Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China

Frontiers in Microbiology

Volumn 6, Issue MAR, 2015, Pages

  Wu, Yucheng ^a   Tan, Liangcheng ^b,c   Liu, Wuxing ^a   Wang, Baozhan ^a   Wang, Jianjun ^d   Cai, Yanjun ^b   Lin, Xiangui ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b Chinese Academy of Sciences   (China)

^c JOINT CENTER FOR GLOBAL CHANGE STUDIES   (China)

^d NANJING INSTITUTE OF GEOGRAPHY AND LIMNOLOGY   (China)

Author keywords

16S rRNA; Bacterial diversity; Cave; Elemental composition; Pyrosequencing; Rock surface

Indexed keywords

LIMESTONE; PLASMID DNA; RIBOSOME RNA; RNA 16S;

ARTICLE; AUTOTROPHY; BACTERIAL COLONIZATION; BACTERIAL GROWTH; BACTERIAL IMMUNITY; BIOGEOCHEMICAL CYCLE; CARBON FIXATION; CHINA; DNA EXTRACTION; ECOSYSTEM; GENE AMPLIFICATION; GENETIC ANALYSIS; GENETIC HETEROGENEITY; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; POLYMERASE CHAIN REACTION; PYROSEQUENCING; SAMPLING; SEQUENCE ANALYSIS;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); GAMMAPROTEOBACTERIA;

EID: 84927511769     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2015.00244     Document Type: Article

References (41)

1. Barton, H. A., and Jurado, V. (2007). What's up down there? Microbial diversity in caves. Microbe 2, 132-138.
2. Barton, H. A., Taylor, N. M., Kreate, M. P., Springer, A. C., Oehrle, S. A., and Bertog., J. L. (2007). The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments. Int. J. Speleol. 36, 93-104. doi: 10.5038/1827-806X.36.2.5.
3. Carmichael, M. J., Carmichael, S. K., Santelli, C. M., Strom, A., and Bräuer, S. L. (2013). Mn(II)-oxidizing bacteria are abundant and environmentally relevant members of ferromanganese deposits in caves of the Upper Tennessee river basin. Geomicrobiol. J. 30, 779-800. doi: 10.1080/01490451.2013.769651.
4. Chen, Y., Wu, L., Boden, R., Hillebrand, A., Kumaresan, D., Moussard, H., et al. (2009). Life without light: microbial diversity and evidence of sulfur-and ammonium-based chemolithotrophy in Movile Cave. ISME J. 3, 1093-1104. doi: 10.1038/ismej.2009.57.
5. Cuezva, S., Fernandez-Cortes, A., Porca, E., Pašic, L., Jurado, V., Hernandez-Marine, M., et al. (2012). The biogeochemical role of actinobacteria in Altamira cave, Spain. FEMS Microbiol. Ecol. 81, 281-290. doi: 10.1111/j.1574-6941.2012.01391.x.
6. Desai, M. S., Assig, K., and Dattagupta, S. (2013). Nitrogen fixation in distinct microbial niches within a chemoautotrophy-driven cave ecosystem. ISME J. 7, 2411-2423. doi: 10.1038/ismej.2013.126.
7. Diaz-Herraiz, M., Jurado, V., Cuezva, S., Laiz, L., Pallecchi, P., Tiano, P., et al. (2013). The actinobacterial colonization of Etruscan paintings. Sci. Rep. 3, 1440. doi: 10.1038/srep01440.
8. Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., and Knight, R. (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200. doi: 10.1093/bioinformatics/btr381.
9. Engel, A. S., Stern, L. A., and Bennett, P. C. (2004). Microbial contributions to cave formation: new insights into sulfuric acid speleogenesis. Geology 32, 369-372. doi: 10.1130/G20288.1.
10. Francis, C. A., and Tebo, B. M. (2002). Enzymatic manganese(II) oxidation by metabolically dormant spores of diverse Bacillus species. Appl. Environ. Microbiol. 68, 874-880. doi: 10.1128/AEM.68.2.874-880.2002.
11. Gihring, T. M., Green, S. J., and Schadt, C. W. (2012). Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environ. Microbiol. 14, 285-290. doi: 10.1111/j.1462-2920.2011.02550.x.
12. Hedrich, S., Schlömann, M., and Johnson, D. B. (2011). The iron-oxidizing proteobacteria. Microbiology 157, 1551-1564. doi: 10.1099/mic.0.045344-0.
13. Hutchens, E., Gleeson, D., Mcdermott, F., Miranda-Casoluengo, R., and Clipson, N. (2010). Meter-scale diversity of microbial communities on a weathered pegmatite granite outcrop in the Wicklow Mountains, Ireland; evidence for mineral induced selection? Geomicrobiol. J. 27, 1-14. doi: 10.1080/01490450903232157.
14. Ikner, L., Toomey, R., Nolan, G., Neilson, J., Pryor, B., and Maier, R. (2007). Culturable microbial diversity and the impact of tourism in Kartchner Caverns, Arizona. Microb. Ecol. 53, 30-42. doi: 10.1007/s00248-006-9135-8.
15. Itoh, T., Yamanoi, K., Kudo, T., Ohkuma, M., and Takashina, T. (2011). Aciditerrimonas ferrireducens gen. nov., sp nov., an iron-reducing thermoacidophilic actinobacterium isolated from a solfataric field./Int. J. Syst. Evol. Microbiol. 61, 1281-1285. doi: 10.1099/ijs.0.023044-0.
16. Koops, H.-P., Purkhold, U., Pommerening-Röser, A., Timmermann, G., and Wagner, M. (2006). "The lithoautotrophic ammonia-oxidizing bacteria, "in The Prokaryotes, eds M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, and E. Stackebrandt (New York, NY: Springer), 778-811.
17. Lu, S., Gischkat, S., Reiche, M., Akob, D. M., Hallberg, K. B., and Küsel, K. (2010). Ecophysiology of Fe-cycling bacteria in acidic sediments. Appl. Environ. Microbiol. 76, 8174-8183. doi: 10.1128/AEM.01931-10.
18. Lücker, S., Wagner, M., Maixner, F., Pelletier, E., Koch, H., Vacherie, B., et al. (2010). A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc. Natl. Acad. Sci. U.S.A. 107, 13479-13484. doi: 10.1073/pnas.1003860107.
19. Macalady, J. L., Jones, D. S., and Lyon, E. H. (2007). Extremely acidic, pendulous cave wall biofilms from the Frasassi cave system, Italy. Environ. Microbiol. 9, 1402-1414. doi: 10.1111/j.1462-2920.2007.01256.x.
20. Mori, K., Suzuki, K.-I., Urabe, T., Sugihara, M., Tanaka, K., Hamada, M., et al. (2011). Thioprofundum hispidum sp. nov., an obligately chemolithoautotrophic sulfur-oxidizing gammaproteobacterium isolated from the hydrothermal field on Suiyo Seamount, and proposal of Thioalkalispiraceae fam. nov. in the order Chromatiales. Int. J. Syst. Evol. Microbiol. 61, 2412-2418. doi: 10.1099/ijs.0.026963-0.
21. Muyzer, G., Teske, A., Wirsen, C., and Jannasch, H. (1995). Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch. Microbiol. 164, 165-172. doi: 10.1007/BF02529967.
22. Ortiz, M., Legatzki, A., Neilson, J. W., Fryslie, B., Nelson, W. M., Wing, R. A., et al. (2013a). Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave. ISME J. 8, 478-491. doi: 10.1038/ismej.2013.159.
23. Ortiz, M., Neilson, J., Nelson, W., Legatzki, A., Byrne, A., Yu, Y., et al. (2013b). Profiling bacterial diversity and taxonomic composition on speleothem surfaces in Kartchner Caverns, AZ. Microb. Ecol. 65, 371-383. doi: 10.1007/s00248-012-0143-6.
24. Pašic, L., Kovce, B., Sket, B., and Herzog-Velikonja, B. (2010). Diversity of microbial communities colonizing the walls of a Karstic cave in Slovenia. FEMS Microbiol. Ecol. 71, 50-60. doi: 10.1111/j.1574-6941.2009.00789.x.
25. Porca, E., Jurado, V., Žgur-Bertok, D., Saiz-Jimenez, C., and Pašic, L. (2012). Comparative analysis of yellow microbial communities growing on the walls of geographically distinct caves indicates a common core of microorganisms involved in their formation. FEMS Microbiol. Ecol. 81, 255-266. doi: 10.1111/j.1574-6941.2012.01383.x.
26. Roesch, L. F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., et al. (2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1, 283-290.
27. Sarbu, S. M., Dane, T. C., and Kinkle, B. K. (1996). A chemoautotrophically based cave ecosystems. Science 272, 1953-1955. doi: 10.1126/science.272.5270.1953.
28. Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., et al. (2009). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541. doi: 10.1128/AEM.01541-09.
29. Shabarova, T., Widmer, F., and Pernthaler, J. (2013). Mass effects meet species sorting: transformations of microbial assemblages in epiphreatic subsurface karst water pools. Environ. Microbiol. 15, 2476-2488. doi: 10.1111/1462-2920.12124.
30. Sorokin, D. Y., Tourova, T. P., Braker, G., and Muyzer, G. (2007). Thiohalomonas denitrificans gen. nov., sp. nov. and Thiohalomonas nitratireducens sp. nov., novel obligately chemolithoautotrophic, moderately halophilic, thiodenitrifying Gammaproteobacteria from hypersaline habitats. Int. J. Syst. Evol. Microbiol. 57, 1582-1589. doi: 10.1099/ijs.0.65112-0.
31. Spilde, M. N., Northup, D. E., Boston, P. J., Schelble, R. T., Dano, K. E., Crossey, L. J., et al. (2005). Geomicrobiology of cave ferromanganese deposits: a field and laboratory investigation. Geomicrobiol. J. 22, 99-116. doi: 10.1080/01490450590945889.
32. Stahl, D. A., and Amann, R. (1991). "Development and application of nucleic acid probes, "in Nucleic Acid Techniques in Bacterial Systematics, eds E. Stackebrandt and M. Goodfellow (New York: Wiley), 205-248.
33. Sun, Y., Wu, F., Clemens, S. C., and Oppo, D. W. (2008). Processes controlling the geochemical composition of the South China Sea sediments during the last climatic cycle. Chem. Geol. 257, 240-246. doi: 10.1016/j.chemgeo.2008.10.002.
34. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739. doi: 10.1093/molbev/msr121.
35. Tan, L. (2008). High-Resolution Monsoon Precipitation Variations in China during the Last 2000 Years. Ph. D. thesis, Chinese Academy of Sciences, Beijing.
36. Tebo, B. M., Johnson, H. A., Mccarthy, J. K., and Templeton, A. S. (2005). Geomicrobiology of manganese(II) oxidation. Trends Microbiol. 13, 421-428. doi: 10.1016/j.tim.2005.07.009.
37. Tetu, S. G., Breakwell, K., Elbourne, L. D., Holmes, A. J., Gillings, M. R., and Paulsen, I. T. (2013). Life in the dark: metagenomic evidence that a microbial slime community is driven by inorganic nitrogen metabolism. ISME J. 7, 1227-1236. doi: 10.1038/ismej.2013.14.
38. Vetrovskỳ, T., and Baldrian, P. (2013). The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS ONE 8:e57923. doi: 10.1371/journal.pone.0057923.
39. Wang, Q., Garrity, G. M., Tiedje, J. M., and Cole, J. R. (2007). Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267. doi: 10.1128/AEM.00062-07.
40. Wu, Y., Ke, X., Hernández, M., Wang, B., Dumont, M. G., Jia, Z., et al. (2013). Autotrophic growth of bacterial and archaeal ammonia oxidizers in freshwater sediment microcosms incubated at different temperatures. Appl. Environ. Microbiol. 79, 3076-3084. doi: 10.1128/AEM.00061-13.
41. Yang, H., Ding, W., Zhang, C. L., Wu, X., Ma, X., He, G., et al. (2011). Occurrence of tetraether lipids in stalagmites: implications for sources and GDGT-based proxies. Org. Geochem. 42, 108-115. doi: 10.1016/j.orggeochem.2010.11.006.