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Influences of plant organ, genotype, and cultivation site on the endophytic bacteriome of maize (Zea mays L.) in the semi-arid region of Pernambuco, Brazil

  • Soil and Agricultural Microbiology - Research Paper
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Abstract

Endophytic bacteria play a crucial role in plant development and adaptation, and the knowledge of how endophytic bacteria assemblage is influenced by cultivation site and plant genotype is an important step to achieve microbiome manipulation. This work aimed to study the roots and stems of endophytic bacteriome of four maize genotypes cultivated in two regions of the semi-arid region of Pernambuco - Brazil. Our hypothesis is that the endophytic community assemblage will be influenced by plant genotypes and cultivation region. Metabarcoding sequencing data revealed significant differences in alfa diversity in function of both factors, genotypes, and maize organs. Beta diversity analysis showed that the bacterial communities differ mainly in function of the plant organ. The most abundant genera found in the samples were Leifsonia, Bacillus, Klebsiella, Streptomyces, and Bradyrhizobium. To understand ecological interactions within each compartment, we constructed co-occurrence network for each organ. This analysis revealed important differences in network structure and complexity and suggested that Leifsonia (the main genera found) had distinct ecological roles depending on the plant organ. Our data showed that root endophytic maize bacteria would be influenced by cultivation site, but not by genotype. We believe that, collectively, our data not only characterize the bacteriome associated with this plant and how different factors shape it, but also increase the knowledge to select potential bacteria for bioinoculant production.

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Data availability

Raw sequences were deposited in the NCBI Sequence Read Archive (SRA) and are available under Bioproject PRJNA846726.

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Funding

The authors thank the Brazilian Council for Scientific and Technological Development (CNPq; Projetos Universal 2018, Grant Numbers 426655/2018-4 and 409519/2018-9). This work is part of the National Observatory of Water and Carbon Dynamics in the Caatinga Biome - NOWCDCB, supported by Fundação de Amparo à Ciência e Tecnologia de Pernambuco (FACEPE; APQ-0498-3.07/17 ONDACBC), CNPq (grants: 441305/2017-2; 465764/2014-2), and CAPES (grants: 88887.136369/2017-00). Part of this study was financed by FACEPE (APQ-0420-5.01/18) and Fundação Carlos Chagas Filho de Apoio à Pesquisa do Estado do Rio de Janeiro (FAPERJ). Freitas ADS and Costa CTRC are CNPq Research Productivity Scholars of CNPq (classes 1D and 2, respectively)

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Authors and Affiliations

  1. Departamento de Agronomia, UFRPE – Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, PE, 52061060, Brazil

    Leandro Reis Costa Santos, Aline Fernandes de Melo, Jéssica Rafaella de Sousa Oliveira & Ana Dolores Santiago de Freitas

  2. Laboratory of Biotechnology and Microbial Ecology (LABEM), Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Av. Carlos Chagas Filho, Rio de Janeiro, 373, Brazil

    Pedro Sodré do Rêgo Barros, Douglas Alfradique Monteiro & Caio Tavora Coelho da Costa Rachid

  3. Laboratory of Genomic, Instituto Agronômico de Pernambuco (IPA), Av. Gen. San Martin 1371, bl D, Pernambuco Agronomic Institute, Recife, Pernambuco, Brazil

    José Nildo Tabosa & Maria do Carmo Catanho Pereira de Lyra

  4. Embrapa Semiárido, Petrolina, PE, Brasil

    Paulo Ivan Fernandes Júnior

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  1. Leandro Reis Costa Santos
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  2. Pedro Sodré do Rêgo Barros
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  3. Douglas Alfradique Monteiro
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  4. José Nildo Tabosa
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  5. Aline Fernandes de Melo
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  10. Caio Tavora Coelho da Costa Rachid
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Contributions

Study conception and design: A.D.S.F, J.N.T, L.R.C.S, and C.T.R.C.C. Field experimentation: L.R.C.S, A.F.M, J.N.T, M.C.C.P.L, and A.D.S.F. Laboratory procedures: L.R.C.S, A.F.M, and M.C.C.P.L. Bioinformatic and statistical analysis: P.S.R.B, D.A.M, and C.T.R.C.C. Drafting of the manuscript: L.R.C.S, P.S.R.B, D.A.M, M.C.C.P.L, and C.T.R.C.C. Critical revision of the manuscript: all authors.

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Correspondence to Caio Tavora Coelho da Costa Rachid.

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Santos, L.R.C., Barros, P.S.d., Monteiro, D.A. et al. Influences of plant organ, genotype, and cultivation site on the endophytic bacteriome of maize (Zea mays L.) in the semi-arid region of Pernambuco, Brazil. Braz J Microbiol 55, 789–797 (2024). https://doi.org/10.1007/s42770-023-01221-w

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