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Bacterial diversity changes in agricultural soils influenced by poultry litter fertilization

  • Environmental Microbiology - Research Paper
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Abstract

Poultry litter is widely applied as agricultural fertilizer and can affect the soil microbiome through nutrient overload and antibiotic contamination. In this study, we assessed changes in soil bacterial diversity using high-throughput sequencing approaches. Four samples in triplicate were studied: soils with short- and long-term fertilization by poultry litter (S1 = 10 months and S2 = 30 years, respectively), a soil inside a poultry shed (S3), and a forest soil used as control (S0). Samples S0, S1, and S2 revealed a relatively high richness, with confirmed operational taxonomic units (OTUs) in the three replicates of each sample ranging from 1243 to 1279, while richness in S3 was about three times lower (466). The most abundant phyla were Proteobacteria, Bacteroidetes, and Actinobacteria. Acidobacteria, Planctomycetes, and Verrucomicrobia were also abundant but highly diminished in S3, while Firmicutes was less abundant in S0. Changes in bacterial communities were very evident at the genera level. The genera Gaiella, Rhodoplanes, Solirubacter, and Sphingomonas were predominant in S0 but strongly decreased in the other soils. Pedobacter and Devosia were the most abundant in S1 and were diminished in S2, while Herbiconiux, Brevundimonas, Proteiniphilum, and Petrimonas were abundant in S2. The most abundant genera in S3 were Deinococcus, Truepera, Rhodanobacter, and Castellaniella. A predictive analysis of the metabolic functions with Tax4Fun2 software suggested the potential presence of enzymes associated with antibiotic resistance as well as with denitrification pathways, indicating that the S3 soil is a potential source of nitrous oxide, a powerful greenhouse gas.

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Data availability

The raw sequences were deposited in the Sequence Read Archive (SRA) database of National Center for Biotechnology Information (NCBI) - project PRJNA577278.

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Acknowledgements

The authors would like to thank the poultry farmers from SJVRP for their essential contribution to the work.

Code availability

Accession numbers SAMN13023011–SAMN13023014.

Funding

This work was supported by the Brazilian Ministry of Science, Technology, Innovations and Communications/National Council for Scientific and Technological Development (MCTI/CNPq-Universal-01/2016), process 426192/2016-8 and Dirección de Apoyo a la Investigación y al Posgrado (DAIP, Universidad de Guanajuato-UG, project 206/2019, in Mexico. C.E.T.P. has a PNPD grant from Brazilian Foundation for the Coordination and Improvement of Higher Level of Education Personnel (CAPES); E.A.C.R and A.P.F.C. received undergraduate scholarships from DAIP-UG; O.M. has a grant “Cientista do Nosso Estado” from Carlos Chagas Filho Research Support Foundation of Rio de Janeiro State (FAPERJ).

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Authors and Affiliations

  1. Laboratório de Radioisótopos Eduardo Penna Franca, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, s/n, bloco G0, sala 60, subsolo, Rio de Janeiro, 21941-902, RJ, Brasil

    Cláudio E. T. Parente & Olaf Malm

  2. Laboratorio de Microbiología Ambiental y Biología Molecular Aplicada, Depto. de Ingeniería Civil y Ambiental, Div. Ingenierías (CGT), Universidad de Guanajuato, Av. Juárez, 77; Zona Centro, Guanajuato, Gto., México, 36000

    Elcia M. S. Brito, Erick A. Cervantes-Rodríguez & Andrea P. Fábila-Canto

  3. Departamento. de Astronomía, Div. Ciencias Naturales y Exactas (CGT), Universidad de Guanajuato, Callejón de Jalisco, s/n; Col. Valenciana, Guanajuato, Gto., México, 36023

    César A. Caretta

  4. Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, s/n, bloco I, sala 60, Rio de Janeiro, 21941-902, RJ, Brasil

    Renata E. Vollú & Lucy Seldin

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Contributions

All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by Cláudio Ernesto Taveira Parente, Elcia Margareth Souza Brito, César Augusto Caretta, Renata Estebanez Vollú, and Lucy Seldin. The first draft of the manuscript was written by Cláudio Ernesto Taveira Parente, Elcia Margareth Souza Brito, and César Augusto Caretta. All authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Elcia M. S. Brito.

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Parente, C.E.T., Brito, E.M.S., Caretta, C.A. et al. Bacterial diversity changes in agricultural soils influenced by poultry litter fertilization. Braz J Microbiol 52, 675–686 (2021). https://doi.org/10.1007/s42770-021-00437-y

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