Climate change, snow cover and microbial diversity in mountain soils: critical processes during snowmelt

In alpine zones, soil microbial diversity and activity are strongly dependent on the annual patterns of snowpack formation. It is under the insulating winter snowpack that a large and stable winter microbial community thrives, which is believed to die during thaw, when the soil rapidly dries up and temperatures start fluctuating again. We investigated the dynamics of soil microbiomes along altitudinal gradients above the tree line in three mountains in the Swiss Alps. This wide-scale soil sampling (160 samples in total) took place before, during and immediately after snowmelt, and later in summer; concomitantly vegetation, and relevant edaphic and climatic parameters were recorded. We used Illumina Novaseq high-throughput sequencing of RNAs (metatranscriptomics) to assess the whole community composition, e.g. prokaryotes and eukaryotes, including the often neglected protists. From the c. 400 million sequences obtained, we found an overall diversity differing from that usually retrieved using metabarcoding: Amoebozoa was the most abundant protistan lineage, followed by Rhizaria and Alveolata. We annotated the taxonomic output according to feeding modes and living styles, to track the dynamics of the soil food web. We found striking differences in community composition and preys/predators proportions between spring and summer, but, contrary to what is usually assumed, there is no rapid microbial turnover at snowmelt. The analyses of this wealth of data are still in progress. This is an unusually large-scale metatranscriptomics study of whole soil communities, with a high potential to unravel also seasonal bacterial and fungal functional profiles.

在高山带中，土壤微生物多样性与活性高度依赖于积雪形成的年度节律。冬季积雪层具有保温作用，其下会孕育出庞大且稳定的冬季微生物群落，而该群落被认为会在融雪期消亡——此时土壤快速干燥，温度再次出现波动。本研究针对瑞士阿尔卑斯山区三座山脉的林线以上海拔梯度，开展了土壤微生物组动态调查。此次大范围土壤采样（总计160份样品）分别在融雪前、融雪中、融雪后即刻以及夏末进行；同步记录了植被状况、相关土壤理化参数与气候参数。我们采用Illumina NovaSeq高通量测序平台对RNA进行测序（宏转录组学，metatranscriptomics），以解析完整微生物群落的组成，包括原核生物（prokaryotes）与真核生物（eukaryotes），乃至常被忽视的原生生物（protists）。从获取的约4亿条序列中，我们发现整体群落多样性与常规宏条形码（metabarcoding）技术得到的结果存在差异：变形虫门（Amoebozoa）是丰度最高的原生生物类群，其次为丝足虫类（Rhizaria）与顶复门（Alveolata）。我们根据营养模式与生活方式对分类学产出结果进行注释，以追踪土壤食物网的动态变化。研究发现，春季与夏季的群落组成及捕食者/猎物比例存在显著差异，但与通常的假设相悖，融雪期并未发生微生物的快速更替。目前针对这批海量数据的分析工作仍在进行中。本研究是针对完整土壤群落的一项超大规模宏转录组学研究，其在解析季节性细菌与真菌功能特征方面具备极高的研究潜力。