Genetically related genotypes of cowpea present similar bacterial community in the rhizosphere

www.nature.com/scientificreports OPEN Genetically related genotypes of cowpea present similar bacterial community in the rhizosphere Tayná Mendes de Albuquerque1, Lucas William Mendes2, Sandra Mara Barbosa Rocha3, Jadson Emanuel Lopes Antunes3, Louise Melo de Souza Oliveira3, Vania Maria Maciel Melo4, Francisca Andrea Silva Oliveira4, Arthur Prudêncio de Araujo Pereira5, Veronica Brito da Silva1, Regina Lucia Ferreira Gomes1, Francisco de Alcantara Neto1, Angela Celis de Almeida Lopes1, Maurisrael de Moura Rocha6 & Ademir Sergio Ferreira Araujo3* Plant breeding reduces the genetic diversity of plants and could influence the composition, structure, and diversity of the rhizosphere microbiome, selecting more homogeneous and specialized microbes. In this study, we used 16S rRNA sequencing to assess the bacterial community in the rhizosphere of different lines and modern cowpea cultivars, to investigate the effect of cowpea breeding on bacterial community assembly. Thus, two African lines (IT85F-2687 and IT82D-60) and two Brazilian cultivars (BRS-Guariba and BRS-Tumucumaque) of cowpea were assessed to verify if the generation advance and genetic breeding influence the bacterial community in the rhizosphere. No significant differences were found in the structure, richness, and diversity of bacterial community structure between the rhizosphere of the different cowpea genotypes, and only slight differences were found at the OTU level. The complexity of the co-occurrence network decreased from African lines to Brazilian cultivars. Regarding functional prediction, the core functions were significantly altered according to the genotypes. In general, African lines presented a more abundance of groups related to chemoheterotrophy, while the rhizosphere of the modern cultivars decreased functions related to cellulolysis. This study showed that the genetic breeding process affects the dynamics of the rhizosphere community, decreasing the complexity of interaction in one cultivar. As these cowpea genotypes are genetically related, it could suggest a new hypothesis of how genetic breeding of similar genotypes could influence the rhizosphere microbiome. The interaction between plants and microorganisms in the rhizosphere regulates several biological processes important to plants. The rhizosphere is known as the narrow zone of soil, which is driven by root traits, being a specific zone where thousands of microbial species live in close association with plants1. Particularly, studies about plant-microorganism interactions in the rhizosphere have focused on bacterial communities that represent the most versatile and diverse groups of microbes found in soils2. Recently, Geisen et al.2 have estimated more than one million bacterial species in soils acting on some important biological processes, such as primary production and nutrient cycling. In the rhizosphere, the bacterial community interacts with plant roots and stimulates plant development, inhibits pathogens, and solubilizes nutrients, so conferring positive effects on p lants3. On the other hand, different traits of the rhizosphere presented by distinct plants species can shape the pattern of the bacterial community. Indeed, different plant species4, the stage of development5, characteristics of root exudation6, and different cultivars7,8, can select specific bacterial groups and contribute to change diversity and richness of species. For instance, Araujo et al.5 assessed the influence of the stage of development in maize and cowpea on bacterial community in the rhizosphere and found that the structure and diversity of bacterial community varied significantly according to different plant species and, to a minor extent, to their development stage. 1 Plant Genetic Resource Group, Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil. 2Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, Brazil. 3Soil Microbial Ecology Group, Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil. 4Laboratório de Ecologia Microbiana E Biotecnologia, Federal University of Ceará, Fortaleza, CE, Brazil. 5Soil Science Department, Federal University of Ceará, Fortaleza, CE, Brazil. 6Embrapa Meio Norte, Teresina, PI, Brazil. *email: Scientific Reports | (2022) 12:3472 | https://doi.org/10.1038/s41598-022-06860-x 1 Vol.:(0123456789) www.nature.com/scientificreports/ The influence of the rhizosphere on the response of the bacterial community in several plants species and conditions is well known, but it remains unclear how plant breeding shapes the assembly of the bacterial community in the rhizosphere. Plant breeding is a process involving the changes in plant traits to obtain superior characteristics, such as biotic and abiotic stress tolerance and grain y ield9. This process is usually done with the use of advancing generations and selection of lines with the obtention of modern cultivars10. Although being positive to humans being, plant breeding promotes a reduction in the genetic diversity of plants11 and it can, consequently, select more homogeneous and specialized m icrobes12. Therefore, plant breeding can potentially modify the composition, structure, and diversity of the bacterial community in the rhizosphere. Indeed, previous studies have reported that plant breeding and the advance of generation significantly impacted rhizosphere microbial communities and network a ssembly7,13,14, promoting a homogenization and specialization of the bacterial community in the rhizosphere as influenced by the decreased genetic diversity12,15,16. As an important tropical plant species, cowpea (Vigna unguiculata L. Walp.) has been submitted to intensive plant breeding, mainly to figure out modern cultivars with higher tolerance to biotic and abiotic factors and yield17. However, little attention has been paid to the effect of cowpea breeding on the bacterial community in the rhizosphere. The knowledge of the behavior of the bacterial community in the rhizosphere of cowpea is important since it could positively influence plant performance. Here, we hypothesized that the process of cowpea breeding would influence plants traits and consequently drive the pattern of the bacterial community. Thus, we used 16S rRNA sequencing to assess the bacterial community in the rhizosphere of different lines and modern cowpea cultivars, to investigate the effect of cowpea breeding on bacterial community assembly. Results Bacterial community structure and diversity. The principal component analysis (PCA) explained 58.9% of the total variation in bacterial operational taxonomic units (OTU) of which 41.8% and 17.1% are displayed on the first two axes, respectively (Fig. 1A). As expected, the PCA showed significant differences in bacterial community structure between bulk soil and rhizosphere of cowpea genotypes (PERMANOVA Bulk x Rhizosphere F = 0.5281, p = 0.0023). However, no significant differen (...truncated)