Kushwaha Priyanka, Soto Velázquez Ana L, McMahan Colleen, Neilson Julia W
Department of Environmental Science, The University of Arizona, Tucson, AZ 85721, USA.
USDA Agricultural Research Service, Western Regional Research Center, Albany, CA 94710, USA.
Microorganisms. 2024 Jan 5;12(1):110. doi: 10.3390/microorganisms12010110.
Plant-soil feedback (PSF) processes impact plant productivity and ecosystem function, but they are poorly understood because PSFs vary significantly with plant and soil type, plant growth stage, and environmental conditions. Controlled greenhouse studies are essential to unravel the mechanisms associating PSFs with plant productivity; however, successful implementation of these controlled experiments is constrained by our understanding of the persistence of the soil microbiome during the transition from field to greenhouse. This study evaluates the preservation potential of a field soil microbiome when stored in the laboratory under field temperature and moisture levels. Soil microbial diversity, taxonomic composition, and functional potential were evaluated via amplicon sequencing at the start of storage (W0), week 3 (W3), week 6 (W6), and week 9 (W9) to determine the effect of storage time on soil microbiome integrity. Though microbial richness remained stable, Shannon diversity indices decreased significantly at W6 for bacteria/archaea and W3 for fungi. Bacterial/archaeal community composition also remained stable, whereas the fungal community changed significantly during the first 3 weeks. Functional predictions revealed increased capacity for chemoheterotrophy for bacteria/archaea and decreased relative proportions of arbuscular mycorrhizal and ectomycorrhizal fungi. We show that preservation of the field soil microbiome must be a fundamental component of experimental design. Either greenhouse experiments should be initiated within 3 weeks of field soil collection, or a preliminary incubation study should be conducted to determine the time and storage conditions required to sustain the integrity of the specific field soil microbiome being studied.
植物-土壤反馈（PSF）过程影响植物生产力和生态系统功能，但由于PSF会因植物和土壤类型、植物生长阶段以及环境条件的不同而有显著差异，所以人们对其了解甚少。可控温室研究对于揭示PSF与植物生产力之间的关联机制至关重要；然而，这些可控实验的成功实施受到我们对土壤微生物群落从田间到温室过渡期间持久性的理解的限制。本研究评估了田间土壤微生物群落在实验室中于田间温度和湿度水平下储存时的保存潜力。在储存开始时（W0）、第3周（W3）、第6周（W6）和第9周（W9），通过扩增子测序评估土壤微生物多样性、分类组成和功能潜力，以确定储存时间对土壤微生物群落完整性的影响。尽管微生物丰富度保持稳定，但细菌/古菌的香农多样性指数在W6时显著下降，真菌的香农多样性指数在W3时显著下降。细菌/古菌群落组成也保持稳定，而真菌群落在最初3周内发生了显著变化。功能预测显示，细菌/古菌的化学异养能力增强，丛枝菌根真菌和外生菌根真菌的相对比例降低。我们表明，田间土壤微生物群落的保存必须是实验设计的一个基本组成部分。要么在采集田间土壤后的3周内启动温室实验，要么进行初步培养研究，以确定维持所研究的特定田间土壤微生物群落完整性所需的时间和储存条件。
