Bacterial community structure in fumigated soil

Soil Biology and Biochemistry

Volumn 73, Issue , 2014, Pages 122-129

  Domínguez Mendoza, Cristina A ^a   Bello López, Juan M ^a   Navarro Noya, Yendi E ^a   de León Lorenzana, Arit S ^a   Delgado Balbuena, Laura ^a   Gómez Acata, Selene ^a   Ruíz Valdiviezo, Victor M ^a   Ramirez Villanueva, Daniel A ^a   Luna Guido, Marco ^a   Dendooven, Luc ^a  

^a DEPARTAMENTO DE FÍSICA   (Mexico)

Author keywords

Bacillus; C and N mineralization; Cohnella; Fumigated and unfumigated arable soil; Micromonospora; Paenibacillus

Indexed keywords

AGRICULTURE; BACILLI; BACTERIA; BACTERIOLOGY; BIOGEOCHEMISTRY; CHLORINE COMPOUNDS; MINERALOGY; ORGANIC COMPOUNDS; RNA;

ARABLE SOILS; C AND N MINERALIZATION; COHNELLA; MICROMONOSPORA; PAENIBACILLUS;

SOILS;

ABUNDANCE; CHLOROFORM; COMMUNITY STRUCTURE; FUMIGANT; METABOLISM; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; POLLUTION TOLERANCE; RECOLONIZATION; SOIL EMISSION; SOIL MICROORGANISM;

EID: 84896510175     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2014.02.012     Document Type: Article

References (52)

1. Abera G., Wolde-meskel E., Bakken L.R. Carbon and nitrogen mineralization dynamics in different soils of the tropics amended with legume residues and contrasting soil moisture contents. Biology and Fertility of Soils 2012, 48:51-66.
2. Acinas S.G., Klepac-Ceraj V., Hunt D.E., Pharino C., Ceraj I., Distel D.L., Polz M.F. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 2004, 430:551-553.
3. Aguilar-Chávez A., Díaz-Rojas M., Cárdenas-Aquino M.R., Dendooven L., Luna-Guido M. Greenhouse gas emissions from a wastewater sludge-amended soil cultivated with wheat (Triticum spp. L.) as affected by different application rates of charcoal. Soil Biology and Biochemistry 2012, 52:90-95.
4. Bandounas L., Wierckx N.J.P., de Winde J.H., Ruijssenaars H.J. Isolation and characterization of novel bacterial strains exhibiting ligninolytic potential. BMC Biotechnology 2011, 11:94.
5. Cano R.J., Borucki M.K. Revival and identification of bacterial spores in 25- to 40-million-year-old dominican amber. Science 1995, 268:1060-1064.
6. Caporaso J.G., Bittinger K., Bushman F.D., DeSantis T.Z., Andersen G.L., Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 2010, 26:266e267.
7. Caporaso J.G., Kuczynski J., Stombaugh J., Bittinger K., Bushman F.D., Costello E.K., Fierer N., Peña A.G., Goodrich J.K., Gordon J.I., Huttley G.A., Kelley S.T., Knights D., Koenig J.E., Ley R.E., Lozupone C.A., McDonald D., Muegge B.D., Pirrung M., Reeder J., Sevinsky J.R., Turnbaugh P.J., Walters W.A., Widmann J., Yatsunenko T., Zaneveld J., Knight R. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 2010, 7:335-336.
8. Ceja-Navarro J.A., Rivera-Orduña F.N., Patiño-Zúñiga L., Vila-Sanjurjo A., Crossa J., Govaerts B., Dendooven L. Phylogenetic and multivariate analyses to determine the effects of different tillage and residue management practices on soil bacterial communities. Applied and Environmental Microbiology 2010, 76:3685-3691.
9. Chandra R., Raj A., Purohit H.J., Kapley A. Characterization and optimization of three potential aerobic bacterial strains for kraft lignin degradation from pulp paper waste. Chemosphere 2007, 67:839-846.
10. Cucurachi M., Busconi M., Marudelli M., Soffritti G., Fogher C. Direct amplification of new cellulase genes from woodland soil purified DNA. Molecular Biology Reports 2013, 40:4317-4325.
11. de Gannes V., Eudoxie G., Hickey W.J. Prokaryotic successions and diversity in composts as revealed by 454-pyrosequencing. Bioresource Technology 2013, 133:573-580.
12. de Menezes A.B., McDonald J.E., Allison H.E., McCarthy A.J. Importance of Micromonospora spp. as colonizers of cellulose in freshwater lakes as demonstrated by quantitative reverse transcriptase PCR of 16S rRNA. Applied and Environmental Microbiology 2012, 78:3495-3499.
13. D'haeseleer P., Gladden J.M., Allgaier M., Chain P.S.G., Tringe S.G., Malfatti S.A., Aldrich J.T., Nicora C.D., Robinson E.W., Paša-Tolić L., Hugenholtz P., Simmons B.A., Singer S.W. Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PLoS One 2013, 8:e68465.
14. Dungait J.A.J., Kemmitt S.J., Michallon L., Guo S., Wen Q., Brookes P.C. The variable response of soil microorganisms to trace concentrations of low molecular weight organic substrates of increasing complexity. Soil Biology & Biochemistry 2013, 64:57-64.
15. Edgar R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26:2460-2461.
16. Eida M.F., Nagaoka T., Kouno K. Isolation and characterization of cellulose-decomposing bacteria inhabiting sawdust and coffee residue composts. Microbes and Environments 2012, 27:226-233.
17. El-Katatny M.H., Gudelj M., Robra K.H., Elnaghy M.A., Gubitz G.M. Characterization of a chitinase and an endo-beta-1,3-glucanase from Trichoderma harzianum Rifai T24 involved in control of the phytopathogen Sclerotium rolfsii. Applied Microbiology and Biotechnology 2001, 56:137-143.
18. El-Tarabily K.A., Nassar A.H., Sivasithamparam K. Promotion of growth of bean (Phaseolus vulgaris L.) in a calcareous soil by a phosphate-solubilizing, rhizosphere-competent isolate of Micromonospora endolithica. Applied Soil Ecology 2008, 39:161-171.
19. 15N-DNA stable isotope probing. Pedobiologia 2011, 54:187-193.
20. Fierer N., Bradford M.A., Jackson R.B. Toward an ecological classification of soil bacteria. Ecology 2007, 88:1354-1364.
21. Fierer N., Strickland M.S., Liptzin D., Bradford M.A., Cleveland C.C. Global patterns in belowground communities. Ecology Letters 2009, 12:1238-1249.
22. García-Fraile P., Velázquez E., Mateos P.F., Martínez-Molina E., Rivas R. Cohnella phaseoli sp. nov., isolated from root nodules of Phaseolus coccineus in Spain, and emended description of the genus Cohnella. International Journal of Systematic and Evolutionary Microbiology 2008, 58:1855-1859.
23. Genilloud O. Genus I. Micromonospora. Bergey's Manual of Systematic Bacteriology: the Actinobacteria 2012, 1039-1057. Bergey's Manual Trust, Springer, Athens, GA. second ed. M. Goodfellow, P. Kämpfer, H.-J. Busse, M.E. Trujillo, K.I. Suzuki, W. Ludwig, W.B. Whitman (Eds.).
24. Goldfarb K.C., Karaoz U., Hanson C.A., Santee C.A., Bradford M.A., Treseder K.K., Wallenstein M.D., Brodie E.L. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Frontiers in Microbiology 2011, 2:94.
25. Haas B.J., Gevers D., Earl A.M., Feldgarden M., Ward D.V., Giannoukos G., Ciulla D., Tabbaa D., Highlander S.K., Sodergren E., Methé B., DeSantis T.Z., Petrosino J.F., Knight R., Birren B.W. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Research 2011, 21:494e504. The Human Microbiome Consortium.
26. Hamady M., Lozupone C., Knight R. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. The ISME Journal 2010, 4:17-27.
27. Hardisson C., Suarez J.E. Fine structure of spore formation and germination in Micromonospora chalcea. Journal of General Microbiology 1979, 110:233-237.
28. Hatayama K., Shoun H., Ueda Y., Nakamura A. Tuberibacillus calidus gen. nov., sp. nov., isolated from a compost pile and reclassification of Bacillus naganoensis Tomimura etal. 1990 as Pullulanibacillus naganoensis gen. nov., comb. nov. and Bacillus laevolacticus Andersch etal. 1994 as Sporolactobacillus laevolacticus comb. nov. International Journal of Systematic and Evolutionary Microbiology 2006, 56:2545-2551.
29. He Y.M., Xie K.Z., Xu P.Z., Huang X., Gu W.J., Zhang F.B., Tang S.H. Evolution of microbial community diversity and enzymatic activity during composting. Research in Microbiology 2013, 164:189-198.
30. Jendrossek D., Tomasi G., Kroppenstedt R.M. Bacterial degradation of natural rubber: a privilege of actinomycetes?. FEMS Microbiology Letters 1997, 150:179-188.
31. Jenkinson D.S., Powlson D.S. The effects of biocidal treatments on metabolism in soil. V. A method for measuring soil biomass. Soil Biology and Biochemistry 1976, 8:209-213.
32. Kemmit S.J., Lanyon C.V., Waite I.S., Wen Q., Addiscott T.M., Bird N.R.A., O'Donnell A.G., Brookes P.C. Mineralization of native soil organic matter is not regulated by the size, activity or composition of the soil microbial biomass-a new perspective. Soil Biology & Biochemistry 2008, 40:61-73.
33. Kim B.C., Lee K.H., Kim M.N., Kim E.M., Rhee M.S., Kwon O.Y., Shin K.S. Paenibacillus pinihumi sp. nov., a cellulolytic bacterium isolated from the rhizosphere of Pinus densiflora. Journal of Microbiology 2009, 47:530-535.
34. Kirchman D.L. Processes in Microbial Ecology 2012, Oxford University Press Inc., New York. first ed.
35. Ko C.H., Lin Z.P., Tu J., Tsai C.H., Liu C.C., Chen H.T., Wang T.P. Xylanase production by Paenibacillus campinasensis BL11 and its pretreatment of hardwood kraft pulp bleaching. International Biodeterioration and Biodegradation 2010, 64:13-19.
36. Ko C.H., Tsai C.H., Lin P.H., Chang K.C., Tu J., Wang Y.N., Yang C.Y. Characterization and pulp refining activity of a Paenibacillus campinasensis cellulase expressed in Escherichia coli. Bioresource Technology 2010, 101:7882-7888.
37. Kolter R., Siegele D.A., Tormo A. The stationary phase of the bacterial life cycle. Annual Review of Microbiology 1993, 47:855-874.
38. Martins L.F., Antunes L.P., Pascon R.C., de Oliveira J.C.F., Digiampietri L.A., Barbosa D., Peixoto B.M., Vallim M.A., Viana-Niero C., Ostroski E.H., Telles G.P., Dias Z., da Cruz J.B., Juliano L., Verjovski-Almeida S., da Silva A.M., Setubal J.C. Metagenomic analysis of a tropical composting operation at the São Paulo Zoo Park reveals diversity of biomass degradation functions and organisms. PLoS One 2013, 8:e61928.
39. Mead D.A., Lucas S., Copeland A., Lapidus A., Cheng J.F., Bruce D.C., Goodwin L.A., Pitluck S., Chertkov O., Zhang X., Detter J.C., Han C.S., Tapia R., Land M., Hauser L.J., Chang Y.J., Kyrpides K.C., Ivanova N.N., Ovchinnikova G., Woyke T., Brumm C., Hochstein R., Schoenfeld T., Brumm P. Complete genome sequence of Paenibacillus strain Y4.12MC10, a novel Paenibacillus lautus strain isolated from obsidian hot spring in Yellowstone National Park. Standards in Genomic Sciences 2012, 6:381-400.
40. Mueller T., Joergensen R.G., Meyer B. Estimation of soil microbial biomass-C in the presence of living roots by fumigation extraction. Soil Biology and Biochemistry 1992, 24:179-181.
41. Navarro-Noya Y.E., Gómez-Acata S., Montoya-Ciriaco N., Rojas-Valdez A., Suárez-Arriaga M.C., Valenzuela-Encinas C., Jiménez-Bueno N., Verhulst N., Govaerts B., Dendooven L. Relative impacts of tillage, residue management and crop-rotation on soil bacterial communities in a semi-arid agroecosystem. Soil Biology and Biochemistry 2013, 65:86-95.
42. Partanen P., Hultman J., Paulin L., Auvinen P., Romantschuk M. Bacterial diversity at different stages of the composting process. BMC Microbiology 2010, 10:94.
43. Pathma J., Sakthivel N. Molecular and functional characterization of bacteria isolated from straw and goat manure based vermicompost. Applied Soil Ecology 2013, 70:33-47.
44. Price M.N., Dehal P.S., Arkin A.P. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Molecular Biology and Evolution 2009, 26:1641-1650.
45. Rousk J., Brookes P.C., Bååth E. Contrasting soil pH effects on fungal and bacterial growth suggests functional redundancy in carbon mineralization. Applied and Environmental Microbiology 2009, 75:1589-1596.
46. Ruíz-Valdiviezo V.M., Luna-Guido M., Galzy A., Gutiérrez-Miceli F.A., Dendooven L. Greenhouse gas emissions and C and N mineralization in soils of Chiapas (México) amended with leaves of piñón (Jatropha curcas L.). Applied Soil Ecology 2010, 46:17-25.
47. SAS Institute Statistic Guide for Personal Computers, Version 6.04 1989, SAS Institute, Cary.
48. Sirota-Madi A., Olender T., Helman Y., Ingham C., Brainis I., Roth D., Hagi E., Brodsky L., Leshkowitz D., Galatenko V., Nikolaev V., Mugasimangalam R.C., Bransburg-Zabary S., Gutnick D.L., Lancet D., Ben-Jacob E. Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments. BMC Genomics 2010, 11:710.
49. Talia P., Sede S.M., Campos E., Rorig M., Principi D., Tosto D., Hopp H.E., Grasso D., Cataldi A. Biodiversity characterization of cellulolytic bacteria present on native Chaco soil by comparison of ribosomal RNA genes. Research in Microbiology 2012, 163:221-232.
50. Wang Q., Garrity G.M., Tiedje J.M., Cole J.R. Native bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 2007, 73:5261-5267.
51. Wang Y.X., Liu Q., Yan L., Gao Y.M., Wang Y.J., Wang W.D. Anovel lignin degradation bacterial consortium for efficient pulping. Bioresource Technology 2013, 139:113-119.
52. Wohl D.L., McArthur J.V. Aquatic actinomycete-fungal interactions and their effects on organic matter decomposition: a microcosm study. Microbial Ecology 2001, 42:446-457.