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\uffe2\uff80\uff93Chernozem-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.
ResultsTaxonomic 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.
ConclusionsOn 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.
", "keywords": ["2. Zero hunger", "570", "Soil microbial diversity", "Metagenomically assembled genomes", "Research", "European soil", "Open metagenome data analysis", "15. Life on land", "Microbiology", "Thaumarchaeota", "QR1-502", "Environmental sciences", "Agricultural microbiome", "Soil health", "GE1-350"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1186/s40793-023-00479-9.pdf"}, {"href": "https://doi.org/10.1186/s40793-023-00479-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40793-023-00479-9", "name": "item", "description": "10.1186/s40793-023-00479-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40793-023-00479-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-03-30T00:00:00Z"}}, {"id": "10.4067/s0718-58392014000300012", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:25:40Z", "type": "Journal Article", "created": "2014-07-30", "description": "Fertilization is an important agricultural practice for increasing crop yields and influencing soil properties. A field experiment was conducted in the period of 2006-2011 in southeastern China, to investigate the effects of fertilization regimes on tea (Camellia sinensis [L.] Kuntze) yields, soil chemical properties, and soil bacterial and fungal communities. The field experiment included six treatments: (1) unfertilized control (CON); (2) chemical fertilizers (NPK); (3) half-chemical fertilizers plus half-organic manure (1/2NPKOM); (4) organic manure fertilizers (OM); (5) half-chemical fertilizers plus half-organic manure plus legume stover returned (1/2NPKOM+L), and (6) chemical fertilizers plus legume stover returned (NPKL). Results showed that, compared to the control, NPK treatment showed no significant effect on soil organic matter (SOM), total N (TN), total P (TP), total K (TK), available N (AN), available K (AK) and tea yields, but showed the lowest bacterial Shannon index of 1.714 and the lowest value of 2.002 for fungal Shannon index. Organic manure treatment had the richest diversity of soil bacterial community with Shannon index of 2.542, and the highest levels of soil essential nutrients, including SOM (30.03%), TN (2.90 g kg-1), TP (1.35 g kg-1), AN (245.30 mg kg-1), AP (57.00 mg kg-1), and AK (271.80 mg kg-1), followed by 1/2NPKOM+L, which appeared the maximal tea yields of 6772 kg ha-1. Organic manure amendment was a key factor in determining soil properties and productivity. Base on soil quality and tea yields, both OM and 1/2NPKOM+L treatments were recommended as better choices of fertilization practices for tea soils in southeastern China. These findings provided a better understanding of the importance of fertilizations in promoting soil fertility, crop yields, and altering soil microbial diversity, leading to selection of scientific fertilization practices for sustainable development of agroecosystems.", "keywords": ["2. Zero hunger", "soil chemical properties", "tea yields", "fertilization", "soil microbial diversity", "", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "Camellia sinensis", "6. Clean water"], "contacts": [{"organization": "Qiu, Shan-Lian, Wang, Li-Min, Huang, Dong-Feng, Lin, Xin-Jian,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.4067/s0718-58392014000300012"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Chilean%20journal%20of%20agricultural%20research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.4067/s0718-58392014000300012", "name": "item", "description": "10.4067/s0718-58392014000300012", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.4067/s0718-58392014000300012"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-09-01T00:00:00Z"}}, {"id": "11585/996222", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:31:49Z", "type": "Journal Article", "created": "2021-07-10", "title": "A critical perspective on interpreting amplicon sequencing data in soil ecological research", "description": "Abstract Microbial community analysis via marker gene amplicon sequencing has become a routine method in the field of soil research. In this perspective, we discuss technical challenges and limitations of amplicon sequencing and present statistical and experimental approaches that can help addressing the spatio-temporal complexity of soil and the high diversity of organisms therein. We illustrate the impact of compositionality on the interpretation of relative abundance data and discuss effects of sample replication on the statistical power in soil community analysis. Additionally, we argue for the need of increased study reproducibility and data availability, as well as complementary techniques for generating deeper ecological insights into microbial roles and our understanding thereof in soil ecosystems. At this stage, we call upon researchers and specialized soil journals to consider the current state of data analysis, interpretation, and availability to improve the rigor of future studies.", "keywords": ["0301 basic medicine", "2. Zero hunger", "Soil microbial diversity", "0303 health sciences", "Soil metabarcoding", "DIVERSITY", "Ecology; Soil microbes; Amplicon sequencing", "Compositional data", "SCALE SPATIAL HETEROGENEITY", "15. Life on land", "BIOMASS", "03 medical and health sciences", "106026 \u00d6kosystemforschung", "Soil complexity", "CARBON-USE EFFICIENCY", "BACTERIA", "DNA EXTRACTION", "MICROORGANISMS", "MICROBIAL COMMUNITIES", "106026 Ecosystem research", "RIBOSOMAL-RNA", "Amplicon sequencing", "Soil microorganisms", "GENERATION"]}, "links": [{"href": "https://doi.org/11585/996222"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11585/996222", "name": "item", "description": "11585/996222", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11585/996222"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-09-01T00:00:00Z"}}, {"id": "PMC10064710", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:37:10Z", "type": "Journal Article", "created": "2023-03-30", "title": "Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis", "description": "Abstract BackgroundFor 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\uffe2\uff80\uff93Chernozem-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.
ResultsTaxonomic 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.
ConclusionsOn 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.
", "keywords": ["2. Zero hunger", "570", "Soil microbial diversity", "Metagenomically assembled genomes", "Research", "European soil", "Open metagenome data analysis", "15. Life on land", "Microbiology", "Thaumarchaeota", "QR1-502", "Environmental sciences", "Agricultural microbiome", "Soil health", "GE1-350"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1186/s40793-023-00479-9.pdf"}, {"href": "https://doi.org/PMC10064710"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC10064710", "name": "item", "description": "PMC10064710", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC10064710"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-03-30T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Soil+microbial+diversity&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Soil+microbial+diversity&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Soil+microbial+diversity&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Soil+microbial+diversity&offset=5", "hreflang": "en-US"}], "numberMatched": 5, "numberReturned": 5, "distributedFeatures": [], "timeStamp": "2026-06-25T21:26:24.157080Z"}