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PMID: 17892477 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Review

Multivariate analyses in microbial ecology.

FEMS microbiology ecology ·Vol. 62 ·No. 2 ·2007-11-00 ·Pages 142-60

Ramette A

Abstract

Environmental microbiology is undergoing a dramatic revolution due to the increasing accumulation of biological information and contextual environmental parameters. This will not only enable a better identification of diversity patterns, but will also shed more light on the associated environmental conditions, spatial locations, and seasonal fluctuations, which could explain such patterns. Complex ecological questions may now be addressed using multivariate statistical analyses, which represent a vast potential of techniques that are still underexploited. Here, well-established exploratory and hypothesis-driven approaches are reviewed, so as to foster their addition to the microbial ecologist toolbox. Because such tools aim at reducing data set complexity, at identifying major patterns and putative causal factors, they will certainly find many applications in microbial ecology.

MeSH Terms
Data Interpretation, Statistical Ecosystem Environmental Microbiology Multivariate Analysis
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Ramette Alban
Microbial habitat group, Max Planck Institute for Marine Microbiology, Bremen, Germany. aramette@mpi-bremen.de
References (42)
42 references, click to expand
  1. Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil.
    Appl Environ Microbiol. 2000 Dec;66(12):5448-56 PMID: 11097926
  2. Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern.
    Environ Microbiol. 2002 Jun;4(6):338-48 PMID: 12071979
  3. Relationship between bacterial community composition and bottom-up versus top-down variables in four eutrophic shallow lakes.
    Appl Environ Microbiol. 2002 Oct;68(10):4740-50 PMID: 12324315
  4. Inability to find consistent bacterial biocontrol agents of Pythium aphanidermatum in cucumber using screens based on ecophysiological traits.
    Microb Ecol. 2003 Jan;45(1):72-87 PMID: 12469246
  5. Seasonal variation in microbial communities and organic malodor indicator compound concentrations in various types of swine manure storage systems.
    J Environ Qual. 2002 Nov-Dec;31(6):2074-85 PMID: 12469859
  6. Geographic barriers isolate endemic populations of hyperthermophilic archaea.
    Science. 2003 Aug 15;301(5635):976-8 PMID: 12881573
  7. Size and shape variation in the painted turtle. A principal component analysis.
    Growth. 1960 Dec;24:339-54 PMID: 13790416
  8. Environmental genome shotgun sequencing of the Sargasso Sea.
    Science. 2004 Apr 2;304(5667):66-74 PMID: 15001713
  9. Multivariate analyses of Burkholderia species in soil: effect of crop and land use history.
    Appl Environ Microbiol. 2004 Jul;70(7):4012-20 PMID: 15240277
  10. Fine-scale phylogenetic architecture of a complex bacterial community.
    Nature. 2004 Jul 29;430(6999):551-4 PMID: 15282603
  11. RAPD-PCR analysis of Staphylococcus aureus strains isolated from bovine and human hosts.
    Microbiol Res. 2004;159(3):245-55 PMID: 15462524
  12. A taxa-area relationship for bacteria.
    Nature. 2004 Dec 9;432(7018):750-3 PMID: 15592412
  13. Geographic and environmental sources of variation in lake bacterial community composition.
    Appl Environ Microbiol. 2005 Jan;71(1):227-39 PMID: 15640192
  14. Abundance of three bacterial populations in selected streams.
    Microb Ecol. 2005 Apr;49(3):461-7 PMID: 16003475
  15. Island size and bacterial diversity in an archipelago of engineering machines.
    Environ Microbiol. 2005 Aug;7(8):1220-6 PMID: 16011759
  16. A multivariate statistical approach to spatial representation of groundwater contamination using hydrochemistry and microbial community profiles.
    Environ Sci Technol. 2005 Oct 1;39(19):7551-9 PMID: 16245827
  17. Characterization of bacterial communities in four freshwater lakes differing in nutrient load and food web structure.
    FEMS Microbiol Ecol. 2005 Jul 1;53(2):205-20 PMID: 16329941
  18. Microbial biogeography: putting microorganisms on the map.
    Nat Rev Microbiol. 2006 Feb;4(2):102-12 PMID: 16415926
  19. Genetic diversity and pathogenicity of the grass pathogen Xanthomonas translucens pv. graminis.
    Syst Appl Microbiol. 2006 Mar;29(2):109-19 PMID: 16464692
  20. Dynamic of the genetic structure of bacterial and fungal communities at different developmental stages of Medicago truncatula Gaertn. cv. Jemalong line J5.
    New Phytol. 2006;170(1):165-75 PMID: 16539613
  21. Using pyrosequencing to shed light on deep mine microbial ecology.
    BMC Genomics. 2006 Mar 20;7:57 PMID: 16549033
  22. Diversity, composition, and geographical distribution of microbial communities in California salt marsh sediments.
    Appl Environ Microbiol. 2006 May;72(5):3357-66 PMID: 16672478
  23. Sequencing genomes from single cells by polymerase cloning.
    Nat Biotechnol. 2006 Jun;24(6):680-6 PMID: 16732271
  24. Metagenomic analysis of the human distal gut microbiome.
    Science. 2006 Jun 2;312(5778):1355-9 PMID: 16741115
  25. Spatial scaling of microbial biodiversity.
    Trends Ecol Evol. 2006 Sep;21(9):501-7 PMID: 16815589
  26. Comparison of virulence gene profiles of Escherichia coli strains isolated from healthy and diarrheic swine.
    Appl Environ Microbiol. 2006 Jul;72(7):4782-95 PMID: 16820472
  27. An assessment of the hypervariable domains of the 16S rRNA genes for their value in determining microbial community diversity: the paradox of traditional ecological indices.
    FEMS Microbiol Ecol. 2006 Sep;57(3):496-503 PMID: 16907762
  28. Variation in microbial community composition and culturability in the rhizosphere of Leucanthemopsis alpina (L.) Heywood and adjacent bare soil along an alpine chronosequence.
    Microb Ecol. 2006 Nov;52(4):679-92 PMID: 16909346
  29. Annually reoccurring bacterial communities are predictable from ocean conditions.
    Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):13104-9 PMID: 16938845
  30. How do we compare hundreds of bacterial genomes?
    Curr Opin Microbiol. 2006 Oct;9(5):499-504 PMID: 16942900
  31. Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices.
    Appl Environ Microbiol. 2006 Dec;72(12):7804-12 PMID: 17041161
  32. The bacterial species definition in the genomic era.
    Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29;361(1475):1929-40 PMID: 17062412
  33. Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution.
    Microb Ecol. 2007 Feb;53(2):197-207 PMID: 17106806
  34. Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem.
    Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2761-6 PMID: 17296935
  35. A molecular comparison of plumage and soil bacteria across biogeographic, ecological, and taxonomic scales.
    Microb Ecol. 2007 Jul;54(1):65-81 PMID: 17334855
  36. Bacterial community dynamics during the winter-spring transition in the North Sea.
    FEMS Microbiol Ecol. 2007 Mar;59(3):622-37 PMID: 17381518
  37. Coral microbial communities, zooxanthellae and mucus along gradients of seawater depth and coastal pollution.
    Environ Microbiol. 2007 May;9(5):1291-305 PMID: 17472641
  38. Synchrony in aquatic microbial community dynamics.
    ISME J. 2007 May;1(1):38-47 PMID: 18043612
  39. How well do multivariate data sets match? The advantages of a Procrustean superimposition approach over the Mantel test.
    Oecologia. 2001 Oct;129(2):169-178 PMID: 28547594
  40. Ecologically meaningful transformations for ordination of species data.
    Oecologia. 2001 Oct;129(2):271-280 PMID: 28547606
  41. The detection of disease clustering and a generalized regression approach.
    Cancer Res. 1967 Feb;27(2):209-20 PMID: 6018555
  42. Cluster analysis and display of genome-wide expression patterns.
    Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8 PMID: 9843981
Article Info
Journal
FEMS microbiology ecology
Abbr.
FEMS Microbiol Ecol
ISSN
0168-6496
Published
2007-11-00
Epub
2007-00-20
Pages
142-60
Language
English
Region
England
NLM ID
8901229
PMCID
PMC2121141
Subset
IM
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