Where the bugs are: analyzing distributions of bacterial phyla by descriptor keyword search in the nucleotide database
Tóm tắt
The associations between bacteria and environment underlie their preferential interactions with given physical or chemical conditions. Microbial ecology aims at extracting conserved patterns of occurrence of bacterial taxa in relation to defined habitats and contexts. In the present report the NCBI nucleotide sequence database is used as dataset to extract information relative to the distribution of each of the 24 phyla of the bacteria superkingdom and of the Archaea. Over two and a half million records are filtered in their cross-association with each of 48 sets of keywords, defined to cover natural or artificial habitats, interactions with plant, animal or human hosts, and physical-chemical conditions. The results are processed showing: (a) how the different descriptors enrich or deplete the proportions at which the phyla occur in the total database; (b) in which order of abundance do the different keywords score for each phylum (preferred habitats or conditions), and to which extent are phyla clustered to few descriptors (specific) or spread across many (cosmopolitan); (c) which keywords individuate the communities ranking highest for diversity and evenness. A number of cues emerge from the results, contributing to sharpen the picture on the functional systematic diversity of prokaryotes. Suggestions are given for a future automated service dedicated to refining and updating such kind of analyses via public bioinformatic engines.
Tài liệu tham khảo
Horner-Devine MC, Carney KM, Bohannan BJ: An ecological perspective on bacterial biodiversity. Proc Biol Sci. 2004, 271: 113-122. 10.1098/rspb.2003.2549.
Horner-Devine MC, Bohannan BJ: Phylogenetic clustering and overdispersion in bacterial communities. Ecology. 2006, 87 (7 Suppl): S100-108.
Green J, Bohannan BJ: Spatial scaling of microbial biodiversity. Trends Ecol Evol. 2006, 21: 501-507. 10.1016/j.tree.2006.06.012.
Martiny JB, Bohannan BJ, Brown JH, Colwell RK, Fuhrman JA, Green JL, Horner-Devine MC, Kane M, Krumins JA, Kuske CR, Morin PJ, Naeem S, Øvreås L, Reysenbach A-L, Smith VH, Staley JT: Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol. 2006, 4: 102-112. 10.1038/nrmicro1341.
Lozupone CA, Knight R: Global patterns in bacterial diversity. Proc Natl Acad Sci USA. 2007, 104: 11436-11440. 10.1073/pnas.0611525104.
von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P: Quantitative phylogenetic assessment of microbial communities in diverse environments. Science. 2007, 315: 1126-1130. 10.1126/science.1133420.
Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R, Rohwer F, Jackson RB: Metagenomics and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol. 2007, 73: 7059-7066. 10.1128/AEM.00358-07.
Pignatelli M, Moya A, Tamames J: EnvDB, a database for describing the environmental distribution of prokaryotic taxa. Environ Microbiol Reports. 2009, 1: 191-197. 10.1111/j.1758-2229.2009.00030.x.
Tamames J, Abellán JJ, Pignatelli M, Camacho A, Moya A: Environmental distribution of prokaryotic taxa. BMC Microbiol. 2010, 22 (10): 85-
Demergasso C, Casamayor EO, Chong G, Galleguillos P, Escudero L, Pedrós-Alió C: Distribution of prokaryotic genetic diversity in athalassohaline lakes of the Atacama Desert, Northern Chile. FEMS Microbiol Ecol. 2004, 48: 57-69. 10.1016/j.femsec.2003.12.013.
Schloss PD, Handelsman J: Towards a census of bacteria in soil. PLoS Comput Biol. 2006, 2 (7): e92-10.1371/journal.pcbi.0020092.
Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ: Microbial diversity in the deep sea and the unexplored "rare biosphere". Proc Natl Acad Sci USA. 2006, 103: 15-20. 10.1073/pnas.0509693102.
Kuczynski J, Costello EK, Nemergut DR, Zaneveld J, Lauber CL, Knights D, Koren O, Fierer N, Kelley ST, Ley RE, Gordon JI, Knight R: Direct sequencing of the human microbiome readily reveals community differences. Genome Biology. 2010, 11: 210-10.1186/gb-2010-11-5-210.
Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS: Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol. 2003, 69: 1800-1809. 10.1128/AEM.69.3.1800-1809.2003.
Hamady M, Lozupone C, Knight R: Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. The ISME Journal. 2010, 4: 17-27. 10.1038/ismej.2009.97.
Kemp PF, Aller JY: Estimating prokaryotic diversity: when are 16S rDNA libraries large enough?. Limnol Oceanogr Methods. 2004, 2: 114-125.
Curtis TP, Sloan WT: Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Current Opinion in Microbiology. 2004, 7: 221-226. 10.1016/j.mib.2004.04.010.
Curtis TP, Wallbridge NC, Sloan W: Theory, community assembly, diversity and evolution in the microbial world. Speciation and Patterns of Diversity. Edited by: Butlin R, Bridle J. 2008, Cambridge University Press, 59-76.
Quince C, Curtis TP, Sloan WT: The rational exploration of microbial diversity. ISME Journal. 2008, 2: 997-1006. 10.1038/ismej.2008.69.
Roesch LF, Fulthrope RR, Riva A, Casella G, Hadwin AKM, Kent AD, Daroub SM, Camargo FAO, Farmerie WG, Triplett EW: Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 2007, 1: 283-290.
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Paulsen IT, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson JD, Hoffman J, Parsons R, Baden-Tillson H, Pfannkock C, Rogers Y-H, Smith HO: Environmental whole genome shotgun sequencing: the Sargasso Sea. Science. 2004, 304: 66-74. 10.1126/science.1093857.
Magurran AE: Ecological Diversity and Its Measurement. 1988, Princeton University Press. Princeton NJ
Baas-Becking L: Geobiologie of Inleiding Tot de Milieukunde. 1934, Van Stockkum & Zoon. The Hague