GeoChip 4: a functional gene‐array‐based high‐throughput environmental technology for microbial community analysis

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.

Aridity threshold in controlling ecosystem nitrogen cycling in arid and semi-arid grasslands

“…GeoChip 5.0S was manufactured by Agilent (Agilent Technologies Inc., Santa Clara, CA) in the 8 Â 60 K format. The purified soil DNAs (0.6 mg) was used for GeoChip 5.0S hybridization, which was labelled with Cy 3 as described previously [48][49][50] . Before hybridization, the labelled DNA was re-suspended and hybridized with GeoChip 5.0S.…”

“…The images data were extracted by Agilent Feature Extraction program. The microarray data were preprocessed for subsequent analysis as described previously [48][49][50] in terms of poor and outlying spot removal, background subtraction, normalization and sample.…”

Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships

“…GeoChip 4.0 analysis was performed as described previously (He et al, 2010;Tu et al, 2014). Briefly, DNA samples were labelled with the fluorescent dye Cy-5 by a random priming method (Tu et al, 2014;Su et al, 2015), followed by purification with a QIA Quick Purification Kit (Qiagen, Valencia, CA, USA). Dye incorporation was measured by a Nano-Drop ND--1000 spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA), and DNA was dried using a SpeedVac (ThermoSavant) at 45°C for 45 min.…”

Elevated temperature alters proteomic responses of individual organisms within a biofilm community

“…Many microbial community studies have evaluated the effect of warming on overall community structure and on specific metabolic processes such as respiration (for example, Zogg et al, 1997;Finke and Jørgensen, 2008;Rose et al, 2009;Yergeau et al, 2012;Lindh et al, 2013;Wu et al, 2013;von Scheibner et al, 2014). Far fewer studies have comprehensively assessed functional responses across the entire community (for example, using 'omic' approaches (Luo et al, 2013;Toseland et al, 2013) or functional gene arrays (Yergeau et al, 2012;Tu et al, 2014)). …”