Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis

Abstract

Background 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. Results 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$$_2$$ 2 ) 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. Conclusions 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.

The Microbiomes of Various Types of Abandoned Fallow Soils of South Taiga (Novgorod Region, Russian North-West)

“…This is consistent with the findings that Bacillota appeared after the initial stage of lignocellulose decomposition [40]. The highest portion of Thermoproteota was in plaggen soils, which well corresponds with data on a high content of this group of microorganisms in fertile black soils of central Europe [41]. The plaggen soil was similar to black soils in terms of humus content, but not in terms of soil acidity; thus, the organic matter content may be a key factor of specificity of the soil microbiome of old cultivated soil.…”

“…The plaggen soil was similar to black soils in terms of humus content, but not in terms of soil acidity; thus, the organic matter content may be a key factor of specificity of the soil microbiome of old cultivated soil. The phylum (Thermoproteota) is also known as a predictor of soil aggregation [41], and the aggregation intensively depends on organic matter content. The portion of Myxococcota was increased in all altered soil in comparison with benchmark (initial) one.…”

Unraveling the Spatio-Temporal Dynamics of Soil and Root-Associated Microbiome in Texas Olive Orchards: A Comprehensive Analysis

“…However, the rhizosphere soil was enriched with Creanarcheota (now known as Thermoproteota). Members of this species are keystone members of agricultural soil communities due to their ability to promote the nitrogen cycle, x carbon dioxide, and possess genes linked to plant growth promotion (PGP), suggesting their importance in these microbiomes [75]. The greater abundance of Candidatus_Nitrososphaeria in the rhizospheric soil of Berclair in the spring and fall seasons was an intriguing nding.…”

A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions

“…Nelkner et al ( 2023 ) conducted a meta-analysis using data from 16 primary studies, examining microbial communities in agricultural soils across Europe. They aimed to understand how European soil characteristics influence microbial community composition, particularly focusing on Thaumarchaeota members.…”