Nelkner Johanna, Huang Liren, Lin Timo W, Schulz Alexander, Osterholz Benedikt, Henke Christian, Blom Jochen, Pühler Alfred, Sczyrba Alexander, Schlüter Andreas
Genome Research of Industrial Microorganisms, CeBiTec - Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
Nucleic Acids Core Facility, Faculty of Biology, Johannes Gutenberg University Mainz, Germany, Mainz.
Environ Microbiome. 2023 Mar 30;18(1):26. doi: 10.1186/s40793-023-00479-9.
For a sustainable production of food, research on agricultural soil microbial communities is inevitable. Due to its immense complexity, soil is still some kind of black box. Soil study designs for identifying microbiome members of relevance have various scopes and focus on particular environmental factors. To identify common features of soil microbiomes, data from multiple studies should be compiled and processed. Taxonomic compositions and functional capabilities of microbial communities associated with soils and plants have been identified and characterized in the past few decades. From a fertile Loess-Chernozem-type soil located in Germany, metagenomically assembled genomes (MAGs) classified as members of the phylum Thaumarchaeota/Thermoproteota were obtained. These possibly represent keystone agricultural soil community members encoding functions of relevance for soil fertility and plant health. Their importance for the analyzed microbiomes is corroborated by the fact that they were predicted to contribute to the cycling of nitrogen, feature the genetic potential to fix carbon dioxide and possess genes with predicted functions in plant-growth-promotion (PGP). To expand the knowledge on soil community members belonging to the phylum Thaumarchaeota, we conducted a meta-analysis integrating primary studies on European agricultural soil microbiomes.
Taxonomic classification of the selected soil metagenomes revealed the shared agricultural soil core microbiome of European soils from 19 locations. Metadata reporting was heterogeneous between the different studies. According to the available metadata, we separated the data into 68 treatments. The phylum Thaumarchaeota is part of the core microbiome and represents a major constituent of the archaeal subcommunities in all European agricultural soils. At a higher taxonomic resolution, 2074 genera constituted the core microbiome. We observed that viral genera strongly contribute to variation in taxonomic profiles. By binning of metagenomically assembled contigs, Thaumarchaeota MAGs could be recovered from several European soil metagenomes. Notably, many of them were classified as members of the family Nitrososphaeraceae, highlighting the importance of this family for agricultural soils. The specific Loess-Chernozem Thaumarchaeota MAGs were most abundant in their original soil, but also seem to be of importance in other agricultural soil microbial communities. Metabolic reconstruction of Switzerland_1_MAG_2 revealed its genetic potential i.a. regarding carbon dioxide (CO[Formula: see text]) fixation, ammonia oxidation, exopolysaccharide production and a beneficial effect on plant growth. Similar genetic features were also present in other reconstructed MAGs. Three Nitrososphaeraceae MAGs are all most likely members of a so far unknown genus.
On a broad view, European agricultural soil microbiomes are similarly structured. Differences in community structure were observable, although analysis was complicated by heterogeneity in metadata recording. Our study highlights the need for standardized metadata reporting and the benefits of networking open data. Future soil sequencing studies should also consider high sequencing depths in order to enable reconstruction of genome bins. Intriguingly, the family Nitrososphaeraceae commonly seems to be of importance in agricultural microbiomes.
为了实现粮食的可持续生产，对农业土壤微生物群落的研究必不可少。由于土壤具有极大的复杂性，它在某种程度上仍是一个未知领域。用于识别相关微生物群落成员的土壤研究设计具有不同的范围，并侧重于特定的环境因素。为了识别土壤微生物群落的共同特征，应汇总和处理来自多项研究的数据。在过去几十年中，已经确定并表征了与土壤和植物相关的微生物群落的分类组成和功能能力。从德国一种肥沃的黄土 - 黑钙土型土壤中，获得了分类为 Thaumarchaeota/Thermoproteota 门成员的宏基因组组装基因组（MAGs）。这些可能代表了对土壤肥力和植物健康具有重要功能的关键农业土壤群落成员。它们对所分析的微生物群落的重要性得到了以下事实的证实：据预测它们有助于氮循环，具有固定二氧化碳的遗传潜力，并拥有具有促进植物生长（PGP）预测功能的基因。为了扩展对属于 Thaumarchaeota 门的土壤群落成员的认识，我们进行了一项荟萃分析，整合了关于欧洲农业土壤微生物群落的初步研究。
对所选土壤宏基因组的分类分析揭示了来自 19 个地点的欧洲土壤共有的农业土壤核心微生物群落。不同研究之间的元数据报告存在异质性。根据可用的元数据，我们将数据分为 68 种处理方式。Thaumarchaeota 门是核心微生物群落的一部分，是所有欧洲农业土壤中古菌亚群落的主要组成部分。在更高的分类分辨率下，2074 个属构成了核心微生物群落。我们观察到病毒属对分类图谱的变化有很大贡献。通过对宏基因组组装的重叠群进行分箱，可以从几个欧洲土壤宏基因组中回收 Thaumarchaeota MAGs。值得注意的是，其中许多被分类为 Nitrososphaeraceae 科的成员，突出了该科对农业土壤的重要性。特定的黄土 - 黑钙土 Thaumarchaeota MAGs 在其原始土壤中最为丰富，但在其他农业土壤微生物群落中似乎也很重要。对 Switzerland_1_MAG_2 的代谢重建揭示了其在二氧化碳（CO₂）固定、氨氧化、胞外多糖产生以及对植物生长的有益影响等方面的遗传潜力。其他重建的 MAGs 也具有类似的遗传特征。三个 Nitrososphaeraceae MAGs 很可能都是一个迄今未知属的成员。
从广义上看，欧洲农业土壤微生物群落结构相似。尽管元数据记录的异质性使分析变得复杂，但仍可观察到群落结构的差异。我们的研究强调了标准化元数据报告的必要性以及开放数据联网的好处。未来的土壤测序研究还应考虑高测序深度，以便能够重建基因组 bins。有趣的是，Nitrososphaeraceae 科在农业微生物群落中似乎通常很重要。
