Phylogenetic clustering of soil microbial communities by 16S rRNA but Not 16S rRNA genes

Applied and Environmental Microbiology

Volumn 78, Issue 7, 2012, Pages 2459-2461

  DeAngelis, Kristen M ^a,b   Firestone, Mary K ^b,c  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ARCHAEON; BACTERIUM; BIODIVERSITY; CLASSIFICATION; CLUSTER ANALYSIS; DNA MICROARRAY; ECOSYSTEM; GENETICS; MICROBIOLOGY; NOTE; OXIDATION REDUCTION REACTION; PHYLOGENY; RNA GENE; TREE; TROPIC CLIMATE;

ARCHAEA; BACTERIA; BIODIVERSITY; CLUSTER ANALYSIS; ECOSYSTEM; GENES, RRNA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OXIDATION-REDUCTION; PHYLOGENY; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY; TREES; TROPICAL CLIMATE;

ARCHAEA; BACTERIA (MICROORGANISMS);

EID: 84861177989     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.07547-11     Document Type: Note

References (27)

1. Binder BJ, Liu YC. 1998. Growth rate regulation of rRNA content of a marine Synechococcus (Cyanobacterium) strain. Appl. Environ. Microbiol. 64:3346 -3351.
2. Brodie EL, et al. 2007. Urban aerosols harbor diverse and dynamic bacterial populations. Proc. Natl. Acad. Sci. U. S. A. 104:299 -304.
3. Bryant JA, et al. 2008. Microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proc. Natl. Acad. Sci. U. S. A. 105:11505-11511.
4. Cavender-Bares J, Kozak KH, Fine PVA, Kembel SW. 2009. The merging of community ecology and phylogenetic biology. Ecol. Lett. 12:693-715.
5. DeAngelis KM, Silver WL, Thompson AW, Firestone MK. 2010. Microbial communities acclimate to recurring changes in soil redox potential status. Environ. Microbiol. 12:3137-3149.
6. De Nobili M, Contin M, Mondini C, Brookes P. 2001. Soil microbial biomass is triggered into activity by trace amounts of substrate. Soil Biol. Biochem. 33:1163-1170.
7. Dortch Q, Roberts TL, Clayton J, Jr, Ahmed S. 1983. RNA/DNA ratios and DNA concentrations as indicators of growth rate and biomass in planktonic marine organisms. Mar. Ecol. Prog. Ser. 13:61-71.
8. Reference deleted
9. Reference deleted
10. Griffiths RI, Whiteley AS, O'Donnell AG, Bailey MJ. 2000. Rapid method for coextraction ofDNAandRNAfrom natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl. Environ. Microbiol. 66:5488 -5491.
11. Horner-Devine MC, Bohannan BJM. 2006. Phylogenetic clustering and overdispersion in bacterial communities. Ecology 87:100 -108.
12. Horner-Devine MC, et al. 2007. A comparison of taxon co-occurrence patterns for macro- and microorganisms. Ecology 88:1345-1353.
13. Kerkhof L, Kemp P. 1999. Small ribosomal RNA content in marine Proteobacteria during non-steady-state growth. FEMS Microbiol. Ecol. 30:253-260.
14. Lennon JT, Jones SE. 2011. Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat. Rev. Microbiol. 9:119 -130.
15. Reference deleted
16. Manini E, Danovaro R. 2006. Synoptic determination of living/dead and active/dormant bacterial fractions in marine sediments. FEMS Microbiol. Ecol. 55:416-423.
17. Reference deleted
18. Polz MF, Cavanaugh CM. 1998. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64:3724 -3730.
19. Poulsen L, Ballard G, Stahl D. 1993. Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl. Environ. Microbiol. 59:1354 -1360.
20. Rastogi R, Wu M, DasGupta I, Fox G. 2009. Visualization of ribosomal RNA operon copy number distribution. BMC Microbiol. 9:208.
21. Steinberger R, Holden P. 2005. Extracellular DNA in single- and multiple-species unsaturated biofilms. Appl. Environ. Microbiol. 71:5404.
22. Stevenson BS, Schmidt TM. 2004. Life history implications of rRNA gene copy number in Escherichia coli. Appl. Environ. Microbiol. 70:6670-6677.
23. Suzuki MT, Giovannoni SJ. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625- 630.
24. Vamosi S, Heard S, Vamosi J, Webb C. 2009. Emerging patterns in the comparative analysis of phylogenetic community structure. Mol. Ecol. 18:572-592.
25. Vandenkoornhuyse P, et al. 2007. Active root-inhabiting microbes identified by rapid incorporation of plant-derived carbon into RNA. Proc. Natl. Acad. Sci. U. S. A. 104:16970.
26. Webb CO, Ackerly DD, Kembel SW. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24:2098 -2100.
27. Webb CO, Ackerly DD, McPeek MA, Donoghue MJ. 2002. Phylogenies and community ecology. Annu. Rev. Ecol. Syst. 33:475-505.