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

Acácio A Navarrete,Siu M Tsai,Fabiana S Cannavan,Rodrigo G Taketani

doi:10.3390/d2050787

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-and-Burn”) 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 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.

Highlights

The Brazilian Amazon represents half of the world's rainforest and is home to one-third of theEarth's species, yet the Amazon has one of the highest rates of deforestation due to anthropogenic activities and dramatic changes in land use [1]
Our results extend the understanding about the bacterial phyla present in Amazonian Dark Earth (ADE) soil, such as those published by Kim et al [55] and add information about the bacterial community composition in black carbon (BC), unknown until now
The molecular methods used to study the microbial communities in two agricultural systems that are practiced in Amazonia, based upon the soil attributes, have enabled us to view a better but quite complex picture of the conditions of soil management by stakeholders or end-users who are looking to develop agricultural sustainability in tropical rain forest ecosystems without serious disturbance to these ecosystems

Summary

Introduction

The Brazilian Amazon represents half of the world's rainforest and is home to one-third of theEarth's species, yet the Amazon has one of the highest rates of deforestation due to anthropogenic activities and dramatic changes in land use [1]. Agriculture is one of the largest and most dynamic parts of the Brazilian economy, and those working to preserve the Amazonia biome are unlikely to be able to slow or stop the expansion of this sector. In this post-genomic era, the application of advanced technologies to solve agricultural issues while maintaining environmental quality is of great importance, as the Brazilian economy relies, to a high degree, on crop and food production. Agricultural systems of indigenous people based primarily on annual crops in shifting cultivation and long fallow, which involves the abandonment of areas coverage with annual cultivation allowing natural regeneration and fallow for approximately three years [6]

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Results

Conclusion