Effect of Low-Input Organic and Conventional Farming Systems on Maize Rhizosphere in Two Portuguese Open-Pollinated Varieties (OPV), "Pigarro" (Improved Landrace) and "SinPre" (a Composite Cross Population)

Abstract

Maize is one of the most important crops worldwide and is the number one arable crop in Portugal. A transition from the conventional farming system to organic agriculture requires optimization of cultivars and management, the interaction of plant-soil rhizosphere microbiota being pivotal. The objectives of this study were to unravel the effect of population genotype and farming system on microbial communities in the rhizosphere of maize. Rhizosphere soil samples of two open-pollinated maize populations ("SinPre" and "Pigarro") cultivated under conventional and organic farming systems were taken during flowering and analyzed by next-generation sequencing (NGS). Phenological data were collected from the replicated field trial. A total of 266 fungi and 317 bacteria genera were identified in "SinPre" and "Pigarro" populations, of which 186 (69.9%) and 277 (87.4%) were shared among them. The microbiota of "Pigarro" showed a significant higher (P < 0.05) average abundance than the microbiota of "SinPre." The farming system had a statistically significant impact (P < 0.05) on the soil rhizosphere microbiota, and several fungal and bacterial taxa were found to be farming system-specific. The rhizosphere microbiota diversity in the organic farming system was higher than that in the conventional system for both varieties. The presence of arbuscular mycorrhizae (Glomeromycota) was mainly detected in the microbiota of the "SinPre" population under the organic farming systems and very rare under conventional systems. A detailed metagenome function prediction was performed. At the fungal level, pathotroph-saprotroph and pathotroph-symbiotroph lifestyles were modified by the farming system. For bacterial microbiota, the main functions altered by the farming system were membrane transport, transcription, translation, cell motility, and signal transduction. This study allowed identifying groups of microorganisms known for their role as plant growth-promoting rhizobacteria (PGPR) and with the capacity to improve crop tolerance for stress conditions, allowing to minimize the use of synthetic fertilizers and pesticides. Arbuscular mycorrhizae (phyla Glomeromycota) were among the most important functional groups in the fungal microbiota and Achromobacter, Burkholderia, Erwinia, Lysinibacillus, Paenibacillus, Pseudomonas, and Stenotrophomonas in the bacterial microbiota. In this perspective, the potential role of these microorganisms will be explored in future research.

Keywords: maize; microbiota; next-generation sequencing; open-pollinated populations; organic and conventional farming system; rhizosphere.

FIGURE 1

Relative abundance of different fungal (A) and bacterial (B) phyla in the soil rhizosphere in both populations. PC_A, “Pigarro” conventional plant A; PC_B, “Pigarro” conventional plant B; PC_C, “Pigarro” conventional plant C; PO_A, “Pigarro” organic plant A; PO_B, “Pigarro” organic plant B; PO_C, “Pigarro” organic plant C; SC_A, “SinPre” conventional plant A; SC_B, “SinPre” conventional plant B; SC_C, “SinPre” conventional plant C; SO_A, “SinPre” organic plant A; SO_B, “SinPre” organic plant B; SO_C, “SinPre” organic plant C.

FIGURE 2

Relative abundance of different fungal (A) and bacterial (B) genera in the soil rhizosphere in both populations representing the genera showing more than 1% relative abundance of all reads. The genera representing less than 1% of the total reads are grouped into “Others.” Venn diagrams showing the common and exclusive fungal (C) and bacterial (D) genera of the rhizosphere of the maize populations “SinPre” and “Pigarro.” PC_A, “Pigarro” conventional plant A; PC_B, “Pigarro” conventional plant B; PC_C, “Pigarro” conventional plant C; PO_A, “Pigarro” organic plant A; PO_B, “Pigarro” organic plant B; PO_C, “Pigarro” organic plant C; SC_A, “SinPre” conventional plant A; SC_B, “SinPre” conventional plant B; SC_C, “SinPre” conventional plant C; SO_A, “SinPre” organic plant A; SO_B, “SinPre” organic plant B; SO_C, “SinPre” organic plant C.

FIGURE 3

Box plot illustrating statistically significant α diversity measures of the effect of farming system in fungal (A) and bacterial (B) communities in the maize rhizosphere. Principal coordinate analysis (PCoA) was performed using the prcomp package to illustrate the effect of farming system on the fungal (C) and bacterial (D) communities in the maize rhizosphere. The calculation is based on singular value decomposition of the fungal and bacterial communities for the farming system. A greater distance between the two samples indicates low similarity. The percentage of variation is explained by component 1 (PC1) and by component 2 (PC2).

FIGURE 4

Linear discriminant analysis (LDA) combined with effect size (LEfSe) was used to identify the most differentially abundant taxa among the population genotypes in the rhizosphere of maize. Cladogram generated by LEfSe indicating differences of fungi (A,B) and bacteria (C,D) at the phylum, class, family, and genus levels (relative abundance, ≤0.5%). Each successive circle represents a phylogenetic level. The red and green circles mean that “Pigarro” conventional and organic (red) and “SinPre” conventional and organic (green) showed differences in relative abundance; yellow circles mean non-significant differences. Differing taxa are listed on the right side of the cladogram. Bar graph showing the LDA scores for bacteria is represented in Supplementary Figure 1. Only taxa meeting an LDA significant threshold >2 are shown.

FIGURE 5

Linear discriminant analysis (LDA) combined with effect size (LEfSe) was used to identify the most differentially abundant taxa among farming systems in the rhizosphere of maize. Cladogram generated by LEfSe indicating differences of fungi (A,B) and bacteria (C,D) at the phylum, class, family, and genus levels (relative abundance, ≤0.5%). Each successive circle represents a phylogenetic level. The red and green circles mean that conventional (red) and organic (green) showed differences in relative abundance; yellow circles mean non-significant differences. Differing taxa are listed on the right side of the cladogram. Bar graph showing the LDA scores for bacteria is represented in Supplementary Figure 1. Only taxa meeting an LDA significant threshold >2 are shown.

FIGURE 6

Metagenome predicted functions classified using FUNGuild for fungi (A) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) level 2 database in PICRUSt software for bacteria (B) showing the most abundant functions throughout the rhizospheric soil samples.