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Community Analysis-Based Methods

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Book cover Microbial Source Tracking: Methods, Applications, and Case Studies

Abstract

Microbial communities are each a composite of populations whose presence and relative abundance in water or other environmental samples are a direct manifestation of environmental conditions, including the introduction of microbe-rich fecal material and factors promoting persistence of the microbes therein. As shown by culture-independent methods, different animal-host fecal microbial communities are distinctive, suggesting that their community profiles can be used to differentiate fecal samples and to potentially reveal the presence of host fecal material in environmental waters. Cross-comparisons of microbial communities from different hosts also reveal relative abundances of genetic groups that can be used to distinguish sources. In increasing order of their information richness, several community analysis methods hold promise for MST applications: phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP), cloning/sequencing, and PhyloChip. Specific case studies involving TRFLP and PhyloChip approaches demonstrate the ability of community-based analyses of contaminated waters to confirm a diagnosis of water quality based on host-specific marker(s). The success of community-based MST for comprehensively confirming fecal sources relies extensively upon using appropriate multivariate statistical approaches. While community-based MST is still under evaluation and development as a primary diagnostic tool, results presented herein demonstrate its promise. Coupled with its inherently comprehensive ability to capture an unprecedented amount of microbiological data that is relevant to water quality, the tools for microbial community analysis are increasingly accessible, and community-based approaches have unparalleled potential for translation into rapid, perhaps real-time, monitoring platforms.

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References

  • An PL, Hua JM, Franz M et al. (2004) Changes of chemical and biological parameters in soil caused by trickling sewage. Acta Hydrochim Hydrobiol 32: 296–303.

    Article  CAS  Google Scholar 

  • Andersen GL, He Z, DeSantis TZ et al. (2010) The use of microarrays in microbial ecology. In Environmental Molecular Microbiology. Liu W-T, and Jansson JK (eds). Caister Academic Press, Norfolk, UK, pp. 87–109.

    Google Scholar 

  • Bernhard AE, and Field KG (2000a) Identification of nonpoint sources of fecal pollution in coastal waters by using host-specific 16S ribosomal DNA genetic markers from fecal anaerobes. Appl Environ Microbiol 66: 1587–1594.

    Article  PubMed  CAS  Google Scholar 

  • Bernhard AE, and Field KG (2000b) A PCR assay to discriminate human and ruminant feces on the basis of host differences in Bacteroides-Prevotella genes encoding 16S rRNA. Appl Environ Microbiol 66: 4571–4574.

    Article  PubMed  CAS  Google Scholar 

  • Blanch AR, Belanche-Munoz L, Bonjoch X et al. (2006) Integrated analysis of established and novel microbial and chemical methods for microbial source tracking. Appl Environ Microbiol 72: 5915–5926.

    Article  PubMed  CAS  Google Scholar 

  • Bodrossy L, and Sessitsch A (2004) Oligonucleotide microarrays in microbial diagnostics. Current Opinion in Microbiology 7: 245–254.

    Article  PubMed  CAS  Google Scholar 

  • Boehm AB, Fuhrman JA, Mrse RD et al. (2003) Tiered approach for identification of a human fecal pollution source at a recreational beach: Case study at Avalon Bay, Catalina Island, California. Environ Sci Technol 37: 673–680.

    Article  PubMed  CAS  Google Scholar 

  • Braker G, Ayala-del-Rio HL, Devol AH et al. (2001) Community structure of denitrifiers, bacteria, and archaea along redox gradients in pacific northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes. Appl Environ Microbiol 67: 1893–1901.

    Article  PubMed  CAS  Google Scholar 

  • Breitbart M, Hewson I, Felts B et al. (2003) Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol 185: 6220–6223.

    Article  PubMed  CAS  Google Scholar 

  • Brinkmann T, Abbt-Braun G, Karle E et al. (2004) Transformation of wastewater-derived dissolved organic matter below leaky sewers - Fate of amino acids and carbohydrates. Acta Hydrochim Hydrobiol 32: 316–327.

    Article  CAS  Google Scholar 

  • Brodie EL, DeSantis TZ, Parker JPM et al. (2007) Urban aerosols harbor diverse and dynamic bacterial populations. Proceedings of the National Academy of Sciences of the United States of America 104: 299–304.

    Article  PubMed  CAS  Google Scholar 

  • Brodie EL, DeSantis TZ, Joyner DC et al. (2006) Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72: 6288–6298.

    Article  PubMed  CAS  Google Scholar 

  • Cabelli VJ, Dufour AP, McCabe LJ et al. (1982) Swimming-associated gastroenteritis and water quality. Am J Epidemiol 115: 606–616.

    PubMed  CAS  Google Scholar 

  • Cao Y, Green PG, and Holden PA (2008) Microbial community composition and denitrifying enzyme activities in salt marsh sediments. Appl Environ Microbiol 74: 7585–7595.

    Article  PubMed  CAS  Google Scholar 

  • Cao Y, Cherr GN, Córdova-Kreylos AL et al. (2006) Relationships between sediment microbial communities and pollutants in two California salt marshes. Microb Ecol 52: 619–633.

    Article  PubMed  CAS  Google Scholar 

  • Chivian D, Brodie EL, Alm EJ et al. (2008) Environmental genomics reveals a single-species ecosystem deep within earth. Science 322: 275–278.

    Article  PubMed  CAS  Google Scholar 

  • Clarke KR, and Warwick RM (2001) Change in marine communities: An approach to statistical analysis and interpretation, 2nd edition. PRIMER-E, Plymouth.

    Google Scholar 

  • Clement BG, Kehl LE, DeBord KL et al. (1998) Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities. J Microbiol Methods 31: 135–142.

    Article  CAS  Google Scholar 

  • Córdova-Kreylos AL, Cao Y, Green PG et al. (2006) Diversity, composition and geographical distribution of microbial communities in California salt marsh sediments. Appl Environ Microbiol 72: 3357–3366.

    Article  PubMed  Google Scholar 

  • Cruz-Martinez K, Suttle KB, Brodie EL et al. (2009) Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME J 3: 738–744.

    Article  PubMed  CAS  Google Scholar 

  • DeAngelis KM, Brodie EL, DeSantis TZ et al. (2009) Selective progressive response of soil microbial community to wild oat roots. ISME J 3: 168–178.

    Article  PubMed  CAS  Google Scholar 

  • DeSantis TZ, Brodie EL, Moberg JP et al. (2007) High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 53: 371–383.

    Article  PubMed  CAS  Google Scholar 

  • DeSantis TZ, Hugenholtz P, Larsen N et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069–5072.

    Article  PubMed  CAS  Google Scholar 

  • Dick LK, Stelzer EA, Bertke EE et al. (2010) Relative decay of Bacteroidales microbial source tracking markers and cultivated Escherichia coli in freshwater microcosms. Appl Environ Microbiol 76: 3255–3262.

    Article  PubMed  CAS  Google Scholar 

  • Dick LK, Bernhard AE, Brodeur TJ et al. (2005) Host distribution of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification. Appl Environ Microbiol 71: 3184–3191.

    Article  PubMed  CAS  Google Scholar 

  • Dorigo U, Volatier L, and Humbert JF (2005) Molecular approaches to the assessment of biodiversity in aquatic microbial communities. Water Res 39: 2207–2218.

    Article  PubMed  CAS  Google Scholar 

  • Dubinsky E, Wu C, Hulls J et al. (2009) A complete microbial community approach to tracking fecal pollution in coastal waters. In State of the Estuary Conference. Oakland, CA.

    Google Scholar 

  • Dunbar J, Ticknor LO, and Kuske CR (2001) Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl Environ Microbiol 67: 190–197.

    Article  PubMed  CAS  Google Scholar 

  • Eaton AD, Clesceri LS, Greenberg AE et al. (1998) Standard Methods for The Examination of Water and Wastewater. American Public Health Association, Washington, DC.

    Google Scholar 

  • Eckburg PB, Bik EM, Bernstein CN et al. (2010) Diversity of the human intestinal microbial flora. Science 308: 1635–1638.

    Article  Google Scholar 

  • Ercolini D (2004) PCR-DGGE fingerprinting: Novel strategies for detection of microbes in food. J Microbiol Methods 56: 297–314.

    Article  PubMed  CAS  Google Scholar 

  • Esseili MA, Kassen II, and Sigler V (2008) Optimization of DGGE community fingerprinting for characterizing Escherichia coli communities associated with fecal pollution. Water Res 42: 4467–4476.

    Article  PubMed  CAS  Google Scholar 

  • Farnleitner AH, Kreuzinger N, Kavka GG et al. (2000) Simultaneous detection and differentiation of Escherichia coli populations from environmental freshwaters by means of sequence variations in a fragment of the beta-D-glucuronidase gene. Appl Environ Microbiol 66: 1340–1346.

    Article  PubMed  CAS  Google Scholar 

  • Field KG, and Samadpour M (2007) Fecal source tracking, the indicator paradigm, and managing water quality. Water Res 41: 3517–3538.

    Article  PubMed  CAS  Google Scholar 

  • Field KG, Bernhard AE, and Brodeur TJ (2003a) Molecular approaches to microbiological monitoring: Fecal source detection. Environmental Monitoring and Assessment 81: 313–326.

    Article  PubMed  CAS  Google Scholar 

  • Field KG, Chern EC, Dick LK et al. (2003b) A comparative study of culture-independent, library-independent genotypic methods of fecal source tracking. J Water Health 1: 181–194.

    PubMed  Google Scholar 

  • Flanagan JL, Brodie EL, Weng L et al. (2007) Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. J Clin Microbiol 45: 1954–1962.

    Article  PubMed  CAS  Google Scholar 

  • Fogarty LR, and Voytek MA (2005) Comparison of Bacteroides-Prevotella 16S rRNA genetic markers for fecal samples from different animal species. Appl Environ Microbiol 71: 5999–6007.

    Article  PubMed  CAS  Google Scholar 

  • Frostegard A, Tunlid A, and Baath E (1993) Phospholipid fatty acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals. Appl Environ Microbiol 59: 3605–3617.

    PubMed  CAS  Google Scholar 

  • Hazen TC (1988) Fecal coliforms as indicators in tropical waters–a review. Toxicity Assessment 3: 461–477.

    Article  CAS  Google Scholar 

  • Hua JM, An PL, Winter J et al. (2003) Elimination of COD, microorganisms and pharmaceuticals from sewage by trickling through sandy soil below leaking sewers. Water Res 37: 4395–4404.

    Article  PubMed  CAS  Google Scholar 

  • Hua JM, An PL, Winter J et al. (2004) Elimination of organic compounds of sewage or sewage fractions in sandy soil below leaking sewers. Acta Hydrochim Hydrobiol 32: 287–295.

    Article  CAS  Google Scholar 

  • Hwang CC, Wu WM, Gentry TJ et al. (2009) Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths. ISME J 3: 47–64.

    Article  PubMed  CAS  Google Scholar 

  • Ibekwe AM, Bold RM, Lyon SR et al. (2008) Microbial community composition in middle Santa Ana River watershed impacted by non-point source pollutants. In the 108th general meeting for American Society of Microbiology. Boston, MA.

    Google Scholar 

  • Ishii S, Hansen DL, Hicks RE et al. (2007) Beach sand and sediments are temporal sinks and sources of Escherichia coli in Lake Superior. Environ Sci Technol 41: 2203–2209.

    Article  PubMed  CAS  Google Scholar 

  • Izbicki JA, Swarzenski PW, Reich CD et al. (2009) Sources of fecal indicator bacteria in urban streams and ocean beaches, Santa Barbara, California. Annals of Environmental Sciences 3: 139–178.

    CAS  Google Scholar 

  • Jeter SN, McDermott CM, Bower PA et al. (2009) Bacteroidales diversity in Ring-Billed Gulls (Laurus delawarensis) residing at Lake Michigan beaches. Appl Environ Microbiol 75: 1525–1533.

    Article  PubMed  CAS  Google Scholar 

  • Kaur A, Chaudhary A, Kaur A et al. (2005) Phospholipid fatty acid - A bioindicator of environment monitoring and assessment in soil ecosystem. Curr Sci 89: 1103–1112.

    CAS  Google Scholar 

  • Kent AD, Smith DJ, Benson BJ et al. (2003) Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities. Appl Environ Microbiol 69: 6768–6776.

    Article  PubMed  CAS  Google Scholar 

  • La Duc MT, Osman S, Vaishampayan P et al. (2009) Comprehensive census of bacteria in clean rooms by using DNA microarray and cloning methods. Appl Environ Microbiol 75: 6559–6567.

    Article  PubMed  Google Scholar 

  • Lamendella R, Santo Domingo JW, Oerther DB et al. (2007) Assessment of fecal pollution sources in a small northern-plains watershed using PCR and phylogenetic analyses of Bacteroidetes 16S rRNA gene. FEMS Microbiol Ecol 59: 651–660.

    Article  PubMed  CAS  Google Scholar 

  • LaMontagne MG, Schimel JP, and Holden PA (2003a) Comparison of subsurface and surface soil bacterial communities in California grassland as assessed by terminal restriction fragment length polymorphisms of PCR-amplified 16S rRNA genes. Microb Ecol 46: 216–227.

    Article  PubMed  CAS  Google Scholar 

  • LaMontagne MG, Griffith JF, and Holden PA (2003b) Comparative analysis of animal fecal bacterial communities using terminal restriction fragment length polymorphisms of bacterial 16S rDNA PCR-amplified from fecal community DNA. In American Society for Microbiology General Meeting. Washington, DC.

    Google Scholar 

  • LaMontagne MG, Leifer I, Bergmann S et al. (2004) Bacterial diversity in marine hydrocarbon seep sediments. Environ Microbiol 6: 799–808.

    Article  PubMed  Google Scholar 

  • Leadbetter ER (1997) Prokaryotic diversity: form, ecophysiology, and habitat. In Manual of Environmental Microbiology. Hurst CJ, Knudsen GR, McInerney MJ et al. (eds). American Society for Microbiology, Washington, D.C., pp. 14–24.

    Google Scholar 

  • Legendre P, and Legendre L (1998) Numerical Ecology. Elsevier Science BV, Amsterdam.

    Google Scholar 

  • Ley RE, Hamady M, Lozupone C et al. (2008) Evolution of mammals and their gut microbes. Science 32: 1647–1651.

    Article  Google Scholar 

  • Li F, Hullar MAJ, and Lampe JW (2007) Optimization of terminal restriction fragment polymorphism (TRFLP) analysis of human gut microbiota. J Microbiol Methods 68: 303–311.

    Article  PubMed  CAS  Google Scholar 

  • Liu W-T, and Jansson JK (eds) (2010) Environmental Molecular Microbiology. Caister Academic Press, Norfolk, U.K.

    Google Scholar 

  • Liu W-T, Marsh TL, Cheng H et al. (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63: 4516–4522.

    PubMed  CAS  Google Scholar 

  • Loffhagen N, Härtig C, and Babel W (2004) Pseudomonas putida NCTC 10936 balances membrane fluidity in response to physical and chemical stress by changing the saturation degree and the trans/cis ratio of fatty acids. Biosci Biotechnol Biochem 68: 317–323.

    Article  PubMed  CAS  Google Scholar 

  • Lu JR, Santo Domingo JW, Lamendella R et al. (2008) Phylogenetic diversity and molecular detection of bacteria in gull feces. Appl Environ Microbiol 74: 3969–3976.

    Article  PubMed  CAS  Google Scholar 

  • Macalady JL, Mack EE, Nelson DC et al. (2000) Sediment microbial community structure and mercury methylation in mercury-polluted Clear Lake, California. Appl Environ Microbiol 66: 1479–1488.

    Article  PubMed  CAS  Google Scholar 

  • Maidak BL, Cole JR, Lilburn TG et al. (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res 29: 173–174.

    Article  PubMed  CAS  Google Scholar 

  • Muyzer G, and Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek International Journal of General & Molecular Microbiology 73: 127–141.

    Article  CAS  Google Scholar 

  • National Research Council (1993) Managing Wastewater in Coastal Urban Areas. National Academy Press, Washington, D.C.

    Google Scholar 

  • Nocker A, Burr M, and Camper AK (2007) Genotypic microbial community profiling: A critical technical review. Microb Ecol 54: 276–289.

    Article  PubMed  CAS  Google Scholar 

  • Osborn AM, and Smith CJ (2005) Molecular Microbial Ecology. Taylor & Francis, New York, NY, USA.

    Google Scholar 

  • Palmer MW (2006). Ordination methods for ecologists: The ordination webpage. http://ordination.okstate.edu/. Accessed May 11, 2011

    Google Scholar 

  • Pennanen T, Frostegard A, Fritze H et al. (1996) Phospholipid fatty acid composition and heavy metal tolerance of soil microbial communities along two heavy metal-polluted gradients in coniferous forests. Appl Environ Microbiol 62: 420–428.

    PubMed  CAS  Google Scholar 

  • R Core Development Team (2008) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.

  • Ramette A (2007) Multivariate analyses in microbial ecology. FEMS Microbiol Ecol 62: 142–160.

    Article  PubMed  CAS  Google Scholar 

  • Rastogi G, Osman S, Vaishampayan PA et al. (2010) Microbial diversity in uranium mining-impacted soils as revealed by high-density 16S microarray and clone library. Microb Ecol 59: 94–108.

    Article  PubMed  CAS  Google Scholar 

  • Sagaram US, DeAngelis KM, Trivedi P et al. (2009) Bacterial diversity analysis of Huanglongbing pathogen-infected citrus, using PhyloChip arrays and 16S rRNA gene clone library sequencing. Appl Environ Microbiol 75: 1566–1574.

    Article  PubMed  CAS  Google Scholar 

  • Santo Domingo JW, Bambic DG, Edge TA et al. (2007) Quo vadis source tracking? Towards a strategic framework for environmental monitoring of fecal pollution. Water Res 41: 3539–3552.

    Article  PubMed  CAS  Google Scholar 

  • Schütte UME, Abdo Z, Bent SJ et al. (2008) Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Appl Microbiol Biotechnol 80: 365–380.

    Article  PubMed  Google Scholar 

  • Sercu B, Van De Werfhorst LC, Murray J et al. (2009) Storm drains are sources of human fecal pollution during dry weather in three urban southern California watersheds. Environ Sci Technol 43: 293–298.

    Article  PubMed  CAS  Google Scholar 

  • Seurinck S, Defoirdt T, Verstraete W et al. (2005) Detection and quantification of the human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater. Environ Microbiol 7: 249–259.

    Article  PubMed  CAS  Google Scholar 

  • Shendure J, and Ji HL (2008) Next-generation DNA sequencing. Nature Biotechnology 26: 1135–1145.

    Article  PubMed  CAS  Google Scholar 

  • Shiu SH, and Borevitz JO (2008) The next generation of microarray research: Applications in evolutionary and ecological genomics. Heredity 100: 141–149.

    Article  PubMed  CAS  Google Scholar 

  • Shyu C, Soule T, Bent SJ et al. (2007) MiCA: A web-based tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphism of 16S and 18S rRNA genes. Microb Ecol 53: 562–570.

    Article  PubMed  CAS  Google Scholar 

  • Sigler V, and Pasutti L (2006) Evaluation of denaturing gradient gel electrophoresis to differentiate Escherichia coli populations in secondary environments. Environ Microbiol 8: 1703–1711.

    Article  PubMed  CAS  Google Scholar 

  • Simpson JM, Santo Domingo JW, and Reasoner DJ (2004) Assessment of equine fecal contamination: the search for alternative bacterial source-tracking targets. FEMS Microbiol Ecol 47: 65.

    Article  PubMed  CAS  Google Scholar 

  • Stogbauer A, Berner Z, and Stuben D (2004) Redox control on the isotopic composition of dissolved sulfate in percolating sewage - An experimental study. Acta Hydrochim Hydrobiol 32: 304–315.

    Article  Google Scholar 

  • Sunagawa S, DeSantis TZ, Piceno YM et al. (2009) Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata. ISME J 3: 512–521.

    Article  PubMed  CAS  Google Scholar 

  • ter Braak CJF (1986) Canonical correspondence analysis: A new eigenvector technique for multivariate direct gradient analysis. Ecology 67: 1167–1179.

    Article  Google Scholar 

  • ter Braak CJF (1995) Ordination. In Data analysis in community and landscape ecology. Jongman RHG, ter Braak CJF, and van Tongeren OFR (eds). Cambridge University Press, New York, pp. 91–173.

    Chapter  Google Scholar 

  • ter Braak CJF, and Prentice IC (1988) A theory of gradient analysis. Advances in Ecological Research 18: 271–317.

    Article  Google Scholar 

  • ter Braak CJF, and Smilauer P (2002) CANOCO reference manual and CanoDraw for windows user’s guide: Software for canonical community ordination (version 4.5). Microcomputer Power, Ithaca, NY, USA.

    Google Scholar 

  • Thies JE (2007) Soil microbial community analysis using terminal restriction fragment length polymorphisms. Soil Sci Soc Am J 71: 579–591.

    Article  CAS  Google Scholar 

  • Tsiamis G, Katsaveli K, Ntougias S et al. (2008) Prokaryotic community profiles at different operational stages of a Greek solar saltern. Res Microbiol 159: 609–627.

    Article  PubMed  Google Scholar 

  • U.S. Environmental Protection Agency (2005) Microbial Source Tracking Guide Document. In. Cincinnati, OH: Office of Research and Development, p. 150.

    Google Scholar 

  • Vogel JR, Stoeckel DM, Lamendella R et al. (2007) Identifying fecal sources in a selected catchment reach using multiple source-tracking tools. J Environ Qual 36: 718–729.

    Article  PubMed  CAS  Google Scholar 

  • Wade TJ, Calderon RL, Sams E et al. (2006) Rapidly measured indicators of recreational water quality are predictive of swimming-associated gastrointestinal illness. Environ Health Perspect 114: 24–28.

    Article  PubMed  Google Scholar 

  • Weidhaas JL, Macbeth TW, Olsen RL et al. (2010) Identification of a Brevibacterium marker gene specific to poultry litter and development of a quantitative PCR assay. J Appl Microbiol 109: 334–347.

    PubMed  CAS  Google Scholar 

  • White DC (1994) Is there anything else you need to understand about the microbiota that cannot be derived from analysis of nucleic acids? Microb Ecol 28: 163–166.

    Article  CAS  Google Scholar 

  • Wright CF, and Kroese M (2010) Evaluation of genetic tests for susceptibility to common complex diseases: why, when and how? Hum Genet 127: 125–134.

    Article  PubMed  Google Scholar 

  • Wrighton KC, Agbo P, Warnecke F et al. (2008) A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. ISME J 2: 1146–1156.

    Article  PubMed  CAS  Google Scholar 

  • Wu CH, Sercu B, Van De Werfhorst LC et al. (2010) Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators. PLoS One 5(6): e11285. doi: 10.1371/journal.pone.0011285.

    Google Scholar 

  • Yergeau E, Schoondermark-Stolk SA, Brodie EL et al. (2009) Environmental microarray analyses of Antarctic soil microbial communities. ISME J 3: 340–351.

    Article  PubMed  CAS  Google Scholar 

  • Zelles L (1999) Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: A review. Biol Fertil Soils 29: 111–129.

    Article  CAS  Google Scholar 

  • Zhang R, Lau SCK, Ki J-S et al. (2009) Response of bacterioplankton community structures to hydrological conditions and anthropogenic pollution in contrasting subtropical environments. FEMS Microbiol Ecol 69: 449–460.

    Article  PubMed  CAS  Google Scholar 

  • Zoetendal EG, Collier CT, Koike S et al. (2004) Molecular ecological analysis of the gastrointestinal microbiota: A review. J Nutr 134: 465–472.

    PubMed  CAS  Google Scholar 

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Acknowledgments

The authors acknowledge the City of Santa and the Switzer Foundation for support, and the NSF-funded Santa Barbara Long Term Ecological Research project (NSF OCE 9982105 and OCE 0620276) for assistance including stream flow data in Santa Barbara, and the work of Laurie C. Van De Werfhorst and Bram Sercu in sampling, and sample and data processing for the AB and MC case studies herein. Other attributions for the Arroyo Burro and Mission Creek fecal source and sample acquisition plus analysis are as per Sercu et al. (2009). Part of this work was performed at Lawrence Berkeley National Laboratory under Department of Energy contract number DE-AC02-05CH11231.

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  1. Southern California Coastal Water Research Project, 3535 Harbor Blvd, Suite 110, Costa Mesa, CA, 92626, USA

    Yiping Cao

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  1. Yiping Cao
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  2. Cindy H. Wu
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  4. Patricia A. Holden
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Correspondence to Yiping Cao .

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  1. Dept. Crop & Soil Environmental Sciences, Virginia Tech, Prince Hall 401, Blacksburg, 24061, Virgin Islands, USA

    Charles Hagedorn

  2. Fac. Biologia, Depto. Microbiologia, Universitat Barcelona, Avenida Diagonal 645, Barcelona, 08028, Spain

    Anicet R. Blanch

  3. Dept. Biology, Div. Integrative Biology (IB), University of South Florida, E. Fowler Ave. 4202, Tampa, 33620, Florida, USA

    Valerie J. Harwood

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Cao, Y., Wu, C.H., Andersen, G.L., Holden, P.A. (2011). Community Analysis-Based Methods. In: Hagedorn, C., Blanch, A., Harwood, V. (eds) Microbial Source Tracking: Methods, Applications, and Case Studies. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-9386-1_11

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