The National Academies Press

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1 Why Metagenomics?
Pages 12-32

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From page 12... ... These functions are conducted within complex communities -- intricate, balanced, and integrated entities that adapt swiftly and flexibly to environmental change. But historically, the study of microbes has focused on single species in pure culture, so understanding of these complex communities lags behind understanding of their individual members. Read the entire page →
From page 13... ... Thus, almost all knowledge about microbes is largely "laboratory knowledge," attained in the unusual and unnatural circumstances of growing them optimally in artificial media in pure culture without ecological context. The science of metagenomics, only a few years old, will make it possible to investigate microbes in their natural environments, the complex communities in which they normally live. Read the entire page →
From page 14... ... Although in its current early implementation (and for the purposes of this report) metagenomics focuses on non-eukaryotic microbes (see Box 1-2) Read the entire page →
From page 15... ... Microbes Modulate and Maintain the Atmosphere Carbon is the most abundant chemical element in all living things, including humans (excluding the hydrogen and oxygen in the water, which makes up the bulk of our weight) Read the entire page →
From page 16... ... . Chemical transformations mediated by marine microbes play a critical role in global biogeochemical cycles (see Figure 1-1) Read the entire page →
From page 17... ... In essence, the combined activities of microbial communities affect the chemistry of the entire ocean and maintain the habitability of the entire planet. Hidden within the population dynamics of these complex communities are fundamental lessons of environmental response and sensing, species and community interactions, gene regulation, and genomic plasticity and evolution. Read the entire page →
From page 18... ... . Microbes Support Plant Growth and Suppress Plant Disease The microbial communities on and around plants play a central role in the health and productivity of crops. Read the entire page →
From page 19... ... INVISIBLE COMMUNITIES: GLOBAL IMPACT Modulating the atmosphere, keeping humans and plants healthy, and cleaning up leaking gasoline are just a few examples of the many things that microbial communities can do. The combined activities of microbial communities shape the face of the biosphere on a global scale. Read the entire page →
From page 20... ... Larger organisms play key roles, too, of course: about half of all carbon is fixed and half of all oxygen produced by trees, grasses, and other macroscopic plant life. But these larger organisms also depend on microbes; for example, plants depend on the nitrogen fixation carried out by symbiotic microbes in the roots of legumes and other plants that form symbiotic associations. Read the entire page →
From page 21... ... Never before have such questions had such urgency. UNDERSTANDING MICROBIAL COMMUNITIES Given that the microbial collective profoundly influences geochemical and greenhouse-gas cycles, as well as climate and environmental change, it is relevant to ask how well we understand microbial communities. Read the entire page →
From page 22... ... , pure cultures became a gold standard for experimentation and the basis of almost all recent knowledge of medical bacteriology, biochemistry, and molecular biology. In the pure-culture paradigm, the presence of multiple species in the same culture medium means "contamination," and species whose growth requires metabolic products of other species are impossible to detect, study, or even name. Read the entire page →
From page 23... ... The study of microbes in culture will continue to be important, but it falls short of telling us about environmental processes, biofilms, microbial bucket brigades of energy and matter flux, and the future trajectory of biogeochemical cycles. Understanding microbial communities will require that the traditional techniques of pure culture be supplemented with new approaches. Read the entire page →
From page 24... ... Soon, there will be thousands of sequenced microbial genomes. If all microbial species were culturable and if such species were easily defined and limited in number (even a number in the tens of thousands) Read the entire page →
From page 25... ... Indeed, two recent successes are the cultivation (and genome sequencing) of Pelagibacter ubique, a bacterium representative of one of the most common microbial phylogenetic groups found in the open ocean, and the isolation of several acidobacteria, the most abundant organisms in soil (Sait et al. Read the entire page →
From page 26... ... THE NEW SCIENCE OF METAGENOMICS BOX 1-4 Ribosomal RNA and the Tree of Life Ribosomal RNAs (rRNAs) are essential structural and functional components of ribosomes, the cellular factories on which proteins are made according to the information encoded in DNA. Read the entire page →
From page 27... ... But also it reflects genomic diversity within what scientists had been calling species. Almost all phylotyping surveys of almost all environments yield not a single phylotype for each likely microbial species contributor to community dynamics, but dozens or hundreds of very close but unquestionably nonidentical phylotypes that form microdiverse clusters (see Figure 1-2) Read the entire page →
From page 28... ... THE NEW SCIENCE OF METAGENOMICS FIGURE 1-2 Microdiversity of environmental 16S rRNA sequences. PCR-amplified 16S rRNA gene sequences from an environmental DNA sample, showing a pattern of clustering often interpreted to be indicative of species divisions. Read the entire page →
From page 29... ... ." All this means that no single collection of genes can be said to be "the V. splendidus genome" or "the E. coli genome" or indeed the genome of almost any designated bacterial or archaeal species, and no amount of complete genome sequencing will be enough to map the genomic diversity of the microbial world. Perhaps the biggest challenge faced by microbial ecology as a science today is to understand the ecological significance of such phylotypic microdiversity and genomic variability, and this challenge cannot be met with a traditional genomic approach. Read the entire page →
From page 30... ... genomics FIGURE 1-3 How metagenomics differs from microbial genomics. Image provided by W Read the entire page →
From page 31... ... Metagenomics provides a means for studying microbial communities on their own "turf." Complex ecological interactions -- including lateral gene transfer, phage-host dynamics, and metabolic complementation -- can now be studied with the lens of metagenomics. Community composition, function, and dynamics can now be measured and modeled in the environment with universal microbial-community genomic approaches. Read the entire page →
From page 32... ... and food safety (monitoring and early detection of dangerous microbial contaminants) and the development of management practices that maximize the beneficial attributes of microbial communities in and around domestic plants and animals. Read the entire page →

From page 12...

... These functions are conducted within complex communities -- intricate, balanced, and integrated entities that adapt swiftly and flexibly to environmental change. But historically, the study of microbes has focused on single species in pure culture, so understanding of these complex communities lags behind understanding of their individual members.

1 Why Metagenomics? Pages 12-32

1 Why Metagenomics?
Pages 12-32