Department of Botany, University of Wyoming, 1000 E. University Ave., Laramie, WY 82071, United States.
Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, 7 MBL Street, Woods Hole, MA 02543, United States.
FEMS Microbiol Lett. 2024 Jan 9;371. doi: 10.1093/femsle/fnae044.
Soil microbial communities are fundamental to ecosystem processes and plant growth, yet community composition is seasonally and successionally dynamic, which interferes with long-term iterative experimentation of plant-microbe interactions. We explore how soil sample handling (e.g. filtering) and sample storage conditions impact the ability to revive the original, physiologically active, soil microbial community. We obtained soil from agricultural fields in Montana and Oklahoma, USA and samples were sieved to 2 mm or filtered to 45 µm. Sieved and filtered soil samples were archived at -20°C or -80°C for 50 days and revived for 2 or 7 days. We extracted DNA and the more transient RNA pools from control and treatment samples and characterized microbial communities using 16S amplicon sequencing. Filtration and storage treatments significantly altered soil microbial communities, impacting both species richness and community composition. Storing sieved soil at -20°C did not alter species richness and resulted in the least disruption to the microbial community composition in comparison to nonarchived controls as characterized by RNA pools from soils of both sites. Filtration significantly altered composition but not species richness. Archiving sieved soil at -20°C could allow for long-term and repeated experimentation on preserved physiologically active microbial communities.
土壤微生物群落是生态系统过程和植物生长的基础，但群落组成具有季节性和演替性动态，这干扰了植物-微生物相互作用的长期迭代实验。我们探讨了土壤样本处理（例如过滤）和样本储存条件如何影响恢复原始生理活性土壤微生物群落的能力。我们从美国蒙大拿州和俄克拉荷马州的农业田中获取土壤，然后将样本筛至 2 毫米或过滤至 45 微米。将筛选和过滤后的土壤样本在-20°C 或-80°C 下储存 50 天，并在 2 天或 7 天后复苏。我们从对照和处理样本中提取 DNA 和更短暂的 RNA 池，并使用 16S 扩增子测序来描述微生物群落。过滤和储存处理显著改变了土壤微生物群落，影响了物种丰富度和群落组成。与未存档的对照相比，-20°C 下储存的筛土并未改变物种丰富度，并且对两个地点的土壤 RNA 池所描述的微生物群落组成的干扰最小。过滤显著改变了组成，但没有改变物种丰富度。-20°C 下储存筛土可以允许对保存的生理活性微生物群落进行长期和重复的实验。
