Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, 73019, USA.
Mol Ecol Resour. 2014 Sep;14(5):914-28. doi: 10.1111/1755-0998.12239. Epub 2014 Mar 14.
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.
微生物在地球生物圈的许多重要生物地球化学过程中发挥着关键作用。然而，由于大多数微生物具有极其多样且常常无法培养的特性，理解和描述微生物群落的功能能力仍然具有挑战性。在这项研究中，我们开发了一种新的功能基因芯片 GeoChip 4，用于分析微生物群落的功能多样性、组成、结构、代谢潜力/活性和动态。GeoChip 4 包含大约 82000 个探针，涵盖了与微生物碳 (C)、氮 (N)、硫 (S) 和磷 (P) 循环、能量代谢、抗生素抗性、金属抗性/还原、有机修复、应激反应、噬菌体和毒力相关的 410 个功能基因家族的 141995 个编码序列。共靶向了 173 种古菌、4138 种细菌、404 种真核生物和 252 种病毒株，提供了分析包括所有四个领域的微生物目标功能基因家族的能力。使用不同量 DNA 的实验评估表明，只需 500ng 环境 DNA 即可进行良好的杂交，并且检测到的信号强度与使用的 DNA 量密切相关。然后，GeoChip 4 被应用于研究俄克拉荷马中部一个地点的长期变暖对土壤微生物群落的影响，结果表明，微生物群落通过富集碳降解、养分循环（氮和磷）和应激反应基因家族来响应长期变暖。据我们所知，GeoChip 4 是用于微生物群落分析的最全面的功能基因芯片。
