. However, li...Limited oxygen supply to anaerobic wastewater treatment systems had been demonstrated as an effective strategy to improve elemental sulfur （So） recovery, coupling sulfate reduction and sulfide oxidation. However, little is known about the impact of dissolved oxygen （DO） on the microbial functional structures in these systems. We used a high throughput tool （GeoChip） to evaluate the microbial community structures in a biological desulfurization reactor under micro-aerobic conditions （DO： 0.02-0.33 rag/L）. The results indicated that the microbial community functional compositions and structures were dramatically altered with elevated DO levels. The abundances of dsrA/B genes involved in sulfate reduction processes significantly decreased （p 〈 0.05, LSD test） at relatively high DO concentration （DO： 0.33 mg/L）. The abundances of sox and fccA/B genes involved in sulfur/sulfide oxidation processes significantly increased （p 〈 0.05, LSD test） in low DO concentration conditions （DO： 0.09 mg/L） and then gradually decreased with continuously elevated DO levels. Their abundances coincided with the change of sulfate removal efliciencies and elemental sulfur （S^0） conversion efficiencies in the bioreactor. In addition, the abundance of carbon degradation genes increased with the raising of DO levels, showing that the heterotrophic microorganisms （e.g., fermentative microorganisms） were thriving under micro-aerobic condition. This study provides new insights into the impacts of micro-aerobic conditions on the microbial functional structure of sulfate- reducing sulfur-producing bioreactors, and revealed the potential linkage between functional microbial communities and reactor performance.展开更多
基金This work has been partially supported through contracts DE-SC0004601 and DE-AC02-05CH11231(as part of ENIGMA,a Scientific Focus Area)by the U.S.Department of Energy,Office of Science,Office of Biologic and Environmental Research,Genomics:GTL Foundational Science and Environmental Remediation Science Program(ERSP)Programs,and Oklahoma Applied Research Support(OARS),Oklahoma Center for the Advancement of Science and Technology(OCAST),the Oklahoma Bioenergy Center(OBC),and the State of Oklahoma through the Project AR062-034.
文摘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 responses.GeoChips are considered as the most comprehensive FGAs.Experimentally 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 technology.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 manner.Several 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 ecosystems.GeoChip 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.
基金Projects(51604308,41771300,41301274)supported by the National Natural Science Foundation of ChinaProject(2017QNCXTD_GTD)supported by the Youth Innovation Team Project of Institute of Subtropical Agriculture,Chinese Academy of Sciences+1 种基金Project(2017YFD0202000)supported by the National Key Research and Development Program of ChinaProject(2020GDASYL-20200402001)supported by the special Project of Science and Technology Development,China。
文摘A new method designated cDNA array was developed by hybridization of quantitatively arrayed DNA samples isolated randomly from a cDNA library with probes reverse-transcribed from mRNAs of different sources or treatments. The gene expression patterns of 1 000 randomly chosen clones from an Arabidopsis library were analyzed with green seedlings versus suspension cells and seedlings irradiated under UV light. Northern blot and sequence analysis of some differentially expressed clones confirmed the results revealed by cDNA array, indicating that this method is efficient and reliable to monitor gene expression.
基金supported by the National High-Tech Research and Development Program(863)of China(No.2011AA060904)the National Natural Science Foundation of China(No.51111140388,51176037 and 51308147)+2 种基金the National Creative Research Groups Project(No.51121062)the State Key Laboratory of Urban Water Resource and Environment(No.2012DX06)Liaoning Provincial Science and Technology Project(No.L2010169)
文摘Limited oxygen supply to anaerobic wastewater treatment systems had been demonstrated as an effective strategy to improve elemental sulfur （So） recovery, coupling sulfate reduction and sulfide oxidation. However, little is known about the impact of dissolved oxygen （DO） on the microbial functional structures in these systems. We used a high throughput tool （GeoChip） to evaluate the microbial community structures in a biological desulfurization reactor under micro-aerobic conditions （DO： 0.02-0.33 rag/L）. The results indicated that the microbial community functional compositions and structures were dramatically altered with elevated DO levels. The abundances of dsrA/B genes involved in sulfate reduction processes significantly decreased （p 〈 0.05, LSD test） at relatively high DO concentration （DO： 0.33 mg/L）. The abundances of sox and fccA/B genes involved in sulfur/sulfide oxidation processes significantly increased （p 〈 0.05, LSD test） in low DO concentration conditions （DO： 0.09 mg/L） and then gradually decreased with continuously elevated DO levels. Their abundances coincided with the change of sulfate removal efliciencies and elemental sulfur （S^0） conversion efficiencies in the bioreactor. In addition, the abundance of carbon degradation genes increased with the raising of DO levels, showing that the heterotrophic microorganisms （e.g., fermentative microorganisms） were thriving under micro-aerobic condition. This study provides new insights into the impacts of micro-aerobic conditions on the microbial functional structure of sulfate- reducing sulfur-producing bioreactors, and revealed the potential linkage between functional microbial communities and reactor performance.
