Multi-analytical approach reveals potential microbial indicators in soil for sugarcane model systems

Journal Article · Tue Jun 09 00:00:00 EDT 2015 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0129765· OSTI ID:1212414

Navarrete, Acacio Aparecido ^[1]; Diniz, Tatiana Rosa ^[1]; Braga, Lucas Palma Perez ^[1]; Silva, Genivaldo Gueiros Zacarias ^[2]; Franchini, Julio Cezar ^[3]; Rossetto, Raffaella ^[4]; Edwards, Robert Alan ^[5]; Tsai, Siu Mui ^[1]; Lehman, R. Michael ^[6]

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1. Univ. of Sao Paulo, Piracicaba (Brazil). Cell and Molecular Biology Lab.
2. San Diego State Univ., San Diego, CA (United States). Computational Science Research Center.
3. Brazilian Agricultural Research Corp., Londrina (Brazil)
4. Sao Paulo's Agency for Agribusiness Technology, Piracicaba (Brazil)
5. San Diego State Univ., CA (United States). Computational Science Research Center and Dept. of Computer Science; Argonne National Lab. (ANL), Argonne, IL (United States). Div. of Mathematics and Computer Science.
6. USDA-ARS (United States)

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.

• Research Organization: Argonne National Laboratory (ANL), Argonne, IL (United States)
• Sponsoring Organization: USDOE
• Grant/Contract Number: AC02-06CH11357
• OSTI ID: 1212414
• Journal Information: PLoS ONE, Vol. 10, Issue 6; ISSN 1932-6203
• Publisher: Public Library of Science
• Country of Publication: United States
• Language: English

Related Subjects

60 APPLIED LIFE SCIENCES
fertilizers
soil chemistry
agricultural soil science
actinobacteria
straw
metagenomics
shotgun sequencing
polymerase chain reaction