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The discovery of complete ammonia oxidizers, comammox Nitrospira, represents a breakthrough in the history of nitrification research. Nitrospira inopinata, which was obtained from an aquatic ecosystem, is the only pure comammox bacterial isolate reported so far. Ammonia oxidation kinetics of N. inopinata indicated that they prefer an oligotrophic lifestyle and may directly compete with ammonia-oxidizing archaea (AOA), but representatives of comammox Nitrospira from terrestrial ecosystems are lacking. Current studies demonstrate that the functionally dominant comammox Nitrospira in terrestrial ecosystems are separated from most sequences obtained from aquatic and engineering systems. Clades A and B of comammox Nitrospira seemingly have different ecological preferences in soils, possibly due to their different ammonium uptake systems. Analyses of the evolutionary history indicate that some genes of comammox Nitrospira involved in ammonia oxidation could be laterally transferred from β-ammonia-oxidizing bacteria (AOB). Some comammox Nitrospira species may have similar ecological preferences with AOB and be functionally active in the niches where nitrification was previously considered to be dominated by AOB. Taken together, this review summarizes the recent findings of the biogeographical distribution and ecological preference of comammox Nitrospira in large-scale soil surveys, the responses of comammox Nitrospira to nitrogen application in soil, and the putative mechanisms underpinning the ecological niche of terrestrial comammox Nitrospira. These studies from terrestrial ecosystems suggest that comammox Nitrospira are not strictly oligotrophic but both oligotrophic and copiotrophic with a broader ecological niche breadth. Comammox Nitrospira in terrestrial ecosystems are abundant and active in both oligotrophic and copiotrophic environments. These findings have profoundly expanded our knowledge of the environmental niches of comammox Nitrospira and their relative contribution to nitrification in soils.

Additional file 1. Fig. S1. The distribution of the soil sampling sites. Fig. S2. Variable importance plot of contigs from random forest classification analysis based on geographical distribution. Fig. S3. Two complete viral genomes contain a P metabolism module.

Additional file 1: Fig. S1. Heatmap of the relative abundance of ARGs. The column is labeled with the content of available Se content of each sampling from low to high. The row is the ARGs detected in each sample and grouped according to antibiotic resistance type.

Additional file 8: Text S1. Determination of total and available Se contents of soil.

Additional file 7: Table S1. Sampling site locations and soil chemical properties. Table S2. Primer sequences and quantitative PCR reaction conditions of 16 selenium resistance genes. Table S3. Pearson correlation between soil chemical properties. “*” significant correlations at P < 0.05; “**” Significant correlations at P < 0.001. Table S4. The detected concentration of antibiotic residues (µg kg−1). Table S5. The absolute copy numbers of selenium resistance genes (copies g−1).

Latitudinal gradients provide opportunities to better understand soil fungal community assembly and its relationship with vegetation, climate, soil and ecosystem function. Understanding the mechanisms underlying community assembly is essential for predicting compositional responses to changing environments. - We quantified the relative importance of stochastic and deterministic processes in structuring soil fungal communities using patterns of community dissimilarity observed within and between twelve natural forests and related these to environmental variation within and among sites. - The results revealed that whole fungal communities and communities of arbuscular and ectomycorrhizal fungi consistently exhibited divergent patterns but with less divergence for ectomycorrhizal fungi at most sites. Within those forests, no clear relationships were observed between the degree of divergence within fungal and plant communities. When comparing communities at larger spatial scales, among the twelve forests, we observed distinct separation in all three fungal groups among tropical, subtropical and temperate climatic zones. Soil fungal β-diversity patterns between forests were also greater when comparing forests exhibiting high environmental heterogeneity. - Taken together, although large-scale community turnover could be attributed to specific environmental drivers, the differences among fungal communities in soils within forests was high even at local scales.

Additional file 1. Supplementary information.

Additional file 1. Supplementary information.

9 páginas.- 5 figuras.- 51 referencias.- Supplementary information The online version contains supplementary material available at https://doi.org/10.1038/s41561-023-01170-x, Soil mosses are among the most widely distributed organisms on land. Experiments and observations suggest that they contribute to terrestrial soil biodiversity and function, yet their ecological contribution to soil has never been assessed globally under natural conditions. Here we conducted the most comprehensive global standardized field study to quantify how soil mosses influence 8 ecosystem services associated with 24 soil biodiversity and functional attributes across wide environmental gradients from all continents. We found that soil mosses are associated with greater carbon sequestration, pool sizes for key nutrients and organic matter decomposition rates but a lower proportion of soil-borne plant pathogens than unvegetated soils. Mosses are especially important for supporting multiple ecosystem services where vascular-plant cover is low. Globally, soil mosses potentially support 6.43 Gt more carbon in the soil layer than do bare soils. The amount of soil carbon associated with mosses is up to six times the annual global carbon emissions from any altered land use globally. The largest positive contribution of mosses to soils occurs under a high cover of mat and turf mosses, in less-productive ecosystems and on sandy and salty soils. Our results highlight the contribution of mosses to soil life and functions and the need to conserve these important organisms to support healthy soils., The study work associated with this paper was funded by a Large Research Grant from the British Ecological Society (no. LRB17\1019; MUSGONET). D.J.E. is supported by the Hermon Slade Foundation. M.D.-B. was supported by a Ramón y Cajal grant from the Spanish Ministry of Science and Innovation (RYC2018-025483-I), a project from the Spanish Ministry of Science and Innovation for the I + D + i (PID2020-115813RA-I00 funded by MCIN/AEI/10.13039/501100011033a) and a project PAIDI 2020 from the Junta de Andalucía (P20_00879). E.G. is supported by the European Research Council grant agreement 647038 (BIODESERT). M.B. is supported by a Ramón y Cajal grant from Spanish Ministry of Science (RYC2021-031797-I). A.d.l.R is supported by the AEI project PID2019-105469RB-C22. L.W. and Jianyong Wang are supported by the Program for Introducing Talents to Universities (B16011) and the Ministry of Education Innovation Team Development Plan (2013-373). The contributions of T.G. and T.U.N. were supported by the Research Program in Forest Biology, Ecology and Technology (P4-0107) and the research projects J4-3098 and J4-4547 of the Slovenian Research Agency. The contribution of P.B.R. was supported by the NSF Biological Integration Institutes grant DBI-2021898. J. Durán and A. Rodríguez acknowledge support from the FCT (2020.03670.CEECIND and SFRH/BDP/108913/2015, respectively), as well as from the MCTES, FSE, UE and the CFE (UIDB/04004/2021) research unit financed by FCT/MCTES through national funds (PIDDAC).

22 páginas.-. 5 figuras.- 64 referencias.- Supplementary Information This pdf file includes: Supplementary Figs. 1–5, Tables 1–11 and references. https://static-content.springer.com/esm/art%3A10.1038%2Fs41559-022-01935-4/MediaObjects/41559_2022_1935_MOESM1_ESM.pdf, While the contribution of biodiversity to supporting multiple ecosystem functions is well established in natural ecosystems, the relationship of the above- and below-ground diversity with ecosystem multifunctionality remains virtually unknown in urban greenspaces. Here we conducted a standardized survey of urban greenspaces from 56 municipalities across six continents, aiming to investigate the relationships of plant and soil biodiversity (diversity of bacteria, fungi, protists and invertebrates, and metagenomics-based functional diversity) with 18 surrogates of ecosystem functions from nine ecosystem services. We found that soil biodiversity across biomes was significantly and positively correlated with multiple dimensions of ecosystem functions, and contributed to key ecosystem services such as microbially driven carbon pools, organic matter decomposition, plant productivity, nutrient cycling, water regulation, plant–soil mutualism, plant pathogen control and antibiotic resistance regulation. Plant diversity only indirectly influenced multifunctionality in urban greenspaces via changes in soil conditions that were associated with soil biodiversity. These findings were maintained after controlling for climate, spatial context, soil properties, vegetation and management practices. This study provides solid evidence that conserving soil biodiversity in urban greenspaces is key to supporting multiple dimensions of ecosystem functioning, which is critical for the sustainability of urban ecosystems and human wellbeing., This study was supported by a 2019 Leonardo Grant for Researchers and Cultural Creators, BBVA Foundation (URBANFUN), and by the BES grant agreement number LRB17\1019 (MUSGONET). M.D.-B. acknowledges support from the Spanish Ministry of Science and Innovation for the I+D+i project PID2020-115813RA-I00 funded by MCIN/AEI/10.13039/501100011033. M.D.-B. is also supported by a project of the Fondo Europeo de Desarrollo Regional (FEDER) and the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía (FEDER Andalucía 2014-2020 Objetivo temático ‘01-Refuerzo de la investigación, el desarrollo tecnológico y la innovación’) associated with the research project P20_00879 (ANDABIOMA). H.C. was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDA28020202), National Key R&D Program of China (2022YFD1500202) and the National Natural Science Foundation of China (91951109, 42230511, 92251305). K.F. was supported by Young Elite Scientist Sponsorship Program by CAST (2021QNRC001) and China Postdoctoral Science Foundation (2021M703302). F.D.A. and S.A. were supported by ANID FONDECYT 11180538 and 1170995. J.P.V. was supported by SERB (SIR/2022/000626, EEQ/2021/001083), DST (DST/INT/SL/P-31/2021) and Banaras Hindu University, IoE (6031) incentives grant for plant-microbe interaction and soil microbiome research. T.G. and T.U.N were supported by the Slovenian Research Agency grants P4-0107, J4-3098 and J4-4547.

14 páginas.- 7 figuras.- 49 referencias, Background Little is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth’s largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents and created the first global atlas with the distributions of topsoil ARGs. Results We show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs. Conclusions Together, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome., This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement 702057 (CLIMIFUN), a Large Research Grant from the British Ecological Society (agreement no. LRA17\1193; MUSGONET), and from the European Research Council (ERC grant agreement no. 647038, BIODESERT). M. D. B. was also supported by a Ramón y Cajal grant (RYC2018-025483-I). M.D-B. also acknowledges support from the Spanish Ministry of Science and Innovation for the I+D+i project PID2020-115813RA-I00 funded by MCIN/AEI/10.13039/501100011033. M.D-B. is also supported by a project of the Fondo Europeo de Desarrollo Regional (FEDER) and the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía (FEDER Andalucía 2014-2020 Objetivo temático “01 - Refuerzo de la investigación, el desarrollo tecnológico y la innovación”) associated with the research project P20_00879 (ANDABIOMA). FTM acknowledges support from Generalitat Valenciana (CIDEGENT/2018/041). J. Z. H and H. W. H. are financially supported by Australian Research Council (DP210100332). We also thank the project CTM2015-64728-C2-2-R from the Ministry of Science of Spain. C. A. G. and N. E. acknowledge funding by the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, funded by the German Research Foundation (FZT 118). TG was financially supported by Slovenian Research Agency (P4-0107, J4-3098 and J4-4547)