Microorganisms actively participate in biogeochemical cycling processes and play a crucial role in maintaining the dynamic balance of hot spring ecosystems.However,the distribution of microbial functional genes and th...Microorganisms actively participate in biogeochemical cycling processes and play a crucial role in maintaining the dynamic balance of hot spring ecosystems.However,the distribution of microbial functional genes and their influencing factors in hot springs remain largely unclear.Therefore,this study investigated the microbial functional genes and their potential for controlling biogeochemical cycles(C,N,S,and P) in the hot Springs of Tengchong,China,using the Geochip method,a functional gene microarray technology.The examined hot springs have very different microbial functional genes.A total of 22 736 gene probe signals were identified,belonging to 567 functional genes and associated with 15 ecological functions,mainly involving stress response,carbon cycle,nitrogen cycle,sulfur cycle,phosphorus cycle and energy processes.The amyA,narG,dsrA and ppx genes were most abundant in carbon,nitrogen,sulfur and phosphorus cycles,respectively,and were significantly correlated with pH,temperature and SO_(4)^(2-).The diversity and abundance of detected gene probes were negatively correlated with temperature.The α-diversity(i.e.,Shannon index) was high at low temperature and low pH.Molecular functional interactions revealed by the gene connectivity levels were negatively correlated with temperature,pH and SO_(4)^(2-).These results suggested that the abundance,diversity and interactions of microbial functional genes were significantly influenced by geochemical parameters.-In addition,some genera possessed functional genes related to carbon,nitrogen,sulfur,and phosphorus cycles and can synergistically control the biogeochemical cycles of carbon,nitrogen,sulfur and phosphorus.These findings provide new insights into the functional potentials of microorganisms to participate in biogeochemical cycles and their responses to environmental factors in hot springs.展开更多
Nitrogenous heterocyclic compounds are key pollutants in coking wastewater; however, the functional potential of microbial communities for biodegradation of such contaminants during biological treatment is still elusi...Nitrogenous heterocyclic compounds are key pollutants in coking wastewater; however, the functional potential of microbial communities for biodegradation of such contaminants during biological treatment is still elusive. Herein, a high throughput functional gene array（Geo Chip 5.0）in combination with Illumina Hi Seq2500 sequencing was used to compare and characterize the microbial community functional structure in a long run（500 days） bench scale bioreactor treating coking wastewater, with a control system treating synthetic wastewater. Despite the inhibitory toxic pollutants, Geo Chip 5.0 detected almost all key functional gene（average61,940 genes） categories in the coking wastewater sludge. With higher abundance, aromatic ring cleavage dioxygenase genes including multi ring1,2 diox; one ring2,3 diox; catechol represented significant functional potential for degradation of aromatic pollutants which was further confirmed by Illumina Hi Seq2500 analysis results. Response ratio analysis revealed that three nitrogenous compound degrading genes-nbz A（nitro-aromatics）, tdn B（aniline）, and scn ABC（thiocyanate） were unique for coking wastewater treatment, which might be strong cause to increase ammonia level during the aerobic process. Additionally, Hi Seq2500 elucidated carbozole and isoquinoline degradation genes in the system. These findings expanded our understanding on functional potential of microbial communities to remove organic nitrogenous pollutants;hence it will be useful in optimization strategies for biological treatment of coking wastewater.展开更多
Metagenomic studies have demonstrated the existence of ammonia-oxidizing archaea(AOA) and revealed they are responsible for ammoxidation in some extreme environments. However, the changes in compositional structure an...Metagenomic studies have demonstrated the existence of ammonia-oxidizing archaea(AOA) and revealed they are responsible for ammoxidation in some extreme environments. However, the changes in compositional structure and ammonia-oxidation capacity of AOA communities in biological soil crusts(BSCs) of desert ecosystems remain poorly understood.Here, we utilized Illumina MiSeq sequencing and microbial functional gene array(GeoChip 5.0) to assess the above changes along a 51-year revegetation chronosequence in the Tengger Desert, China. The results showed a significant difference in AOA-community richness between 5-year-old BSCs and older ones. The most dominant phylum during BSC development was Crenarchaeota, and the corresponding species were ammonia-oxidizing_Crenarchaeote and environmental_samples_Crenarchaeota. Network analysis revealed that the positive correlations among dominant taxa increased, and their cooperation was reinforced in AOA communities during BSC succession. Redundancy analysis showed that the dominant factor influencing the change in AOA-community structure was soil texture. GeoChip 5.0 indicated that the amoA gene abundances of AOA and ammonia-oxidizing bacteria(AOB) were basically the same, demonstrating that AOA and AOB played an equally important role during BSCs development. Our study of the long-term succession of BSC demonstrated a persistent response of AOA communities to revegetation development in desert ecosystems.展开更多
Our previously described environmental DNA extraction method has been widely used in environmental microbial community analysis. However, residual humic substances may remain with obtained environmental DNA, which int...Our previously described environmental DNA extraction method has been widely used in environmental microbial community analysis. However, residual humic substances may remain with obtained environmental DNA, which interferes downstream molecular analyses. To remedy this situation, two DNA extraction buffers （PIPES and Tris-HCl） and four purification strategies including our new modified low melting point gel purification method and three commercial kits from QIAEX, Omega and Promega were evaluated with diverse soil samples. The PIPES buffer （pH 6.5） is found to be more effective for removing the humic substances, but it leads to lower DNA yield and causes more severe DNA shearing than using the Tris-HC1 buffer （pH 8.0）. Gel purification and the Promega purification kit achieve much higher DNA recoveries than QIAEX or Omega kit, and higher purity of DNA is obtained by gel purification than by the Promega kit with both DNA extraction buffers mentioned above. Considering all results together, two alternative methods for DNA extraction and purification are proposed： one uses Tris-HCl buffer extraction and gel purification as the primary approach when the amount of soil or biomass is not a major concern, and the other uses PIPES buffer extraction and the Promega kit purification when severe DNA shearing and/or limited biomass occurs. Purified DNA samples by both methods are amenable for use as templates for whole community genome amplifications and PCR amplifications of bacterial 16S rRNA genes. It is demonstrated that these two alternative methods could be applied to a wide variety of environmental samples.展开更多
【目的】结合中温与高温消化两者优势的两相厌氧消化工艺可能是推进污泥厌氧消化发展的重要方向,因此,探究和比较中温和高温污泥厌氧消化系统中微生物群落组成的异同具有重要意义。【方法】利用高通量测序技术检测中温和高温厌氧消化系...【目的】结合中温与高温消化两者优势的两相厌氧消化工艺可能是推进污泥厌氧消化发展的重要方向,因此,探究和比较中温和高温污泥厌氧消化系统中微生物群落组成的异同具有重要意义。【方法】利用高通量测序技术检测中温和高温厌氧消化系统中细菌与古菌的16S r RNA基因序列信息和真菌的内转录间隔(ITS)序列信息,利用基因芯片(Geo Chip 5.0)检测病毒和病原菌致病基因的信息,以对比中温和高温条件下微生物群落在物种组成和功能基因层面上的异同。【结果】中温和高温条件下细菌和古菌在群落物种组成上存在显著差异,病毒和病原菌毒性基因也显著不同,而两种系统中真菌群落的物种组成相似且丰度相对较低。中温条件下产甲烷古菌和未分类微生物相对丰度较高,而高温条件下产酸及嗜热菌相对丰度较高,且高温消化后病毒和病原菌毒性基因相对丰度下降。微生物群落结构与COD、TS和VS有着显著相关性。【结论】微生物群落组成和功能基因在中高温的污泥厌氧消化系统中显著不同,从而解释了两个系统功能的差异。微生物群落的形成与进水参数相关,说明微生物对进水条件敏感。展开更多
The GeoChip is a glass slide containing oligonucleotide probes targeting genes that confer specific function to micro-organism. The GeoChip has been used to dissect the microbial community functional structure of envi...The GeoChip is a glass slide containing oligonucleotide probes targeting genes that confer specific function to micro-organism. The GeoChip has been used to dissect the microbial community functional structure of environmental samples. The PhyloChip is a glass slide containing oligonucleotide probes of the 16S rRNA genes and it offers tremendous potential to monitor microbial population. Below ground microbial community can be linked to the above ground plant community by the use of these Chips in a high throughput manner. This review seeks to determine the various roles of the GeoChip and the PhyloChip in soil microbial ecology studies. During biostimulation of uranium in groundwater, microbial community dynamics was linked to functional processes and in global warming studies, microbial response to functional gene structure has been possible by the use of the GeoChip. The PhyloChip, on the other hand, provides more comprehensive survey of the microbial diversity, composition and structure and are less susceptible to the influence of dominance in microbial community. Some of the concerns regarding the use of compost in agricultural soils i.e. the spread of human, animal and plant pathogens were reduced when the PhyloChip was used to monitor composting.展开更多
基金supported by grants from the National Natural Science Foundation of China(Nos.42172339,91951205)。
文摘Microorganisms actively participate in biogeochemical cycling processes and play a crucial role in maintaining the dynamic balance of hot spring ecosystems.However,the distribution of microbial functional genes and their influencing factors in hot springs remain largely unclear.Therefore,this study investigated the microbial functional genes and their potential for controlling biogeochemical cycles(C,N,S,and P) in the hot Springs of Tengchong,China,using the Geochip method,a functional gene microarray technology.The examined hot springs have very different microbial functional genes.A total of 22 736 gene probe signals were identified,belonging to 567 functional genes and associated with 15 ecological functions,mainly involving stress response,carbon cycle,nitrogen cycle,sulfur cycle,phosphorus cycle and energy processes.The amyA,narG,dsrA and ppx genes were most abundant in carbon,nitrogen,sulfur and phosphorus cycles,respectively,and were significantly correlated with pH,temperature and SO_(4)^(2-).The diversity and abundance of detected gene probes were negatively correlated with temperature.The α-diversity(i.e.,Shannon index) was high at low temperature and low pH.Molecular functional interactions revealed by the gene connectivity levels were negatively correlated with temperature,pH and SO_(4)^(2-).These results suggested that the abundance,diversity and interactions of microbial functional genes were significantly influenced by geochemical parameters.-In addition,some genera possessed functional genes related to carbon,nitrogen,sulfur,and phosphorus cycles and can synergistically control the biogeochemical cycles of carbon,nitrogen,sulfur and phosphorus.These findings provide new insights into the functional potentials of microorganisms to participate in biogeochemical cycles and their responses to environmental factors in hot springs.
基金National Key Basic Research Program of China(No.2013CB956601,2013CB956000)National High Technology Research and Development Program of China(863 Program,No.2012AA061401)National Natural Science Foundation of China(No.41471202,41171201,41230750,41430856)
基金supported by the National Natural Scientific Foundation of China(No.21437005)the State Hi-tech Research and Development Project of the Ministry of Science and Technology,Peoples Republic of China(No.2012AA063401)the special fund of State Key Joint Laboratory of Environmental Simulation and Pollution Control(No.15L03ESPC)
文摘Nitrogenous heterocyclic compounds are key pollutants in coking wastewater; however, the functional potential of microbial communities for biodegradation of such contaminants during biological treatment is still elusive. Herein, a high throughput functional gene array（Geo Chip 5.0）in combination with Illumina Hi Seq2500 sequencing was used to compare and characterize the microbial community functional structure in a long run（500 days） bench scale bioreactor treating coking wastewater, with a control system treating synthetic wastewater. Despite the inhibitory toxic pollutants, Geo Chip 5.0 detected almost all key functional gene（average61,940 genes） categories in the coking wastewater sludge. With higher abundance, aromatic ring cleavage dioxygenase genes including multi ring1,2 diox; one ring2,3 diox; catechol represented significant functional potential for degradation of aromatic pollutants which was further confirmed by Illumina Hi Seq2500 analysis results. Response ratio analysis revealed that three nitrogenous compound degrading genes-nbz A（nitro-aromatics）, tdn B（aniline）, and scn ABC（thiocyanate） were unique for coking wastewater treatment, which might be strong cause to increase ammonia level during the aerobic process. Additionally, Hi Seq2500 elucidated carbozole and isoquinoline degradation genes in the system. These findings expanded our understanding on functional potential of microbial communities to remove organic nitrogenous pollutants;hence it will be useful in optimization strategies for biological treatment of coking wastewater.
基金supported financially by the Strategic Priority Research Program of Chinese Academy of Sciences (Grant No. XDA2003010301)the National Natural Science Foundation of China (Grant No. 41621001)
文摘Metagenomic studies have demonstrated the existence of ammonia-oxidizing archaea(AOA) and revealed they are responsible for ammoxidation in some extreme environments. However, the changes in compositional structure and ammonia-oxidation capacity of AOA communities in biological soil crusts(BSCs) of desert ecosystems remain poorly understood.Here, we utilized Illumina MiSeq sequencing and microbial functional gene array(GeoChip 5.0) to assess the above changes along a 51-year revegetation chronosequence in the Tengger Desert, China. The results showed a significant difference in AOA-community richness between 5-year-old BSCs and older ones. The most dominant phylum during BSC development was Crenarchaeota, and the corresponding species were ammonia-oxidizing_Crenarchaeote and environmental_samples_Crenarchaeota. Network analysis revealed that the positive correlations among dominant taxa increased, and their cooperation was reinforced in AOA communities during BSC succession. Redundancy analysis showed that the dominant factor influencing the change in AOA-community structure was soil texture. GeoChip 5.0 indicated that the amoA gene abundances of AOA and ammonia-oxidizing bacteria(AOB) were basically the same, demonstrating that AOA and AOB played an equally important role during BSCs development. Our study of the long-term succession of BSC demonstrated a persistent response of AOA communities to revegetation development in desert ecosystems.
基金Project(51104189)supported by the National Natural Science Foundation of ChinaProject(2010CB630901)supported by the National Basic Research Program of China+1 种基金Project(1343-77341)supported by the Graduate Education Innovative Program of Central South University,ChinaProject(DOE-ER64125)supported by Department of Energy,Office of Science under the Environmental Remediation Science Program of the United States
文摘Our previously described environmental DNA extraction method has been widely used in environmental microbial community analysis. However, residual humic substances may remain with obtained environmental DNA, which interferes downstream molecular analyses. To remedy this situation, two DNA extraction buffers （PIPES and Tris-HCl） and four purification strategies including our new modified low melting point gel purification method and three commercial kits from QIAEX, Omega and Promega were evaluated with diverse soil samples. The PIPES buffer （pH 6.5） is found to be more effective for removing the humic substances, but it leads to lower DNA yield and causes more severe DNA shearing than using the Tris-HC1 buffer （pH 8.0）. Gel purification and the Promega purification kit achieve much higher DNA recoveries than QIAEX or Omega kit, and higher purity of DNA is obtained by gel purification than by the Promega kit with both DNA extraction buffers mentioned above. Considering all results together, two alternative methods for DNA extraction and purification are proposed： one uses Tris-HCl buffer extraction and gel purification as the primary approach when the amount of soil or biomass is not a major concern, and the other uses PIPES buffer extraction and the Promega kit purification when severe DNA shearing and/or limited biomass occurs. Purified DNA samples by both methods are amenable for use as templates for whole community genome amplifications and PCR amplifications of bacterial 16S rRNA genes. It is demonstrated that these two alternative methods could be applied to a wide variety of environmental samples.
文摘【目的】结合中温与高温消化两者优势的两相厌氧消化工艺可能是推进污泥厌氧消化发展的重要方向,因此,探究和比较中温和高温污泥厌氧消化系统中微生物群落组成的异同具有重要意义。【方法】利用高通量测序技术检测中温和高温厌氧消化系统中细菌与古菌的16S r RNA基因序列信息和真菌的内转录间隔(ITS)序列信息,利用基因芯片(Geo Chip 5.0)检测病毒和病原菌致病基因的信息,以对比中温和高温条件下微生物群落在物种组成和功能基因层面上的异同。【结果】中温和高温条件下细菌和古菌在群落物种组成上存在显著差异,病毒和病原菌毒性基因也显著不同,而两种系统中真菌群落的物种组成相似且丰度相对较低。中温条件下产甲烷古菌和未分类微生物相对丰度较高,而高温条件下产酸及嗜热菌相对丰度较高,且高温消化后病毒和病原菌毒性基因相对丰度下降。微生物群落结构与COD、TS和VS有着显著相关性。【结论】微生物群落组成和功能基因在中高温的污泥厌氧消化系统中显著不同,从而解释了两个系统功能的差异。微生物群落的形成与进水参数相关,说明微生物对进水条件敏感。
文摘The GeoChip is a glass slide containing oligonucleotide probes targeting genes that confer specific function to micro-organism. The GeoChip has been used to dissect the microbial community functional structure of environmental samples. The PhyloChip is a glass slide containing oligonucleotide probes of the 16S rRNA genes and it offers tremendous potential to monitor microbial population. Below ground microbial community can be linked to the above ground plant community by the use of these Chips in a high throughput manner. This review seeks to determine the various roles of the GeoChip and the PhyloChip in soil microbial ecology studies. During biostimulation of uranium in groundwater, microbial community dynamics was linked to functional processes and in global warming studies, microbial response to functional gene structure has been possible by the use of the GeoChip. The PhyloChip, on the other hand, provides more comprehensive survey of the microbial diversity, composition and structure and are less susceptible to the influence of dominance in microbial community. Some of the concerns regarding the use of compost in agricultural soils i.e. the spread of human, animal and plant pathogens were reduced when the PhyloChip was used to monitor composting.
