Frontiers in Sustainable Food Systems (Nov 2020)
Temporal Dynamics of Rhizobacteria Found in Pequin Pepper, Soybean, and Orange Trees Growing in a Semi-arid Ecosystem
Abstract
Harsh environmental conditions in drylands force plants and their associated microbial communities to adapt to abiotic stresses. In semi-arid environments, climatic conditions and poor agricultural management have a strong impact on plant yield and thus, enhancing soil fertility by means of beneficial microorganisms such as plant growth-promoting rhizobacteria (PGPR) has been proposed as part of sustainable agricultural management. As drylands will increase due to climate change, studying microbial community dynamics of crops under such conditions is crucial as it might favor rhizobacteria adapted to drought. While the microbiome of many native dryland crops has been characterized, the microbial community composition from non-native crops under semi-arid environmental conditions is understudied. Thus, the aim of this study was to characterize the bacterial community associated with the roots of three crops with different growth cycles, cultivated in the same semi-arid environment, to understand their microbial community composition during the season with the highest temperature in northeast Mexico. We performed high throughput sequencing of the V3-V4 region of the 16S rRNA gene from root samples of Pequin pepper, soybean and orange trees. Classified taxa were evaluated according to crop, sampling time and climatological parameters. Our findings revealed that changes in temporal dynamics of microbial communities correlate with environmental temperature. Moreover, the microbial community of pepper was more diverse and differed from that of soybean and orange. Regarding PGPR, 47.6% of the genera were shared among crops with a high relative abundance of Bacillus, but we also detected crop-specific microbial associations where Serratia was specific to orange trees and Rhodobacter to pepper. When analyzing PGPR in correlation to climatological parameters, Bacillus was found to thrive under lower precipitation rates, higher temperatures and higher evaporation rates in pepper and orange. In contrast, some PGPR commonly used in commercial biofertilizers such as Rhizobium and Azospirillum were affected by high temperatures. This study provides a better understanding of the rhizobacterial assemblies of economically relevant crops grown under a semi-arid environment.
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