title: Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems.
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.
authors.affiliation: Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Piracicaba, SP, Brazil.
authors.forename: Acacio Aparecido
authors.initials: AA
authors.lastname: Navarrete
authors.affiliation: Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Piracicaba, SP, Brazil.
authors.forename: Tatiana Rosa
authors.initials: TR
authors.lastname: Diniz
authors.affiliation: Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Piracicaba, SP, Brazil.
authors.forename: Lucas Palma Perez
authors.initials: LP
authors.lastname: Braga
authors.affiliation: Computational Science Research Center, San Diego State University, San Diego, California, United States of America.
authors.forename: Genivaldo Gueiros Zacarias
authors.initials: GG
authors.lastname: Silva
authors.affiliation: Brazilian Agricultural Research Corporation, Londrina, PR, Brazil.
authors.forename: Julio Cezar
authors.initials: JC
authors.lastname: Franchini
authors.affiliation: São Paulo's Agency for Agribusiness Technology, Piracicaba, SP, Brazil.
authors.forename: Raffaella
authors.initials: R
authors.lastname: Rossetto
authors.affiliation: Computational Science Research Center, San Diego State University, San Diego, California, United States of America; Department of Computer Science, San Diego State University, San Diego, California, United States of America; Division of Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois, United States of America.
authors.forename: Robert Alan
authors.initials: RA
authors.lastname: Edwards
authors.affiliation: Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Piracicaba, SP, Brazil.
authors.forename: Siu Mui
authors.initials: SM
authors.lastname: Tsai
mesh_terms: D061271:Acidobacteria / Q000502:physiology*; D039903:Actinobacteria / Q000502:physiology*; D000704:Analysis of Variance; D018533:Biomass; D002245:Carbon Dioxide / Q000032:analysis; D005308:Fertilizers; D008962:Models, Theoretical; D009609:Nitrous Oxide / Q000032:analysis; D060888:Real-Time Polymerase Chain Reaction; D031786:Saccharum / Q000502:physiology*; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology; D012989:Soil Pollutants / Q000032:analysis; D018709:Statistics, Nonparametric
chemical_list: D005308:Fertilizers; D012987:Soil; D012989:Soil Pollutants; D002245:Carbon Dioxide; D009609:Nitrous Oxide