Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems.

Acacio Aparecido Navarrete,Robert Alan Edwards,Tatiana Rosa Diniz,Siu Mui Tsai,Julio Cezar Franchini,Genivaldo Gueiros Zacarias Silva,Raffaella Rossetto,Lucas Palma Perez Braga,R Michael Lehman

doi:10.1371/journal.pone.0129765

Abstract

This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB) and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N), vinasse (V; a liquid waste from ethanol production), and sugarcane-straw blankets. Increases in CO2-C and N2O-N emissions were identified shortly after the addition of both N and V to the soils, thus increasing MB nitrogen (MB-N) and decreasing MB carbon (MB-C) in the N+V-amended soils and altering soil chemical factors that were correlated with the MB. Across 57 soil metagenomic datasets, Actinobacteria (31.5%), Planctomycetes (12.3%), Deltaproteobacteria (12.3%), Alphaproteobacteria (12.0%) and Betaproteobacteria (11.1%) were the most dominant bacterial groups during the experiment. Differences in relative abundance of metagenomic sequences were mainly revealed for Acidobacteria, Actinobacteria, Gammaproteobacteria and Verrucomicrobia with regard to N+V fertilization and straw retention. Differential abundances in bacterial groups were confirmed using 16S rRNA gene-targeted phylum-specific primers for real-time PCR analysis in all soil samples, whose results were in accordance with sequence data, except for Gammaproteobacteria. Actinobacteria were more responsive to straw retention with Rubrobacterales, Bifidobacteriales and Actinomycetales related to the chemical factors of N+V-amended soils. Acidobacteria subgroup 7 and Opitutae, a verrucomicrobial class, were related to the chemical factors of soils without straw retention as a surface blanket. Taken together, the results showed that MB-C and MB-N responded to changes in soil chemical factors and CO2-C and N2O-N emissions, especially for N+V-amended soils. The results also indicated that several taxonomic groups of bacteria, such as Acidobacteria, Actinobacteria and Verrucomicrobia, and their subgroups acted as early-warning indicators of N+V amendments and straw retention in sugarcane-cultivated soils, which can alter the soil chemical factors.

Highlights

Quantitative and qualitative changes in soil characteristics are expected when using different types of soil agricultural management, which leads to different nutrient availability to the soil that will determine, favor or inhibit the establishment of different microbial groups [1,2,3]
N fertilization use combined with V and straw retention improves soil fertility and sugarcane productivity, there is a lack of information on the impacts of such combinations on the microbiological properties of tropical soils
A verrucomicrobial class, was related to the chemical factors of uncovered soils after three fertilizer applications with N and V (Fig 4). This short-term study showed that the use of synthetic N and V as amendments may affect the microbial biomass (MB) and relative abundance of taxonomic groups of bacteria in sugarcane-cultivated soils through alterations of the soil chemical factors

Summary

Introduction

Quantitative and qualitative changes in soil characteristics are expected when using different types of soil agricultural management, which leads to different nutrient availability to the soil that will determine, favor or inhibit the establishment of different microbial groups [1,2,3]. Organic and inorganic fertilizer amendments are primarily used to increase nutrient availability to plants, but they can affect soil microbial community composition [4,5]. Soil management practices used in sugarcane agriculture in Brazil, which is the largest world’s producer of sugarcane, require synthetic mineral fertilizers (nitrogen/phosphorus/potassium—NPK) [6] and full recycling of waste products from ethanol production to sugarcane fields in the form of organic fertilizer [7]. Vinasse is a by-product of the sugar-ethanol industry produced in large quantities, and it is composed of water, organic matter, and mineral elements [8]. N fertilization use combined with V and straw retention improves soil fertility and sugarcane productivity, there is a lack of information on the impacts of such combinations on the microbiological properties of tropical soils

Methods

Results

Conclusion