Diversity, Ecology and Evolution of Microorganisms Inhabiting Hot Spring Microbial Mats

Relevant Publications [* = recommended]

Ward Lab

                        Reviews and book chapters:  

*Ward, D.M., R. Thane Papke, U. Nübel and M.C. McKitrick.  2002.  Natural history of microorganisms inhabiting hot spring microbial mat communities:  clues to the origin of microbial diversity and implications for micro- and macro-biology, pp. 25-48 in Biodiversity of Microbial Life: Foundation of Earth’s Biosphere (J.T. Staley and A.-L. Reysenbach, eds.). John Wiley and Sons, NY. 

Ferris, M.J., S.C. Nold, C.M. Santegoeds and D. M. Ward.  2001.  Examining bacterial population diversity within the Octopus Spring microbial mat community, pp. 51-64 in Thermophiles: biodiversity, ecology and evolution (Reysenback, A.-L., Voytek, M. and Mancinelli, R., eds). Kluwer Academic/Plenum Publishers, NY. 

Ward, D.M., M.M. Bateson and J.W. deLeeuw.  2001.  Use of 16S rRNA, lipid and naturally preserved components of hot spring mats and microorganisms to help interpret the record of microbial evolution, pp. 167-181 in Thermophiles: biodiversity, ecology and evolution (Reysenback, A.-L., Voytek, M. and Mancinelli, R., eds). Kluwer Academic/Plenum Publishers, NY. 

Ward, D.M. and R.W. Castenholz.  2000.  Cyanobacteria in geothermal habitats, p. 37-59 in (M. Potts and B. Whitton, eds.)  Ecology of Cyanobacteria.  Kluwer Academic Publishers, The Netherlands. 

*Ward, D.M., Bateson, M.M., Ferris, M.J. and S.C. Nold. 1998.  A natural view of microbial biodiversity within hot spring cyanobacterial mat communities.  Microbiol. Mol. Biol. Rev.  62:1353-1370.

     [http://mmbr.asm.org/cgi/reprint/62/4/1353.pdf] 

*Ward, D.M. 1998. A natural species concept for prokaryotes. Curr. Opinion in Microbiol. 1:271-277.

     [http://sciserver.lanl.gov/pdflinks/02092716503523344--journals--13695274--v01i0003--271_anscfp.pdf]  

Ward, D.M., M.J. Ferris, and M.M. Bateson. 1997. Organization of native populations within hot spring microbial mat communities:  Need for a more ecological approach, p.147-153 in M.T. Martins, M.I.Z. Sato, J.M. Tiedje, L.C.N. Hagler, J. Dobereiner, and P.S. Sanchez(ed.). Progress in Microbial Ecology, SBM - Brazilian Society for Microbiology / ICOME - International Committee on Microbial Ecology, Sao Paulo, Brazil. 

Bateson, M.M. and D.M. Ward. 1995.  Methods for extracting DNA from microbial mats and cultivated microorganisms--high molecular weight DNA from French Press lysis, section 1.1.4, p. 1-7 in Molecular Microbial Ecology Manual (A.D.L. Akkermans, J.D. van Elsas and F.J.  de Bruijn, eds.). Kluwer Acad. Publ., Dordrecht, The Netherlands.  

Ward, D.M., A.L. Ruff-Roberts and R. Weller.  1995.  Methods for extracting RNA or ribosomes from microbial mats and cultivated microorganisms, section, 1.2.3, p. 1-14 in Molecular Microbial Ecology Manual (A.D.L. Akkermans, J.D. van Elsas and F.J. de Bruijn, eds.). Kluwer Acad. Publ., Dordrecht, The Netherlands.  

Ward, D.M., M.J. Ferris, S.C. Nold, M.M. Bateson, E.D. Kopczynski and A.L. Ruff-Roberts.  1994.  Species diversity in hot spring microbial mats as revealed by both molecular and enrichment culture approaches--relationship between biodiversity and community structure, p. 33-44 in Microbial mats: structure, development and environmental significance (L. J. Stal and P. Coumette, eds.), Series G: Ecological Sciences, vol. 35, NATO/ASI Series, Springer-Verlag, Heidelberg. 

Ward, D.M., M.M. Bateson, R. Weller and A.L. Ruff‑Roberts. 1992. Ribosomal analysis of microorganisms as they occur in nature.  Adv. Microbial Ecology 12:219‑286. 

                    Primary literature: 

*Papke, R.T., N.B. Ramsing, M.M. Bateson and D.M. Ward. 2003.  Geographical isolation in hot spring cyanobacteria.   Environ. Microbiol. 5:650-659. 

*Ferris, M.J., M. Kühl, A. Wieland and D.M. Ward.  2003.  Cyanobacterial ecotypes in different optical microenvironments of a 68°C hot spring mat community revealed by 16S-23S rRNA internal transcribed spacer region variation.  Appl. Environ. Microbiol. 69:2893-2898. 

*Nübel, U., M.M. Bateson, V. Vandieken, M. Kühl and D.M. Ward. 2002. Microscopic examination of distribution and phenotypic properties of phylogenetically diverse Chloroflexaceae-related bacteria in hot spring microbial mats.  Appl. Environ. Microbiol.  68:4593-4603. [http://aem.asm.org/cgi/reprint/68/9/4593.pdf] 

*Ramsing, N.B., M.J. Ferris and D.M. Ward.  2000.  Highly ordered vertical structure of Synechococcus populations within the one-millimeter thick photic zone of a hot spring cyanobacterial mat.  Appl. Environ. Microbiol. 66:1038-1049. [http://aem.asm.org/cgi/reprint/66/3/1038.pdf] 

*Ferris, M.J. S.C. Nold, N.P. Revsbech and D.M. Ward.  1997.  Population structure and physiological changes within a hot spring microbial mat community following disturbance.  Appl. Environ. Microbiol.  63:1367-1374. 

*Ramsing, N.B., M.J. Ferris and D.M. Ward.  1997.  Light-induced motility of thermophilic Synechococcus isolates from Octopus Spring, Yellowstone National Park.  Appl. Environ. Microbiol.  63:2347-2354. 

*Ferris, M.J. and D.M. Ward.  1997. Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis.  Appl. Environ. Microbiol.  63:1375-1381. 

Ward, D.M., C.M. Santegoeds, S.C. Nold, N.B. Ramsing, M.J. Ferris and M.M. Bateson.  1997.  Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures.  Antonie van Leeuwenhoek 71:143-150. 

Ferris, M.J., A.L. Ruff-Roberts, E.D. Kopczynski, M.M. Bateson and D.M. Ward. 1996.  Enrichment culture and microscopy conceal diverse thermophilic Synechococcus populations in a single hot spring microbial mat habitat.  Appl. Environ. Microbiol. 62:1045-1050. 

Santegoeds, C.M., S.C. Nold and D.M. Ward.  1996.  Denaturing gradient gel electrophoresis used to monitor the enrichment culture of aerobic chemoorganotrophic bacteria from a hot spring cyanobacterial mat.  Appl. Environ. Microbiol.  62:3922-3928. 

Nold, S.C., E.D. Kopczynski and D.M. Ward.  1996.  Cultivation of aerobic chemoorganotrophic Proteobacteria and Gram-positive bacteria from a hot spring microbial mat.  Appl. Environ. Microbiol.  62:3917-3921. 

Ferris, M.J., G. Muyzer and D.M. Ward.  1996.  Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community.  Appl. Environ. Microbiol. 62:340-346. 

Nold, S.C. and D.M. Ward.  1995.  Diverse Thermus species inhabit a single hot spring microbial mat.  System. Appl. Microbiol. 18:274-278. 

Robison-Cox, J., M.M. Bateson and D.M. Ward. 1995.  Evaluation of nearest-neighbor methods of detection of chimeric small- subunit rRNA sequences.  Appl. Environ. Microbiol. 61:1240-1245. 

*Ruff-Roberts, A.L., J.G. Kuenen and D.M. Ward.  1994.  Distribution of cultivated and uncultivated cyanobacteria and Chloroflexus-like bacteria in hot spring microbial mats.  Appl. Environ. Microbiol. 60:697-704. 

Kopczynski, E.D., M.M. Bateson and D.M. Ward. 1994. Recognition of chimeric small-subunit ribosomal RNA sequences composed of genes from uncultivated microorganisms. Appl. Environ. Microbiol. 60:746-748.      

Weller, R., M.M. Bateson, B.K. Heimbuch, E.D. Kopczynski and D.M. Ward.  1992.  Uncultivated cyanobacteria, Chloroflexus-like inhabitants, and spirochete-like inhabitants of a hot spring microbial mat.  Appl. Environ. Microbiol.  58:3964-3969. 

Weller, R., F.W. Weller and D.M. Ward.  1991. 16S rRNA sequences retrieved as randomly primed cDNA from a hot spring cyanobacterial mat community.  Appl. Environ. Microbiol. 57:1146-1151. 

Bateson, M.M., K. Thibault and D.M. Ward. 1990. Comparative analysis of partial 16S ribosomal RNA sequences of Thermus species.  System. Appl. Microbiol.  13: 8-13. 

Ward, D.M., R. Weller and M.M. Bateson. 1990. 16S rRNA sequences reveal uncultured inhabitants of a well-studied thermal community.  FEMS Microbiology Rev. 75:105-116. 

*Ward, D.M., Weller, R. and M.M. Bateson.  1990.  16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature  345: 63-65. 

Weller, R. and D.M. Ward.  1989. Selective recovery of 16S ribosomal RNA sequences from natural microbial communities in the form of cDNA. Appl. Environ. Microbiol.  55: 1818-1822. 

Bateson, M.M., J. Wiegel and D.M. Ward. 1989.  Comparative analysis of 16S ribosomal RNA sequences of thermophilic fermentative bacteria isolated from hot spring cyanobacterial mats. System. Appl. Microbiol. 12:1-7. 

Non-Ward Lab Citations 

*Begon, M, J.L. Harper and C.R. Townsend. 1990. Ecology: individuals, populations and communities. 2^nd ed. Blackwell Sci. Publ., Cambridge, MA. [link: I'm seeking this.]  [This is an excellent introduction to how diversity is linked to evolution and ecology.  I highly recommend it for a more natural view than microbiologists usually acquire through their own texts.]