Bacterial diversity in a large, temperate, heavily modified river, as determined by pyrosequencing

Aquatic Microbial Ecology

Volumn 70, Issue 2, 2013, Pages 169-179

  Schultz, Gary E ^a   Kovatch, Jeffrey J ^a   Anneken, Emily M ^a,b  

^a MARSHALL UNIVERSITY   (United States)

^b U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

Author keywords

Bacterial community; Molecular diversity; Ohio river; Pyrosequencing; Richness

Indexed keywords

EID: 84884471401     PISSN: 09483055     EISSN: None     Source Type: Journal    
DOI: 10.3354/ame01646     Document Type: Article

References (50)

1. Andreotti R, Pérez de León A, Dowd S, Guerrero F, Bendele K, Scoles G (2011) Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus) microplus through tag-encoded pyrosequencing. BMC Microbiol 11: 6-16.
2. Battin TJ, Wille A, Sattler B, Psenner R (2001) Phylogenetic and functional heterogeneity of sediment biofilms along environmental gradients in a glacial stream. Appl Environ Microbiol 67: 799-807.
3. Berdjeb L, Pollet T, Domaizon I, Jacquet S (2011) Effect of grazers and viruses on bacterial community structure and production in two contrasting trophic lakes. BMC Microbiol 11: 88, doi:10.1186/1471-218U-11-88.
4. Bloom SA (1981) Similarity indices in community studies: potential pitfalls. Mar Ecol Prog Ser 5: 125-128.
5. Böckelmann U, Manz W, Neu TR, Szewzyk U (2000) Characterization of the microbial community of lotic organic aggregates ('river snow') in the Elbe River of Germany by cultivation and molecular methods. FEMS Microbiol Ecol 33: 157-170.
6. Bray JR, Curtis JT (1957) An ordination of upland forest communities of southern Wisconsin. Ecol Monograph 27: 325-349.
7. Callaway TR, Dowd SE, Edrington TS, Anderson RC and others (2010) Evaluation of bacterial diversity in the rumen and feces of cattle fed different levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing. J Anim Sci 88: 3977-3983.
8. Chao A (1987) Estimating the population size for capturerecapture data with unequal catchability. Biometrics 43: 783-791.
9. Chow VT, Maidment DR, Mays LW (1988) Applied hydrology. McGraw Hill, New York, NY.
10. Cole JJ, Prairie YT, Caraco NF, McDowell WH and others (2007) Plumbing the global carbon cycle: integrating inland waters into the terrestrial carbon budget. Ecosystems 10: 172-185.
11. Crump BC, Hobbie JE (2005) Synchrony and seasonality of bacterioplankton communities in two temperate rivers. Limnol Oceanogr 50: 1718-1729.
12. Crump BC, Peterson BJ, Raymond PA, Amon RM, Rinehart A, McClelland JW, Holmes RM (2009) Circumpolar syn- chrony in big river bacterioplankton. Proc Natl Acad Sci USA 106: 21208-21212.
13. Crump BC, Amaral-Zettler LA, Kling GW (2012) Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils. ISME J 6: 1629-1639.
14. Dowd SE, Zaragoza J, Rodriguez JR, Oliver MJ, Payton PR (2005) Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST). BMC Bioinformatics 6: 93-106.
15. Dowd SE, Callaway TR, Wolcott RD, Sun Y, McKeehan T, Hagevoort RG, Edrington TS (2008) FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol 8: 125-132.
16. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
17. Faith DP, Minchin PR, Belbin L (1987) Compositional dissimilarity as a robust measure of ecological distance. Vegetatio 69: 57-68.
18. Ghai R, Rodriguez-Valera F, McMahon KD, Toyama D and others (2011) Metagenomics of the water column in the pristine upper course of the Amazon river. PLoS ONE 6: e23785.
19. Gihring TM, Green SJ, Schadt CW (2012) Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environ Microbiol 14: 285-290.
20. Handl S, Dowd SE, Garcia-Mazcorro JF, Steiner JM, Suchodolski JS (2011) Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats. FEMS Microbiol Ecol 76: 301-310.
21. Ishak HD, Plowes R, Sen R, Kellner K and others (2011) Bacterial diversity in Solenopsis invicta and Solenopsis geminata ant colonies characterized by 16S amplicon 454 pyrosequencing. Microb Ecol 61: 821-831.
22. Lemke MJ, Lienau EK, Rothe J, Pagioro TA, Rosenfeld J, Desalle R (2009) Description of freshwater bacterial assemblages from the upper Parana River floodpulse system, Brazil. Microb Ecol 57: 94-103.
23. Leopold LB, Wolman MG, Miller JP (1964) Fluvial processes in geomorphology. WH Freeman, San Francisco, CA.
24. Li D, Yang M, Li Z, Qi R, He J, Liu H (2008) Change of bacterial communities in sediments along Songhua River in Northeastern China after a nitrobenzene pollution event. FEMS Microbiol Ecol 65: 494-503.
25. Liu Z, Huang S, Sun G, Xu Z, Xu M (2012) Phylogenetic diversity, composition and distribution of bacterioplankton community in the Dongjiang River, China. FEMS Microbiol Ecol 80: 30-44.
26. Lundin D, Severin I, Logue JB, Östman O, Andersson AF, Lindström EF (2012) Which sequencing depth is sufficient to describe patterns in bacterial ?- and ?-diversity? Environ Microbiol Rep 4: 367-372.
27. Magurran AE (2004) Measuring biological diversity. Blackwell Publishing, Malden, MA.
28. Metzker ML (2010) Sequencing technologies-the next generation. Nat Rev Genet 11: 31-46.
29. Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S (2011) A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol Rev 75: 14-49.
30. Oksanen J, Kindt R, Legendre P, O'Hara RB (2007) vegan: community ecology package for R, version 1.9-25. R Foundation for Statistical Computing, Vienna. Available at http://cran.r-project.org.
31. Olsen G, Lane D, Giovannoni S, Pace N, Stahl D (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40: 337-365.
32. Pace N, Stahl D, Lane D, Olsen G (1986) The analysis of natural microbial populations by rRNA sequences. Adv Microb Ecol 9: 1-55.
33. Pedrós-Alió C (2006) Marine microbial diversity: can it be determined? Trends Microbiol 14: 257-263.
34. Pedrós-Alió C (2007) Dipping into the rare biosphere. Science 315: 192-193.
35. Pernthaler J (2005) Predation on prokaryotes in the water column and its ecological implications. Nat Rev Microbiol 3: 537-546.
36. Pielou EC (1969) An introduction to mathematical ecology. Wiley-Interscience, New York, NY.
37. Pielou EC (1975) Ecological diversity. Wiley, New York, NY.
38. R Development Core Team (2007) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. www.R-project.org.
39. Ronaghi M, Uhlén M, Nyrén P (1998) A sequencing method based on real-time pyrophosphate. Science 281: 363-365.
40. Sekiguchi H, Watanabe M, Nakahara T, Xu B, Uchiyama H (2002) Succession of bacterial community structure along the Changjiang River determined by denaturing gradient gel electrophoresis and clone library analysis. Appl Environ Microbiol 68: 5142-5150.
41. Sen R, Ishak HD, Estrada D, Dowd SE, Hong E, Mueller UG (2009) Generalized antifungal activity and 454-screening of Pseudonocardia and Amycolatopsis bacteria in nests of fungus-growing ants. Proc Natl Acad Sci USA 106: 17805-17810.
42. Shannon CE, Weaver W (1963) The mathematical theory of communication. University of Illinois Press, Urbana, IL.
43. Šimek K, Weinbauer MG, Hornák K, Jezbera J, Nedoma J, Dolan JR (2007) Grazer and virus-induced mortality of bacterioplankton accelerates development of Flectobacillus populations in a freshwater community. Environ Microbiol 9: 789-800.
44. Simpson EH (1949) Measurement of diversity. Nature 163: 688.
45. Sørensen T (1948) A method of establishing groups of equal amplitude in plant sociology based on similarity of species content and its application to analyses of the vegetation on Danish commons. Biol Skr K Danske Vidensk Selsk 5: 1-34.
46. Suchodolski JS, Dowd SE, Westermarck E, Steiner JM, Wolcott RD, Spillmann T, Harmoinen JA (2009) The effect of the macrolide antibiotic tylosin on microbial diversity in the canine small intestine as demonstrated by massive parallel 16S rRNA gene sequencing. BMC Microbiol 9: 210-225.
47. Vannote RL, Minshall GW, Cummins KW, Sedell JR, Cushing CE (1980) The river continuum concept. Can J Fish Aquat Sci 37: 130-137.
48. Vörösmarty CJ, McIntyre PB, Gessner MO, Dudgeon D and others (2010) Global threats to human water security and river biodiversity. Nature 467: 555-561.
49. Winter C, Hein T, Kavka G, Mach RL, Farnleitner AH (2007) Longitudinal changes in the bacterial community composition of the Danube River: a whole-river approach. Appl Environ Microbiol 73: 421-431.
50. Zhang R, Weinbauer MG, Qian PY (2007) Viruses and flagellates sustain apparent richness and reduce biomass accumulation of bacterioplankton in coastal marine waters. Environ Microbiol 9: 3008-3018.