Microbial phylogeny

Martin W (2005) Woe is the tree of life. In Sapp J (ed) Microbial phylogeny and evolution concepts and controversies. Oxford University Press, New York Martin W, Muller M (1998) The hydrogen hypothesis for the first eukaryote. Nature 392 37-41... 

Sapp J (1994) Evolution by association a history of symbiosis. Oxford University Press, New York Sapp J (2002) Paul Buchner and hereditary symbiosis in insects. Int Microbiol 5 145-160 Sapp J (2003) Genesis the evolution of biology. Oxford University Press, New York Sapp J (2005a) The bacterium s place in nature. In Sapp J (ed) Microbial phylogeny and evolution concepts and controversies. Oxford University Press, New York, pp 1-52 Sapp J (2005b) The Prokaryote-eukaryote dichotomy meanings and mythology. Microbiol Mol Biol Rev 69 292-305... 

Behrens, S., Losekann, T., Pett-Padge, J., Weber, P. K., Ng, W. O., Stevenson, B. S., et al. (2008). Linking microbial phylogeny to metabolic activity at the single-cell level by using enhanced element labeHng-catalyzed reporter deposition fluorescence in situ hybridization (EL-FISH) and NanoSIMS. Appl. Environ. Microbiol. 74, 3143—3150. 

This model is also unable to explain microbial phylogeny. For example, the origins of thermophily, sulfur metabolism, and the differentiation of Bacteria and Archaea are not immediately apparent. There are some other specific constraints of clay-life theory and those who are interested can find the details in T. Fenchel et al., 1998 (see Further reading list). 

RNAs, has yielded the most complete understanding of microbial phylogeny (4,6). This, and a clear evolutionary perspective has served as the foundation for the explicit characterization of natural microbial communities (7,8,9,10). 

The use of ribosomal RNAs to infer evolutionary relationships is now well documented (4). These ubiquitous biopolymers are ideally suited to studies of microbial phylogeny and to studies in microbial ecology for the following reasons. 

Microbial Ecology and Microbial Phylogeny Common Ground... 

Rajendhran J, Gunasekaran P. Microbial phylogeny and diversity small subunit ribosomal RNA sequence analysis and beyond. Microbiol Res. 2011 166 99-110. 

L. F. Wu, M. A. Mandrand (1993) Microbial hydrogenases primary structure, classification, signatures and phylogeny. FEMS Microbiol. Rev., 104 243-270... 

Nealson KH, Saffarini D (1994) Iron and manganese in anaerobic respiration environmental significance, phylogeny, and regulation. Ann Rev Microbio 48 311-343 Nealson KH, Stahl DA (1997) Microorganisms and biogeochemical cycles what can we learn from layered microbial communities Rev Mineral 35 5-34... 

Symbiobacterium thermophilum is an uncultivable bacterium isolated from compost that depends on microbial commensalism. The 16S ribosomal DNA-based phylogeny suggests that this bacterium belongs to an unknown taxon in the Gram-positive bacterial cluster (Ueda et al., 2004), low G + C Gram-positive bacteria... 

Manefield, M., Wtuteley, A. S., Griffiths, R. I., and Bailey, M. J. (2002a). RNA stable isotope probing, a novel means of linking microbial community function to Phylogeny. Appl. Environ. Microbiol. 68, 5367-5373. 

Paulsen FT, Sliwinski MK, Saier MH Jr. Microbial genome analyses Global comparisons of transport capabilities based on phylogenies, bioenergetics and substrate specificities. J Mol Biol 1998 277 573-92. 

Standard rRNA molecular phylogeny (Woese, 1987 Barnes et al, 1996 Stetter, 1996 Pace, 1997) implies the antiquity of hyperthermophile organisms. Though there has been much dispute about the rRNA interpretation, there is some consensus that, whether or not it is the very most ancient, life around hot-water vents is certainly of great antiquity. The implication is that by mid-Archean, hyperthermophile habitats around hot vents were populated by microbial mats, and the waters around hot vents were occupied by free-swimming cells. Mesophile prephotosynthetic plankton probably existed in the open seas, and, distal to the thermophile life in the surroundings of vents, the mesophile habitats further from the hot springs were also occupied. 

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