Biology's next revolution

The interpretation of recent environmental genomics data exposes the far-reaching influence of horizontal gene transfer, and is changing our basic concepts of organism, species and evolution itself.Comment: Slightly expanded version of invited essay published in Nature. The most important addition is a complete set of references that could not be included in the published version due to space limitations and acknowledgment of the grant that supported our wor

IGB Outreach Annual Report 2018

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The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota

<p>Abstract</p> <p>Background</p> <p><it>Staphylothermus marinus </it>is an anaerobic, sulfur-reducing peptide fermenter of the archaeal phylum Crenarchaeota. It is the third heterotrophic, obligate sulfur reducing crenarchaeote to be sequenced and provides an opportunity for comparative analysis of the three genomes.</p> <p>Results</p> <p>The 1.57 Mbp genome of the hyperthermophilic crenarchaeote <it>Staphylothermus marinus </it>has been completely sequenced. The main energy generating pathways likely involve 2-oxoacid:ferredoxin oxidoreductases and ADP-forming acetyl-CoA synthases. <it>S. marinus </it>possesses several enzymes not present in other crenarchaeotes including a sodium ion-translocating decarboxylase likely to be involved in amino acid degradation. <it>S. marinus </it>lacks sulfur-reducing enzymes present in the other two sulfur-reducing crenarchaeotes that have been sequenced – <it>Thermofilum pendens </it>and <it>Hyperthermus butylicus</it>. Instead it has three operons similar to the <it>mbh </it>and <it>mbx </it>operons of <it>Pyrococcus furiosus</it>, which may play a role in sulfur reduction and/or hydrogen production. The two marine organisms, <it>S. marinus </it>and <it>H. butylicus</it>, possess more sodium-dependent transporters than <it>T. pendens </it>and use symporters for potassium uptake while <it>T. pendens </it>uses an ATP-dependent potassium transporter. <it>T. pendens </it>has adapted to a nutrient-rich environment while <it>H. butylicus </it>is adapted to a nutrient-poor environment, and <it>S. marinus </it>lies between these two extremes.</p> <p>Conclusion</p> <p>The three heterotrophic sulfur-reducing crenarchaeotes have adapted to their habitats, terrestrial vs. marine, via their transporter content, and they have also adapted to environments with differing levels of nutrients. Despite the fact that they all use sulfur as an electron acceptor, they are likely to have different pathways for sulfur reduction.</p

Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens

BACKGROUND:Methanomicrobiales is the least studied order of methanogens. While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens. METHODOLOGY/PRINCIPAL FINDINGS:In order to improve our understanding of this lineage, we have completely sequenced the genomes of two members of this order, Methanocorpusculum labreanum Z and Methanoculleus marisnigri JR1, and compared them with the genome of a third, Methanospirillum hungatei JF-1. Similar to Class I methanogens, Methanomicrobiales use a partial reductive citric acid cycle for 2-oxoglutarate biosynthesis, and they have the Eha energy-converting hydrogenase. In common with Methanosarcinales, Methanomicrobiales possess the Ech hydrogenase and at least some of them may couple formylmethanofuran formation and heterodisulfide reduction to transmembrane ion gradients. Uniquely, M. labreanum and M. hungatei contain hydrogenases similar to the Pyrococcus furiosus Mbh hydrogenase, and all three Methanomicrobiales have anti-sigma factor and anti-anti-sigma factor regulatory proteins not found in other methanogens. Phylogenetic analysis based on seven core proteins of methanogenesis and cofactor biosynthesis places the Methanomicrobiales equidistant from Class I methanogens and Methanosarcinales. CONCLUSIONS/SIGNIFICANCE:Our results indicate that Methanomicrobiales, rather than being similar to Class I methanogens or Methanomicrobiales, share some features of both and have some unique properties. We find that there are three distinct classes of methanogens: the Class I methanogens, the Methanomicrobiales (Class II), and the Methanosarcinales (Class III)

Astrophysics in 2005

We bring you, as usual, the Sun and Moon and stars, plus some galaxies and a new section on astrobiology. Some highlights are short (the newly identified class of gamma-ray bursts, and the Deep Impact on Comet 9P/ Tempel 1), some long (the age of the universe, which will be found to have the Earth at its center), and a few metonymic, for instance the term "down-sizing" to describe the evolution of star formation rates with redshift

How We Do, Don’t, and Should Look at Bacteria and Bacteriology

Microbiology today has a new-found wealth far greater than any it possessed before. The source of that wealth is the universal phylogenetic tree—the framework essential for understanding organismal relationships. The power that flows from phylogenetic ordering permeates the field. Microbiologists now accomplish with ease things that were previously impossible and approach bacteria in ways that 20 years ago were unthinkable. Microbial ecology is no longer the faux ecology it had been—when defining a niche in organismal terms was not an option. Today, the field rests on a par with plant and animal ecology and exceeds them in importance, for it is in the microbial realm that the base and fount of the global ecosystem lie. Studying microbial diversity used to be the equivalent of hunting through antique shops for curios—which resulted in a collection of species no more connected to one another than the items in a bower bird’s nest. Now all organisms sit on the well-ordered tips of branches on the universal phylogenetic tree (Woese 1987; Olsen et al. 1994), and the study of one, far from being an isolated adventure, can contribute to the study of all. An interest in bacterial evolution used to be perceived as metaphysical and worthless. Today, evolutionary relationships are the foundation and motive force behind a new and resurgent microbiology and hence biology as a whole

A New Biology for a New Century

Biology today is at a crossroads. The molecular paradigm, which so successfully guided the discipline throughout most of the 20th century, is no longer a reliable guide. Its vision of biology now realized, the molecular paradigm has run its course. Biology, therefore, has a choice to make, between the comfortable path of continuing to follow molecular biology's lead or the more invigorating one of seeking a new and inspiring vision of the living world, one that addresses the major problems in biology that 20th century biology, molecular biology, could not handle and, so, avoided. The former course, though highly productive, is certain to turn biology into an engineering discipline. The latter holds the promise of making biology an even more fundamental science, one that, along with physics, probes and defines the nature of reality. This is a choice between a biology that solely does society's bidding and a biology that is society's teacher