Robust estimation of microbial diversity in theory and in practice

ISME Journal

Volumn 7, Issue 6, 2013, Pages 1092-1101

  Haegeman, Bart ^a   Hamelin, Jérôme ^b   Moriarty, John ^c   Neal, Peter ^d   Dushoff, Jonathan ^e   Weitz, Joshua S ^f  

^a Station d'Ecologie Expérimentale du Centre National de la Recherche Scientifique   (France)

^b LABORATOIRE DE BIOTECHNOLOGIE DE L ENVIRONNEMENT   (France)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

^d LANCASTER UNIVERSITY   (United Kingdom)

^e MCMASTER UNIVERSITY   (Canada)

^f GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Chao estimator; Hill diversities; Metagenomics; Shannon diversity; Simpson diversity; Species abundance distribution

Indexed keywords

SEA WATER;

ABUNDANCE; CHAOS THEORY; DIVERSITY INDEX; GENOMICS; MICROBIAL COMMUNITY; RARE SPECIES; SPECIES DIVERSITY; SPECIES RICHNESS;

ARCHAEON; ARTICLE; BACTERIUM; BIODIVERSITY; CLASSIFICATION; COMPUTER SIMULATION; METAGENOMICS; MICROBIOLOGY; REGRESSION ANALYSIS;

ARCHAEA; BACTERIA; BIODIVERSITY; COMPUTER SIMULATION; METAGENOMICS; REGRESSION ANALYSIS; SEAWATER; SOIL MICROBIOLOGY;

EID: 84878270728     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2013.10     Document Type: Article

References (55)

1. Bent SJ, Forney LJ. (2008). The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. ISME J 2: 689-695.
2. Bohannan BJM, Hughes JB. (2003). New approaches to analyzing microbial biodiversity data. Curr Opin Microbiol 6: 282-287.
3. Brose U, Martinez ND, Williams RJ. (2003). Estimating species richness: sensitivity to sample coverage and insensitivity to spatial patterns. Ecology 84: 2364-2377.
4. Bunge J. (2009). Statistical estimation of uncultivated microbial diversity. In: Epstein SS (ed) Uncultivated Microorganisms. Springer-Verlag, pp 1-18.
5. Bunge J, Fitzpatrick M. (1993). Estimating the number of species: a review. J Amer Statist Assoc 88: 364-373.
6. Chao A. (1984). Nonparametric estimation of the number of classes in a population. Scand J Statist 11: 265-270.
7. Chao A, Colwell RK, Lin CW, Gotelli NJ. (2009). Sufficient sampling for asymptotic minimum species richness estimators. Ecology 90: 1125-1133.
8. Colwell RK, Mao CX, Chang J. (2004). Interpolating, extrapolating, and comparing incidence-based species accumulation curves. Ecology 85: 2717-2727.
9. Curtis TP, Sloan WT, Scannell JW. (2002). Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 99: 10494-10499.
10. Dykhuizen DE. (1998). Santa Rosalia revisited: why are there so many species of bacteria? Antonie Van Leeuwenhoek 73: 25-33.
11. Engen S. (1978). Stochastic Abundance Models. Chapman & Hall.
12. Fromin N, Hamelin J, Tarnawski S, Roesti D, Jourdain-Miserez K, Forestier N et al. (2002). Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ Microbiol 4: 634-643.
13. Gans J, Wolinsky M, Dunbar J. (2005). Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387-1390.
14. Gobet A, Quince C, Ramette A. (2010). Multivariate cutoff level analysis (Multi CoLA) of large community data sets. Nucl Acids Res 38: e155.
15. Gotelli NJ, Colwell RK. (2001). Quantifying biodiversity: Procedures and pitfalls in the measurement and comparison of species richness. Ecol Lett 4: 379-391.
16. Gotelli NJ, Colwell RK. (2011). Estimating species richness. In: Magurran AE, McGill BJ (eds). Biological Diversity: Frontiers in Measurement and Assessment. Oxford University Press, pp 39-54.
17. Green JL, Bohannan BJM, Whitaker RJ. (2008). Microbial biogeography: from taxonomy to traits. Science 320: 1039-1043.
18. Haegeman B, Vanpeteghem D, Godon JJ, Hamelin J. (2008). DNA reassociation kinetics and diversity indices: richness is not rich enough. Oikos 117: 177-181.
19. Hill MO. (1973). Diversity and evenness: A unifying notation and its consequences. Ecology 54: 427-432.
20. Hong SH, Bunge J, Jeon SO, Epstein SS. (2006). Predicting microbial species richness. Proc Natl Acad Sci USA 103: 117-122.
21. Horner-Devine MC, Bohannan BJM. (2006). Phylogenetic clustering and overdispersion in bacterial communities. Ecology 87: S100-S108.
22. Huber JA, Welch DBM, Morrison HG, Huse SM, Neal PR, Butterfield DA et al. (2007). Microbial population structures in the deep marine biosphere. Science 318: 97-100.
23. Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJM. (2001). Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67: 4399-4406.
24. Ives A, Carpenter S. (2007). Stability and diversity of ecosystems. Science 317: 58-68.
25. Jost L. (2006). Entropy and diversity. Oikos 113: 363-375.
26. Kemp P, Aller J. (2004). Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us. FEMS Microbiol Ecol 47: 161-171.
27. Kislyuk AO, Haegeman B, Bergman NH, Weitz JS. (2011). Genomic fluidity: an integrative view of gene diversity within microbial populations. BMC Genomics 12: 32.
28. Lande R, DeVries PJ, Walla TR. (2000). When species accumulation curves intersect: implications for ranking diversity using small samples. Oikos 89: 601-605.
29. Loisel P, Harmand J, Zemb O, Latrille E, Lobry C, Delgenès JP et al. (2006). Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity. Environ Microbiol 8: 720-731.
30. Loreau M. (2010). From Populations to Ecosystems: Theoretical Foundations for a New Ecological Synthesis. Princeton University Press.
31. Loreau M, Naeem S, Inchausti P, Bengtsson J, Grime JP, Hector A et al. (2001). Biodiversity and ecosystem functioning: Current knowledge and future challenges. Science 294: 804-808.
32. Lozupone CA, Knight R. (2007). Global patterns in bacterial diversity. Proc Natl Acad Sci USA 104: 11436-11440.
33. Magurran AE. (2004). Measuring Biological Diversity. Blackwell Publishing.
34. Mao CX, Colwell RK. (2005). Estimation of species richness: Mixture models, the role of rare species, and inferential challenges. Ecology 86: 1143-1153.
35. May RM. (1988). How many species are there on earth? Science 241: 1441-1449.
36. Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B. (2011). How many species are there on earth and in the ocean? PLoS Biol 9: e1001127.
37. Øvreås L, Curtis TP. (2011). Microbial diversity and ecology. In: Magurran AE, McGill BJ (eds) Biological Diversity: Frontiers in Measurement and Assessment. Oxford University Press, pp 221-236.
38. Pedrós-Alió C. (2006). Marine microbial diversity: can it be determined? Trends Microbiol 14: 257-263.
39. Pedrós-Alió C. (2007). Dipping into the rare biosphere. Science 315: 192-193.
40. Quince C, Curtis TP, Sloan WT. (2008). The rational exploration of microbial diversity. Isme J 2: 997-1006.
41. Roesch LFW, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, Kent AD et al. (2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1: 283-290.
42. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S et al. (2007). The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol 5: e77.
43. 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.
44. Schloss PD, Handelsman J. (2006). Toward a census of bacteria in soil. PLoS Comput Biol 2: e92.
45. Shannon CE. (1948). A mathematical theory of communication. Bell System Tech J 27: 623-656.
46. Shaw AK, Halpern AL, Beeson K, Tran B, Venter JC, Martiny JBH. (2008). It's all relative: ranking the diversity of aquatic bacterial communities. Environ Microbiol 10: 2200-2210.
47. Shen TJ, Chao A, Lin CF. (2003). Predicting the number of new species in further taxonomic sampling. Ecology 84: 798-804.
48. Simpson EH. (1949). Measurement of diversity. Nature 163: 688.
49. Sloan WT, Quince C, Curtis TP. (2008). The uncountables. In: Zengler K (ed) Accessing Uncultivated Microorganisms: From the Environment to Organisms and Genomes and Back. ASM Press, pp 35-54.
50. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR et al. (2006). Microbial diversity in the deep sea and the underexplored 'rare biosphere'. Proc Natl Acad Sci USA 103: 12115-12120.
51. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, K̈ampfer P, Maiden MCJ et al. (2002). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52: 1043-1047.
52. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL et al. (2005). Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial 'pan-genome'. Proc Natl Acad Sci USA 102: 13950-13955.
53. Torsvik V, Salte K, Sorheim R, Goksoyr J. (1990). Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria. Appl Environ Microbiol 56: 776-781.
54. Whitman WB, Coleman DC, Wiebe WJ. (1998). Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95: 6578-6583.
55. Wilson EO. (1999). The Diversity of Life. W.W. Norton & Company.