Data_Sheet_2_Temporal Dynamics of Rhizobacteria Found in Pequin Pepper, Soybean, and Orange Trees Growing in a Semi-arid Ecosystem.PDF

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.

干旱地区严苛的环境条件迫使植物及其附属微生物群落应对非生物胁迫。在半干旱环境中，气候条件与粗放的农业管理会严重影响作物产量，因此学界提出借助植物促生根际菌（plant growth-promoting rhizobacteria, PGPR）这类有益微生物提升土壤肥力，以此作为可持续农业管理的组成部分。由于气候变化导致干旱地区面积扩张，研究此类环境下作物的微生物群落动态至关重要，因为这可能筛选出适应干旱的根际菌。尽管诸多本土旱地作物的微生物组已被解析，但半干旱环境下非本土作物的微生物群落组成仍未得到充分研究。因此本研究旨在解析种植于墨西哥东北部同一半干旱环境中的三种生长周期各异作物的根系细菌群落，以明确其在当地最热季节的微生物群落组成特征。我们对皮奎恩辣椒、大豆与柑橘树根系样本的16S rRNA基因V3-V4区进行了高通量测序。我们依据作物种类、采样时间与气候参数对分类单元进行了评估。研究结果显示，微生物群落的时间动态变化与环境温度显著相关。此外，辣椒的微生物群落多样性更高，且与大豆和柑橘的微生物群落存在显著差异。针对PGPR而言，共有47.6%的菌属在各作物中均存在，其中芽孢杆菌属（Bacillus）相对丰度较高；同时我们还检测到了作物特异性的微生物关联：沙雷氏菌属（Serratia）仅存在于柑橘树根系，红杆菌属（Rhodobacter）仅存在于辣椒根系。在分析PGPR与气候参数的相关性时，我们发现芽孢杆菌属在辣椒与柑橘样本中，于低降水量、高温度与高蒸发量的环境下生长旺盛。与之相反，部分常用于商业生物肥料的PGPR，如根瘤菌属（Rhizobium）与固氮螺菌属（Azospirillum），会受到高温的负面影响。本研究有助于加深对半干旱环境下经济作物根际细菌群落组装机制的理解。