Using genomics, metagenomics and other omics to assess valuable microbial ecosystem services and novel biotechnological applications

Abstract

Metagenomics and other "omics" are among the fastest advancing scientific tools, underpinning the recent and unprecedented access to genetic and functional information of entire communities of bacteria, virus and fungi. These remarkable advances contribute greatly to expanding our understanding of the diversity, ecology, evolution and functioning of the microbial world. There is a continuous and dynamic development of faster and cheaper sequencing and other "omics" techniques. This, combined with the development of analytical tools to deal with the exponentially increasing amount of data generated, allows access to microbial communities from a wide range of habitats and environments. The synergy between metagenomics and other ?omics? is paving the path to functional, integrative, and wider analyses including systems biology. All these new developments are increasingly contributing to the understanding of the mechanisms and processes of essential microbial ecosystem services, and to the emergence of innovative applications in many different areas.Ecosystems support life on Earth, and human existence relies heavily on ecosystem goods and services. Although only recently recognized, most of these services and goods are provided by microbial populations and communities. Many of the provisioning services (e.g. food and enzymes for industrial processes); regulating services (e.g. water quality, contamination alleviation and biological processes such as pollination and symbioses); and supporting services (e.g. nutrient cycling, agricultural production and biodiversity), are produced or mediated by microbes. Indeed, for example, many of the nitrogen cycle pathways are known to be driven by different microbial guilds. For instance, atmospheric nitrogen fixation for plant crops utilization is a microbial process, which raises agricultural productivity while decreasing the use of nitrogen fertilizers. These, when used in excess, cause water eutrophication, decrease water quality and increase the emission of the greenhouse gas N2O. Recent functional metagenomic studies have shown in freshwater relationships between the microbial nitrogen cycle and the microbial cycle of methane, another source of global warming, thus revealing the intricacy of microbial ecosystem services.A recently discovered ecosystem service performed by microbial communities is based on their ability to metabolize halogenated organic compounds. These compounds, are diverse and widespread in nature, and come from both anthropogenic and natural origins. Metagenomics has revealed a high diversity and abundance of genes encoding for halogenating and dehalogenating enzymes in soil. These discoveries are highly relevant to industrial biotechnologies and to the development of bioremediation applications.Metagenomics and other "omics" methods are also playing pivotal roles in the following areas: the development of novel antibiotics, by accessing in situ antimicrobial biosynthesis and resistance within microbiomes; the identification of new enzymes like esterases with novel properties of industrial interest; the optimization of biogas-producing microbial reactors; the understanding of the implication of microbiomes in metal corrosion processes; the prevention of microbial food spoilage, not only dependent on microbiome composition but also on the interactions between the microorganisms present naturally or as contaminants in food; the development of culture-independent surveillance of commercially available probiotics. These are only a few examples as ?omics? technologies are continuously opening new areas of research.There is virtually no limitations to the investigation of the microbial world using metagenomics, other "omics" and/or integrative approaches like systems biology. Articles in this Frontiers Topic are expected to contribute to a better understanding of microbial ecosystem services and to expand the horizon for finding and developing new and more efficient biotechnological applications.