Erlandson Sonya R, Ewing Patrick M, Osborne Shannon L, Lehman R Michael
USDA-ARS-North Central Agricultural Research Laboratory, Brookings, SD, 57006, USA.
USDA-ARS-Food Systems Research Unit, Burlington, VT, 57006, USA.
Environ Microbiome. 2024 May 7;19(1):30. doi: 10.1186/s40793-024-00571-8.
Soil microbial communities are difficult to measure and critical to soil processes. The bulk soil microbiome is highly diverse and spatially heterogeneous, which can make it difficult to detect and monitor the responses of microbial communities to differences or changes in management, such as different crop rotations in agricultural research. Sampling a subset of actively growing microbes should promote monitoring how soil microbial communities respond to management by reducing the variation contributed by high microbial spatial and temporal heterogeneity and less active microbes. We tested an in-growth bag method using sterilized soil in root-excluding mesh, "sterile sentinels," for the capacity to differentiate between crop rotations. We assessed the utility of different incubation times and compared colonized sentinels to concurrently sampled bulk soils for the statistical power to differentiate microbial community composition in low and high diversity crop rotations. We paired this method with Oxford Nanopore MinION sequencing to assess sterile sentinels as a standardized, fast turn-around monitoring method.
Compared to bulk soil, sentinels provided greater statistical power to distinguish between crop rotations for bacterial communities and equivalent power for fungal communities. The incubation time did not affect the statistical power to detect treatment differences in community composition, although longer incubation time increased total biomass. Bulk and sentinel soil samples contained shared and unique microbial taxa that were differentially abundant between crop rotations.
Overall, compared to bulk soils, the sentinels captured taxa with copiotrophic or ruderal traits, and plant-associated taxa. The sentinels show promise as a sensitive, scalable method to monitor soil microbial communities and provide information complementary to traditional soil sampling.
土壤微生物群落难以测量，但对土壤过程至关重要。土壤整体微生物组具有高度多样性和空间异质性，这可能使得难以检测和监测微生物群落对管理差异或变化的响应，例如农业研究中的不同作物轮作。对一部分活跃生长的微生物进行采样，应能通过减少高微生物空间和时间异质性以及活性较低的微生物所造成的变异，促进对土壤微生物群落如何响应管理的监测。我们测试了一种在根系排斥网中使用灭菌土壤的内生长袋方法，即“无菌哨兵”，以区分作物轮作的能力。我们评估了不同培养时间的效用，并将定殖的哨兵与同时采集的土壤整体样本进行比较，以确定在低多样性和高多样性作物轮作中区分微生物群落组成的统计功效。我们将此方法与牛津纳米孔MinION测序相结合，以评估无菌哨兵作为一种标准化、快速周转的监测方法。
与土壤整体相比，哨兵在区分细菌群落作物轮作方面提供了更大的统计功效，在区分真菌群落方面提供了相当的功效。培养时间并未影响检测群落组成中处理差异的统计功效，尽管较长的培养时间增加了总生物量。土壤整体和哨兵土壤样本包含在作物轮作之间丰度不同的共享和独特微生物分类群。
总体而言，与土壤整体相比，哨兵捕获了具有富营养或杂草性特征的分类群以及与植物相关的分类群。哨兵有望成为一种敏感、可扩展的方法，用于监测土壤微生物群落，并提供与传统土壤采样互补的信息。
