GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis
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‐organi...
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Published in | Molecular ecology resources Vol. 14; no. 5; pp. 914 - 928 |
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Main Authors | , , , , , , , , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
England
Blackwell Publishing Ltd
01.09.2014
Wiley Subscription Services, Inc |
Subjects | |
Online Access | Get full text |
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Summary: | 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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Bibliography: | U. S. Department of Energy - No. DE-AC02-05CH11231 Office of Science, Office of Biological and Environmental Research (OBER) OBER Biological Systems Research - No. DE-SC0004601 U.S. National Science Foundation MacroSystems Biology program - No. NSF EF-1065844 ArticleID:MEN12239 Figure S1 Flowchart of GeoChip 4.0 design pipeline. Figure S2 Illustration of the layout of GeoChip 4.0 probes. Figure S3 The normalized average signal intensity of genes involved in carbon degradation process under warming and the control conditions. Figure S4 The normalized average signal intensity of genes involved in nitrogen cycling process under warming and the control. Figure S5 The normalized average signal intensity of genes involved in phosphorus cycling process under warming and the control. Figure S6 The normalized average signal intensity of genes related with bacteriophage under warming and the control. Oklahoma Applied Research Support (OARS) Oklahoma Center for the Advancement of Science and Technology (OCAST) - No. AR062-034; No. AR11-035 istex:34DD3CB6CD44D0EAADCC795CD77E36C559897D26 ark:/67375/WNG-1B89HQRX-W ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
ISSN: | 1755-098X 1755-0998 |
DOI: | 10.1111/1755-0998.12239 |