Unearthing the soil-borne microbiome of land plants

Plant–soil biodiversity interactions are fundamental for the functioning of terrestrial ecosystems. Yet, the existence of a set of globally distributed topsoil microbial and small invertebrate organisms consistently associated with land plants (i.e., their consistent soil-borne microbiome), together with the environmental preferences and functional capabilities of these organisms, remains unknown. We conducted a standardized field survey under 150 species of land plants, including 58 species of bryophytes and 92 of vascular plants, across 124 locations from all continents. We found that, despite the immense biodiversity of soil organisms, the land plants evaluated only shared a small fraction (less than 1%) of all microbial and invertebrate taxa that were present across contrasting climatic and soil conditions and vegetation types. These consistent taxa were dominated by generalist decomposers and phagotrophs and their presence was positively correlated with the abundance of functional genes linked to mineralization. Finally, we showed that crossing environmental thresholds in aridity (aridity index of 0.65, i.e., the transition from mesic to dry ecosystems), soil pH (5.5; i.e., the transition from acidic to strongly acidic soils), and carbon (less than 2%, the lower limit of fertile soils) can result in drastic disruptions in the associations between land plants and soil organisms, with potential implications for the delivery of soil ecosystem processes under ongoing global environmental change

Unearthing the soil-borne microbiome of land plants

DATA AVAILABILITY STATEMENT : Data from this manuscript is available at 10.6084/m9.figshare.25254673.Plant–soil biodiversity interactions are fundamental for the functioning of terrestrial ecosystems. Yet, the existence of a set of globally distributed topsoil microbial and small invertebrate organisms consistently associated with land plants (i.e., their consistent soil-borne microbiome), together with the environmental preferences and functional capabilities of these organisms, remains unknown. We conducted a standardized field survey under 150 species of land plants, including 58 species of bryophytes and 92 of vascular plants, across 124 locations from all continents. We found that, despite the immense biodiversity of soil organisms, the land plants evaluated only shared a small fraction (less than 1%) of all microbial and invertebrate taxa that were present across contrasting climatic and soil conditions and vegetation types. These consistent taxa were dominated by generalist decomposers and phagotrophs and their presence was positively correlated with the abundance of functional genes linked to mineralization. Finally, we showed that crossing environmental thresholds in aridity (aridity index of 0.65, i.e., the transition from mesic to dry ecosystems), soil pH (5.5; i.e., the transition from acidic to strongly acidic soils), and carbon (less than 2%, the lower limit of fertile soils) can result in drastic disruptions in the associations between land plants and soil organisms, with potential implications for the delivery of soil ecosystem processes under ongoing global environmental change.British Ecological Society; Slovenian Research Agency; Junta de Andalucía; Spanish Ministry of Science and Innovation.http://www.wileyonlinelibrary.com/journal/gcbhj2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-15:Life on lan

Potential Link between Ectomycorrhizal Community Composition and Host Tree Phenology

The timing of leaf phenology tends to be crucial in controlling ecosystem processes such as the acquisition of carbon and water loss as well as in controlling tree nutrient cycling. To date, tree phenology has mostly been associated with environmental control (e.g., temperature and photoperiod) in a relationship with inheritance, while it has rarely been linked with ectomycorrhizal community compositional changes through the host tree’s phenological stages. Seasonal variations of fungal communities have been widely studied, but little is known about mycorrhiza community composition changes along phenological stages. Therefore, we analyzed ectomycorrhizal communities associated with silver fir and their compositional changes during the transition between phenological stages. The phenological stages of each individual tree and time of bud break were monitored weekly for two years and, at the same time, ectomycorrhiza was harvested from selected silver fir trees. In total, 60 soil cores were analyzed for differences in the ectomycorrhizal community between phenological stages using Sanger sequencing of individual ectomycorrhizal morphotypes. A significant difference in beta diversity for an overall ectomycorrhizal community was confirmed between analyzed time periods for both sampled years. Species-specific reactions to transitions between phenological stages were confirmed for 18 different ectomycorrhizal taxa, where a positive correlation of Russula ochroleuca, Russula illota, Tomentella sublilacina, and Tylospora fibrillosa was observed with the phenological stage of bud burst

Buckwheat Milling Waste Effects on Root Morphology and Mycorrhization of Silver Fir Seedlings Inoculated with Black Summer Truffle (Tuber aestivum Vittad.)

Large amounts of buckwheat waste are generated annually by the industry and are used in several different ways. To date, there has been little research regarding its suitability as a medium for growing seedlings in nurseries. The aim of this study was therefore to analyze the suitability of common and Tartary buckwheat wastes (brans and husks) as media used for raising seedlings. A pot experiment with five different treatments was carried out, in which silver fir root parameters were analyzed and compared 6 and 12 months after summer truffle-spore inoculation. A significantly higher concentration of the antioxidant rutin was confirmed in Tartary buckwheat bran compared to other buckwheat waste used. We also confirmed a significantly positive effect of added Tartary buckwheat husks on specific root length, root tip density, and specific root tip density compared to added common buckwheat husks or Tartary buckwheat bran, for which a significantly negative effect on branching density was confirmed. A significantly negative effect of added buckwheat husks and Tartary buckwheat bran was confirmed for summer truffle mycorrhization level

Ectomycorrhizal symbionts of silver fir (Abies alba Mill.)

Poznavanje ektomikoriznih (ECM) simbiontov bele jelke do zdaj po večini temelji na morfološko-anatomskih opisih tipov ektomikorize ali pojavljanju trosnjakov. Ektomikoriza bele jelke v Sloveniji še ni bila ciljno raziskana. V okviru raziskave smo na treh klimatološko in pedološko različnih vzorčnih ploskvah v obdobju dveh let v rastnih sezonah enkrat mesečno vzorčili drobne korenine bele jelke in jih analizirali z morfološko-anatomsko metodo. Na podlagi opaženih morfološko-anatomskih lastnosti tipov ektomikorize smo ločili posamezne tipe ektomikorize in jih v naslednjem koraku identificirali še z analizo molekularnih markerjev. Z uporabljenimi pristopi smo ločili 86 tipov ektomikorize oziroma glivnih ECM-simbiontov in s tem prispevali k boljšemu poznavanju ECM-simbiontov bele jelke. Glede na do zdaj znane podatke smo kar 48 tipov ektomikorize v asociaciji z belo jelko identificirali prvič. V raziskavi so nas zanimali tudi vplivi abiotskih dejavnikov na vzorčnih ploskvah in načini, kako ti vplivajo na sestavo združb ECM-gliv in na njihove eksploracijske tipe. Potrdili smo statistično značilne razlike v sestavi združb ECM-gliv in v številčnosti eksploracijskih tipov ektomikorize med vzorčnimi ploskvami ter značilen vpliv nekaterih abiotskih dejavnikov tako na združbo ECM-simbiontov kot tudi na številčnost eksploracijskih tipov. Potrdili smo statistično značilno nihanje številčnosti tipov ECM-simbiontov ter eksploracijskih tipov med rastno sezono. V okviru raziskave smo vzpostavili lončni poskus za ugotavljanje, ali je bela jelka primeren ECM-gostitelj za nekatere vrste gomoljik (rod Tuber), in za ugotavljanje pomena deževnikov za uspešno mikorizacijo. Uspešnost mikorizacije v kontroliranih pogojih in vivo smo analizirali po 6 mesecih ter po enem letu od inokulacije s trosi vrst Tuber aestivum, T. borchii in T. melanosporum. Po enem letu od inokulacije smo potrdili, da je v naši študiji bela jelka primeren gostitelj gomoljike T. aestivum, ne pa tudi gomoljik T. borchii in T. melanosporum. Opazili pa smo negativen vpliv deževnikov na mikorizacijo in drobne korenine, kar kaže na pomanjkanje virov hrane in posledično objedanje koreninskih vršičkov.Knowledge of ectomycorrhizal (ECM) symbionts of silver fir is till date generally based on morphological-anatomical descriptions of ECM fruit bodies and/or ECM root tips, meanwhile ECM symbionts of silver fir in Slovenia have not been targeted analyzed. Within this research, silver fir’s fine roots were sampled at three climatologically and pedologically different sampling plots, where silver fir fine roots were sampled once per month during growth season, in a period of two years, and were further analyzed with stereo microscope and light microscope. Based on morphological-anatomical characteristics, individual ECM morphotypes were separated and further analyzed with molecular methods, for more reliable identification. In total, we identified 86 different ECM symbionts of silver fir, by which we contributed to better knowledge of silver fir ECM symbionts, as based on published data,48 ECM symbionts were in association with silver fir identified for the first time. We were also interested in possible significant effects of certain abiotic factors linked to individual sampling plot, on changes of ECM community composition as well as on abundances of individual exploration types. We confirmed statistically significant changes of ECM community composition and exploration types between sampled plots, by which we also confirmed significant effects of some abiotic factors as on ECM community composition as well as on abundances of exploration types. Also, statistically significant temporal changes of ECM species abundances and exploration types abundances were confirmed along to growing season. As a part of research, a pot experiment was established, by which silver fir as an appropriate host for commercially valuable truffles form genus Tuber was analyzed. Mycorrhization success in vitro was assessed after 6 months and after 1 year from spore inoculation with T. aestivum, T. borchii and T. melanosporum. At the same time, we wanted to highlight the key importance of earthworms on mycorrhization success, however after one year from spore inoculation, negative effects of added earthworms on mycorrhization level was observed, suggesting on lacking appropriate food source, which leaded to earthworms root grazing. After one year from spore inoculation, silver fir was confirmed as a appropriate host partner for truffle T. aestivum, but not also for truffles T. borchii and T. melanosporum, which\u27s presence on silver fir root tips was not observed

How beech provenance affects the structure of secondary xylem, leaf traits, and the ectomycorrhizal community under optimal growth conditions

Beyond growth parameters and drought tolerance, comparatively little is known about the functioning of different beech (Fagus sylvatica L.) provenances. We investigated properties of leaves, stem secondary xylem, and ectomycorrhiza (ECM), and explored their interdependencies to identify the best performing beech provenance in optimal growth conditions. The study was conducted on 23-year-old trees in a provenance trial. The investigated provenances originated from Atlantic (Belgium—BE), Alpine (Italy—IT, Slovenia—SI), and continental climates (the Czech Republic—CZ). A significant effect of provenance was observed for stem vessel diameters and conductive area, as well as for foliar %C, δ13C, δ15N, and δ18O. δ13C as a proxy of intrinsic water use efficiency (iWUE) showed that the highest iWUE was achieved in BE provenance. Individuals with a better iWUE had wider growth rings regardless of provenance. Better iWUE was associated with lower specific leaf area (SLA). ECM community composition and diversity indices did not differ significantly among the provenances. Specific ECM taxa were associated with individuals with high SLA, δ13C, δ15N, and δ18O. In optimal growth conditions with no stress events, BE is a promising provenance due to an efficient water conducting system with high vessel diameters and conductive area, and high iWUE, while Alpine provenances showed an adaptation of their water conducting system to freezing conditions at their original locations. Integrating findings from different compartments improves our understanding of functioning of different beech provenances

Urban greenspaces and nearby natural areas support similar levels of soil ecosystem services

Greenspaces are important for sustaining healthy urban environments and their human populations. Yet their capacity to support multiple ecosystem services simultaneously (multiservices) compared with nearby natural ecosystems remains virtually unknown. We conducted a global field survey in 56 urban areas to investigate the influence of urban greenspaces on 23 soil and plant attributes and compared them with nearby natural environments. We show that, in general, urban greenspaces and nearby natural areas support similar levels of soil multiservices, with only six of 23 attributes (available phosphorus, water holding capacity, water respiration, plant cover, arbuscular mycorrhizal fungi (AMF), and arachnid richness) significantly greater in greenspaces, and one (available ammonium) greater in natural areas. Further analyses showed that, although natural areas and urban greenspaces delivered a similar number of services at low (>25% threshold) and moderate (>50%) levels of functioning, natural systems supported significantly more functions at high (>75%) levels of functioning. Management practices (mowing) played an important role in explaining urban ecosystem services, but there were no effects of fertilisation or irrigation. Some services declined with increasing site size, for both greenspaces and natural areas. Our work highlights the fact that urban greenspaces are more similar to natural environments than previously reported and underscores the importance of managing urban greenspaces not only for their social and recreational values, but for supporting multiple ecosystem services on which soils and human well-being depends

Unearthing the soil-borne microbiome of land plants

Plant–soil biodiversity interactions are fundamental for the functioning of terrestrial ecosystems. Yet, the existence of a set of globally distributed topsoil microbial and small invertebrate organisms consistently associated with land plants (i.e., their consistent soil-borne microbiome), together with the environmental preferences and functional capabilities of these organisms, remains unknown. We conducted a standardized field survey under 150 species of land plants, including 58 species of bryophytes and 92 of vascular plants, across 124 locations from all continents. We found that, despite the immense biodiversity of soil organisms, the land plants evaluated only shared a small fraction (less than 1%) of all microbial and invertebrate taxa that were present across contrasting climatic and soil conditions and vegetation types. These consistent taxa were dominated by generalist decomposers and phagotrophs and their presence was positively correlated with the abundance of functional genes linked to mineralization. Finally, we showed that crossing environmental thresholds in aridity (aridity index of 0.65, i.e., the transition from mesic to dry ecosystems), soil pH (5.5i.e., the transition from acidic to strongly acidic soils), and carbon (less than 2%, the lower limit of fertile soils) can result in drastic disruptions in the associations between land plants and soil organisms, with potential implications for the delivery of soil ecosystem processes under ongoing global environmental change

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

Dataset of "Unearthing the soil-borne microbiome of land plants"

We described the soil-borne microbiome of land plants</p