A Molecular Survey of the Diversity of Microbial Communities in Different Amazonian Agricultural Model Systems

Abstract

Abstract:The processes of land conversion and agricultural intensification are a significant cause of biodiversity loss, with consequent negative effects both on the environment and the sustainability of food production. The anthrosols associated with pre-Colombian settlements in the Amazonian region are examples of how anthropogenic activities may sustain the native populations against harsh tropical environments for human establishment, even without a previous intentionality of anthropic soil formation. In a case study (Model I-"Slash-andBurn") the community structures detected by automated ribosomal intergenic spacer analysis (ARISA) revealed that soil archaeal, bacterial and fungal communities are heterogeneous and each capable of responding differently to environmental characteristics. ARISA data evidenced considerable difference in structure existing between microbial communities in forest and agricultural soils. In a second study (Model II-"Anthropogenic Soil"), the bacterial community structures revealed by terminal restriction fragment length polymorphism (T-RFLP) differed among an Amazonian Dark Earth (ADE), black carbon (BC) and its adjacent non-anthropogenic oxisoil. The bacterial 16S rRNA gene (OTU) richness estimated by pyrosequencing was higher in ADE than BC. The most abundant bacterial phyla in ADE soils and BC were Proteobacteria-24% ADE, 15% BC; Acidobacteria-10% ADE, 21% BC; Actinobacteria-7% ADE, 12% BC; Verrucomicrobia, 8% ADE; 9% BC; Firmicutes-3% ADE, 8% BC. Overall, unclassified bacteria corresponded to 36% ADE, and 26% BC. Regardless of current land uses, our data suggest OPEN ACCESSDiversity 2010, 2 788 that soil microbial community structures may be strongly influenced by the historical soil management and that anthrosols in Amazonia, of anthropogenic origins, in addition to their capacity of enhancing crop yields, may also improve microbial diversity, with the support of the black carbon, which may sustain a particular and unique habitat for the microbes.

Land-use systems affect Archaeal community structure and functional diversity in western Amazon soils

“…The molecular data from the DGGE analysis of 16S rRNA for the Archaea domain showed that soil archaeal communities tended to become more similar to those of the primary forest when the forest was allowed to regenerate in an area under controlled agricultural use. Recent results from the same Amazon soils as in this study showed that archaeal and bacterial communities, evaluated by automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphism (T-RFLP), respectively, presented similar ecological patterns to the archaeal communities in this investigation Navarrete et al, 2010). Interestingly, Moreira et al (2009) reported that secondary forest is similar to primary forest regarding the fertility of the Inceptisols in the upper Solimões river region.…”

Functional diversity of bacterial genes associated with aromatic hydrocarbon degradation in anthropogenic dark earth of Amazonia

“…In both cases, the number of OPC was higher in the SF libraries, suggesting a significant influence of land use on microbial functional diversity. According to Jesus et al (2009), when studying land conversion from tropical forest to agricultural use, several alterations may occur in the size, activity and composition of the microbial communities, and unusual microbial communities, like specific functional bacterial groups, may prevail during shifts associated with deforestation (Borneman & Triplett, 1997;Navarrete et al, 2010). These findings stimulated studies on ADE at high concentrations of BC, as these particles are the oldest form of carbon in the soil (Pessenda et al, 2001), and were found to host a large number of microbes .…”

Genetic and Functional Diversities of Microbial Communities in Amazonian Soils Under Different Land Uses and Cultivation

“…While T-RFLP provided a good fingerprinting between Anthrosols and Adjacent soils, 16S rRNA sequencing provided better resolution of the changes, indicating Verrucomicrobia as an important group to the Anthrosols, Proteobacteria and Cyanobacteria for Adjacent soils; while Pseudomonas, Acidobacteria and Flexibacter were found in both sites. Studying the "Hatahara" site, differences in bacterial communities were also observed among Amazonian Dark Earth, black carbon and an adjacent oxisol by T-RFLP (Navarrete et al, 2010). By pyrosequencing it was shown that the most predominant phyla were Proteobacteria, Acidobacteria, Actinobacteria and Verrucomicrobia.…”

“…Secondary forest presented similar diversity with the community structure of the primary forest, showing that bacterial community can be restored after agricultural use of the soils. Using the automated ribosomal intergenic spacer amplification (ARISA) technique distinct microbial structures were also observed between agricultural and forest soils (Navarrete et al, 2010). Seasonal changes in the two different years of sampling and distinct band patterns were observed for fungal, bacterial and archaeal richness.…”