Characterization of the microbiome of Caatinga semiarid soils and its potential for lignocellulose degradation

Author(s)

Gileno Vieira Lacerda Júnior

• Document type: Doctoral Thesis
• Institution: Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia
• Defense date: 2017-08-31

Examining board members

Anete Pereira de Souza; Renato Vicentini; Rodrigo Mendes; Fernando Dini Andreote

• Advisor: Valeria Maia Merzel

Abstract

Caatinga is an exclusively Brazilian biome, poorly studied and preserved, with an exuberant and exclusive biological diversity. This ecosystem consists of a dry tropical forest adapted to severe climatic conditions, including high temperatures and solar irradiation, soil acidity, and water deficit caused by the seasonal rainfall regime. Therefore, it is expected to harbor a soil microbiota carrying unique and versatile enzymatic arsenals with a potential biotechnological application. Resident soil microorganisms are capable of decomposing lignin (second most abundant biopolymer of the biosphere) using a set of ligninolytic enzymes which can also be applied in the treatment of effluents, pulp and paper industry, biofuels productions, among other industrial processes. Considering that about 99% of soil microorganisms cannot be isolated by conventional culture methods, molecular approaches based on the direct extraction of environmental genetic material, such as "metagenomics", are needed to provide more precise information about the diversity and biotechnological potential of the native microbial community. Thus, this study uses an integrated approach of functional (based on biological activity and sequence similarity) and descriptive metagenomics, with the aim of identifying new lignocellulolytic enzymes, in addition to analyzing the impact of seasonality and agricultural practices (irrigation/fertilization) in the community structure and functional responses of the Caatinga soil microbiome. The functional screening based on the phenotypic expression of 40,000 metagenomic clones did not show any ligninolytic activity. However, the molecular screening by PCR allowed the identification of a bacterial Laccase-like Multicopper oxidase, affiliated with the genus Mesorhizobium. The large-scale sequencing of a soil metagenomic library and subsequent in silico analysis revealed a large enzymatic repertoire related to the lignocellulosic degradation carried by different bacterial groups with potential application in the biofuels production as well as other environmental processes. In an ecological approach, it was observed the enrichment of the phyla Actinobacteria and Proteobacteria in the drought and rainy seasonal period, respectively. The data suggest that microorganisms thriving on native soils of the dry period are specialized in monosaccharides and disaccharides utilization, as well as osmoprotective sugars such as trehalose. In contrast, the soil microbiome affected by land use was mainly driven by chemical factors, with the enrichment of the Acidobacteria phylum and genes related to nitrification and denitrification processes, and to oxidative stress. These results suggest that the nutrients input and the breakdown of the natural cycles of the water regime may impact the biogeochemical cycles, affecting the natural functionality of the Caatinga semiarid soils (AU)

• FAPESP's process: 13/09386-9 - Integrated metatranscriptomic and metagenomic analyses of Caatinga soil and genes prospection involved on the liginin degradation.
• Grantee: Gileno Vieira Lacerda Júnior
• Support Opportunities: Scholarships in Brazil - Doctorate