Advances in Microbial Physiology: 55

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cszplayers.com/16.php When we were done sorting the trees, what we found in our analysis were genes that depict LUCA as an anaerobic autotroph that lived in a hot, gas-rich, metal-rich environment [47]. Its inferred energy metabolism was dependent upon H 2 and CO 2 , it could fix N 2 , it had a heavy dependence upon transition metals, its metabolism revealed an extremely prominent role for methyl groups, one electron transfers, radical reactions, and redox chemistry. Its carbon metabolism was based on the acetyl-CoA pathway, the oldest of the six known CO 2 fixation pathways.

It was capable of substrate level phosphorylation using the acetyl-CoA pathway and it could harness chemiosmotic potential. It had modified bases, mostly involving methylations, suggesting that not only LUCA, but also the genetic code arose in an environment where reactive methyl groups were abundant. That is probably because earlier studies had focused on genes that are universally distributed or nearly so.

Advances in Microbial Physiology, Volume 60

We also found that the trees of genes that trace to LUCA implicate clostridia which harbour many acetogens and methanogens as the earliest-branching forms of bacteria and archaea respectively. That fits with the functions of the genes we found, because acetogens and methanogens have carbon and energy metabolism that depends upon H 2 and CO 2 , they can fix N 2 , they have a heavy dependence upon transition metals, and their core physiology reveals an extremely prominent role for methyl groups, one electron transfers, radical reactions, and redox chemistry.

The results that we obtained fit very well with the idea that life arose in submarine hydrothermal vents and that the first cells were autotrophs that satisfy both their carbon and their energy needs from the reduction of CO 2 with electrons from H 2 [52] [53] [54]. Rather we found evidence linking LUCA to known forms of microbial physiology — acetogenesis and methanogenesis without cytochromes [58] — that are manifest among the strictest anaerobes [59] [60] , with evidence for a role of sulfur metabolism [61] , and with a very important role for Fe, Ni, Mo, and Co, transition metals that play a central role in the metabolism of anaerobic autotrophs today.

Our recent findings depart from phylogeny-based views of LUCA germane to the three domain tree and uncover connections between modern microbial physiology and geochemical environments on the early Earth.

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How can anything live without that? Transdomain LGT is both normal and natural, and all theories for the origin of cells, without exception, require abiotic syntheses, hence we do not see any fundamental problems in that regard. There was a time on the early Earth when there was no life and there was a time when there was life. If we filter out the effects of 4 billion years of LGT — which is, in essence, what we did — a picture of LUCA emerges that represents something that was half-alive, an intermediate in the transition from rocks and water on a young, barren planet to something that could scratch a living out of gasses and mineral salts.

For some reason, that sounds quite reasonable to us, others will surely disagree. It is very interesting that acetogens and methanogens inhabit the crust today [10] [62]. Let us presume, just for a moment, that the first bacteria and archaea were acetogens and methanogens respectively. On an uninhabited planet, they have no competitors, and life multiplies quickly given ample growth substrates. The founders of their respective domains would have bubbled off into the ocean bottom waters to be spread around by currents and eventually to be introduced back into hydrothermal systems in the crust, where they would have found the diet that they were raised on.

It is possible that some anaerobic autotrophs that live from the reduction of CO 2 with H 2 still inhabit the same niche in which life arose, albeit not the same rocks because during Earth history oceanic crust is constantly recycled into the mantle via subduction. In that sense, acetogens and methanogens really might provide a glimpse into the biology of the very first microbes on Earth, as some microbiologists familiar with the physiology of these organisms have been saying for some time [45] [61] [64].

Over four decades ago, biochemists thought that FeS clusters are ancient [65] and that acetogens and methanogens are ancient [45] , based on good intuition, common sense, and some straightforward principles of physiology. With the discovery of archaea, the three domain tree led to avenues of thought about early evolution that were guided by phylogeny rather than physiology. LGT conflates phylogeny.

But LGT does not conflate physiology, it just decouples it from phylogeny. If we return to the geochemical record, the first evidence for life we see is evidence for autotrophs [3] [4] , which is also what genomes recently uncovered about LUCA [47]. Thus, on the issue of autotrophs being ancient, geology and physiology converge. The version of LUCA that is obtained by taking all the data and simply removing the obvious LGT interfaces well with Earth history, with microbial physiology, and even with the new two domain tree.

It also bears out the predictions of some specific formulations the theory that life arose at submarine hydrothermal vents. Martin et al.

Advances in Microbial Physiology, Volume 44

Viewpoint: Microbial Cell, Vol. Abstract Genomes record their own history. References E. Gaidos, and A. Mojzsis, G. Arrhenius, K. McKeegan, T. Harrison, A. Nutman, and C. Friend, "Evidence for life on Earth before 3, million years ago", Nature , vol. Ueno, H. Yurimoto, H. Yoshioka, T. Komiya, and S. Maruyama, "Ion microprobe analysis of graphite from ca.

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Bell, P. Boehnke, T. Harrison, and W. Mao, "Potentially biogenic carbon preserved in a 4. Fischer, J. Hemp, and J. Rabus, S. Venceslau, L.

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Voordouw, J. Wall, and I. Marreiros, F. Calisto, P. Castro, A. Duarte, F. Sena, A. Silva, F. Sousa, M. Teixeira, P. Refojo, and M. Raymann, C. Brochier-Armanet, and S. Gribaldo, "The two-domain tree of life is linked to a new root for the Archaea", Proceedings of the National Academy of Sciences , vol.

Evans, D. Parks, G.

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Orphan, S. The first study on biogeographical variability hundreds to thousands of kilometres comprised a comprehensive phylogenetic analysis of bacteria associated with the distantly related sponges Theonella swinhoei from the western Pacific and Aplysina aerophoba from the Mediterranean Hentschel et al. Skip this list. How to write a great review. Lake, "Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences", Nature , vol. Thoms, P. The chemically stable C was then determined based on the differences in C remaining in the non-acid hydrolysable residues and the initial C content of the sample.

Chadwick, S. Robbins, V.

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Orphan, S. Golding, and G. Tyson, "Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics", Science , vol. Nelson-Sathi, F. Roettger, N. Thiergart, A. Janssen, D. Bryant, G. Landan, P. Siebers, J. McInerney, and W. Martin, "Origins of major archaeal clades correspond to gene acquisitions from bacteria", Nature , vol. Woese, O. Kandler, and M. Wheelis, "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

Ouzounis, V. Kunin, N. Darzentas, and L. Goldovsky, "A minimal estimate for the gene content of the last universal common ancestor—exobiology from a terrestrial perspective", Research in Microbiology , vol. Castresana, "Comparative genomics and bioenergetics. Nitschke, and M. Kannan, H. Li, B. Rubinstein, and A.

Mushegian, "Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life", Biology Direct , vol. Martin, and R. Cerff, "Prokaryotic features of a nucleus-encoded enzyme. Nelson-Sathi, T. Dagan, G. Landan, A. Janssen, M. Steel, J.

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McInerney, U. Deppenmeier, and W. Martin, "Acquisition of 1, eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea", Proceedings of the National Academy of Sciences , vol. Iwabe, K. Description Advances in Microbial Physiology is one of the most successful and prestigious series from Academic Press, an imprint of Elsevier. It publishes topical and important reviews, interpreting physiology to include all material that contributes to our understanding of how microorganisms and their component parts work.

First published in , it is now in its 54th volume.

Advances in Microbial Physiology: Volume 54

The Editors have always striven to interpret microbial physiology in the broadest context and have never restricted the contents to "traditional" views of whole cell physiology. Now edited by Professor Robert Poole, University of Sheffield, Advances in Microbial Physiology continues to be an influential and very well reviewed series. Product details Format Hardback pages Dimensions x x 24mm Other books in this series. Add to basket. Table of contents 1. Complex regulatory pathways coordinate cell cycle progression and development in Caulobacter crescentus Pamela J.

Brown, Gail G. Journal of molecular biology 3 , , Antimicrobial agents and chemotherapy 48 10 , , Journal of Antimicrobial Chemotherapy 70 7 , , Articles 1—20 Show more. Help Privacy Terms. Energetics of bacterial growth: balance of anabolic and catabolic reactions. Microbiology 2 , , Redundancy of aerobic respiratory chains in bacteria? Isolation and characterization of arsenate-reducing bacteria from arsenic-contaminated sites in New Zealand CR Anderson, GM Cook Current microbiology 48 5 , , The ISME journal 10 3 , , Unique flexibility in energy metabolism allows mycobacteria to combat starvation and hypoxia M Berney, GM Cook PloS one 5 1 , e , Advances in microbial physiology 55, ,