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Microbial Ecology Research

They control our planet, but are invisible to our naked eye. There are millions of different kinds, but they remain a mystery to us. The truth is, we would not be here without our microbial friends.

Microbial diversity is mind-blowing. One gram of soil has the potential to harbor over 10 billion bacterial and archaeal cells, representing thousands of species, yet only few of them are validly described to date (www.bacterio.cict.fr). Interdependent constituents of this vast microbiota play fundamental roles in organic matter decomposition, carbon sequestration, nitrogen cycling, and virtually every other chemical cycling process on our planet. They degrade and immobilize toxic compounds, control pests and diseases, promote plant growth, and ultimately shape our climate.

Our inadequate understanding of microbial communities and their metabolic activities limits our ability to manage our environment for sustainability. At the system level, microbial metabolism regulates ecosystem functionality and modulates resilience to internal and external stresses. In this light, intact and functional microbial communities are key for ecosystem health, which can be defined as the integrative ecological and socio-economic unit that is stable, viable, resilient, and sustainable by maintaining its characteristic composition, organization, and function over time. Since microbial processes regulate soil ecology and biogeochemistry, it is likely that microbial community structure, gene expression patterns, and metabolic activities can serve as indicators of ecosystem health. Such indicators might improve our ability to monitor ecosystems, to evaluate effects of management practices, and perhaps, to detect changes in nutrient and energy flow patterns before they have irreversible effects.

Traditional tools largely fail to adequately survey the microbiome of any given environment. Cultivation-dependent approaches are yet impracticable to capture the true extent of microbial diversity in any ecosystem as less than 1% of indigenous microorganisms are readily culturable. The development of molecular and, more recently, genomic tools have completely revolutionized our understanding of microbial life by giving access to uncultivable organisms. It is now possible to analyze environmental DNA in order to measure microbial populations and to determine the functional and metabolic potential of the soil community. It is possible to analyze RNA extracted from soil in order to measure the expression of genes and estimate metabolic activities. These approaches avoid the need to cultivate organisms and yield a deeper understanding of the composition and functioning of microbial communities than was previously possible. Analysis of structural genes common to all cellular life (i.e. ribosomal RNA genes) enables to target the majority of microbial life and to infer phylogenetic relationships among species. Analysis of functional genes, i.e. genes encoding for enzymes catalyzing specific processes in a metabolic pathway, enables to target communities that share the potential of carrying out this process.

Recent advances in next-generation sequencing technologies such as massively parallel pyrosequencing offer to capture the highly complex soil microbiota by screening for these genes with an adequate resolution. These tools simultaneously assess millions of gene copies in a large number of samples required for robust ecological studies, while providing access to their phylogenetic content essential for inference within the tree of life. In 1987, legendary Carl Woese did not see it coming when he stated “It is reasonable for a properly equipped laboratory in the future to sequence on the order of hundred 16S rRNAs per year”.  Nowadays, novel high-throughput sequencing platforms can sequence millions of gene copies in just a few hours. Given the novelty of these technologies, we are just at the beginning of seeing a substantial shift in our knowledge about the microbial life on our planet.



There are two common definitions for the term microbiome. First, the microbiome can be considered equivalent to the microbial biome, which refers to all microbes of a given system. Alternatively, the microbiome refers to the collective genome of all microbes in a given system. According to Joshua Lederberg who coined the term, I like to understand the microbiome as the ecological community of microorganisms that share an ecosystem, described by their genetic elements and their interactions with this ecosystem. Fact is, unraveling the microbiome of any given environment is extremely challenging and might start with understanding is phylogenetic structure. Or as Slava Epstein put it in 2008: “Can you study a part if you don't have any idea how significant this part is of a whole? My feeling is not really.”

The Earth Microbiome Projecthttp://www.earthmicrobiome.org/