Genotypic Distribution of a Specialist Model Microorganism, Methanosaeta, along an Estuarine Gradient: Does Metabolic Restriction Limit Niche Differentiation Potential?

Microbial Ecology

Volumn 63, Issue 4, 2012, Pages 856-864

  Carbonero, Franck ^a,c   Oakley, Brian B ^a,d   Hawkins, Robert J ^b   Purdy, Kevin J ^a  

^a UNIVERSITY OF WARWICK   (United Kingdom)

^b UNIVERSITY OF READING   (United Kingdom)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^d AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL DNA; ARCHAEAL RNA;

ARTICLE; CLASSIFICATION; DELTAPROTEOBACTERIA; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA SEQUENCE; ECOSYSTEM; ESTUARY; GENE LIBRARY; GENETICS; GENOTYPE; ISOLATION AND PURIFICATION; METABOLISM; METHANOSARCINALES; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

CLONING, MOLECULAR; DELTAPROTEOBACTERIA; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA, ARCHAEAL; ECOSYSTEM; ESTUARIES; GENE LIBRARY; GENOTYPE; METHANOSARCINALES; MOLECULAR SEQUENCE DATA; RNA, ARCHAEAL; SEQUENCE ANALYSIS, DNA;

DESULFOBULBUS; METHANOSAETA;

EID: 84864349619     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-011-9993-6     Document Type: Article

References (42)

1. Boone DR, Mah RA (2001) Methanosarcina. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey's manual of systematic bacteriology volume 1: the Archaea and deeply branching and phototrophic Bacteria. Springer, New York, pp 269-276.
2. Carbonero F, Oakley BB, Purdy KJ (2010) Improving the isolation of anaerobes on solid media: the example of the fastidious Methanosaeta. J Microbiol Meth 80: 203-205.
3. Cermeno P, Falkowski PG (2009) Controls on diatom biogeography in the ocean. Science 325: 1539-1541.
4. Crump BC, Hopkinson CS, Sogin ML, Hobbie JE (2004) Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time. Appl Environ Microbiol 70: 1494-1505.
5. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072.
6. Dixon P (2003) VEGAN, a package of R functions for community ecology. J Veg Sci 14: 927-930.
7. Doebeli M, Dieckmann U (2003) Speciation along environmental gradients. Nature 421: 259-264.
8. Dunbar J, Barns SM, Ticknor LO, Kuske CR (2002) Empirical and theoretical bacterial diversity in four Arizona soils. Appl Environ Microbiol 68: 3035-3045.
9. Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103: 626-631.
10. Hawkins RJ, Purdy KJ (2007) Genotypic distribution of an indigenous model microorganism along an estuarine gradient. FEMS Microbiol Ecol 62: 187-194.
11. Jetten MSM, Stams AJM, Zehnder AJB (1990) Acetate threshold values and acetate activating enzymes in methanogenic bacteria. FEMS Microbiol Ecol 73: 339-344.
12. Kassen R, Rainey PB (2004) The ecology and genetics of microbial diversity. Annu Rev Microbiol 58: 207-231.
13. Kuever J, Rainey FA, Widdel F (2005) Desulfobacter. In: Brenner DJ, Krieg NR, Staley JT (eds) Bergey's manual of systematic bacteriology volume 2: the Proteobacteria; part C the Alpha-, Beta-, Delta and Epsilon-proteobacteria. Springer, New York, pp 961-964.
14. Kuever J, Rainey FA, Widdel F (2005) Desulfobulbus. In: Brenner DJ, Krieg NR, Staley JT (eds) Bergey's manual of systematic bacteriology volume 2: the Proteobacteria; part C the Alpha-, Beta-, Delta and Epsilon-proteobacteria. Springer, New York, pp 988-992.
15. Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75: 5111-5120.
16. Lozupone C, Hamady M, Knight R (2006) UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinforma 7: 371.
17. Lubchenco J (1991) The sustainable biosphere initiative-an ecological research agenda-a report from the Ecological Society of America. Ecology 72: 371-412.
18. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar BA, Lai T, Steppi S, Jobb G, Forster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Konig A, Liss T, Lussmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
19. Mantel N, Fleiss JL (1980) Minimum expected cell-size requirements for the Mantel-Haenszel one-degree-of-freedom chi-square test and a related rapid procedure. Am J Epidemiol 112: 129-134.
20. Munson MA, Nedwell DB, Embley TM (1997) Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Appl Environ Microbiol 63: 4729-4733.
21. Oakley BB, Carbonero F, van der Gast CJ, Hawkins RJ, Purdy KJ (2010) Evolutionary divergence and biogeography of sympatric niche-differentiated bacterial populations. ISME J 4: 488-497.
22. Oakley BB, Carbonero F, Dowd SE, Hawkins RH, Purdy KJ (2011) Contrasting patterns of niche partitioning between two anaerobic terminal oxidizers of organic matter. ISME J doi: 10. 1038/ismej. 2011. 165.
23. Øvreås L, Forney L, Daae FL, Torsvik V (1997) Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63: 3367-3373.
24. Patel GB, Sprott GD (1990) Methanosaeta concilii gen. nov., sp. nov. (Methanothrix concilii) and Methanosaeta thermoacetophila nom. rev., comb. nov. Int J Syst Bacteriol 40: 79-82.
25. Patel GB (2001) Methanosaeta. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey's manual of systematic bacteriology volume 1: the Archaea and deeply branching and phototrophic Bacteria. Springer, New York, pp 289-294.
26. Peres-Neto PR, Legendre P, Dray S, Borcard D (2006) Variation partitioning of species data matrices: estimation and comparison of fractions. Ecology 87: 2614-2625.
27. Prosser JI, Bohannan BJM, Curtis TP, Ellis RJ, Firestone MK, Freckleton RP, Green JL, Green LE, Killham K, Lennon JJ, Osborn AM, Solan M, van der Gast CJ, Young JPW (2007) The role of ecological theory in microbial ecology. Nat Rev Microbiol 5: 384-392.
28. Prosser JI, Head IM (2007) Microorganisms, macroorganisms and ecology. FEMS Microbiol Ecol 62: 133-134.
29. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig WG, Peplies J, Glockner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
30. Pulliam HR (1988) Sources, sinks, and population regulation. Am Nat 132: 652-661.
31. Purdy KJ, Embley TM, Takii S, Nedwell DB (1996) Rapid extraction of DNA and rRNA from sediments by a novel hydroxyapatite spin-column method. Appl Environ Microbiol 62: 3905-3907.
32. Purdy KJ, Munson MA, Nedwell DB, Embley TM (2002) Comparison of the molecular diversity of the methanogenic community at the brackish and marine ends of a UK estuary. FEMS Microbiol Ecol 39: 17-21.
33. Purdy KJ, Munson MA, Cresswell-Maynard T, Nedwell DB, Embley TM (2003) Use of 16S rRNA-targeted oligonucleotide probes to investigate function and phylogeny of sulphate-reducing bacteria and methanogenic archaea in a UK estuary. FEMS Microbiol Ecol 44: 361-371.
34. Purdy KJ, Cresswell-Maynard TD, Nedwell DB, McGenity TJ, Grant WD, Timmis KN, Embley TM (2004) Isolation of haloarchaea that grow at low salinities. Environ Microbiol 6: 591-595.
35. Purdy KJ (2005) Nucleic acid recovery from complex environmental samples. Meth Enzymol 397: 271-292.
36. Schafer H, Muyzer G (2001) Denaturing gradient gel electrophoresis in marine microbial ecology. Meth Microbiol 30: 425-468.
37. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-1506.
38. Silva SQ (2004) Activity and diversity of sulphate-reducing bacteria and methanogenic archaea in contrasting sediments from the River Colne estuary. University of Essex, Colchester.
39. Spooner GM (1947) The distribution of Gammarus species in estuaries. J Mar Biol Assoc 27: 1-52.
40. Tsai YL, Olson BH (1991) Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57: 1070-1074.
41. Westermann P, Ahring BK, Mah RA (1989) Threshold acetate concentrations for acetate catabolism by aceticlastic methanogenic bacteria. Appl Environ Microbiol 55: 514-515.
42. Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301: 976-978.