RNA preservation agents and nucleic acid extraction method bias perceived bacterial community composition

PLoS ONE

Volumn 10, Issue 3, 2015, Pages

  McCarthy, Ann ^a   Chiang, Edna ^a   Schmidt, Marian L ^a   Denef, Vincent J ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DNA; FRESH WATER; NUCLEIC ACID; RNA;

AMPLICON; ARTICLE; COMMUNITY STRUCTURE; CONTROLLED STUDY; DNA EXTRACTION; DNA LIBRARY; DNA SEQUENCE; FLUORESCENCE IN SITU HYBRIDIZATION; MICROBIAL COMMUNITY; MICROSCOPY; NONHUMAN; POLYMERASE CHAIN REACTION; PRESERVATION; RNA ANALYSIS; RNA EXTRACTION; RNA SEQUENCE; VERRUCOMICROBIA; BACTERIUM; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PROCEDURES; SEQUENCE ANALYSIS;

BACTERIA (MICROORGANISMS); VERRUCOMICROBIA;

BACTERIA; DNA; FRESH WATER; NUCLEIC ACIDS; RNA; SEQUENCE ANALYSIS;

EID: 84925726130     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0121659     Document Type: Article

References (53)

1. Hugenholtz P, Goebel BM, Pace NR. Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity. J Bacteriol. 1998; 180: 4765-4774. PMID: 9733676
2. Forney LJ, Zhou X, Brown CJ. Molecular microbial ecology: land of the one-eyed king. Curr Opin Microbiol. 2004; 7: 210-220. PMID: 15196487
3. Temperton B, Giovannoni SJ. Metagenomics: microbial diversity through a scratched lens. Curr Opin Microbiol. 2012; 15: 605-612. doi: 10.1016/j.mib.2012.07.001 PMID: 22831844
4. Willner D, Daly J, Whiley D, Grimwood K, Wainwright CE, Hugenholtz P. Comparison of DNA Extraction Methods for Microbial Community Profiling with an Application to Pediatric Bronchoalveolar Lavage Samples. PLoS ONE. 2012; 7: e34605. doi: 10.1371/journal.pone.0034605 PMID: 22514642
5. Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 2011; 6: e27310. doi: 10.1371/journal.pone.0027310 PMID: 22194782
6. Rubin BER, Gibbons SM, Kennedy S, Hampton-Marcell J, Owens S, Gilbert JA. Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples. PLoS ONE. 2013; 8: e70460. doi: 10.1371/journal.pone.0070460 PMID: 23936206
7. Martin-Laurent F, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G, et al. DNA Extraction from Soils: Old Bias for New Microbial Diversity Analysis Methods. Appl Environ Microbiol. 2001; 67: 2354-2359. PMID: 11319122
8. Niemi MR, Heiskanen I, Wallenius K, Lindström K. Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia. J Microbiol Methods. 2001; 45: 155-165. PMID: 11348673
9. Carrigg C, Rice O, Kavanagh S, Collins G, O'Flaherty V. DNA extraction method affects microbial community profiles from soils and sediment. Appl Microbiol Biotechnol. 2007; 77: 955-964. PMID: 17960375
10. Morgan JL, Darling AE, Eisen JA. Metagenomic Sequencing of an In Vitro-Simulated Microbial Community. PLoS ONE. 2010; 5: e10209. doi: 10.1371/journal.pone.0010209 PMID: 20419134
11. Yuan S, Cohen DB, Ravel J, Abdo Z, Forney LJ. Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome. PLoS ONE. 2012; 7: e33865. doi: 10.1371/journal.pone.0033865 PMID: 22457796
12. Vishnivetskaya TA, Layton AC, Lau MCY, Chauhan A, Cheng KR, Meyers AJ, et al. Commercial DNA extraction kits impact observed microbial community composition in permafrost samples. FEMS Microbiol Ecol. 2014; 87: 217-230. doi: 10.1111/1574-6941.12219 PMID: 24102625
13. Wesolowska-Andersen A, Bahl M, Carvalho V, Kristiansen K, Sicheritz-Pontén T, Gupta R, et al. Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis. Microbiome. 2014; 2: 19. doi: 10.1186/2049-2618-2-19 PMID: 24949196
14. Temperton B, Field D, Oliver A, Tiwari B, Muhling M, Joint I, et al. Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing. ISME J. 2009; 3: 792-796. doi: 10.1038/ismej.2009.32 PMID: 19340085
15. Berry D, Mahfoudh KB, Wagner M, Loy A. Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Appl Environ Microbiol. 2011; 77: 7846-7849. doi: 10.1128/AEM.05220-11 PMID: 21890669
16. Pinto AJ, Raskin L. PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets. PLoS ONE. 2012; 7: e43093. doi: 10.1371/journal.pone.0043093 PMID: 22905208
17. Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M. Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environ Microbiol. 2013; 15: 1882-1899. doi: 10.1111/1462-2920.12086 PMID: 23387867
18. Lee CK, Herbold CW, Polson SW, Wommack KE, Williamson SJ, McDonald IR, et al. Groundtruthing Next-Gen Sequencing for Microbial Ecology, Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing. PLoS ONE. 2012; 7: e44224. doi: 10.1371/journal.pone.0044224 PMID: 22970184
19. McMurdie PJ, Holmes S. Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible. PLoS Comput Biol. 2014; 10: e1003531. doi: 10.1371/journal.pcbi.1003531 PMID: 24699258
20. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, et al. Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA. 2008; 105: 3805-3810. doi: 10.1073/pnas.0708897105 PMID: 18316740
21. Poretsky RS, Hewson I, Sun S, Allen AE, Zehr JP, Moran MA. Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. Environ Microbiol. 2009; 11: 1358-1375. doi: 10.1111/j.1462-2920.2008.01863.x PMID: 19207571
22. Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, Niazi F, et al. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci USA. 2010; 107: 7503-7508. doi: 10.1073/pnas.1002355107 PMID: 20363958
23. Lesniewski RA, Jain S, Anantharaman K, Schloss PD, Dick GJ. The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs. ISME J. 2012; 6: 2257-2268. doi: 10.1038/ismej.2012.63 PMID: 22695860
24. Yu K, Zhang T. Metagenomic and Metatranscriptomic Analysis of Microbial Community Structure and Gene Expression of Activated Sludge. PLoS ONE. 2012; 7: e38183. doi: 10.1371/journal.pone.0038183 PMID: 22666477
25. Ottesen EA, Young CR, Gifford SM, Eppley JM, Marin R, Schuster SC, et al. Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages. Science. 2014; 345: 207-212. doi: 10.1126/science.1252476 PMID: 25013074
26. Frostegard A, Courtois S, Ramisse V, Clerc S, Bernillon D, Le Gall F, et al. Quantification of Bias Related to the Extraction of DNA Directly from Soils. Appl Environ Microbiol. 1999; 65: 5409-5420. PMID: 10583997
27. Hurt RA, Qiu X, Wu L, Roh Y, Palumbo AV, Tiedje JM, et al. Simultaneous Recovery of RNA and DNA from Soils and Sediments. Appl Environ Microbiol. 2001; 67: 4495-4503. PMID: 11571148
28. Roume H, Muller EEL, Cordes T, Renaut J, Hiller K, Wilmes P. A biomolecular isolation framework for eco-systems biology. ISME J. 2013; 7: 110-121. doi: 10.1038/ismej.2012.72 PMID: 22763648
29. Muller EEL, Glaab E, May P, Vlassis N, Wilmes P. Condensing the omics fog of microbial communities. Trends Microbiol. 2013; 21: 325-333. doi: 10.1016/j.tim.2013.04.009 PMID: 23764387
30. Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, Walters WA, et al. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem. 2011; 43: 1450-1455. PMID: 22267877
31. Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S. A Guide to the Natural History of Freshwater Lake Bacteria. Microbiol Mol Biol Rev. 2011; 75: 14-49. doi: 10.1128/MMBR.00028-10 PMID: 21372319
32. Halm H, Musat N, Lam P, Langlois R, Musat F, Peduzzi S, et al. Co-occurrence of denitrification and nitrogen fixation in a meromictic lake, Lake Cadagno (Switzerland). Environ Microbiol. 2009; 11: 1945-1958. doi: 10.1111/j.1462-2920.2009.01917.x PMID: 19397681
33. Peng X, Jayakumar A, Ward BB. Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones. Frontiers Microbiol. 2013; 4
34. Rich VI, Konstantinidis K, DeLong EF. Design and testing of 'genome-proxy' microarrays to profile marine microbial communities. Environ Microbiol. 2008; 10: 506-521. PMID: 18028413
35. Anantharaman K, Breier JA, Sheik CS, Dick GJ. Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria. Proc Natl Acad Sci USA. 2013; 110: 330-335. doi: 10.1073/pnas.1215340110 PMID: 23263870
36. Rissanen A, Kurhela E, Aho T, Oittinen T, Tiirola M. Storage of environmental samples for guaranteeing nucleic acid yields for molecular microbiological studies. Appl Microbiol Biotechnol. 2010; 88: 977-984. doi: 10.1007/s00253-010-2838-2 PMID: 20730531
37. Boström KH, Simu K, Hagström A, Riemann L. Optimization of DNA extraction for quantitative marine bacterioplankton community analysis. Limnol Oceanogr Meth. 2004; 2: 365-373.
38. Fuhrman JA, Comeau DE, Hagström Å, Chan AM. Extraction from Natural Planktonic Microorganisms of DNA Suitable for Molecular Biological Studies. Appl Environ Microbiol. 1988; 54: 1426-1429. PMID: 16347652
39. Poretsky R, Rodriguez-R LM, Luo C, Tsementzi D, Konstantinidis KT. Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics. PLoS ONE. 2014; 9: e93827. doi: 10.1371/journal.pone.0093827 PMID: 24714158
40. Kuczynski J, Costello E, Nemergut D, Zaneveld J, Lauber C, Knights D, et al. Direct sequencing of the human microbiome readily reveals community differences. Genome Biol. 2010; 11: 210. doi: 10.1186/gb-2010-11-5-210 PMID: 20441597
41. Tsementzi D, Poretsky R, Rodriguez-R LM, Luo C, Konstantinidis KT. Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities. Environ Microbiol Rep. 2014; 6: 640-655. PMID: 25756118
42. Arnds J, Knittel K, Buck U, Winkel M, Amann R. Development of a 16S rRNA-targeted probe set for Verrucomicrobia and its application for fluorescence in situ hybridization in a humic lake. Syst Appl Microbiol. 2010; 33: 139-148. doi: 10.1016/j.syapm.2009.12.005 PMID: 20226613
43. Dominianni C, Wu J, Hayes R, Ahn J. Comparison of methods for fecal microbiome biospecimen collection. BMC Microbiol. 2014; 14: 103. doi: 10.1186/1471-2180-14-103 PMID: 24758293
44. Tatangelo V, Franzetti A, Gandolfi I, Bestetti G, Ambrosini R. Effect of preservation method on the assessment of bacterial community structure in soil and water samples. FEMS Microbiol Lett. 2014; 356: 32-38. doi: 10.1111/1574-6968.12475 PMID: 24840085
45. Shi Y, Tyson GW, DeLong EF. Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature. 2009; 459: 266-269. doi: 10.1038/nature08055 PMID: 19444216
46. Anantharaman K, Breier JA, Sheik CS, Dick GJ. Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria. Proc Natl Acad Sci USA. 2012; 110: 330-335. doi:10.1073/pnas.1215340110 PMID: 23263870
47. Dick GJ, Tebo BM. Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume. Environ Microbiol. 2010; 12: 1334-1347. doi: 10.1111/j.1462-2920.2010.02177.x PMID: 20192971
48. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol. 2013; 79: 5112-5120. doi: 10.1128/AEM.01043-13 PMID:23793624
49. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012; 6: 1621-1624. doi: 10.1038/ismej.2012.8 PMID: 22402401
50. Allers E, Wright JJ, Konwar KM, Howes CG, Beneze E, Hallam SJ, et al. Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean. ISME J. 2013; 7: 256-268. doi: 10.1038/ismej.2012.108 PMID: 23151638
51. Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol. 1990; 56: 1919-1925. PMID: 2200342
52. Daims H, Brühl A, Amann R, Schleifer K-H, Wagner M. The Domain-specific Probe EUB338 is Insufficient for the Detection of all Bacteria: Development and Evaluation of a more Comprehensive Probe Set. Syst Appl Microbiol. 1999; 22: 434-444. PMID: 10553296
53. Wallner G, Amann R, Beisker W. Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry. 1993; 14: 136-143. PMID: 7679962