Abstract
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.
Highlights
Archaea constitute one of the three major evolutionary lineages of life on Earth (Woese, 1987; Woese et al, 1990)
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
Subtle differences were noted in the soil N-NO3and total N concentrations under different land-use systems, the N-NO3- concentrations were lower in primary forest soils
Summary
Archaea constitute one of the three major evolutionary lineages of life on Earth (Woese, 1987; Woese et al, 1990). For the last two decades, Archaea have been the focus of a growing number of studies on microbial ecology due to their ubiquity and abundance in various natural and anthropogenically influenced terrestrial ecosystems, such as arable land, grassland and forest soils (reviewed by Chaban et al, 2006). The Amazon contains the world’s largest area of contiguous tropical forest and is constantly affected by high rates of deforestation and conversion to cattle pasture and other agricultural uses. In this context, Brazil has been slowing down deforestation by trying to make better use of already cleared land (Tollefson, 2010). The establishment of policies for the sustainable use of land in the Amazon region requires considering the diversity of flora and fauna and the aspects of microbial ecology and biogeochemistry represented in this region as well (Piccolo et al, 1994; Borneman & Triplett, 1997; Moraes et al, 2002; Cenciani et al, 2009; Chaves et al, 2009; Jesus et al, 2009; O’Neill et al, 2009; Pazinato et al, 2010)
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