Environmental filtering controls soil biodiversity in wet tropical ecosystems

9 páginas..- 4 figuras.- referencias.- Supplementary data to this article can be found online at https://doi. org/10.1016/j.soilbio.2022.108571The environmental factors controlling soil biodiversity along resource gradients remain poorly understood in wet tropical ecosystems. Aboveground biodiversity is expected to be driven by changes in nutrient availability in these ecosystems, however, much less is known about the importance of nutrient availability in driving soil biodiversity. Here, we combined a cross-continental soil survey across tropical regions with a three decades' field experiment adding nitrogen (N) and phosphorus (P) (100 kg N ha(-1)y(-1) and 100 kg P ha(-1)y(-1)) to Hawai'ian tropical forests with contrasting substrate ages (300 and 4,100,000 years) to investigate the influence of nutrient availability to explain the biodiversity of soil bacteria, fungi, protists, invertebrates and key functional genes. We found that soil biodiversity was driven by soil acidification during long-term pedogenesis and across environmental gradients, rather than by nutrient limitations. In fact, our results showed that experimental N additions caused substantial acidification in soils from Hawai'i. These declines in pH were related to large decreases in soil biodiversity from tropical ecosystems in four continents. Moreover, the microbial activity did not change in response to long-term N and P additions. We concluded that environmental filtering drives the biodiversity of multiple soil organisms, and that the acidification effects associated with N additions can further create substantial undesired net negative effects on overall soil biodiversity in naturally tropical acid soils. This knowledge is integral for the understanding and management of soil biodiversity in tropical ecosystems globally.Supported by a Ramón y Cajal grant (RYC2018-025483-I), a “Ayuda P.P. 2020. Desarrollo Lineas Investigación Propias (UPO), a project from the Spanish Ministry of Science and Innovation (PID2020-115813RA-I00), and a project PAIDI 2020 from the Junta de Andalucía (P20_00879). H.Y.C. is supported by National Natural Science Foundation of China (32101335), China Postdoctoral Science Foundation (2021M690589), Innovation Project of Young Technological Talents in Changchun City (21QC07), and Fundamental Research Funds for the Central Universities (2412021QD014). J.P.V. is thankful to DST and SERB (Science and Engineering Research Board), India for financial support for plant-microbe interaction research. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.Peer reviewe

Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwide

Soil contamination is one of the main threats to ecosystem health and sustainability. Yet little is known about the extent to which soil contaminants differ between urban greenspaces and natural ecosystems. Here we show that urban greenspaces and adjacent natural areas (i.e., natural/semi-natural ecosystems) shared similar levels of multiple soil contaminants (metal(loid)s, pesticides, microplastics, and antibiotic resistance genes) across the globe. We reveal that human influence explained many forms of soil contamination worldwide. Socio-economic factors were integral to explaining the occurrence of soil contaminants worldwide. We further show that increased levels of multiple soil contaminants were linked with changes in microbial traits including genes associated with environmental stress resistance, nutrient cycling, and pathogenesis. Taken together, our work demonstrates that human-driven soil contamination in nearby natural areas mirrors that in urban greenspaces globally, and highlights that soil contaminants have the potential to cause dire consequences for ecosystem sustainability and human wellbeing

The global distribution and environmental drivers of the soil antibiotic resistome

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)

The global contribution of soil mosses to ecosystem services

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)

Biogenic factors explain soil carbon in paired urban and natural ecosystems worldwide

12 páginas.- 4 figuras.- 49 referencia.- Supplementary information The online version contains supplementary material available at https://doi.org/10.1038/s41558-023-01646-z .- Full-text access to a view-only version (Acceso a texto completo de sólo lectura en este enlace) https://rdcu.be/c8vZiUrban greenspaces support multiple nature-based services, many of which depend on the amount of soil carbon (C). Yet, the environmental drivers of soil C and its sensitivity to warming are still poorly understood globally. Here we use soil samples from 56 paired urban greenspaces and natural ecosystems worldwide and combine soil C concentration and size fractionation measures with metagenomics and warming incubations. We show that surface soils in urban and natural ecosystems sustain similar C concentrations that follow comparable negative relationships with temperature. Plant productivity’s contribution to explaining soil C was higher in natural ecosystems, while in urban ecosystems, the soil microbial biomass had the greatest explanatory power. Moreover, the soil microbiome supported a faster C mineralization rate with experimental warming in urban greenspaces compared with natural ecosystems. Consequently, urban management strategies should consider the soil microbiome to maintain soil C and related ecosystem services.This study was supported by a 2019 Leonardo Grant for Researchers and Cultural Creators, BBVA Foundation (URBANFUN), and by BES Grant Agreement No. LRB17\1019 (MUSGONET). M.D-B., P.G-P., J.D. and A.R. acknowledge support from TED2021-130908B-C41/AEI/10.13039/501100011033/ Unión Europea NextGenerationEU/PRTR. 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. was 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). D.J.E. was supported by the Hermon Slade Foundation. J.P.V. thanks the Science and Engineering Research Board (SERB) (EEQ/2021/001083, SIR/2022/000626) and the Department of Science and Technology (DST), India (DST/INT/SL/P-31/2021) and Banaras Hindu Univeristy-IoE (6031)-incentive grant for financial assistance for research in plant-microbe interaction and soil microbiome. J.D. 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).Peer reviewe

Global hotspots for soil nature conservation

19 páginas.- 5 figuras.- 98 referencias.- Supplementary information The online version contains supplementary material available at https://doi.org/10.1038/s41586-022-05292-xSoils are the foundation of all terrestrial ecosystems1. However, unlike for plants and animals, a global assessment of hotspots for soil nature conservation is still lacking2. This hampers our ability to establish nature conservation priorities for the multiple dimensions that support the soil system: from soil biodiversity to ecosystem services. Here, to identify global hotspots for soil nature conservation, we performed a global field survey that includes observations of biodiversity (archaea, bacteria, fungi, protists and invertebrates) and functions (critical for six ecosystem services) in 615 composite samples of topsoil from a standardized survey in all continents. We found that each of the different ecological dimensions of soils—that is, species richness (alpha diversity, measured as amplicon sequence variants), community dissimilarity and ecosystem services—peaked in contrasting regions of the planet, and were associated with different environmental factors. Temperate ecosystems showed the highest species richness, whereas community dissimilarity peaked in the tropics, and colder high-latitudinal ecosystems were identified as hotspots of ecosystem services. These findings highlight the complexities that are involved in simultaneously protecting multiple ecological dimensions of soil. We further show that most of these hotspots are not adequately covered by protected areas (more than 70%), and are vulnerable in the context of several scenarios of global change. Our global estimation of priorities for soil nature conservation highlights the importance of accounting for the multidimensionality of soil biodiversity and ecosystem services to conserve soils for future generations.This project received funding from the British Ecological Society (agreement LRA17\1193; MUSGONET). C.A.G. and N.E. were funded by DFG–FZT 118, 202548816; C.A.G. was supported by FCT-PTDC/BIA-CBI/2340/2020; M.D.-B. was supported by RYC2018-025483-I, PID2020-115813RA-I00\MCIN/AEI/10.13039/501100011033 and P20_00879. M.A.M.-M. and S.A. were funded by FONDECYT 1181034 and ANID-PIA-Anillo INACH ACT192057. J.D. and A.R. acknowledge support from IF/00950/2014, 2020.03670.CEECIND, SFRH/BDP/108913/2015 and UIDB/04004/2020. Y.-R.L. was supported by 2662019PY010 from the FRFCU. L.T. was supported by the ESF grant PRG632. F.B. and J.L.M. were supported by i-LINK+2018 (LINKA20069) funded by CSIC. C.T.-D. was supported by the Grupo de Biodibersidad & Cambio Global UBB–GI 170509/EF. C.P. was supported by the EU H2020 grant agreement 101000224. H.C. was supported by NSFC32101335, FRFCU2412021QD014 and CPSF2021M690589. J.P.V. was supported by DST (DST/INT/SL/P-31/2021) SERB (EEQ/2021/001083) and BHU-IoE (6031).Peer reviewe

Publisher Correction: Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwide

Correction to: Nature Communications, published online 27 March 2023 In the version of this article originally published, the current affiliation 25, “CEAZA, Universidad Católica del Norte, Coquimbo, Chile,” initially appeared as the last affiliation, offsetting all author footnotes from 25-39. The affiliation order has been restored in the article.Peer reviewe

Differential Effects of Desiccation on Hornworts with Contrasting Life Histories in Tropical Montane Forests: A Functional Trait—Based Perspective

Desiccation tolerance (DT) is the ability of an organism or structure to dry completely and subsequently survive in that air-dry state. Hornworts are excellent plant models to study desiccation effects as they have contrasting life histories which are likely associated with DT. We tested whether (1) epiphytic species had more efficient DT responses to drying and postrehydration than non-epiphytic species and whether (2) “green” spores were more sensitive than non-green spores to extreme drying. Hornwort species were collected from the Atlantic Forest of Rio de Janeiro, Brazil. We studied five species (gametophytes and spores: Dendroceros crispus, D. crispatus, Nothoceros vincentianus, Phaeoceros carolinianus; and only spores of Anthoceros lamellatus), using different relative humidity values, drying durations, and postrehydration conditions. All DT treatments affected the chlorophyll fluorescence (Fv/Fm) of gametophytes, with species-specific responses. D. crispatus and D. crispus (epiphytes) performed better than P. carolinianus and N. vincentianus, with fast recovery of Fv/Fm values postrehydration. The ability of non-green spores of P. carolinianus and A. lamellatus and green spores of D. crispus to support desiccation led us to reject our second hypothesis. The DT strategies of hornworts highlighted the trade-offs that are important in spore dispersal and plant establishment, such as fast colonization in Dendroceros spp. and potential spore soil banks in Phaeoceros and Anthoceros species

Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification

<p class="MsoNormal"><strong><span>Premise</span></strong></p> <p class="MsoNormal"><span>Bryophytes, land plants defined by a free-living gametophyte and an unbranched sporophyte, form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. </span><span>Our understanding of the evolutionary history of hornworts, liverworts and mosses has been significantly reshaped by inferences from molecular data, highlighting extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, and the degree to which the observed homoplasy represents error or biological processes, remain poorly resolved.</span></p> <p class="MsoNormal"><strong><span>Methods</span></strong></p> <p class="MsoNormal"><span>Using the GoFlag probe set, we sampled 405 exons representing 228 nuclear genes for 531 species from 51 of the 53 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations.</span></p> <p class="MsoNormal"><strong><span>Results</span></strong></p> <p class="MsoNormal"><span>The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more, and propose ten new orders of mosses. Most orders originated in the Jurassic or earlier and diversified in the Cretaceous or later. The phylogenomic data also highlight topological conflict in parts of the tree, suggesting complex processes of diversification that cannot be adequately captured in a single gene tree topology. </span></p> <p class="MsoNormal"><strong><span>Conclusions</span></strong></p> <p class="MsoNormal"><span>We sampled hundreds of homologous loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution, and these data resolved many of the critical nodes of the diversification of bryophytes. The data also highlight the need to explore the mechanisms underlying the phylogenetic ambiguity at specific nodes. The phylogenomic data provide an expandable framework toward reconstructing a comprehensive phylogeny of bryophytes and for investigating the transformations of traits in this important group of plants.</span></p><p>Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: https://ror.org/021nxhr62<br>Award Number: 1541506</p><p>Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: https://ror.org/021nxhr62<br>Award Number: 1541545</p><p>Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: https://ror.org/021nxhr62<br>Award Number: 1753811</p><p>Funding provided by: Natural Sciences and Engineering Research Council<br>Crossref Funder Registry ID: https://ror.org/01h531d29<br>Award Number: 05967–2016</p><p>Funding provided by: Canadian Foundation for Innovation*<br>Crossref Funder Registry ID: <br>Award Number: 36781</p><p>Funding provided by: Canadian Foundation for Innovation*<br>Crossref Funder Registry ID: <br>Award Number: 39135</p&gt

Soil biodiversity supports the delivery of multiple ecosystem functions in urban greenspaces

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.pdfWhile 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.Peer reviewe