Chile is topographically and climatically diverse, with a wide array of diverse undisturbed ecosystems that include native plants that are highly adapted to local conditions. However, our understanding of the diversity, activity, and role of rhizobacteria associated with natural vegetation in undisturbed Chilean extreme ecosystems is very poor. In the present study, the combination of denaturing gradient gel electrophoresis and 454-pyrosequencing approaches was used to describe the rhizobacterial community structures of native plants grown in three representative Chilean extreme environments: Atacama Desert (ATA), Andes Mountains (AND), and Antarctic (ANT). Both molecular approaches revealed the presence of Proteobacteria, Bacteroidetes, and Actinobacteria as the dominant phyla in the rhizospheres of native plants. Lower numbers of operational taxonomic units (OTUs) were observed in rhizosphere soils from ATA compared with AND and ANT. Both approaches also showed differences in rhizobacterial community structures between extreme environments and between plant species. The differences among plant species grown in the same environment were attributed to the higher relative abundance of classes Gammaproteobacteria and Alphaproteobacteria. However, further studies are needed to determine which environmental factors regulate the structures of rhizobacterial communities, and how (or if) specific bacterial groups may contribute to the growth and survival of native plants in each Chilean extreme environments.

The rhizosphere (soil zone influenced by roots) is a complex environment that harbors diverse bacterial populations, which have an important role in biogeochemical cycling of organic matter and mineral nutrients. Nevertheless, our knowledge of the ecology and role of these bacteria in the rhizosphere is very limited, particularly regarding how indigenous bacteria are able to communicate, colonize root environments, and compete along the rhizosphere microsites. In recent decades, the development and improvement of molecular techniques have provided more accurate knowledge of bacteria in their natural environment, refining microbial ecology and generating new questions about the roles and functions of bacteria in the rhizosphere. Recently, advances insoil post-genomic techniques (metagenomics, metaproteomics and metatranscriptomics) are being applied to improve our understanding of the microbial communities at a higher resolution. Moreover, advantages and limitations of classical and post-genomic techniques must be considered when studying bacteria in the rhizosphere. This review provides an overview of the current knowledgeon the study of bacterial community in the rhizosphere by using modern molecular techniques, describing the bias of classical molecular techniques, next generation sequencing platforms and post-genomics techniques.

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Bacterial alkaline phosphomonoesterases (APases) are relevant for organic phosphorus (Po) recycling in many soils. However, the abundance and diversity of bacterial APase in the rhizospheres of native plants are poorly known, particularly in extreme environments. In this research work, we studied the composition of total and APase-harboring bacterial communities, abundances of selected APase genes (phoD and phoX), and APase activities in rhizosphere soils from native plants grown in extreme environments of northern (Atacama Desert), central (Andes volcano; Quetrupillan and Mamuil Malal) and hot spring (Liquiñe), and southern polar (Patagonia and Antarctic) regions of Chile. Differences in the composition of bacterial communities in the rhizosphere soils were revealed by denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) of 16S ribosomal RNA (rRNA), phoD, and phoX genes. In general, the significant lowest bacterial diversities, APase gene abundances, and APase activities were observed in rhizosphere soils from Atacama Desert, whereas the highest values were observed in rhizosphere soils of Patagonia. In addition, APase gene abundances were positively correlated among them and with APase activity of rhizosphere soils, but negatively correlated with phosphorus (P) availability in rhizosphere soils. Although bacterial APases were observed in all studied rhizosphere soils, their relevance to soil Po recycling in soils of extreme environments remains unclear and further studies are needed.