Microorganisms are the foundation of the Earth's biosphere, and play integral and unique roles in ecosystem functions and biogeochemical cycling of carbon, nitrogen, sulfur, phosphorus, and various metals. They are the most diverse group of life presently known, inhabiting almost every imaginable environment on Earth. But they never live alone. Instead, they grow together to form complex communities and these communities are always undergoing dynamic structural change over space and time. Understanding the structure, functions, interactions, and population changes of microbial communities over time and space is critical for many aspects of our lives, including science discovery, biotechnology development, sustainable agriculture, energy security, environmental protection, and human health. For instance, sudden, dramatic changes of microbial communities from biological terrorist attacks, human epidemics, plant or animal diseases, or hazardous atmospheric alternations due to global climate change could represent a disaster to us or our environment. But, how do we know "who is there and what are they doing with whom and when" in these ecosystems?
Detection, identification, characterization, and quantification of microbial communities face several grand challenges. First, microbial communities are extremely diverse in familiar environments such as soil, water, food, and within our own bodies. One gram of a typical soil contains more than 5,000 (up to 40,000) microbial species. Characterizing such a vast diversity and understanding the mechanisms shaping it presents numerous obstacles. Second, the majority of these microorganisms (>99%) have not yet been cultured, which presents enormous difficulty for microbiologists to study microbial identity and community structure, activity, and dynamics. In addition, although microorganisms control, at least to some degree, various ecosystem processes, in most cases, we do not know what they are doing. Establishing mechanistic linkages between microbial diversity and ecosystem functioning is even more difficult. To address these challenges, revolutionary high-throughput detection technologies for analyzing microbial communities are needed.
To assess microbial community composition, structure, functions, and dynamics in natural settings, microbial detection tools must be: (i) simple, rapid, and robust; (ii) specific and sensitive with a broad comprehensive coverage of target microorganisms; (iii) quantitative and accurate with wide dynamic ranges; (iv) capable of detecting functions with high resolution; (v) capable of high throughput and in parallel analysis; (vi) capable of making reliable comparisons across different sites, experiments, laboratories and/or time periods; and (vii) cost-effective. No such accurate, comprehensive, high-throughput, and cost-effective approaches have been developed thus far to characterize microbial community functional structure and activity. Traditional culturing techniques have proven difficult and ultimately, provide an extremely limited view of microbial diversity and functions. Although conventional nucleic acid detection approaches, such as 16S rRNA gene-based cloning methods, denaturing gradient gel electrophoresis (DGGE), terminal-restriction fragment length polymorphism (T-RFLP), quantitative PCR, and in situ hybridization remain vital to studies of microbial communities, they do not easily meet these requirements. These individual gene-based molecular approaches are slow, laborious, or low-throughput, have low resolution, are not quantitative and/or provide very limited functional information. Thus, they are not suitable for high throughput and comprehensive functional characterization of microbial communities at the whole community level.
To address those challenges, GeoChips have been developed, which have unique features to answer the question 'who is there and what are they doing?'. First, the GeoChip is a DNA microarray containing oligonucleotide probes for genes involved in biogeochemical ing of carbon, nitrogen, phosphorus, sulfur and various metals, antibiotic resistance, metal resistance, organic contaminant degradation, bacterophages, stress responses, and energy production, as well as gyrB-based phylogenetic markers. Thus, the GeoChip is able to specifically, sensitively, and quantitatively detect hundreds of thousands of microbial functional genes/groups important to biogeochemical, ecological and environmental processes. Second, GeoChip is a generic tool in its ability to analyze microbial samples from any environmental source, such as soil, water, air, and human and animal bodies. Third, GeoChip provides easy operation since it can analyze microbial samples without any culturing required, and without prior knowledge of a sample's microbial composition. In addition, GeoChip is an unprecedented tool in its ability to rapidly and comprehensively identify the microbial community functional structure, activity and dynamics using both community DNA or RNA samples. Finally, one of the bottlenecks in using metagenomic tools for addressing environmental questions is the lack of appropriate standards for data comparison. The GeoChip allows comparable analysis of microarray data across different sites, experiments, laboratories and/or time periods by implementing universal standards.
GeoChips can be fabricated on a glass slide by spotting or in situ synthesis. Once DNA or RNA samples are obtained, numerous samples from one or more specific environments can be analyzed virtually on a daily basis. With the GeoChip pipeline, all results can be processed immediately after hybridization. Such rapid detection enables scientists to track functional processes over a short period of time, which was not previously possible.
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