Acácio Aparecido Navarrete(2), Rodrigo Gouvêa Taketani(3), Lucas William Mendes(4), Fabiana de Souza Cannavan(2), Fatima Maria de Souza Moreira(5) & Siu Mui Tsai(6)
Part of the Master’s Thesis of the first author for the Applied Ecology Program of the University of Sao Paulo (USP). Work
supported by grants from FAPESP, CNPq and GEF/UNEP. Received for publication in December 15, 2010 and approved in
June 27, 2011.
(2) Master’s Degree, Graduate Program in Applied Ecology of the Luiz de Queiroz College of Agriculture – ESALQ. University of Sao Paulo – USP. E- mails: email@example.com; firstname.lastname@example.org
(3) Pos-Doctor, Cell and Molecular Biology Laboratory, CENA-USP. E-mail: email@example.com
(4) Master’s Degree, Graduate Program in Science of the Centre for Nuclear Energy in Agriculture – CENA. University of Sao Paulo – USP. E- mail: firstname.lastname@example.org
(5) Associate Professor of Soil Microbiology and Biochemistry, Soil Science Department, Federal University of Lavras – UFLA. CEP 37200-000, Lavras (MG). E-mail: email@example.com
(6) Full Professor at Cell and Molecular Biology Laboratory, CENA. University of Sao Paulo – USP. Av. Centenário 303, CEP 13400-970 Piracicaba (SP) Brazil. E-mail: firstname.lastname@example.org
The study of the ecology of soil microbial communities at relevant spatial scales is primordial in the wide Amazon region due to the current land use changes. In this study, the diversity of the Archaea domain (community structure) and ammonia-oxidizing Archaea (richness and community composition) were investigated using molecular biology-based techniques in different land-use systems in western Amazonia, Brazil. Soil samples were collected in two periods with high precipitation (March 2008 and January 2009) from Inceptisols under primary tropical rainforest, secondary forest (5–20 year old), agricultural systems of indigenous people and cattle pasture. Denaturing gradient gel electrophoresis of polymerase chain reaction-amplified DNA (PCR-DGGE) using the 16S rRNA gene as a biomarker showed that archaeal community structures in crops and pasture soils are different from those in primary forest soil, which is more similar to the community structure in secondary forest soil. Sequence analysis of excised DGGE bands indicated the presence of crenarchaeal and euryarchaeal organisms. Based on clone library analysis of the gene coding the subunit of the enzyme ammonia monooxygenase (amoA) of Archaea (306 sequences), the Shannon-Wiener function and Simpson’s index showed a greater ammonia-oxidizing archaeal diversity in primary forest soils (H’ = 2.1486; D = 0.1366), followed by a lower diversity in soils under pasture (H’ = 1.9629; D = 0.1715), crops (H’ = 1.4613; D = 0.3309) and secondary forest (H’ = 0.8633; D = 0.5405). All cloned inserts were similar to the Crenarchaeota amoA gene clones (identity ≥ 95 %) previously found in soils and sediments and distributed primarily in three major phylogenetic clusters. The findings indicate that agricultural systems of indigenous people and cattle pasture affect the archaeal community structure and diversity of ammonia-oxidizing Archaea in western Amazon soils.
Index terms: soil microbial ecology; soil microbiology; microbial diversity; land use changes; tropical soils.
Revista Brasileira de Ciência do Solo, 35:1527-1540, 2011.