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).

Aitana Ares,Pedro M Mendes-Moreira,Duarte Pintado,Daniela Santos,Carolina Joaquim,Joana Costa,Monika M Messmer

doi:10.3389/fmicb.2021.636009

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.

Highlights

Maize (Zea mays) is one of the most important cereal crops in human and animal diets worldwide
The phenotypic characterization indicates that “SinPre” in conventional farming was significantly higher than in organic farming for plant and first ear height, but no differences were observed for “Pigarro.” Within farming systems, there were no significant differences between the tested populations (“SinPre” × ”Pigarro”) for the measured parameters
In the current context of climate change, environmental degradation, and misuse of natural resources, the transition from conventional to organic farming requires the optimization of cultivars and management, with the rhizosphere microbiota playing an important role

Summary

Introduction

Maize (Zea mays) is one of the most important cereal crops in human and animal diets worldwide. Together with rice and wheat, it provides at least 30% of the food calories to more than 4.5 billion people in 94 developing countries (Shiferaw et al, 2011). Aside from providing nutrients for humans and animals, maize serves as a basic raw material to produce starch, oil, protein, alcoholic beverages, food sweeteners, and fuel (Wu and Guclu, 2013). According to FAOSTAT, from 2012 to 2017, the average world production per year of corn was around 1,036,263,896 t. In Portugal, maize is the most important arable crop, occupying an area of approximately 150,000 ha (ANPROMIS, 2019), producing an annual average of 826,417 Mg from 2012 to 2017 (FAOSTAT, 2019). Improvements on both agronomic practices and breeding related with microorganism interactions (e.g., control of root diseases) and organic management are appellative proposals since the rhizosphere microbial communities are critically important for soil nitrogen cycling and plant productivity (Schmidt et al, 2016; Emmett et al, 2017; Wille et al, 2018)

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