The New Science of Metagenomics Revealing the Secrets of Our Microbial Planet (2007) / Chapter Skim
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2 A New Light on Biology
2 A New Light on Biology
Pages 33-46
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From page 33... ...
Although there is much more to learn even about model organisms, such as E. coli, many individual pathways for nutrient cycling, gene regulation, and reproduction are understood at a satisfying level of precision. But these processes in the majority of microbes remain unknown and knowledge of the evolution and ecology of microbial communities lags far behind cellular microbiology.
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From page 34... ...
It is, however, the pervasiveness of lateral gene transfer between species that most profoundly challenges the notion that a single bacterial species has a single genome. Several natural processes -- transport by viruses, bacterial "mating," and the direct uptake of DNA from the environment -- carry genetic information from one species to another.
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From page 35... ...
With suitable experimental and computational methods, environmental gene sequences can be binned (statistically grouped) into provisional pangenomes on the basis of compositional characteristics and site of recovery.
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From page 36... ...
, have transformed bacterial classification in the field and in the clinical laboratory, they have not provided entirely satisfying or conclusive answers. Bacteria or archaea that carry similar or even identical rRNA genes can have deeply diverging genomic structure and content because of horizontal gene transfer.
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From page 37... ...
What we call bacteria does make a difference. less important than intelligent and flexible application of species concepts so that estimates of species richness or organisms' names imply a similar degree of relatedness across groups and can be of genuine utility in the development of ecological theory and environmental applications.
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From page 38... ...
How redundant or how modular are the contributions of individual microbial constituents to community function and to host biology? How should such constituents be defined given that mutualists, like pathogens, do not have a single genomic structure but rather have pangenomes with various degrees of openness to acquisition of genes from other microbes?
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From page 39... ...
CO 2 D Odds ratio C 0 5 10 15 20 25 coenzyme F420 COG1152 CO dehydrogenase, alpha subunit reduced coenzyme F420 methylene-H4MPT COG1614 CO dehydrogenase, beta subunit acetyl-CoA COG4059 H4MPT S-methyltransferase, E subunit 5-methyl-H4MPT F420-reducing hydrogenase , delta subunit 5-methyl-H 4 SPT COG1908 methyl-CoM COG1148 Heterodisulfide reductase , subunit A Methyl coenzyme M reductase, subunit C CoM -S-S-CoB COG4056 CoB METHANE CoM FIGURE 2-2 Some of the metabolism on our own distal gut (isoprenoid synthesis and methane formation) that is the responsibility of genes encoded in the genomes of our microbiota.
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From page 40... ...
For other purposes, it may be that what is important is the overall genetic content of an environment, not the number of species it contains. The degree to which genetic diversity and species composition affect the capabilities and stability of a microbial community is another fundamental conceptual question to which metagenomics can contribute.
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From page 41... ...
Proteorhodopsin genes show a distribution characteristic of lateral gene transfer. As with many other genes, environmental surveys reveal vast and hitherto unexpected 2-3.eps numbers and variations of gene sequences.
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From page 42... ...
For example, metagenomic datasets provide information about the structure, type, and organization of genes in individual genomes, about withinpopulation allelic variability, and about the patterns of organismal and gene occurrence. Reading metagenomic information may make it possible to infer emergent properties and dynamics of interacting genomes and the relationship of the interactions to the functionality of natural microbial ecosystems.
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From page 43... ...
If genetic instructions in part encode species interactions and community assembly, what are the "assembly rules"? Do founder effects influence the nature of spatially structured microbial ecosystems?
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From page 44... ...
Current understanding of evolution in general is built on eukaryotes, so a more broadly synthetic evolutionary theory is needed to reconstruct the history of microbial life, to model microbial ecology, and to integrate microbial with eukaryotic evolutionary theory. The microbial evolutionary model that dominated until recently emphasized clonality and periodic selection.
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From page 45... ...
Indeed, recombination may well be the principal generator of evolutionary novelty in such groups and has parallels to the role of sex in the evolution of animal species. But in other respects there are important differences between microbes and animals: the boundaries of cross-species homologous recombination may be much less distinct, and lateral gene transfer, almost by definition a transgressor of species boundaries, clearly is an important cause of divergence and adaptation in bacteria.
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From page 46... ...
WHAT ECOLOGICAL AND EVOLUTIONARY ROLES DO VIRUSES PLAY? Viruses are important not only as pathogens, but also as agents of lateral gene transfer and catalysts that generate tremendous genetic variation in their specific hosts.
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