Soil microbiome responses to the short-term effects of Amazonian deforestation

Molecular Ecology

Volumn 24, Issue 10, 2015, Pages 2433-2448

  Navarrete, Acacio A ^a,b   Tsai, Siu M ^a   Mendes, Lucas W ^a,b   Faust, Karoline ^c   De Hollander, Mattias ^b   Cassman, Noriko A ^b   Raes, Jeroen ^c   Van Veen, Johannes A ^b,d   Kuramae, Eiko E ^b  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b NETHERLANDS INSTITUTE OF ECOLOGY NIOO KNAW   (Netherlands)

^c REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^d LEIDEN UNIVERSITY   (Netherlands)

Author keywords

16S rRNA gene; bacterial networks; metagenomics; slash and burning; soil microbial ecology; tropical rainforest

Indexed keywords

ACTINOBACTERIA; ACTINOMYCETALES; BACTERIA (MICROORGANISMS); CHLAMYDIAE; PLANCTOMYCETES; VERRUCOMICROBIA;

BACTERIAL DNA; RNA 16S; SOIL;

AGRICULTURE; BACTERIUM; CHEMISTRY; CLASSIFICATION; ENVIRONMENTAL PROTECTION; FOREST; GENETICS; HIGH THROUGHPUT SEQUENCING; MICROBIOLOGY; MICROFLORA; PROCEDURES; SOIL;

AGRICULTURE; BACTERIA; CONSERVATION OF NATURAL RESOURCES; DNA, BACTERIAL; FORESTS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROBIOTA; RNA, RIBOSOMAL, 16S; SOIL; SOIL MICROBIOLOGY;

EID: 84928353254     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.13172     Document Type: Article

References (57)

1. Aziz RK, Bartels D, Best AA, et al,. (2008) The RAST server: rapid annotation using subsystems technology. BMC Genomics, 9, 75.
2. Barberan A, Bates ST, Casamayor EO, Fierer N, (2012) Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME Journal, 6, 343-351.
3. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate-a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B-Methodological, 57, 289-300.
4. Bibb MJ, (2005) Regulation of secondary metabolism in streptomycetes. Current Opinion in Microbiology, 8, 208-215.
5. Brown MB, (1975) 400: A method for combining non-independent one-sided tests of significance. Biometrics, 31, 987-992.
6. Buckley DH, Schmidt TM, (2001) The structure of microbial communities in soil and the lasting impact of cultivation. Microbial Ecology, 42, 11-21.
7. Buckley DH, Huangyutitham V, Nelson TA, Rumberger A, Thies JE, (2006) Diversity of Planctomycetes in soil in relation to soil history and environmental heterogeneity. Applied and Environmental Microbiology, 72, 4522-4531.
8. Caporaso JG, Kuczynski J, Stombaugh J, et al,. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7, 335-336.
9. Certini G, (2005) Effects of fire on properties of forest soils: A review. Oecologia, 143, 1-10.
10. Clauset A, Newman M, Moore C, (2004) Finding community structure in very large networks. Physical Review E, 70, 066111.
11. Edgar RC, (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
12. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R, (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27, 2194-2200.
13. Faust K, Sathirapongsasuti JF, Izard J, et al,. (2012) Microbial co-occurrence relationships in the human microbiome. PLoS Computational Biology, 8, e1002606.
14. Fearnside PM, (2005) Desmatamento na Amazônia brasileira: Histõria, índices e consequências. Megadiversidade, 1, 113-122.
15. Fierer N, Jackson JA, Vilgalys R, Jackson RB, (2005) Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Applied and Environmental Microbiology, 71, 4117-4120.
16. Fierer N, Bradford MA, Jackson RB, (2007) Toward an ecological classification of soil bacteria. Ecology, 88, 1354-1364.
17. Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R, (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME Journal, 6, 1007-1017.
18. Fisher WD, (1958) On grouping for maximum homogeneity. Journal of the American Statistical Association, 53, 789-798.
19. Fujisaka S, Bell W, Thomas N, Hurtado L, Crawford E, (1996) Slash-and-burn agriculture, conversion to pasture, and deforestation in two Brazilian Amazon colonies. Agriculture, Ecosystems and Environment, 59, 115-130.
20. Fujisaka S, Castilla C, Escobar G, et al,. (1998) The effects of forest conversion on annual crops and pastures: estimates of carbon emissions and plant species loss in a Brazilian Amazon colony. Agriculture, Ecosystems and Environment, 69, 17-26.
21. Giardina CP, Sanford RL, Dockersmith IC, Jaramillo VJ, (2000) The effects of slash burning on ecosystem nutrients during the land preparation phase of shifting cultivation. Plant and Soil, 220, 247-260.
22. Goecks J, Nekrutenko A, Taylor J, Galaxy T, (2010) Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology, 11, R86.
23. González-Pérez JA, González-Vila FJ, Almendros G, Knicker H, (2004) The effect of fire on soil organic matter-a review. Environment International, 30, 855-870.
24. Hamady M, Lozupone C, Knight R, (2010) Fast UniFrac: facilitating high-throughput phylogenetic analysis of microbial communities including analysis of pyrosequencing and phylochip data. ISME Journal, 4, 17-27.
25. Isanapong J, Goodwin L, Bruce D, Chen A, Detter C, (2012) High-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, a symbiont of the wood-feeding termite Reticulitermes flavipes. Journal of Bacteriology, 194, 2744-2745.
26. Jesus ED, Marsh TL, Tiedje JM, Moreira FMD, (2009) Changes in land use alter the structure of bacterial communities in Western Amazon soils. ISME Journal, 3, 1004-1011.
27. Jiricny J, (1998) Replication errors: cha(lle)nging the genome. The EMBO Journal, 17, 6427-6436.
28. Juo ASR, Manu A, (1996) Chemical dynamics in slash-and-burn agriculture. Agriculture, Ecosystems and Environment, 58, 49-60.
29. Lane D, (1991) 16S/23S rRNA sequencing. In: Nucleic Acid Techniques in Bacterial Systematics (eds, Stackebrandtand E, Goodfellow M,), pp. 115-175. John Wiley & Sons, West Sussex, UK.
30. Lauber CL, Hamady M, Knight R, Fierer N, (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and Environmental Microbiology, 75, 5111-5120.
31. Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell J, (2000) Molecular Cell Biology, 4th edn. W. H. Freeman, New York. Section 3.2, Folding, modification, and degradation of proteins. Available from: http://www.ncbi.nlm.nih.gov/books/NBK21750/
32. Lozupone C, Hamady M, Knight R, (2006) UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics, 7, 371.
33. MacArthur R, Wilson E, (1967) The Theory of Island Biogeography. Princeton University Press, Princeton, New Jersey.
34. Maeder P, Fließach A, Dubois D, Gunst L, Fried P, Niggli U, (2002) Soil fertility and biodiversity in organic farming. Science, 296, 1694-1697.
35. McBride MB, (1994) Environmental Chemistry of Soils. Oxford University Press, New York.
36. Mendes LW, Tsai SM, Navarrete AA, de Hollander M, van Veen JA, Kuramae EE, (2015) Soil-borne microbiome: linking diversity to function. Microbial Ecology. doi: 10.1007/s00248-014-0559-2
37. Meyer F, Paarman D, D'Souza M, et al,. (2008) The Metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics, 9, 386.
38. Morton DC, DeFries RS, Shimabukuro YE, et al,. (2006) Cropland expansion changes deforestation dynamics in the southern Brazilian Amazon. Proceedings of the National Academy of Sciences of the United States of America, 103, 14637-14641.
39. Navarrete AA, Taketani RG, Mendes LW, Cannavan FS, Moreira FMS, Tsai SM, (2011) Land-use systems affect archaeal community structure and functional diversity in western Amazon soils. Revista Brasileira de Ciência do Solo, 35, 1527-1540.
40. Navarrete AA, Kuramae EE, de Hollander M, Pijl AS, van Veen JA, Tsai SM, (2013) Acidobacterial community responses to agricultural management of soybean in Amazon forest soils. FEMS Microbiology Ecology, 83, 607-621.
41. Newcombe RG, (1998) Improved confidence intervals for the difference between binomial proportions based on paired data. Statistics in Medicine, 17, 2635-2650.
42. Noll M, Matthies D, Frenzel P, Derakshani M, Liesack W, (2005) Succession of bacterial community structure and diversity in a paddy soil oxygen gradient. Environmental Microbiology, 7, 382-395.
43. Nye P, Greenland D, (1960) The soil under shifting cultivation. Technical Communication Common Wealth Agricultural Bureau, 51, 156.
44. Olden JD, Poff NL, (2003) Toward a mechanistic understanding and prediction of biotic homogenization. The American Naturalist, 162, 442-460.
45. Overbeek R, Begley T, Butler RM, et al,. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Research, 33, 5691-5702.
46. Parks DH, Beiko RG, (2010) Identifying biologically relevant differences between metagenomic communities. Bioinformatics, 26, 715-721.
47. Ramirez KS, Craine JM, Fierer N, (2012) Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes. Global Change Biology, 18, 1918-1927.
48. Reeder J, Knight R, (2010) Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nature Methods, 7, 668-669.
49. Rodrigues JLM, Pellizari VH, Mueller R, et al,. (2013) Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America, 110, 988-993.
50. Shange RS, Ankumah RO, Ibekwe AM, Zabawa R, Dowd SE, (2012) Distinct soil bacterial communities revealed under a diversely managed agroecosystem. PLoS ONE, 7, e40338.
51. Smoot M, Ono K, Ruscheinski J, Wang P-L, Ideker T, (2012) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics, 27, 431-432.
52. Sonia MT, Naceur J, Abdennaceur H, (2011) Studies on the ecology of actinomycetes in an agricultural soil amended with organic residues: I. Identification of the dominant groups of Actinomycetales. World Journal of Microbiology and Biotechnology, 27, 2239-2249.
53. Sul WJ, Asuming-Brempong S, Wang Q, et al,. (2013) Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon. Soil Biology and Biochemistry, 65, 33-38.
54. Wagner M, Horn M, (2006) The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Current Opinion in Biotechnology, 17, 241-249.
55. Wakelin SA, Barratt BIP, Gerard E, et al,. (2013) Shifts in the phylogenetic structure and functional capacity of soil microbial communities follow alteration of native tussock grassland ecosystems. Soil Biology and Biochemistry, 57, 675-682.
56. Wang Q, Garrity GM, Tiedje JM, Cole JR, (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73, 5261-5267.
57. Zhang X, Chen Q, Han X, (2013) Soil bacterial communities respond to mowing and nutrient addition in a steppe ecosystem. PLoS ONE, 8, e84210.