101
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Xu M, Zhang Q, Xia C, Zhong Y, Sun G, Guo J, Yuan T, Zhou J, He Z. Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments. ISME JOURNAL 2014; 8:1932-44. [PMID: 24671084 DOI: 10.1038/ismej.2014.42] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 02/17/2014] [Accepted: 02/19/2014] [Indexed: 02/02/2023]
Abstract
Nitrate is an important nutrient and electron acceptor for microorganisms, having a key role in nitrogen (N) cycling and electron transfer in anoxic sediments. High-nitrate inputs into sediments could have a significant effect on N cycling and its associated microbial processes. However, few studies have been focused on the effect of nitrate addition on the functional diversity, composition, structure and dynamics of sediment microbial communities in contaminated aquatic ecosystems with persistent organic pollutants (POPs). Here we analyzed sediment microbial communities from a field-scale in situ bioremediation site, a creek in Pearl River Delta containing a variety of contaminants including polybrominated diphenyl ethers (PBDEs) and polycyclic aromatic hydrocarbons (PAHs), before and after nitrate injection using a comprehensive functional gene array (GeoChip 4.0). Our results showed that the sediment microbial community functional composition and structure were markedly altered, and that functional genes involved in N-, carbon (C)-, sulfur (S)-and phosphorus (P)- cycling processes were highly enriched after nitrate injection, especially those microorganisms with diverse metabolic capabilities, leading to potential in situ bioremediation of the contaminated sediment, such as PBDE and PAH reduction/degradation. This study provides new insights into our understanding of sediment microbial community responses to nitrate addition, suggesting that indigenous microorganisms could be successfully stimulated for in situ bioremediation of POPs in contaminated sediments with nitrate addition.
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Affiliation(s)
- Meiying Xu
- 1] Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, China [2] State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Qin Zhang
- 1] Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, China [2] College of Environmental Sciences and Engineering, Guilin University of Technology, Guilin, China
| | - Chunyu Xia
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, China
| | - Yuming Zhong
- 1] Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, China [2] State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Guoping Sun
- 1] Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, China [2] State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Jun Guo
- 1] Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, China [2] State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Tong Yuan
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Zhili He
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
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102
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Wang X, Xia Y, Wen X, Yang Y, Zhou J. Microbial community functional structures in wastewater treatment plants as characterized by GeoChip. PLoS One 2014; 9:e93422. [PMID: 24671164 PMCID: PMC3966879 DOI: 10.1371/journal.pone.0093422] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 03/06/2014] [Indexed: 11/23/2022] Open
Abstract
Background Biological WWTPs must be functionally stable to continuously and steadily remove contaminants which rely upon the activity of complex microbial communities. However, knowledge is still lacking in regard to microbial community functional structures and their linkages to environmental variables. Aims To investigate microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs) and to understand the effects of environmental factors on their structure. Methods 12 activated sludge samples were collected from four WWTPs in Beijing. A comprehensive functional gene array named GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes such as carbon, nitrogen, phosphorous and sulfur cycles, metal resistance, antibiotic resistance and organic contaminant degradation. Results High similarities of the microbial community functional structures were found among activated sludge samples from the four WWTPs, as shown by both diversity indices and the overlapped genes. For individual gene category, such as egl, amyA, lip, nirS, nirK, nosZ, ureC, ppx, ppk, aprA, dsrA, sox and benAB, there were a number of microorganisms shared by all 12 samples. Canonical correspondence analysis (CCA) showed that the microbial functional patterns were highly correlated with water temperature, dissolved oxygen (DO), ammonia concentrations and loading rate of chemical oxygen demand (COD). Based on the variance partitioning analyses (VPA), a total of 53% of microbial community variation from GeoChip data can be explained by wastewater characteristics (25%) and operational parameters (23%), respectively. Conclusions This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs.
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Affiliation(s)
- Xiaohui Wang
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing, China; Department of Environmental Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Yu Xia
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing, China
| | - Xianghua Wen
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing, China
| | - Yunfeng Yang
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing, China
| | - Jizhong Zhou
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing, China; Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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103
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Tu Q, Yu H, He Z, Deng Y, Wu L, Van Nostrand JD, Zhou A, Voordeckers J, Lee YJ, Qin Y, Hemme CL, Shi Z, Xue K, Yuan T, Wang A, Zhou J. GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis. Mol Ecol Resour 2014; 14:914-28. [PMID: 24520909 DOI: 10.1111/1755-0998.12239] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 02/02/2014] [Accepted: 02/05/2014] [Indexed: 01/21/2023]
Abstract
Micro-organisms play critical roles in many important biogeochemical processes in the Earth's biosphere. However, understanding and characterizing the functional capacity of microbial communities are still difficult due to the extremely diverse and often uncultivable nature of most micro-organisms. In this study, we developed a new functional gene array, GeoChip 4, for analysing the functional diversity, composition, structure, metabolic potential/activity and dynamics of microbial communities. GeoChip 4 contained approximately 82 000 probes covering 141 995 coding sequences from 410 functional gene families related to microbial carbon (C), nitrogen (N), sulphur (S), and phosphorus (P) cycling, energy metabolism, antibiotic resistance, metal resistance/reduction, organic remediation, stress responses, bacteriophage and virulence. A total of 173 archaeal, 4138 bacterial, 404 eukaryotic and 252 viral strains were targeted, providing the ability to analyse targeted functional gene families of micro-organisms included in all four domains. Experimental assessment using different amounts of DNA suggested that as little as 500 ng environmental DNA was required for good hybridization, and the signal intensities detected were well correlated with the DNA amount used. GeoChip 4 was then applied to study the effect of long-term warming on soil microbial communities at a Central Oklahoma site, with results indicating that microbial communities respond to long-term warming by enriching carbon degradation, nutrient cycling (nitrogen and phosphorous) and stress response gene families. To the best of our knowledge, GeoChip 4 is the most comprehensive functional gene array for microbial community analysis.
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Affiliation(s)
- Qichao Tu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, 73019, USA
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104
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Sun B, Wang F, Jiang Y, Li Y, Dong Z, Li Z, Zhang XX. A long-term field experiment of soil transplantation demonstrating the role of contemporary geographic separation in shaping soil microbial community structure. Ecol Evol 2014; 4:1073-87. [PMID: 24772284 PMCID: PMC3997323 DOI: 10.1002/ece3.1006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 01/29/2014] [Accepted: 01/30/2014] [Indexed: 11/30/2022] Open
Abstract
The spatial patterns of microbial communities are largely determined by the combined effects of historical contingencies and contemporary environmental disturbances, but their relative importance remains poorly understood. Empirical biogeographic data currently available are mostly based on the traditional method of observational survey, which typically involves comparing indigenous microbial communities across spatial scales. Here, we report a long-term soil transplantation experiment, whereby the same two soils (red Acrisol and purple Cambisol from Yingtan) were placed into two geographic locations of ∼1000 km apart (i.e., Yingtan in the mid-subtropical region and Fengqiu in warm-temperate region; both located in China). Twenty years after the transplantation, the resulting soil microbial communities were subject to high-throughput 454 pyrosequencing analysis of 16S and 18S rRNA genes. Additionally, bacteria and archaea involved in nitrogen cycling were estimated using clone library analysis of four genes: archaeal amoA, bacterial amoA,nirK, and nifH. Data of subsequent phylogenetic analysis show that bacteria, fungi, and other microbial eukaryotes, as well as the nitrogen cycling genes, are grouped primarily by the factor of geographic location rather than soil type. Moreover, a shift of microbial communities toward those in local soil (i.e., Chao soil in Fengqiu) has been observed. The results thus suggest that the historical effects persistent in the soil microbial communities can be largely erased by contemporary disturbance within a short period of 20 years, implicating weak effects of historical contingencies on the structure and composition of microbial communities in the soil.
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Affiliation(s)
- Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences 71 East Beijing Road, Nanjing, 210008, China
| | - Feng Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences 71 East Beijing Road, Nanjing, 210008, China ; University of the Chinese Academy of Sciences Beijing, 100049, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences 71 East Beijing Road, Nanjing, 210008, China
| | - Yun Li
- College of Resource & Environment, Sichuan Agricultural University Chengdu, 611130, China
| | - Zhixin Dong
- Institute of Mountain Hazards and Environment, Chinese Academy of Science Chengdu, 610041, China
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences 71 East Beijing Road, Nanjing, 210008, China
| | - Xue-Xian Zhang
- Institute of Natural and Mathematical Sciences, Massey University at Albany Auckland, 0745, New Zealand
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105
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Tu Q, He Z, Li Y, Chen Y, Deng Y, Lin L, Hemme CL, Yuan T, Van Nostrand JD, Wu L, Zhou X, Shi W, Li L, Xu J, Zhou J. Development of HuMiChip for functional profiling of human microbiomes. PLoS One 2014; 9:e90546. [PMID: 24595026 PMCID: PMC3942451 DOI: 10.1371/journal.pone.0090546] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 02/01/2014] [Indexed: 02/05/2023] Open
Abstract
Understanding the diversity, composition, structure, function, and dynamics of human microbiomes in individual human hosts is crucial to reveal human-microbial interactions, especially for patients with microbially mediated disorders, but challenging due to the high diversity of the human microbiome. Here we have developed a functional gene-based microarray for profiling human microbiomes (HuMiChip) with 36,802 probes targeting 50,007 protein coding sequences for 139 key functional gene families. Computational evaluation suggested all probes included are highly specific to their target sequences. HuMiChip was used to analyze human oral and gut microbiomes, showing significantly different functional gene profiles between oral and gut microbiome. Obvious shifts of microbial functional structure and composition were observed for both patients with dental caries and periodontitis from moderate to advanced stages, suggesting a progressive change of microbial communities in response to the diseases. Consistent gene family profiles were observed by both HuMiChip and next generation sequencing technologies. Additionally, HuMiChip was able to detect gene families at as low as 0.001% relative abundance. The results indicate that the developed HuMiChip is a useful and effective tool for functional profiling of human microbiomes.
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Affiliation(s)
- Qichao Tu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Zhili He
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Yan Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yanfei Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Ye Deng
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Lu Lin
- Chinese Academy of Sciences, Qingdao Institute of Bioenergy and Bioprocess Technology, Qingdao, Shandong, China
| | - Christopher L. Hemme
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Tong Yuan
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Joy D. Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Liyou Wu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Wenyuan Shi
- UCLA School of Dentistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Jian Xu
- Chinese Academy of Sciences, Qingdao Institute of Bioenergy and Bioprocess Technology, Qingdao, Shandong, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
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106
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Zhou J, Deng Y, Zhang P, Xue K, Liang Y, Van Nostrand JD, Yang Y, He Z, Wu L, Stahl DA, Hazen TC, Tiedje JM, Arkin AP. Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proc Natl Acad Sci U S A 2014; 111:E836-45. [PMID: 24550501 PMCID: PMC3948316 DOI: 10.1073/pnas.1324044111] [Citation(s) in RCA: 450] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unraveling the drivers of community structure and succession in response to environmental change is a central goal in ecology. Although the mechanisms shaping community structure have been intensively examined, those controlling ecological succession remain elusive. To understand the relative importance of stochastic and deterministic processes in mediating microbial community succession, a unique framework composed of four different cases was developed for fluidic and nonfluidic ecosystems. The framework was then tested for one fluidic ecosystem: a groundwater system perturbed by adding emulsified vegetable oil (EVO) for uranium immobilization. Our results revealed that groundwater microbial community diverged substantially away from the initial community after EVO amendment and eventually converged to a new community state, which was closely clustered with its initial state. However, their composition and structure were significantly different from each other. Null model analysis indicated that both deterministic and stochastic processes played important roles in controlling the assembly and succession of the groundwater microbial community, but their relative importance was time dependent. Additionally, consistent with the proposed conceptual framework but contradictory to conventional wisdom, the community succession responding to EVO amendment was primarily controlled by stochastic rather than deterministic processes. During the middle phase of the succession, the roles of stochastic processes in controlling community composition increased substantially, ranging from 81.3% to 92.0%. Finally, there are limited successional studies available to support different cases in the conceptual framework, but further well-replicated explicit time-series experiments are needed to understand the relative importance of deterministic and stochastic processes in controlling community succession.
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Affiliation(s)
- Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94270
| | - Ye Deng
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
- Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, China
| | - Ping Zhang
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
| | - Kai Xue
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
| | - Yuting Liang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
| | - Joy D. Van Nostrand
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Zhili He
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
| | - Liyou Wu
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
| | - David A. Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195
| | - Terry C. Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824; and
| | - Adam P. Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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107
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He Z, Xiong J, Kent AD, Deng Y, Xue K, Wang G, Wu L, Van Nostrand JD, Zhou J. Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agro-ecosystem. THE ISME JOURNAL 2014; 8:714-726. [PMID: 24108327 PMCID: PMC3930317 DOI: 10.1038/ismej.2013.177] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 08/01/2013] [Accepted: 09/06/2013] [Indexed: 11/08/2022]
Abstract
The concentrations of atmospheric carbon dioxide (CO2) and tropospheric ozone (O3) have been rising due to human activities. However, little is known about how such increases influence soil microbial communities. We hypothesized that elevated CO2 (eCO2) and elevated O3 (eO3) would significantly affect the functional composition, structure and metabolic potential of soil microbial communities, and that various functional groups would respond to such atmospheric changes differentially. To test these hypotheses, we analyzed 96 soil samples from a soybean free-air CO2 enrichment (SoyFACE) experimental site using a comprehensive functional gene microarray (GeoChip 3.0). The results showed the overall functional composition and structure of soil microbial communities shifted under eCO2, eO3 or eCO2+eO3. Key functional genes involved in carbon fixation and degradation, nitrogen fixation, denitrification and methane metabolism were stimulated under eCO2, whereas those involved in N fixation, denitrification and N mineralization were suppressed under eO3, resulting in the fact that the abundance of some eO3-supressed genes was promoted to ambient, or eCO2-induced levels by the interaction of eCO2+eO3. Such effects appeared distinct for each treatment and significantly correlated with soil properties and soybean yield. Overall, our analysis suggests possible mechanisms of microbial responses to global atmospheric change factors through the stimulation of C and N cycling by eCO2, the inhibition of N functional processes by eO3 and the interaction by eCO2 and eO3. This study provides new insights into our understanding of microbial functional processes in response to global atmospheric change in soybean agro-ecosystems.
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Affiliation(s)
- Zhili He
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, the University of Oklahoma, Norman, OK, USA.
| | - Jinbo Xiong
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, the University of Oklahoma, Norman, OK, USA
- Faculty of Marine Sciences, Ningbo University, Ningbo, China
| | - Angela D Kent
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ye Deng
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, the University of Oklahoma, Norman, OK, USA
| | - Kai Xue
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, the University of Oklahoma, Norman, OK, USA
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Liyou Wu
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, the University of Oklahoma, Norman, OK, USA
| | - Joy D Van Nostrand
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, the University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, the University of Oklahoma, Norman, OK, USA.
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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108
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Liu S, Wang F, Xue K, Sun B, Zhang Y, He Z, Van Nostrand JD, Zhou J, Yang Y. The interactive effects of soil transplant into colder regions and cropping on soil microbiology and biogeochemistry. Environ Microbiol 2014; 17:566-76. [DOI: 10.1111/1462-2920.12398] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 01/08/2014] [Accepted: 01/08/2014] [Indexed: 01/18/2023]
Affiliation(s)
- Shanshan Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control; School of Environment; Tsinghua University; Beijing China
| | - Feng Wang
- State Key Laboratory of Soil and Sustainable Agriculture; Institute of Soil Science; Chinese Academy of Sciences; Nanjing China
- University of Chinese Academy of Sciences; Beijing China
| | - Kai Xue
- Institute for Environmental Genomics; Department Microbiology and Plant Science; University of Oklahoma; Norman OK USA
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture; Institute of Soil Science; Chinese Academy of Sciences; Nanjing China
| | - Yuguang Zhang
- Institute of Forestry Ecology, Environment and Protection; Key Laboratory of Forest Ecology and Environment of State Forestry Administration; Chinese Academy of Forestry; Beijing China
| | - Zhili He
- Institute for Environmental Genomics; Department Microbiology and Plant Science; University of Oklahoma; Norman OK USA
| | - Joy D. Van Nostrand
- Institute for Environmental Genomics; Department Microbiology and Plant Science; University of Oklahoma; Norman OK USA
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control; School of Environment; Tsinghua University; Beijing China
- Institute for Environmental Genomics; Department Microbiology and Plant Science; University of Oklahoma; Norman OK USA
- Earth Sciences Division; Lawrence Berkeley National Laboratory; Berkeley CA USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control; School of Environment; Tsinghua University; Beijing China
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109
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Saliva microbiota carry caries-specific functional gene signatures. PLoS One 2014; 9:e76458. [PMID: 24533043 PMCID: PMC3922703 DOI: 10.1371/journal.pone.0076458] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 08/26/2013] [Indexed: 01/05/2023] Open
Abstract
Human saliva microbiota is phylogenetically divergent among host individuals yet their roles in health and disease are poorly appreciated. We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults. Saliva microbiota in the pilot population featured a vast diversity of functional genes. No significant distinction in gene number or diversity indices was observed between healthy and caries-active microbiota. However, co-presence network analysis of functional genes revealed that caries-active microbiota was more divergent in non-core genes than healthy microbiota, despite both groups exhibited a similar degree of conservation at their respective core genes. Furthermore, functional gene structure of saliva microbiota could potentially distinguish caries-active patients from healthy hosts. Microbial functions such as Diaminopimelate epimerase, Prephenate dehydrogenase, Pyruvate-formate lyase and N-acetylmuramoyl-L-alanine amidase were significantly linked to caries. Therefore, saliva microbiota carried disease-associated functional signatures, which could be potentially exploited for caries diagnosis.
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110
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A microarray for assessing transcription from pelagic marine microbial taxa. ISME JOURNAL 2014; 8:1476-91. [PMID: 24477198 DOI: 10.1038/ismej.2014.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 12/16/2013] [Accepted: 12/31/2013] [Indexed: 02/08/2023]
Abstract
Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world's oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions.
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111
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Linking stoichiometric homeostasis of microorganisms with soil phosphorus dynamics in wetlands subjected to microcosm warming. PLoS One 2014; 9:e85575. [PMID: 24475045 PMCID: PMC3903482 DOI: 10.1371/journal.pone.0085575] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 11/29/2013] [Indexed: 12/02/2022] Open
Abstract
Soil biogeochemical processes and the ecological stability of wetland ecosystems under global warming scenarios have gained increasing attention worldwide. Changes in the capacity of microorganisms to maintain stoichiometric homeostasis, or relatively stable internal concentrations of elements, may serve as an indicator of alterations to soil biogeochemical processes and their associated ecological feedbacks. In this study, an outdoor computerized microcosm was set up to simulate a warmed (+5°C) climate scenario, using novel, minute-scale temperature manipulation technology. The principle of stoichiometric homeostasis was adopted to illustrate phosphorus (P) biogeochemical cycling coupled with carbon (C) dynamics within the soil-microorganism complex. We hypothesized that enhancing the flux of P from soil to water under warming scenarios is tightly coupled with a decrease in homeostatic regulation ability in wetland ecosystems. Results indicate that experimental warming impaired the ability of stoichiometric homeostasis (H) to regulate biogeochemical processes, enhancing the ecological role of wetland soil as an ecological source for both P and C. The potential P flux from soil to water ranged from 0.11 to 34.51 mg m−2 d−1 in the control and 0.07 to 61.26 mg m−2 d−1 in the warmed treatment. The synergistic function of C-P acquisition is an important mechanism underlying C∶P stoichiometric balance for soil microorganisms under warming. For both treatment groups, strongly significant (p<0.001) relationships fitting a negative allometric power model with a fractional exponent were found between n-HC∶P (the specialized homeostatic regulation ability as a ratio of soil highly labile organic carbon to dissolved reactive phosphorus in porewater) and potential P flux. Although many factors may affect soil P dynamics, the n-HC∶P term fundamentally reflects the stoichiometric balance or interactions between the energy landscape (i.e., C) and flow of resources (e.g., N and P), and can be a useful ecological tool for assessing potential P flux in ecosystems.
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Singh BK, Quince C, Macdonald CA, Khachane A, Thomas N, Al-Soud WA, Sørensen SJ, He Z, White D, Sinclair A, Crooks B, Zhou J, Campbell CD. Loss of microbial diversity in soils is coincident with reductions in some specialized functions. Environ Microbiol 2014; 16:2408-20. [DOI: 10.1111/1462-2920.12353] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 11/30/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Brajesh K. Singh
- Hawkesbury Institute for the Environment; University of Western Sydney; Penrith NSW Australia
| | | | - Catriona A. Macdonald
- Hawkesbury Institute for the Environment; University of Western Sydney; Penrith NSW Australia
| | - Amit Khachane
- Hawkesbury Institute for the Environment; University of Western Sydney; Penrith NSW Australia
| | | | - Waleed Abu Al-Soud
- Department of Biology; Faculty of Science; University of Copenhagen; Copenhagen Denmark
| | - Søren J. Sørensen
- Department of Biology; Faculty of Science; University of Copenhagen; Copenhagen Denmark
| | - Zhili He
- Department of Botany and Microbiology; Institute for Environmental Genomics; Stephenson Research and Technology Centre; University of Oklahoma; Norman OK USA
| | | | | | - Bill Crooks
- SRUC Auchincruive; Ayr Auchincruive Estate UK
| | - Jizhong Zhou
- Department of Botany and Microbiology; Institute for Environmental Genomics; Stephenson Research and Technology Centre; University of Oklahoma; Norman OK USA
| | - Colin D. Campbell
- The James Hutton Institute; Aberdeen UK
- Department of Soil and Environment; Swedish Agricultural Sciences University; Uppsala Sweden
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113
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Störmer R, Wichels A, Gerdts G. Geo-Chip analysis reveals reduced functional diversity of the bacterial community at a dumping site for dredged Elbe sediment. MARINE POLLUTION BULLETIN 2013; 77:113-122. [PMID: 24229782 DOI: 10.1016/j.marpolbul.2013.10.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 06/02/2023]
Abstract
The dumping of dredged sediments represents a major stressor for coastal ecosystems. The impact on the ecosystem function is determined by its complexity not easy to assess. In the present study, we evaluated the potential of bacterial community analyses to act as ecological indicators in environmental monitoring programmes. We investigated the functional structure of bacterial communities, applying functional gene arrays (GeoChip4.2). The relationship between functional genes and environmental factors was analysed using distance-based multivariate multiple regression. Apparently, both the function and structure of the bacterial communities are impacted by dumping activities. The bacterial community at the dumping centre displayed a significant reduction of its entire functional diversity compared with that found at a reference site. DDX compounds separated bacterial communities of the dumping site from those of un-impacted sites. Thus, bacterial community analyses show great potential as ecological indicators in environmental monitoring.
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Affiliation(s)
- Rebecca Störmer
- Microbial Ecology Group Alfred Wegener, Institute for Polar and Marine Research, Kurpromenade 201, 27498 Helgoland, Germany.
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114
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Duan L, Song Y, Xia S, Hermanowicz SW. Characterization of nitrifying microbial community in a submerged membrane bioreactor at short solids retention times. BIORESOURCE TECHNOLOGY 2013; 149:200-207. [PMID: 24099975 DOI: 10.1016/j.biortech.2013.09.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/07/2013] [Accepted: 09/11/2013] [Indexed: 06/02/2023]
Abstract
This study investigated the nitrifying bacterial community in membrane bioreactor (MBR) at short solids retention times (SRTs) of 3, 5 and 10 days. The denaturing gradient gel electrophoresis results showed that different types of ammonia-oxidizing bacteria (AOB) can survive at different operating conditions. The diversity of AOB increased as the SRT increased. The real-time PCR results showed that the amoA gene concentrations were similar when MBRs were stabilized, and it can be a good indicator of stabilized nitrification. The results of clone library indicated that Nitrosomonas was the dominant group of AOB in three reactors. The microarray results showed that Nitrospira was the dominant group of nitrite-oxidizing bacteria (NOB) in the system. All groups of AOB and NOB except Nitrosolobus and Nitrococcus were found in MBR, indicated that the nitrifying bacterial community structure was more complicated. The combination of some molecular tools can provide more information of microbial communities.
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Affiliation(s)
- Liang Duan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720-1710, USA
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115
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Meslé M, Dromart G, Oger P. Microbial methanogenesis in subsurface oil and coal. Res Microbiol 2013; 164:959-72. [DOI: 10.1016/j.resmic.2013.07.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 07/02/2013] [Indexed: 11/17/2022]
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116
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Antony-Babu S, Deveau A, Van Nostrand JD, Zhou J, Le Tacon F, Robin C, Frey-Klett P, Uroz S. Black truffle-associated bacterial communities during the development and maturation ofTuber melanosporumascocarps and putative functional roles. Environ Microbiol 2013; 16:2831-47. [DOI: 10.1111/1462-2920.12294] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 09/20/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Sanjay Antony-Babu
- INRA; Interactions Arbres - Microorganismes; UMR1136 F-54280 Champenoux France
- Interactions Arbres - Microorganismes; Université de Lorraine; UMR1136 F-54500 Vandoeuvre-lès-Nancy France
| | - Aurélie Deveau
- INRA; Interactions Arbres - Microorganismes; UMR1136 F-54280 Champenoux France
- Interactions Arbres - Microorganismes; Université de Lorraine; UMR1136 F-54500 Vandoeuvre-lès-Nancy France
| | - Joy D. Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology; University of Oklahoma; Norman OK 73072 USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology; University of Oklahoma; Norman OK 73072 USA
- Earth Sciences Division; Lawrence Berkeley National Laboratory; Berkeley CA 94720 USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control; School of Environment; Tsinghua University; Beijing 100084 China
| | - François Le Tacon
- INRA; Interactions Arbres - Microorganismes; UMR1136 F-54280 Champenoux France
- Interactions Arbres - Microorganismes; Université de Lorraine; UMR1136 F-54500 Vandoeuvre-lès-Nancy France
| | - Christophe Robin
- Agronomie & Environnement; Université de Lorraine; Nancy-Colmar UMR 1121 F-54500 Vandoeuvre-lès-Nancy France
- INRA; Agronomie & Environnement; Centre INRA de Nancy-Lorraine; Nancy-Colmar UMR 1121 F-54500 Vandoeuvre-lès-Nancy France
| | - Pascale Frey-Klett
- INRA; Interactions Arbres - Microorganismes; UMR1136 F-54280 Champenoux France
- Interactions Arbres - Microorganismes; Université de Lorraine; UMR1136 F-54500 Vandoeuvre-lès-Nancy France
| | - Stéphane Uroz
- INRA; Interactions Arbres - Microorganismes; UMR1136 F-54280 Champenoux France
- Interactions Arbres - Microorganismes; Université de Lorraine; UMR1136 F-54500 Vandoeuvre-lès-Nancy France
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Microbial diversity in the era of omic technologies. BIOMED RESEARCH INTERNATIONAL 2013; 2013:958719. [PMID: 24260747 PMCID: PMC3821902 DOI: 10.1155/2013/958719] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 08/26/2013] [Accepted: 08/26/2013] [Indexed: 11/17/2022]
Abstract
Human life and activity depends on microorganisms, as they are responsible for providing basic elements of life. Although microbes have such a key role in sustaining basic functions for all living organisms, very little is known about their biology since only a small fraction (average 1%) can be cultured under laboratory conditions. This is even more evident when considering that >88% of all bacterial isolates belong to four bacterial phyla, the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Advanced technologies, developed in the last years, promise to revolutionise the way that we characterize, identify, and study microbial communities. In this review, we present the most advanced tools that microbial ecologists can use for the study of microbial communities. Innovative microbial ecological DNA microarrays such as PhyloChip and GeoChip that have been developed for investigating the composition and function of microbial communities are presented, along with an overview of the next generation sequencing technologies. Finally, the Single Cell Genomics approach, which can be used for obtaining genomes from uncultured phyla, is outlined. This tool enables the amplification and sequencing of DNA from single cells obtained directly from environmental samples and is promising to revolutionise microbiology.
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118
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Zhang Y, Xie J, Liu M, Tian Z, He Z, van Nostrand JD, Ren L, Zhou J, Yang M. Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems. WATER RESEARCH 2013; 47:6298-6308. [PMID: 23981791 DOI: 10.1016/j.watres.2013.08.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 07/15/2013] [Accepted: 08/03/2013] [Indexed: 06/02/2023]
Abstract
It is widely demonstrated that antibiotics in the environment affect microbial community structure. However, direct evidence regarding the impacts of antibiotics on microbial functional structures in wastewater treatment systems is limited. Herein, a high-throughput functional gene array (GeoChip 3.0) in combination with quantitative PCR and clone libraries were used to evaluate the microbial functional structures in two biological wastewater treatment systems, which treat antibiotic production wastewater mainly containing oxytetracycline. Despite the bacteriostatic effects of antibiotics, the GeoChip detected almost all key functional gene categories, including carbon cycling, nitrogen cycling, etc., suggesting that these microbial communities were functionally diverse. Totally 749 carbon-degrading genes belonging to 40 groups (24 from bacteria and 16 from fungi) were detected. The abundance of several fungal carbon-degrading genes (e.g., glyoxal oxidase (glx), lignin peroxidase or ligninase (lip), manganese peroxidase (mnp), endochitinase, exoglucanase_genes) was significantly correlated with antibiotic concentrations (Mantel test; P < 0.05), showing that the fungal functional genes have been enhanced by the presence of antibiotics. However, from the fact that the majority of carbon-degrading genes were derived from bacteria and diverse antibiotic resistance genes were detected in bacteria, it was assumed that many bacteria could survive in the environment by acquiring antibiotic resistance and may have maintained the position as a main player in nutrient removal. Variance partitioning analysis showed that antibiotics could explain 24.4% of variations in microbial functional structure of the treatment systems. This study provides insights into the impacts of antibiotics on microbial functional structure of a unique system receiving antibiotic production wastewater, and reveals the potential importance of the cooperation between fungi and bacteria with antibiotic resistance in maintaining the stability and performance of the systems.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
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119
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Zhang X, Liu W, Schloter M, Zhang G, Chen Q, Huang J, Li L, Elser JJ, Han X. Response of the abundance of key soil microbial nitrogen-cycling genes to multi-factorial global changes. PLoS One 2013; 8:e76500. [PMID: 24124568 PMCID: PMC3790715 DOI: 10.1371/journal.pone.0076500] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 08/28/2013] [Indexed: 12/03/2022] Open
Abstract
Multiple co-occurring environmental changes are affecting soil nitrogen cycling processes, which are mainly mediated by microbes. While it is likely that various nitrogen-cycling functional groups will respond differently to such environmental changes, very little is known about their relative responsiveness. Here we conducted four long-term experiments in a steppe ecosystem by removing plant functional groups, mowing, adding nitrogen, adding phosphorus, watering, warming, and manipulating some of their combinations. We quantified the abundance of seven nitrogen-cycling genes, including those for fixation (nifH), mineralization (chiA), nitrification (amoA of ammonia-oxidizing bacteria (AOB) or archaea (AOA)), and denitrification (nirS, nirK and nosZ). First, for each gene, we compared its sensitivities to different environmental changes and found that the abundances of various genes were sensitive to distinct and different factors. Overall, the abundances of nearly all genes were sensitive to nitrogen enrichment. In addition, the abundances of the chiA and nosZ genes were sensitive to plant functional group removal, the AOB-amoA gene abundance to phosphorus enrichment when nitrogen was added simultaneously, and the nirS and nirK gene abundances responded to watering. Second, for each single- or multi-factorial environmental change, we compared the sensitivities of the abundances of different genes and found that different environmental changes primarily affected different gene abundances. Overall, AOB-amoA gene abundance was most responsive, followed by the two denitrifying genes nosZ and nirS, while the other genes were less sensitive. These results provide, for the first time, systematic insights into how the abundance of each type of nitrogen-cycling gene and the equilibrium state of all these nitrogen-cycling gene abundances would shift under each single- or multi-factorial global change.
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Affiliation(s)
- Ximei Zhang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Michael Schloter
- Environmental Genomics, Helmholtz Center for Environmental Health, Oberschleissheim, Germany
| | - Guangming Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Quansheng Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jianhui Huang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Linghao Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - James J. Elser
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- * E-mail: (JJE); (XH)
| | - Xingguo Han
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- * E-mail: (JJE); (XH)
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120
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Campos-Herrera R, Ali JG, Diaz BM, Duncan LW. Analyzing spatial patterns linked to the ecology of herbivores and their natural enemies in the soil. FRONTIERS IN PLANT SCIENCE 2013; 4:378. [PMID: 24137165 PMCID: PMC3786222 DOI: 10.3389/fpls.2013.00378] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 09/03/2013] [Indexed: 05/11/2023]
Abstract
Modern agricultural systems can benefit from the application of concepts and models from applied ecology. When understood, multitrophic interactions among plants, pests, diseases and their natural enemies can be exploited to increase crop production and reduce undesirable environmental impacts. Although the understanding of subterranean ecology is rudimentary compared to the perspective aboveground, technologies today vastly reduce traditional obstacles to studying cryptic communities. Here we emphasize advantages to integrating as much as possible the use of these methods in order to leverage the information gained from studying communities of soil organisms. PCR-based approaches to identify and quantify species (real time qPCR and next generation sequencing) greatly expand the ability to investigate food web interactions because there is less need for wide taxonomic expertise within research programs. Improved methods to capture and measure volatiles in the soil atmosphere in situ make it possible to detect and study chemical cues that are critical to communication across trophic levels. The application of SADIE to directly assess rather than infer spatial patterns in belowground agroecosystems has improved the ability to characterize relationships between organisms in space and time. We review selected methodology and use of these tools and describe some of the ways they were integrated to study soil food webs in Florida citrus orchards with the goal of developing new biocontrol approaches.
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Affiliation(s)
- R. Campos-Herrera
- Departamento de Contaminación Ambiental, Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones CientíficasMadrid, Spain
- Entomology and Nematology Department, Citrus Research and Education Center, University of FloridaLake Alfred, FL, USA
| | - J. G. Ali
- Entomology and Nematology Department, Citrus Research and Education Center, University of FloridaLake Alfred, FL, USA
- Department of Ecology and Evolutionary Biology, Cornell UniversityIthaca, NY, USA
| | - B. M. Diaz
- Departamento de Protección Vegetal, Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - L. W. Duncan
- Entomology and Nematology Department, Citrus Research and Education Center, University of FloridaLake Alfred, FL, USA
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121
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Zhou A, He Z, Qin Y, Lu Z, Deng Y, Tu Q, Hemme CL, Van Nostrand JD, Wu L, Hazen TC, Arkin AP, Zhou J. StressChip as a high-throughput tool for assessing microbial community responses to environmental stresses. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:9841-9849. [PMID: 23889170 DOI: 10.1021/es4018656] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Microbial community responses to environmental stresses are critical for microbial growth, survival, and adaptation. To fill major gaps in our ability to discern the influence of environmental changes on microbial communities from engineered and natural environments, a functional gene-based microarray, termed StressChip, has been developed. First, 46 functional genes involved in microbial responses to environmental stresses such as changes to temperature, osmolarity, oxidative status, nutrient limitation, or general stress response were selected and curated. A total of 22,855 probes were designed, covering 79,628 coding sequences from 985 bacterial, 76 archaeal, and 59 eukaryotic species/strains. Probe specificity was computationally verified. Second, the usefulness of functional genes as indicators of stress response was examined by surveying their distribution in metagenome data sets. The abundance of individual stress response genes is consistent with expected distributions based on respective habitats. Third, the StressChip was used to analyze marine microbial communities from the Deepwater Horizon oil spill. That functional stress response genes were detected in higher abundance (p < 0.05) in oil plume compared to nonplume samples indicated shifts in community composition and structure, consistent with previous results. In summary, StressChip provides a new tool for accessing microbial community functional structure and responses to environmental changes.
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Affiliation(s)
- Aifen Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
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Li M, Mathieu J, Yang Y, Fiorenza S, Deng Y, He Z, Zhou J, Alvarez PJJ. Widespread distribution of soluble di-iron monooxygenase (SDIMO) genes in Arctic groundwater impacted by 1,4-dioxane. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:9950-9958. [PMID: 23909410 DOI: 10.1021/es402228x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Soluble di-iron monooxygenases (SDIMOs), especially group-5 SDIMOs (i.e., tetrahydrofuran and propane monooxygenases), are of significant interest due to their potential role in the initiation of 1,4-dioxane (dioxane) degradation. Functional gene array (i.e., GeoChip) analysis of Arctic groundwater exposed to dioxane since 1980s revealed that various dioxane-degrading SDIMO genes were widespread, and PCR-DGGE analysis showed that group-5 SDIMOs were present in every tested sample, including background groundwater with no known dioxane exposure history. A group-5 thmA-like gene was enriched (2.4-fold over background, p < 0.05) in source-zone samples with higher dioxane concentrations, suggesting selective pressure by dioxane. Microcosm assays with (14)C-labeled dioxane showed that the highest mineralization capacity (6.4 ± 0.1% (14)CO2 recovery during 15 days, representing over 60% of the amount degraded) corresponded to the source area, which was presumably more acclimated and contained a higher abundance of SDIMO genes. Dioxane mineralization ceased after 7 days and was resumed by adding acetate (0.24 mM) as an auxiliary substrate to replenish NADH, a key coenzyme for the functioning of monoxygenases. Acetylene inactivation tests further corroborated the vital role of monooxygenases in dioxane degradation. This is the first report of the prevalence of oxygenase genes that are likely involved in dioxane degradation and suggests their usefulness as biomarkers of dioxane natural attenuation.
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Affiliation(s)
- Mengyan Li
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, United States
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123
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The microbial gene diversity along an elevation gradient of the Tibetan grassland. ISME JOURNAL 2013; 8:430-40. [PMID: 23985745 DOI: 10.1038/ismej.2013.146] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 07/15/2013] [Accepted: 07/17/2013] [Indexed: 11/08/2022]
Abstract
Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore the potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C-cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations, whereas ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by Canonical correspondence analysis, Mantel tests and the similarity tests that soil pH, temperature, NH4(+)-N and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. On the basis of these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N-cycling genes and consequently microbe-mediated soil N dynamics.
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124
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Yang Y, Xu M, He Z, Guo J, Sun G, Zhou J. Microbial electricity generation enhances decabromodiphenyl ether (BDE-209) degradation. PLoS One 2013; 8:e70686. [PMID: 23940625 PMCID: PMC3734261 DOI: 10.1371/journal.pone.0070686] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 06/21/2013] [Indexed: 01/31/2023] Open
Abstract
Due to environmental persistence and biotoxicity of polybrominated diphenyl ethers (PBDEs), it is urgent to develop potential technologies to remediate PBDEs. Introducing electrodes for microbial electricity generation to stimulate the anaerobic degradation of organic pollutants is highly promising for bioremediation. However, it is still not clear whether the degradation of PBDEs could be promoted by this strategy. In this study, we hypothesized that the degradation of PBDEs (e.g., BDE-209) would be enhanced under microbial electricity generation condition. The functional compositions and structures of microbial communities in closed-circuit microbial fuel cell (c-MFC) and open-circuit microbial fuel cell (o-MFC) systems for BDE-209 degradation were detected by a comprehensive functional gene array, GeoChip 4.0, and linked with PBDE degradations. The results indicated that distinctly different microbial community structures were formed between c-MFCs and o-MFCs, and that lower concentrations of BDE-209 and the resulting lower brominated PBDE products were detected in c-MFCs after 70-day performance. The diversity and abundance of a variety of functional genes in c-MFCs were significantly higher than those in o-MFCs. Most genes involved in chlorinated solvent reductive dechlorination, hydroxylation, methoxylation and aromatic hydrocarbon degradation were highly enriched in c-MFCs and significantly positively correlated with the removal of PBDEs. Various other microbial functional genes for carbon, nitrogen, phosphorus and sulfur cycling, as well as energy transformation process, were also significantly increased in c-MFCs. Together, these results suggest that PBDE degradation could be enhanced by introducing the electrodes for microbial electricity generation and by specifically stimulating microbial functional genes.
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Affiliation(s)
- Yonggang Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, China
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125
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Culture-Independent Molecular Tools for Soil and Rhizosphere Microbiology. DIVERSITY-BASEL 2013. [DOI: 10.3390/d5030581] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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126
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Fraile S, Jiménez JI, Gutiérrez C, de Lorenzo V. NanoPad: An integrated platform for bacterial production of camel nanobodies aimed at detecting environmental biomarkers. Proteomics 2013; 13:2766-75. [DOI: 10.1002/pmic.201300009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 02/11/2013] [Accepted: 03/26/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Sofía Fraile
- Systems Biology Program; Centro Nacional de Biotecnología-CSIC; Campus de Cantoblanco; Madrid Spain
| | - Jose I. Jiménez
- Systems Biology Program; Centro Nacional de Biotecnología-CSIC; Campus de Cantoblanco; Madrid Spain
| | - Carlos Gutiérrez
- Department of Animal Pathology; Faculty of Veterinary Science; Las Palmas University; Canary Islands Spain
| | - Víctor de Lorenzo
- Systems Biology Program; Centro Nacional de Biotecnología-CSIC; Campus de Cantoblanco; Madrid Spain
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127
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He Y, Xiao X, Wang F. Metagenome reveals potential microbial degradation of hydrocarbon coupled with sulfate reduction in an oil-immersed chimney from Guaymas Basin. Front Microbiol 2013; 4:148. [PMID: 23785357 PMCID: PMC3682177 DOI: 10.3389/fmicb.2013.00148] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 05/27/2013] [Indexed: 11/13/2022] Open
Abstract
Deep-sea hydrothermal vent chimneys contain a high diversity of microorganisms, yet the metabolic activity and the ecological functions of the microbial communities remain largely unexplored. In this study, a metagenomic approach was applied to characterize the metabolic potential in a Guaymas hydrothermal vent chimney and to conduct comparative genomic analysis among a variety of environments with sequenced metagenomes. Complete clustering of functional gene categories with a comparative metagenomic approach showed that this Guaymas chimney metagenome was clustered most closely with a chimney metagenome from Juan de Fuca. All chimney samples were enriched with genes involved in recombination and repair, chemotaxis and flagellar assembly, highlighting their roles in coping with the fluctuating extreme deep-sea environments. A high proportion of transposases was observed in all the metagenomes from deep-sea chimneys, supporting the previous hypothesis that horizontal gene transfer may be common in the deep-sea vent chimney biosphere. In the Guaymas chimney metagenome, thermophilic sulfate reducing microorganisms including bacteria and archaea were found predominant, and genes coding for the degradation of refractory organic compounds such as cellulose, lipid, pullullan, as well as a few hydrocarbons including toluene, ethylbenzene and o-xylene were identified. Therefore, this oil-immersed chimney supported a thermophilic microbial community capable of oxidizing a range of hydrocarbons that served as electron donors for sulphate reduction under anaerobic conditions.
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Affiliation(s)
- Ying He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology Shanghai, China ; State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University Shanghai, China
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128
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Lee YJ, van Nostrand JD, Tu Q, Lu Z, Cheng L, Yuan T, Deng Y, Carter MQ, He Z, Wu L, Yang F, Xu J, Zhou J. The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. ISME JOURNAL 2013; 7:1974-84. [PMID: 23765101 DOI: 10.1038/ismej.2013.88] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 04/10/2013] [Accepted: 04/20/2013] [Indexed: 12/21/2022]
Abstract
Pathogens present in the environment pose a serious threat to human, plant and animal health as evidenced by recent outbreaks. As many pathogens can survive and proliferate in the environment, it is important to understand their population dynamics and pathogenic potential in the environment. To assess pathogenic potential in diverse habitats, we developed a functional gene array, the PathoChip, constructed with key virulence genes related to major virulence factors, such as adherence, colonization, motility, invasion, toxin, immune evasion and iron uptake. A total of 3715 best probes were selected from 13 virulence factors, covering 7417 coding sequences from 1397 microbial species (2336 strains). The specificity of the PathoChip was computationally verified, and approximately 98% of the probes provided specificity at or below the species level, proving its excellent capability for the detection of target sequences with high discrimination power. We applied this array to community samples from soil, seawater and human saliva to assess the occurrence of virulence genes in natural environments. Both the abundance and diversity of virulence genes increased in stressed conditions compared with their corresponding controls, indicating a possible increase in abundance of pathogenic bacteria under environmental perturbations such as warming or oil spills. Statistical analyses showed that microbial communities harboring virulence genes were responsive to environmental perturbations, which drove changes in abundance and distribution of virulence genes. The PathoChip provides a useful tool to identify virulence genes in microbial populations, examine the dynamics of virulence genes in response to environmental perturbations and determine the pathogenic potential of microbial communities.
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Affiliation(s)
- Yong-Jin Lee
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
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129
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Strain/species-specific probe design for microbial identification microarrays. Appl Environ Microbiol 2013; 79:5085-8. [PMID: 23747703 DOI: 10.1128/aem.01124-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Specific identification of microorganisms in the environment is important but challenging, especially at the species/strain level. Here, we have developed a novel k-mer-based approach to select strain/species-specific probes for microbial identification with diagnostic microarrays. Application of this approach to human microbiome genomes showed that multiple (≥10 probes per strain) strain-specific 50-mer oligonucleotide probes could be designed for 2,012 of 3,421 bacterial strains of the human microbiome, and species-specific probes could be designed for most of the other strains. The method can also be used to select strain/species-specific probes for sequenced genomes in any environments, such as soil and water.
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130
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Callaghan AV. Metabolomic investigations of anaerobic hydrocarbon-impacted environments. Curr Opin Biotechnol 2013; 24:506-15. [DOI: 10.1016/j.copbio.2012.08.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 08/28/2012] [Accepted: 08/29/2012] [Indexed: 11/26/2022]
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131
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Cavalca L, Corsini A, Zaccheo P, Andreoni V, Muyzer G. Microbial transformations of arsenic: perspectives for biological removal of arsenic from water. Future Microbiol 2013; 8:753-68. [DOI: 10.2217/fmb.13.38] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Arsenic is present in many environments and is released by various natural processes and anthropogenic actions. Although arsenic is recognized to cause a wide range of adverse health effects in humans, diverse bacteria can metabolize it by detoxification and energy conservation reactions. This review highlights the current understanding of the ecology, biochemistry and genomics of these bacteria, and their potential application in the treatment of arsenic-polluted water.
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Affiliation(s)
- Lucia Cavalca
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milano, Italy.
| | - Anna Corsini
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milano, Italy
| | - Patrizia Zaccheo
- Dipartimento di Scienze Agrarie e Ambientali – Produzione, Territorio, Agroenergia (DiSAA), Università degli Studi di Milano, Milano, Italy
| | - Vincenza Andreoni
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milano, Italy
| | - Gerard Muyzer
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milano, Italy
- Institute for Biodiversity & Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
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132
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Xu M, He Z, Deng Y, Wu L, van Nostrand JD, Hobbie SE, Reich PB, Zhou J. Elevated CO₂ influences microbial carbon and nitrogen cycling. BMC Microbiol 2013; 13:124. [PMID: 23718284 PMCID: PMC3679978 DOI: 10.1186/1471-2180-13-124] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 05/24/2013] [Indexed: 11/10/2022] Open
Abstract
Background Elevated atmospheric CO2 (eCO2) has been shown to have significant effects on terrestrial ecosystems. However, little is known about its influence on the structure, composition, and functional potential of soil microbial communities, especially carbon (C) and nitrogen (N) cycling. A high-throughput functional gene array (GeoChip 3.0) was used to examine the composition, structure, and metabolic potential of soil microbial communities from a grassland field experiment after ten-year field exposure to ambient and elevated CO2 concentrations. Results Distinct microbial communities were established under eCO2. The abundance of three key C fixation genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), carbon monoxide dehydrogenase (CODH) and propionyl-CoA/acetyl-CoA carboxylase (PCC/ACC), significantly increased under eCO2, and so did some C degrading genes involved in starch, cellulose, and hemicellulose. Also, nifH and nirS involved in N cycling were significantly stimulated. In addition, based on variation partitioning analysis (VPA), the soil microbial community structure was largely shaped by direct and indirect eCO2-driven factors. Conclusions These findings suggest that the soil microbial community structure and their ecosystem functioning for C and N cycling were altered dramatically at eCO2. This study provides new insights into our understanding of the feedback response of soil microbial communities to elevated CO2 and global change.
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Affiliation(s)
- Meiying Xu
- State Key Laboratory of Applied Microbiology, Ministry-Guangdong Province Jointly Breeding Base, South China, Guangdong Institute of Microbiology, Guangzhou, China.
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133
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Kuang JL, Huang LN, Chen LX, Hua ZS, Li SJ, Hu M, Li JT, Shu WS. Contemporary environmental variation determines microbial diversity patterns in acid mine drainage. THE ISME JOURNAL 2013; 7:1038-50. [PMID: 23178673 PMCID: PMC3635239 DOI: 10.1038/ismej.2012.139] [Citation(s) in RCA: 228] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 10/01/2012] [Accepted: 10/01/2012] [Indexed: 11/17/2022]
Abstract
A wide array of microorganisms survive and thrive in extreme environments. However, we know little about the patterns of, and controls over, their large-scale ecological distribution. To this end, we have applied a bar-coded 16S rRNA pyrosequencing technology to explore the phylogenetic differentiation among 59 microbial communities from physically and geochemically diverse acid mine drainage (AMD) sites across Southeast China, revealing for the first time environmental variation as the major factor explaining community differences in these harsh environments. Our data showed that overall microbial diversity estimates, including phylogenetic diversity, phylotype richness and pairwise UniFrac distance, were largely correlated with pH conditions. Furthermore, multivariate regression tree analysis also identified solution pH as a strong predictor of relative lineage abundance. Betaproteobacteria, mostly affiliated with the 'Ferrovum' genus, were explicitly predominant in assemblages under moderate pH conditions, whereas Alphaproteobacteria, Euryarchaeota, Gammaproteobacteria and Nitrospira exhibited a strong adaptation to more acidic environments. Strikingly, such pH-dependent patterns could also be observed in a subsequent comprehensive analysis of the environmental distribution of acidophilic microorganisms based on 16S rRNA gene sequences previously retrieved from globally distributed AMD and associated environments, regardless of the long-distance isolation and the distinct substrate types. Collectively, our results suggest that microbial diversity patterns are better predicted by contemporary environmental variation rather than geographical distance in extreme AMD systems.
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Affiliation(s)
- Jia-Liang Kuang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Lin-Xing Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Zheng-Shuang Hua
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Sheng-Jin Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Min Hu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jin-Tian Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Wen-Sheng Shu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
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134
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Lin J, Hunkapiller AA, Layton AC, Chang YJ, Robbins KR. Response of Intestinal Microbiota to Antibiotic Growth Promoters in Chickens. Foodborne Pathog Dis 2013; 10:331-7. [DOI: 10.1089/fpd.2012.1348] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jun Lin
- Department of Animal Science, The University of Tennessee, Knoxville, Tennessee
| | | | - Alice C. Layton
- Center for Environmental Microbiology, The University of Tennessee, Knoxville, Tennessee
| | - Yun-Juan Chang
- Department of Animal Science, The University of Tennessee, Knoxville, Tennessee
| | - Kelly R. Robbins
- Department of Animal Science, The University of Tennessee, Knoxville, Tennessee
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135
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Sims A, Zhang Y, Gajaraj S, Brown PB, Hu Z. Toward the development of microbial indicators for wetland assessment. WATER RESEARCH 2013; 47:1711-1725. [PMID: 23384515 DOI: 10.1016/j.watres.2013.01.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 01/10/2013] [Accepted: 01/11/2013] [Indexed: 06/01/2023]
Abstract
Wetland assessment tools are being developed and employed in wetland monitoring and conservation based on physical, chemical and biological characterization. In wetland biological assessment, various ecological functions have been described by biological traits of an entire species pool that adapts to different types of wetland environments. Since microorganisms play a key role in wetland biogeochemical processes and respond quickly to environmental disturbances, this review paper describes the different macro indicators used in wetland biological monitoring and expands the potential use of microbial indicators in wetland assessment and management. Application of molecular microbial technologies paves the path to an integrated measure of wetland health conditions. For example, the ratio of ammonia-oxidizing archaeal and bacterial populations has been proposed to serve as a microbial indicator of wetland nutrient conditions. The microbial indicators coupled with physical, chemical and other biological parameters are vital to the development of multi-metric index for measuring wetland health conditions. Inclusion of microbial indicators will lead to a more comprehensive wetland assessment for wetland restoration and management practices.
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Affiliation(s)
- Atreyee Sims
- Department of Civil and Environmental Engineering, University of Missouri, E2509 Lafferre Hall, Columbia, MO 65211, USA
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136
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Zhang Y, Lu Z, Liu S, Yang Y, He Z, Ren Z, Zhou J, Li D. Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau. BMC Microbiol 2013; 13:72. [PMID: 23537200 PMCID: PMC3617080 DOI: 10.1186/1471-2180-13-72] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 03/20/2013] [Indexed: 12/02/2022] Open
Abstract
Background GeoChip 3.0, a microbial functional gene array, containing ~28,000 oligonucleotide probes and targeting ~57,000 sequences from 292 functional gene families, provided a powerful tool for researching microbial community structure in natural environments. The alpine meadow is a dominant plant community in the Qinghai-Tibetan plateau, hence it is important to profile the unique geographical flora and assess the response of the microbial communities to environmental variables. In this study, Geochip 3.0 was employed to understand the microbial functional gene diversity and structure, and metabolic potential and the major environmental factors in shaping microbial communities structure of alpine meadow soil in Qinghai-Tibetan Plateau. Results A total of 6143 microbial functional genes involved in carbon degradation, carbon fixation, methane oxidation and production, nitrogen cycling, phosphorus utilization, sulphur cycling, organic remediation, metal resistance, energy process and other category were detected in six soil samples and high diversity was observed. Interestingly, most of the detected genes associated with carbon degradation were derived from cultivated organisms. To identify major environmental factors in shaping microbial communities, Mantel test and CCA Statistical analyses were performed. The results indicated that altitude, C/N, pH and soil organic carbon were significantly (P < 0.05) correlated with the microbial functional structure and a total of 80.97% of the variation was significantly explained by altitude, C/N and pH. The C/N contributed 38.2% to microbial functional gene variation, which is in accordance with the hierarchical clustering of overall microbial functional genes. Conclusions High overall functional genes and phylogenetic diversity of the alpine meadow soil microbial communities existed in the Qinghai-Tibetan Plateau. Most of the genes involved in carbon degradation were derived from characterized microbial groups. Microbial composition and structures variation were significantly impacted by local environmental conditions, and soil C/N is the most important factor to impact the microbial structure in alpine meadow in Qinghai-Tibetan plateau.
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Affiliation(s)
- Yuguang Zhang
- Institute of Forestry Ecology, Environment and Protection, and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, the Chinese Academy of Forestry, Beijing 100091, China
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137
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Zhou J, Liu W, Deng Y, Jiang YH, Xue K, He Z, Van Nostrand JD, Wu L, Yang Y, Wang A. Stochastic assembly leads to alternative communities with distinct functions in a bioreactor microbial community. mBio 2013; 4:e00584-12. [PMID: 23462114 PMCID: PMC3585448 DOI: 10.1128/mbio.00584-12] [Citation(s) in RCA: 211] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 01/14/2013] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT The processes and mechanisms of community assembly and its relationships to community functioning are central issues in ecology. Both deterministic and stochastic factors play important roles in shaping community composition and structure, but the connection between community assembly and ecosystem functioning remains elusive, especially in microbial communities. Here, we used microbial electrolysis cell reactors as a model system to examine the roles of stochastic assembly in determining microbial community structure and functions. Under identical environmental conditions with the same source community, ecological drift (i.e., initial stochastic colonization) and subsequent biotic interactions created dramatically different communities with little overlap among 14 identical reactors, indicating that stochastic assembly played dominant roles in determining microbial community structure. Neutral community modeling analysis revealed that deterministic factors also played significant roles in shaping microbial community structure in these reactors. Most importantly, the newly formed communities differed substantially in community functions (e.g., H2 production), which showed strong linkages to community structure. This study is the first to demonstrate that stochastic assembly plays a dominant role in determining not only community structure but also ecosystem functions. Elucidating the links among community assembly, biodiversity, and ecosystem functioning is critical to understanding ecosystem functioning, biodiversity preservation, and ecosystem management. IMPORTANCE Microorganisms are the most diverse group of life known on earth. Although it is well documented that microbial natural biodiversity is extremely high, it is not clear why such high diversity is generated and maintained. Numerous studies have established the roles of niche-based deterministic factors (e.g., pH, temperature, and salt) in shaping microbial biodiversity, the importance of stochastic processes in generating microbial biodiversity is rarely appreciated. Moreover, while microorganisms mediate many ecosystem processes, the relationship between microbial diversity and ecosystem functioning remains largely elusive. Using a well-controlled laboratory system, this study provides empirical support for the dominant role of stochastic assembly in creating variations of microbial diversity and the first explicit evidence for the critical role of community assembly in influencing ecosystem functioning. The results presented in this study represent important contributions to the understanding of the mechanisms, especially stochastic processes, involved in shaping microbial biodiversity.
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Affiliation(s)
| | | | - Ye Deng
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics and University of Oklahoma, Norman, Oklahoma, USA
| | - Yi-Huei Jiang
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics and University of Oklahoma, Norman, Oklahoma, USA
| | - Kai Xue
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics and University of Oklahoma, Norman, Oklahoma, USA
| | - Zhili He
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics and University of Oklahoma, Norman, Oklahoma, USA
| | - Joy D. Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics and University of Oklahoma, Norman, Oklahoma, USA
| | - Liyou Wu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics and University of Oklahoma, Norman, Oklahoma, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
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138
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Li X, Deng Y, Li Q, Lu C, Wang J, Zhang H, Zhu J, Zhou J, He Z. Shifts of functional gene representation in wheat rhizosphere microbial communities under elevated ozone. THE ISME JOURNAL 2013; 7:660-71. [PMID: 23151639 PMCID: PMC3578556 DOI: 10.1038/ismej.2012.120] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 08/21/2012] [Accepted: 08/21/2012] [Indexed: 11/08/2022]
Abstract
Although the influence of ozone (O(3)) on plants has been well studied in agroecosystems, little is known about the effect of elevated O(3) (eO(3)) on soil microbial functional communities. Here, we used a comprehensive functional gene array (GeoChip 3.0) to investigate the functional composition, and structure of rhizosphere microbial communities of Yannong 19 (O(3)-sensitive) and Yangmai 16 (O(3)-relatively sensitive) wheat (Triticum aestivum L.) cultivars under eO(3). Compared with ambient O(3) (aO(3)), eO(3) led to an increase in soil pH and total carbon (C) percentages in grain and straw of wheat plants, and reduced grain weight and soil dissolved organic carbon (DOC). Based on GeoChip hybridization signal intensities, although the overall functional structure of rhizosphere microbial communities did not significantly change by eO(3) or cultivars, the results showed that the abundance of specific functional genes involved in C fixation and degradation, nitrogen (N) fixation, and sulfite reduction did significantly (P<0.05) alter in response to eO(3) and/or wheat cultivars. Also, Yannong 19 appeared to harbor microbial functional communities in the rhizosphere more sensitive in response to eO(3) than Yangmai 16. Additionally, canonical correspondence analysis suggested that the functional structure of microbial community involved in C cycling was largely shaped by soil and plant properties including pH, DOC, microbial biomass C, C/N ratio and grain weight. This study provides new insight into our understanding of the influence of eO(3) and wheat cultivars on soil microbial communities.
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Affiliation(s)
- Xinyu Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- Department of Botany and Microbiology, Institute for Environmental Genomics, The University of Oklahoma, Norman, OK, USA
| | - Ye Deng
- Department of Botany and Microbiology, Institute for Environmental Genomics, The University of Oklahoma, Norman, OK, USA
| | - Qi Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Caiyan Lu
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Jingjing Wang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Huiwen Zhang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, The Chinese Academy of Sciences, Nanjing, China
| | - Jizhong Zhou
- Department of Botany and Microbiology, Institute for Environmental Genomics, The University of Oklahoma, Norman, OK, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zhili He
- Department of Botany and Microbiology, Institute for Environmental Genomics, The University of Oklahoma, Norman, OK, USA
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139
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Yang Y, Wu L, Lin Q, Yuan M, Xu D, Yu H, Hu Y, Duan J, Li X, He Z, Xue K, van Nostrand J, Wang S, Zhou J. Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland. GLOBAL CHANGE BIOLOGY 2013; 19:637-648. [PMID: 23504798 DOI: 10.1111/gcb.12065] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 10/11/2012] [Indexed: 06/01/2023]
Abstract
Microbes play key roles in various biogeochemical processes, including carbon (C) and nitrogen (N) cycling. However, changes of microbial community at the functional gene level by livestock grazing, which is a global land-use activity, remain unclear. Here we use a functional gene array, GeoChip 4.0, to examine the effects of free livestock grazing on the microbial community at an experimental site of Tibet, a region known to be very sensitive to anthropogenic perturbation and global warming. Our results showed that grazing changed microbial community functional structure, in addition to aboveground vegetation and soil geochemical properties. Further statistical tests showed that microbial community functional structures were closely correlated with environmental variables, and variations in microbial community functional structures were mainly controlled by aboveground vegetation, soil C/N ratio, and NH4 (+) -N. In-depth examination of N cycling genes showed that abundances of N mineralization and nitrification genes were increased at grazed sites, but denitrification and N-reduction genes were decreased, suggesting that functional potentials of relevant bioprocesses were changed. Meanwhile, abundances of genes involved in methane cycling, C fixation, and degradation were decreased, which might be caused by vegetation removal and hence decrease in litter accumulation at grazed sites. In contrast, abundances of virulence, stress, and antibiotics resistance genes were increased because of the presence of livestock. In conclusion, these results indicated that soil microbial community functional structure was very sensitive to the impact of livestock grazing and revealed microbial functional potentials in regulating soil N and C cycling, supporting the necessity to include microbial components in evaluating the consequence of land-use and/or climate changes.
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Affiliation(s)
- Yunfeng Yang
- School of Environment, Tsinghua University, Beijing, China.
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140
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Starting Up Microbial Enhanced Oil Recovery. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 142:1-94. [DOI: 10.1007/10_2013_256] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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141
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Leis B, Angelov A, Liebl W. Screening and expression of genes from metagenomes. ADVANCES IN APPLIED MICROBIOLOGY 2013; 83:1-68. [PMID: 23651593 DOI: 10.1016/b978-0-12-407678-5.00001-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Microorganisms are the most abundant and widely spread organisms on earth. They colonize a huge variety of natural and anthropogenic environments, including very specialized ecological niches and even extreme habitats, which are made possible by the immense metabolic diversity and genetic adaptability of microbes. As most of the organisms from environmental samples defy cultivation, cultivation-independent metagenomics approaches have been applied since more than one decade to access and characterize the phylogenetic diversity in microbial communities as well as their metabolic potential and ecological functions. Thereby, metagenomics has fully emerged as an own scientific field for mining new biocatalysts for many industrially relevant processes in biotechnology and pharmaceutics. This review summarizes common metagenomic approaches ranging from sampling, isolation of nucleic acids, construction of metagenomic libraries and their evaluation. Sequence-based screenings implement next-generation sequencing platforms, microarrays or PCR-based methods, while function-based analysis covers heterologous expression of metagenomic libraries in diverse screening setups. Major constraints and advantages of each strategy are described. The importance of alternative host-vector systems is discussed, and in order to underline the role of phylogenetic and physiological distance from the gene donor and the expression host employed, a case study is presented that describes the screening of a genomic library from an extreme thermophilic bacterium in both Escherichia coli and Thermus thermophilus. Metatranscriptomics, metaproteomics and single-cell-based methods are expected to complement metagenomic screening efforts to identify novel biocatalysts from environmental samples.
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Affiliation(s)
- Benedikt Leis
- Lehrstuhl für Mikrobiologie, Technische Universität München, Freising, Bavaria, Germany
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142
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Abell GCJ, Robert SS, Frampton DMF, Volkman JK, Rizwi F, Csontos J, Bodrossy L. High-throughput analysis of ammonia oxidiser community composition via a novel, amoA-based functional gene array. PLoS One 2012; 7:e51542. [PMID: 23284709 PMCID: PMC3526613 DOI: 10.1371/journal.pone.0051542] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 11/08/2012] [Indexed: 11/17/2022] Open
Abstract
Advances in microbial ecology research are more often than not limited by the capabilities of available methodologies. Aerobic autotrophic nitrification is one of the most important and well studied microbiological processes in terrestrial and aquatic ecosystems. We have developed and validated a microbial diagnostic microarray based on the ammonia-monooxygenase subunit A (amoA) gene, enabling the in-depth analysis of the community structure of bacterial and archaeal ammonia oxidisers. The amoA microarray has been successfully applied to analyse nitrifier diversity in marine, estuarine, soil and wastewater treatment plant environments. The microarray has moderate costs for labour and consumables and enables the analysis of hundreds of environmental DNA or RNA samples per week per person. The array has been thoroughly validated with a range of individual and complex targets (amoA clones and environmental samples, respectively), combined with parallel analysis using traditional sequencing methods. The moderate cost and high throughput of the microarray makes it possible to adequately address broader questions of the ecology of microbial ammonia oxidation requiring high sample numbers and high resolution of the community composition.
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Affiliation(s)
- Guy C J Abell
- CSIRO Marine and Atmospheric Research and Wealth from Oceans National Research Flagship, Hobart, Tasmania, Australia
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143
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Functional gene differences in soil microbial communities from conventional, low-input, and organic farmlands. Appl Environ Microbiol 2012; 79:1284-92. [PMID: 23241975 DOI: 10.1128/aem.03393-12] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Various agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO(3)(-), NH(4)(+), available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO(3)(-) concentration and denitrification genes, NH(4)(+) concentration and ammonification genes, and N(2)O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes.
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144
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Microbial mechanisms mediating increased soil C storage under elevated atmospheric N deposition. Appl Environ Microbiol 2012; 79:1191-9. [PMID: 23220961 DOI: 10.1128/aem.03156-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Future rates of anthropogenic N deposition can slow the cycling and enhance the storage of C in forest ecosystems. In a northern hardwood forest ecosystem, experimental N deposition has decreased the extent of forest floor decay, leading to increased soil C storage. To better understand the microbial mechanisms mediating this response, we examined the functional genes derived from communities of actinobacteria and fungi present in the forest floor using GeoChip 4.0, a high-throughput functional-gene microarray. The compositions of functional genes derived from actinobacterial and fungal communities was significantly altered by experimental nitrogen deposition, with more heterogeneity detected in both groups. Experimental N deposition significantly decreased the richness and diversity of genes involved in the depolymerization of starch (∼12%), hemicellulose (∼16%), cellulose (∼16%), chitin (∼15%), and lignin (∼16%). The decrease in richness occurred across all taxonomic groupings detected by the microarray. The compositions of genes encoding oxidoreductases, which plausibly mediate lignin decay, were responsible for much of the observed dissimilarity between actinobacterial communities under ambient and experimental N deposition. This shift in composition and decrease in richness and diversity of genes encoding enzymes that mediate the decay process has occurred in parallel with a reduction in the extent of decay and accumulation of soil organic matter. Our observations indicate that compositional changes in actinobacterial and fungal communities elicited by experimental N deposition have functional implications for the cycling and storage of carbon in forest ecosystems.
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145
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Assessing the microbial community and functional genes in a vertical soil profile with long-term arsenic contamination. PLoS One 2012; 7:e50507. [PMID: 23226297 PMCID: PMC3511582 DOI: 10.1371/journal.pone.0050507] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 10/22/2012] [Indexed: 11/19/2022] Open
Abstract
Arsenic (As) contamination in soil and groundwater has become a serious problem to public health. To examine how microbial communities and functional genes respond to long-term arsenic contamination in vertical soil profile, soil samples were collected from the surface to the depth of 4 m (with an interval of 1 m) after 16-year arsenic downward infiltration. Integrating BioLog and functional gene microarray (GeoChip 3.0) technologies, we showed that microbial metabolic potential and diversity substantially decreased, and community structure was markedly distinct along the depth. Variations in microbial community functional genes, including genes responsible for As resistance, carbon and nitrogen cycling, phosphorus utilization and cytochrome c oxidases were detected. In particular, changes in community structures and activities were correlated with the biogeochemical features along the vertical soil profile when using the rbcL and nifH genes as biomarkers, evident for a gradual transition from aerobic to anaerobic lifestyles. The C/N showed marginally significant correlations with arsenic resistance (p = 0.069) and carbon cycling genes (p = 0.073), and significant correlation with nitrogen fixation genes (p = 0.024). The combination of C/N, NO3− and P showed the highest correlation (r = 0.779, p = 0.062) with the microbial community structure. Contradict to our hypotheses, a long-term arsenic downward infiltration was not the primary factor, while the spatial isolation and nutrient availability were the key forces in shaping the community structure. This study provides new insights about the heterogeneity of microbial community metabolic potential and future biodiversity preservation for arsenic bioremediation management.
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146
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Wang H, He Z, Lu Z, Zhou J, Van Nostrand JD, Xu X, Zhang Z. Genetic linkage of soil carbon pools and microbial functions in subtropical freshwater wetlands in response to experimental warming. Appl Environ Microbiol 2012; 78:7652-61. [PMID: 22923398 PMCID: PMC3485724 DOI: 10.1128/aem.01602-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Accepted: 08/16/2012] [Indexed: 11/20/2022] Open
Abstract
Rising climate temperatures in the future are predicted to accelerate the microbial decomposition of soil organic matter. A field microcosm experiment was carried out to examine the impact of soil warming in freshwater wetlands on different organic carbon (C) pools and associated microbial functional responses. GeoChip 4.0, a functional gene microarray, was used to determine microbial gene diversity and functional potential for C degradation. Experimental warming significantly increased soil pore water dissolved organic C and phosphorus (P) concentrations, leading to a higher potential for C emission and P export. Such losses of total organic C stored in soil could be traced back to the decomposition of recalcitrant organic C. Warming preferentially stimulated genes for degrading recalcitrant C over labile C. This was especially true for genes encoding cellobiase and mnp for cellulose and lignin degradation, respectively. We confirmed this with warming-enhanced polyphenol oxidase and peroxidase activities for recalcitrant C acquisition and greater increases in recalcitrant C use efficiency than in labile C use efficiency (average percentage increases of 48% versus 28%, respectively). The relative abundance of lignin-degrading genes increased by 15% under warming; meanwhile, soil fungi, as the primary decomposers of lignin, were greater in abundance by 27%. This work suggests that future warming may enhance the potential for accelerated fungal decomposition of lignin-like compounds, leading to greater microbially mediated C losses than previously estimated in freshwater wetlands.
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Affiliation(s)
- Hang Wang
- College of Environmental and Resource Science, Research Center of Water and Watershed Sustainability, Zhejiang University, Hangzhou, China
| | - Zhili He
- Institute for Environmental Genomics, Department of Botany, University of Oklahoma, Norman, Oklahoma, USA
| | - Zhenmei Lu
- Institute of Environmental Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Botany, University of Oklahoma, Norman, Oklahoma, USA
| | - Joy D. Van Nostrand
- Institute for Environmental Genomics, Department of Botany, University of Oklahoma, Norman, Oklahoma, USA
| | - Xinhua Xu
- College of Environmental and Resource Science, Research Center of Water and Watershed Sustainability, Zhejiang University, Hangzhou, China
| | - Zhijian Zhang
- College of Environmental and Resource Science, Research Center of Water and Watershed Sustainability, Zhejiang University, Hangzhou, China
- Department of Earth and Environmental Engineering, Columbia University, New York, New York, USA
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147
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Maphosa F, Lieten SH, Dinkla I, Stams AJ, Smidt H, Fennell DE. Ecogenomics of microbial communities in bioremediation of chlorinated contaminated sites. Front Microbiol 2012; 3:351. [PMID: 23060869 PMCID: PMC3462421 DOI: 10.3389/fmicb.2012.00351] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/12/2012] [Indexed: 11/29/2022] Open
Abstract
Organohalide compounds such as chloroethenes, chloroethanes, and polychlorinated benzenes are among the most significant pollutants in the world. These compounds are often found in contamination plumes with other pollutants such as solvents, pesticides, and petroleum derivatives. Microbial bioremediation of contaminated sites, has become commonplace whereby key processes involved in bioremediation include anaerobic degradation and transformation of these organohalides by organohalide respiring bacteria and also via hydrolytic, oxygenic, and reductive mechanisms by aerobic bacteria. Microbial ecogenomics has enabled us to not only study the microbiology involved in these complex processes but also develop tools to better monitor and assess these sites during bioremediation. Microbial ecogenomics have capitalized on recent advances in high-throughput and -output genomics technologies in combination with microbial physiology studies to address these complex bioremediation problems at a system level. Advances in environmental metagenomics, transcriptomics, and proteomics have provided insights into key genes and their regulation in the environment. They have also given us clues into microbial community structures, dynamics, and functions at contaminated sites. These techniques have not only aided us in understanding the lifestyles of common organohalide respirers, for example Dehalococcoides, Dehalobacter, and Desulfitobacterium, but also provided insights into novel and yet uncultured microorganisms found in organohalide respiring consortia. In this paper, we look at how ecogenomic studies have aided us to understand the microbial structures and functions in response to environmental stimuli such as the presence of chlorinated pollutants.
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Affiliation(s)
- Farai Maphosa
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| | | | | | - Alfons J. Stams
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
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148
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Uhlik O, Leewis MC, Strejcek M, Musilova L, Mackova M, Leigh MB, Macek T. Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation. Biotechnol Adv 2012; 31:154-65. [PMID: 23022353 DOI: 10.1016/j.biotechadv.2012.09.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 09/17/2012] [Accepted: 09/17/2012] [Indexed: 12/24/2022]
Abstract
Microbial biodegradation and biotransformation reactions are essential to most bioremediation processes, yet the specific organisms, genes, and mechanisms involved are often not well understood. Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylogenetic and metagenomic information within a community context by tracking isotopically labeled substances into phylogenetically and functionally informative biomarkers. SIP is thus applicable as a tool for the identification of active members of the microbial community and associated genes integral to the community functional potential, such as biodegradative processes. The rapid evolution of SIP over the last decade and integration with metagenomics provide researchers with a much deeper insight into potential biodegradative genes, processes, and applications, thereby enabling an improved mechanistic understanding that can facilitate advances in the field of bioremediation.
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Affiliation(s)
- Ondrej Uhlik
- Institute of Chemical Technology Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Technicka 3, 166 28 Prague, Czech Republic.
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149
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Nostrand JDV, He Z, Zhou J. Use of functional gene arrays for elucidating in situ biodegradation. Front Microbiol 2012; 3:339. [PMID: 23049526 PMCID: PMC3448134 DOI: 10.3389/fmicb.2012.00339] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/03/2012] [Indexed: 12/18/2022] Open
Abstract
Microarrays have revolutionized the study of microbiology by providing a high-throughput method for examining thousands of genes with a single test and overcome the limitations of many culture-independent approaches. Functional gene arrays (FGA) probe a wide range of genes involved in a variety of functions of interest to microbial ecology (e.g., carbon degradation, N fixation, metal resistance) from many different microorganisms, cultured and uncultured. The most comprehensive FGA to date is the GeoChip array, which targets tens of thousands of genes involved in the geochemical cycling of carbon, nitrogen, phosphorus, and sulfur, metal resistance and reduction, energy processing, antibiotic resistance and contaminant degradation as well as phylogenetic information (gyrB). Since the development of GeoChips, many studies have been performed using this FGA and have shown it to be a powerful tool for rapid, sensitive, and specific examination of microbial communities in a high-throughput manner. As such, the GeoChip is well-suited for linking geochemical processes with microbial community function and structure. This technology has been used successfully to examine microbial communities before, during, and after in situ bioremediation at a variety of contaminated sites. These studies have expanded our understanding of biodegradation and bioremediation processes and the associated microorganisms and environmental conditions responsible. This review provides an overview of FGA development with a focus on the GeoChip and highlights specific GeoChip studies involving in situ bioremediation.
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Affiliation(s)
- Joy D Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma Norman, OK, USA ; Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA
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150
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Carter MQ, Xue K, Brandl MT, Liu F, Wu L, Louie JW, Mandrell RE, Zhou J. Functional metagenomics of Escherichia coli O157:H7 interactions with spinach indigenous microorganisms during biofilm formation. PLoS One 2012; 7:e44186. [PMID: 22957052 PMCID: PMC3434221 DOI: 10.1371/journal.pone.0044186] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 07/30/2012] [Indexed: 11/18/2022] Open
Abstract
The increase in foodborne outbreaks worldwide attributed to fresh fruit and vegetables suggests that produce may serve as an ecological niche for enteric pathogens. Here we examined the interaction of E. coli O157:H7 (EcO157) with spinach leaf indigenous microorganisms during co-colonization and establishment of a mixed biofilm on a stainless steel surface. Stainless steel surface was selected to mimic the surface of produce-processing equipment, where retention of foodborne pathogens such as EcO157 could serve as a potential source for transmission. We observed a positive effect of spinach-associated microbes on the initial attachment of EcO157, but an antagonistic effect on the EcO157 population at the later stage of biofilm formation. Metagenomic analyses of the biofilm community with the GeoChip revealed an extremely diverse community (gene richness, 23409; Shannon-Weiner index H, 9.55). Presence of EcO157 in the mixed biofilm resulted in a significant decrease in the community α-diversity (t test, P<0.05), indicating a putative competition between the pathogen and indigenous spinach microbes. The decrease in the β-diversity of the EcO157-inoculated biofilm at 48 h (ANOVA, P<0.05) suggested a convergent shift in functional composition in response to EcO157 invasion. The success of EcO157 in the mixed biofilm is likely associated with its metabolic potential in utilizing spinach nutrients: the generation time of EcO157 in spinach lysates at 28°C is ∼ 38 min, which is comparable to that in rich broth. The significant decrease in the abundance of many genes involved in carbon, nitrogen, and phosphorus cycling in the EcO157-inoculated biofilms (t test, P<0.05) further support our conclusion that competition for essential macronutrients is likely the primary interaction between the EcO157 and indigenous spinach-biofilm species.
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Affiliation(s)
- Michelle Q Carter
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Albany, California, United States of America.
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