The ‘microbiome counterattack’: Insights on the soil and root‐associated microbiome in diverse chickpea and lentil genotypes after an erratic rainfall event

Abstract

Legumes maintain soil fertility thanks to their associated microbiota but are threatened by climate change that causes soil microbial community structural and functional modifications. The core microbiome associated with different chickpea and lentil genotypes was described after an unexpected climatic event. Results showed that chickpea and lentil bulk soil microbiomes varied significantly between two sampling time points, the first immediately after the rainfall and the second 2 weeks later. Rhizobia were associated with the soil of the more productive chickpea genotypes in terms of flower and fruit number. The root‐associated bacteria and fungi were surveyed in lentil genotypes, considering that several parcels showed disease symptoms. The metabarcoding analysis revealed that reads related to fungal pathogens were significantly associated with one lentil genotype. A lentil core prokaryotic community common to all genotypes was identified as well as a genotype‐specific one. A higher number of specific bacterial taxa and an enhanced tolerance to fungal diseases characterized a lentil landrace compared to the commercial varieties. This outcome supported the hypothesis that locally adapted landraces might have a high recruiting efficiency of beneficial soil microbes.

Lentil Landrace Seed Origin and Genotype Affects Rhizosphere Microbiome

“…Eglouvis 1 and Eglouvis 2 displayed almost the same abundance, with almost 300 species. The presence of Kabatiella microsticta, a plant pathogen also known as Aureobasidium microstictum (Bubák), was interestingly noticeable only in sample Eglouvis 4, identified by a large number of reads (12,640). Members of Kabatiella spp.…”

“…Members of Kabatiella spp. belong to fungal phylum Ascomycota, which is reported to cause leaf streak on maize and ornamentals plants The presence of Kabatiella microsticta, a plant pathogen also known as Aureobasidium microstictum (Bubák), was interestingly noticeable only in sample Eglouvis 4, identified by a large number of reads (12,640). Members of Kabatiella spp.…”

“…Whether there are differences in the lentil rhizosphere microbiome among lentil cultivars and landraces under the same field and environmental conditions still remains unexplored. In a recent study it was shown that irregular high precipitation events resulted in a higher number of specific bacterial taxa identified in the rhizosphere of a lentil landrace compared to the commercial cultivars [12]. Nonetheless, whether a landrace maintains a distinct rhizosphere microbiome signature in comparison to modern varieties under the same field and environmental conditions remains unknown.…”

“…Thus, the "rhizosphere effect" label was coined to describe the interplay of genotype-specific signaling molecules that support microbial proliferation and are also responsible for the formation of distinct microbial assemblages between the soil and the rhizosphere, as well as the interactions of the environment, soil type, microbiome, and plant growth and health [15]. It is becoming clear that the soil type and environment affect the legume rhizosphere microbiome [12,16]. Additionally, time of sampling and sampling compartments further impact the microbiome, often resulting in obscuring the genotype effect, which appears more profoundly in the rhizosphere microbiome of wheat genotypes [17].…”

“…Additionally, time of sampling and sampling compartments further impact the microbiome, often resulting in obscuring the genotype effect, which appears more profoundly in the rhizosphere microbiome of wheat genotypes [17]. Studies of the lentil microbiome are scarce and centered in lentil cultivars, in comparison to other legumes and crop species under normal and or erratic climate conditions [12,18].…”