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Although soil ecology has benefited from recent advances in describing the functional and trophic traits of soil organisms, large scale reconstruction of soil food webs is still hampered by the issues that (1) most of the data about trophic interactions and diets are distributed across heterogeneous repositories, (2) no well-established terminology exists for describing trophic groups, feeding processes, and resource types, and (3) large heterogeneity exists in the trophic classification of different soil organisms, or such classifications are lacking. Here, we propose the Soil Food Web Ontology as a new formal framework for representing knowledge on trophic ecology of soil organisms. This ontology captures the semantics of trophic concepts, including consumer-resource interactions, diets and feeding processes, and provides a formalisation of trophic group definitions. This ontology can be used to add semantic annotations to trophic data, thus facilitating the integration of heterogeneous datasets. It also provides lexical resources that can support the development of information extraction tools for the creation of literature-based datasets. Finally, it enables automatic and consistent classification of soil organisms based on their trophic relationships. We argue that, by harmonising the terminology and underlying concepts of soil trophic ecology, our ontology allows a better use of available information on the feeding habits of soil organisms and sounder trophic classifications, thus facilitating the reconstruction of soil food webs and making food web research more accessible, reusable and reproducible.

Earthworms are considered ecosystem engineers due to their fundamental impact on soil structure, soil processes and on other soil biota. An invasion of non-native earthworm species has altered soils of North America since European settlement, a process currently expanding into still earthworm-free forest ecosystems due to continuous spread and increasing soil temperatures owing to climate change. Although earthworms are known to modify soil microbial diversity and activity, it is as yet unclear how eukaryote consumers in soil microbial food webs will be affected. Here, we investigated how earthworm invasion affects the diversity of Cercozoa, one of the most dominant protist taxa in soils. Although the composition of the native cercozoan community clearly shifted in response to earthworm invasion, the communities of the different forests showed distinct responses. We identified 39 operational taxonomic units (OTUs) exclusively indicating earthworm invasion, hinting at an earthworm-associated community of Cercozoa. In particular, Woronina pythii, a hyper-parasite of plant-parasitic Oomycota in American forests, increased strongly in the presence of invasive earthworms, indicating an influence of invasive earthworms on oomycete communities and potentially on forest health, which requires further research.

In natural ecosystems, positive effects of plant diversity on ecosystem functioning have been widely observed, yet whether this is true in cropping systems remains unclear. Here we assessed the impact of crop diversification on soil microbial diversity, soil multifunctionality (SMF) and crop yields in 155 cereal fields across a 3,000 km north–south European gradient. Overall, crop diversity showed a relatively minor effect on soil microbial diversity, SMF and yields. In contrast, the proportion of time with crop cover (including cash crops, cover crops or forage leys) during the past ten-year crop rotation had a much stronger impact. This suggests that increasing crop cover can enhance both yields and soil functioning, while also providing habitat for soil microorganisms. We found that SMF did not positively contribute to crop yields, highlighting that care must be taken to balance the provision of food with environmentally beneficial functions and services, since they do not always go hand in hand. The Digging Deeper project was funded through the 2015–2016 BiodivERsA COg call for research proposals, with the national funders Swiss National Science Foundation (grant 31BD30-172466), Deutsche Forschungsgemeinschaft (317895346), Swedish Research Council Formas contract 2016-0194), Ministerio de Economía y Competitividad (Digging_Deeper, reference PCIN-2016-028) and Agence Nationale de la Recherche (ANR, France, grant ANR-16-EBI3-0004-01).

Background: Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. Here we combined multiple environmental gradients with fine-scale phylogenetic analyses and machine learning for new insights into ecological preferences within Nitrososphaeria. With this approach, we could identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea in arable soils along a 3 000 km European gradient. Results: Mean annual temperature, C:N ratio and pH were the best predictors of diversity, evenness and distribution of Nitrososphaeria and thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Recent adaptations to soil pH were indicated in the Nitrososphaeria phylogeny. Our analyses further suggest the coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria. Only limited insights into the ecology of the low-abundant, but highly diverse classes Thermoplasmata and Woesearchaeia could be inferred. However, for explaining the overall archaeal community composition at the continental scale the contribution of distance (reflecting stochastic assembly processes) and environmental factors (reflecting deterministic processes) were comparable. Conclusions: Our findings underline the multifactorial nature of niche differentiation in soil Nitrososphaeria and the ecophysiological differences between closely related members observed suggest that the phylogeny does not reflect their ecology. Our results also imply multiple, independent specializations to low pH. The study highlights that the ecology of Nitrososphaeria is best studied at fine phylogenetic scale. Finally, the identification of thresholds in the responses show that simple correlations are not sufficient when determining environmental drivers of archaeal diversity.

Phosphorus (P) acquisition is key for global food production. Arbuscular mycorrhizal fungi (AMF) help plants acquire P and are considered key for the design of sustainable agroecosystems. However, how the functioning of AMF varies across agricultural soils and responds to management practices is still unknown. Here, we collected soils from 150 cereal fields and 60 non-cropped grassland sites across Europe, and in a greenhouse experiment, we tested the ability of AMF in these soils to forage for radioisotope-labelled 33P from a hyphal compartment. Hyphal-mediated P uptake was 64% higher in non-cropped grassland compared to cropland soils. Soil pH and organic carbon best explained the hyphal-mediated P uptake in the grasslands, while the use of fungicide in croplands reduced P uptake in the croplands by 43%. Our results suggest that land-use intensity and fungicide use are major deterrents to the natural capacity of AMF to contribute to sustainable crop production.

The Tansley review by Ryan & Graham (2018) provided a welcome critical perspective on the role of arbuscular mycorrhizal (AM) fungi in large‐scale industrial agriculture, with a focus on cereals (wheat, Triticum aestivum). They conclude that there is little evidence that farmers should consider the abundance or diversity of AM fungi when managing crops. We welcome many of the points made in the paper, as they give an opportunity for self‐reflection, considering that the importance of AM fungi in agroecosystems is often taken for granted. However, we suggest that it is too early to draw the overall conclusion that the management of AM fungi by farmers is currently not warranted. We offer the following points to contribute to the discussion. The first point pertains to the overall focus of Ryan & Graham (2018), which strongly determines the recommendations at which the authors arrive. This scope is limited to yield, at the expense of neglecting aspects of sustainability. We then argue that AM fungal communities do respond negatively to aspects of agricultural management, and list evidence for their positive effects to agronomically important traits, including yield in cereals. In our final argument, we advocate for transitioning to agroecosystems that are more AM compatible in order to increasingly take advantage of all the potential services these ancient symbionts, and other soil biota, can provide.

Levels of N-cycle gene transcripts (nirK, nirS, nosZ, amoA) were measured during an N2O emission peak in an agricultural soil. Automated dynamic closed chambers were used to monitor an N2O emission peak on a maize crop after a natural rainfall. The peak occurred rapidly after the rainfall began. Spatial and temporal variability in N2O emission was observed between chambers. An analysis of N-cycle gene transcript levels revealed an increase in bacterial amoA gene transcripts (but not in archaeal amoA transcripts), correlating strongly with N2O emission. This suggests the involvement of nitrification enzymes, despite a high water-filled pore space (80%). Reverse transcription of bacterial 16S rRNA followed by partial sequencing of the resulting cDNAs revealed few rainfall-induced changes in the potentially active bacterial community, and notably no significant change in the relative abundance of 16S rRNAs from the nitrifier genus Nitrosospira. Expression of the amoA gene appears as a possible proxy for monitoring the N2O emission peak. To our knowledge, this is the first experiment to evaluate the expression of N-cycle genes during an N2O emission peak on an agricultural field.

Among the soil management practices used to promote sustainable agriculture, reduced tillage and retention of residues from the previous crop are reported to enhance significantly both soil fertility and crop productivity. Here, high-throughput sequencing (454 technology) was used to see how the tillage regime (conventional vs. reduced tillage) and the fate of crop residues (retention or removal) affect microbial communities at two sampling depths (top soil: 0–5 cm and deeper soil: 15–20 cm) in a fertile silty loam soil in Belgium. All combinations of these three factors were studied. After 6 years of conversion from conventional to reduced tillage, depth emerged as the main factor responsible for variation in microbial diversity, tillage regime ranked second, and finally, crop residue fate had no influence on microbial diversity. For both bacteria and fungi, the diversity appeared higher in the top soil than in the deeper soil, and surprisingly, higher under conventional than under reduced tillage. These differences are explained by changes in community composition due to taxon loss rather than taxon replacement. The specific local set of environmental conditions (a loess-derived soil and an oceanic temperate climate) may explain these results. These observations raise the question: does impoverishment in indicator taxa influence soil processes, and thus crop production? To answer this question, we discuss how the presence of certain indicator taxa liable to play an ecological role might relate to crop productivity.

Soil protists are increasingly appreciated as essential components of soil foodwebs; however, there is a dearth of information on the factors structuring their communities. Here we investigate the importance of different biotic and abiotic factors as key drivers of spatial and seasonal distribution of protistan communities. We conducted an intensive survey of a 10m2 grassland plot in Germany, focusing on a major group of protists, the Cercozoa. From 177 soil samples, collected from April to November, we obtained 694 Operational Taxonomy Units representing >6 million Illumina reads. All major cercozoan groups were present, dominated by the small flagellates of the Glissomonadida. We found evidence of environmental filtering structuring the cercozoan communities both spatially and seasonally. Spatial analyses indicated that communities were correlated within a range of four meters. Seasonal variations of bactevirores and bacteria, and that of omnivores after a time-lapse, suggested a dynamic prey-predator succession. The most influential edaphic properties were moisture and clay content, which differentially affected each functional group. Our study is based on an intense sampling of protists at a small scale, thus providing a detailed description of the niches occupied by different taxa/functional groups and the ecological processes involved.

In soils, bacteria are very abundant and diverse. They are involved in various agro-ecosystem processes such as the nitrogen cycle, organic matter degradation, and soil formation. Yet, little is known about the distribution and composition of bacterial communities through the soil profile, particularly in agricultural soils, as most studies have focused only on topsoils or forest and grassland soils. In the present work, we have used bar-coded pyrosequencing analysis of the V3 region of the 16S rRNA gene to analyze bacterial diversity in a profile (depths 10, 25, and 45 cm) of a well-characterized field of winter wheat. Taxonomic assignment was carried out with the Ribosomal Database Project (RDP) Classifier program with three bootstrap scores: a main run at 0.80, a confirmation run at 0.99, and a run at 0 to gain information on the unknown bacteria. Our results show that biomass and bacterial quantity and diversity decreased greatly with depth. Depth also had an impact, in terms of relative sequence abundance, on 81 % of the most represented taxonomic ranks, notably the ranks Proteobacteria, Bacteroidetes, Actinobacteridae, and Acidobacteria. Bacterial community composition differed more strongly between the topsoil (10 and 25 cm) and subsoil (45 cm) than between levels in the topsoil, mainly because of shifts in the carbon, nitrogen, and potassium contents. The subsoil also contained more unknown bacteria, 53.96 % on the average, than did the topsoil, with 42.06 % at 10 cm and 45.59 % at 25 cm. Most of these unknown bacteria seem to belong to Deltaproteobacteria, Actinobacteria, Rhizobiales, and Acidobacteria.

International audience; Soil microorganisms such as mycorrhizae and plant-growth-promoting rhizobacteria have beneficial effects on crop productivity. Agricultural practices are known to impact soil microbial communities, but past studies examining this impact have focused mostly on one or two taxonomic levels, such as phylum and class, thus missing potentially relevant information from lower levels. Therefore, we propose here an original, sub-phylum method for studying how agricultural practices modify microbial communities. This method involves exploiting the available sequence information at the lowest taxonomic level attainable for each operational taxonomic unit. In order to validate this novel method, we assessed microbial community composition using 454 pyrosequencing of 16S and 28S rRNA genes, and then we compared the results with results of a phylum-level analysis. Agricultural practices included conventional tillage, reduced tillage, residue removal, and residue retention. Results show that, at the lowest taxonomic level attainable, tillage is the main factor influencing both bacterial community composition, accounting for 13 % of the variation, and fungal community composition, accounting for 18 % of the variation. On the other hand, phylum-level analysis failed to reveal any effect of soil practice on bacterial community composition and missed the fact that different members of the same phylum responded differently to tillage practice. For instance, the fungal phylum Chytridiomycota showed no impact of soil treatment, while sub-phylum-level analysis revealed an impact of tillage practice on the Chytridiomycota sub-groups Gibberella, which includes a notorious wheat pathogen, and Trichocomaceae. This clearly demonstrates the necessity of exploiting the information obtainable at sub-phylum level when assessing the effects of agricultural practice on microbial communities.