Microbial diversity involved in the cycling of nitrogen in soil cultivated with sugarcane in São Paulo State

Author(s)

Júlia Elídia de Lima Perim

• Document type: Doctoral Thesis
• Press: Piracicaba.
• Institution: Universidade de São Paulo (USP). Escola Superior de Agricultura Luiz de Queiroz (ESALA/BC)
• Defense date: 2016-10-14

Examining board members

Fernando Dini Andreote; Caio Tavora Rachid Coelho da Costa

• Advisor: Fernando Dini Andreote

Abstract

Brazil is the largest world\'s producer of sugarcane and State of São Paulo accounts for over 50% of this production. This crop has a huge impact on Brazilian agriculture and due to this great importance, a better understanding of the composition of the microbial community related to cycling of nitrogen (N) in these soils is of utmost importance for the improvement in the cultivation of sugarcane. However, little is known about the relationship between microbial groups and this crop. This study aimed to determine changes in microbial communities that participate in the transformation of N in soils derived from three areas used for sugarcane production (named A, F and J), which have a range of different management conditions and soil characteristics. Each area was analyzed in triplicate, and the extracted DNA was used to develop next generation sequencing (shotgun metagenomics and 16S rDNA), quantitative PCR (qPCR) and terminal restriction fragment length polymorphism (T-RFLP). Most of the sequences derived from Bacteria (98%; M5NR database); six stages of nitrogen cycle were annotated by MG-RAST plataform (SEED database): nitrate and nitrite ammonification (NNA); nitrogen fixation; denitrification; nitric oxide synthase; dissimilatory nitrite reductase and ammonia assimilation. This last mentioned step was the most abundant (28%) (gltB and gltD genes) and is directly linked to microbial growth in soil, since the final product of the reaction is glutamate. The second most abundant process was NNA (nir and nar genes), responsible for consuming this substrate during the cycle. Proteobacteria and Chroloflexi are present at all stages of the cycle, representing microorganisms that can participate in the N transformation and, moreover, it was possible to describe a microbial core (at an order level) represented by Sphingomonadales. Some environmental variables, such as the application of filter cake and productivity showed a significant correlation with the structure of the microbial community. This was also found for certain soil characteristics such as phosphorus, magnesium and organic matter. In addition, it was identified a high abundance of microorganisms carrying genes encoding the enzymes for nitrate and nitrite reduction pathway. Therefore, despite its complexity, the study of microbial functions of nitrogen in soils cultivated with sugarcane is innovative by accessing jointly all communities involved in this cycle, characterized by sequencing, which avoids the problems inherent in microbial cultivation and allows to infer about the hierarchy of environmental variables that influence this microbial groups. (AU)

• FAPESP's process: 12/03949-9 - Microbial diversity involved in the cycling of nitrogen in soils cultivated with sugarcane in São Paulo state
• Grantee: Júlia Elidia de Lima Perim
• Support Opportunities: Scholarships in Brazil - Doctorate