Print PageMicroorganisms constitute the most abundant life forms on Earth’s biosphere, and play integral and unique roles in ecosystem functioning, such as biogeochemical cycling of carbon (C), nitrogen (N), sulfur (S), phosphorous (P) and various metals. Understanding the functional diversity, composition, structure, and interactions of microbial communities across different spatial and temporal scales is a critical issue in microbial community ecology. However, analyzing microbial community structure and linking community structure to functions are very difficult. Functional gene arrays such as GeoChip have been demonstrated to be a powerful tool for understanding microbial community composition, structure, function, and dynamics and linking microbial communities with environmental factors and ecosystem functioning.
Results/Conclusions
Based on previous GeoChips, we have developed GeoChip 4.0, a more comprehensive GeoChip to facilitate our analysis of microbial communities from a variety of habitats. GeoChip 4.0 contains more than 135,000 probes from 152,000 genes involved in C, N, S and P cycling, organic contaminant degradation, metal resistance, antibiotic resistance, stress responses, metal resistance, virulence, bacterial phage-mediated lysis, and soil beneficial microorganisms. Experimental evaluation of specificity, sensitivity and quantification using artificial and environmental samples showed that GeoChip hybridization is highly specific, sensitive and quantitative. We have successfully used GeoChips to analyze samples from a variety of environments, including bioreactors, soils, marine sediments, hydrothermal vents, ocean crust, and groundwater. Our results indicate that GeoChip is very valuable for monitoring microbial community dynamics and assessing metabolic functions of microbial communities. For instance, GeoChip has been used to analyze the responses of microbial communities to elevated CO2 and climate warming and many novel critical insights in terms of the feedback responses of ecosystems to climate change were obtained. In addition, based on GeoChip data, novel molecular ecological network framework is developed. Our results indicated that the topological structure of the functional molecular ecological networks is distinctly different between elevated and ambient CO2, at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that elevated CO2 dramatically altered the network interactions among different microbial functional genes/populations. Such shift in network structure is also significantly correlated with soil geochemical variables. To our knowledge, this is the first study to demonstrate the changes in network interactions of microbial communities in response to elevated CO2.
