Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe.

Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.

Ecological drivers of fine-scale distribution of arbuscular mycorrhizal fungi in a semiarid Mediterranean scrubland.

BACKGROUND AND AIMS: Arbuscular mycorrhizal (AM) fungi enhance the uptake of water and minerals by the plant hosts, alleviating plant stress. Therefore, AM fungal-plant interactions are particularly important in drylands and other stressful ecosystems. We aimed to determine the combined and independent effects of above- and below-ground plant community attributes (i.e. diversity and composition), soil heterogeneity and spatial covariates on the spatial structure of the AM fungal communities in a semiarid Mediterranean scrubland. Furthermore, we evaluated how the phylogenetic relatedness of both plants and AM fungi shapes these symbiotic relationships. METHODS: We characterized the composition and diversity of AM fungal and plant communities in a dry Mediterranean scrubland taxonomically and phylogenetically, using DNA metabarcoding and a spatially explicit sampling design at the plant neighbourhood scale. KEY RESULTS: The above- and below-ground plant community attributes, soil physicochemical properties and spatial variables explained unique fractions of AM fungal diversity and composition. Mainly, variations in plant composition affected the AM fungal composition and diversity. Our results also showed that particular AM fungal taxa tended to be associated with closely related plant species, suggesting the existence of a phylogenetic signal. Although soil texture, fertility and pH affected AM fungal community assembly, spatial factors had a greater influence on AM fungal community composition and diversity than soil physicochemical properties. CONCLUSIONS: Our results highlight that the more easily accessible above-ground vegetation is a reliable indicator of the linkages between plant roots and AM fungi. We also emphasize the importance of soil physicochemical properties in addition to below-ground plant information, while accounting for the phylogenetic relationships of both plants and fungi, because these factors improve our ability to predict the relationships between AM fungal and plant communities.

Continuous monitoring of chlorophyll a fluorescence and microclimatic conditions reveals warming-induced physiological damage in biocrust-forming lichens.

Purpose: Biocrust communities, which are important regulators of multiple ecosystem functions in drylands, are highly sensitive to climate change. There is growing evidence of the negative impacts of warming on the performance of biocrust constituents like lichens in the field. Here, we aim to understand the physiological basis behind this pattern. Methods: Using a unique manipulative climate change experiment, we monitored every 30 minutes and for 9 months the chlorophyll a fluorescence and microclimatic conditions (lichen surface temperature, relative moisture and photosynthetically active radiation) of Psora decipiens, a key biocrust constituent in drylands worldwide. This long-term monitoring resulted in 11,847 records at the thallus-level, which allowed us to evaluate the impacts of ~2.3 °C simulated warming treatment on the physiology of Psora at an unprecedented level of detail. Results: Simulated warming and the associated decrease in relative moisture promoted by this treatment negatively impacted the physiology of Psora, especially during the diurnal period of the spring, when conditions are warmer and drier. These impacts were driven by a mechanism based on the reduction of the length of the periods allowing net photosynthesis, and by declines in Yield and Fv/Fm under simulated warming. Conclusion: Our study reveals the physiological basis explaining observed negative impacts of ongoing global warming on biocrust-forming lichens in the field. The functional response observed could limit the growth and cover of biocrust-forming lichens in drylands in the long-term, negatively impacting in key soil attributes such as biogeochemical cycles, water balance, biological activity and ability of controlling erosion. Supplementary Information: The online version contains supplementary material available at 10.1007/s11104-022-05686-w.

Ecological clusters of soil taxa within bipartite networks are highly sensitive to climatic conditions in global drylands.

Determining the influence of climate in driving the global distribution of soil microbial communities is fundamental to help predict potential shifts in soil food webs and ecosystem functioning under global change scenarios. Herein, we used a global survey including 80 dryland ecosystems from six continents, and found that the relative abundance of ecological clusters formed by taxa involved in bacteria-fungi and bacteria-cercozoa bipartite networks was highly sensitive to changes in temperature and aridity. Importantly, such a result was maintained when controlling for soil, geographical location and vegetation attributes, being pH and soil organic carbon important determinants of the relative abundance of the ecological clusters. We also identified potential global associations between important soil microbial taxa, which can be useful to support the conservation of terrestrial ecosystems under global change scenarios. Our results suggest that increases in temperature and aridity such as those forecasted for the next decades in drylands could potentially lead to drastic changes in the community composition of functionally important bipartite networks within soil food webs. This could have important but unknown implications for the provision of key ecosystem functions and associated services driven by the organisms forming these networks if other taxa cannot cope with them. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'.

Fourteen years of continuous soil moisture records from plant and biocrust-dominated microsites.

Drylands cover ~41% of the terrestrial surface. In these water-limited ecosystems, soil moisture contributes to multiple hydrological processes and is a crucial determinant of the activity and performance of above- and belowground organisms and of the ecosystem processes that rely on them. Thus, an accurate characterisation of the temporal dynamics of soil moisture is critical to improve our understanding of how dryland ecosystems function and are responding to ongoing climate change. Furthermore, it may help improve climatic forecasts and drought monitoring. Here we present the MOISCRUST dataset, a long-term (2006-2020) soil moisture dataset at a sub-daily resolution from five different microsites (vascular plants and biocrusts) in a Mediterranean semiarid dryland located in Central Spain. MOISCRUST is a unique dataset for improving our understanding on how both vascular plants and biocrusts determine soil water dynamics in drylands, and thus to better assess their hydrological impacts and responses to ongoing climate change.

Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils.

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. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale.

Crop cover is more important than rotational diversity for soil multifunctionality and cereal yields in European cropping systems.

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 role of root community attributes in predicting soil fungal and bacterial community patterns.

Roots are assumed to play a major role in structuring soil microbial communities, but most studies exploring the relationships between microbes and plants at the community level have only used aboveground plant distribution as a proxy. However, a decoupling between belowground and aboveground plant components may occur due to differential spreading of plant canopies and root systems. Thus, soil microbe-plant links are not completely understood. Using a combination of DNA metabarcoding and spatially explicit sampling at the plant neighbourhood scale, we assessed the influence of the plant root community on soil bacterial and fungal diversity (species richness, composition and ß-diversity) in a dry Mediterranean scrubland. We found that root composition and biomass, but not richness, predict unique fractions of variation in microbial richness and composition. Moreover, bacterial ß-diversity was related to root ß-diversity, while fungal ß-diversity was related to aboveground plant ß-diversity, suggesting that plants differently influence both microbial groups. Our study highlights the role of plant distribution both belowground and aboveground, soil properties and other spatially structured factors in explaining the heterogeneity in soil microbial diversity. These results also show that incorporating data on both plant community compartments will further our understanding of the relationships between soil microbial and plant communities.

Impacts of climate, soil and biotic interactions on the interplay of the different facets of alpine plant diversity.

Disentangling the processes that drive plant community assembly is critical for understanding the patterns of plant diversity. We studied how different abiotic and biotic factors shape the interplay between the facets of alpine plant diversity, functional (FD), phylogenetic (PD) and taxonomic diversity (TD), in three different mountain ranges with contrasting evolutionary histories and climate conditions (Pyrenees and Mediterranean-type mountains in central Spain and Chilean Andes). We hypothesized that the causal links vary in strength and sign across regions. We used species inventories, functional trait data, and a phylogeny from 84 plant communities spread throughout three high-mountain alpine grasslands. Structural equation models were used to test our causal hypotheses on the relationships observed between the three diversity facets, and the abiotic (elevation, potential solar radiation and soil total nitrogen) and biotic factors (C-score). Despite our causal model presented a high variability in each mountain range, TD always decreased with increasing elevation (sum of direct and indirect effects). We also found some patterns suggesting that assembly processes could be climatically/biogeographically structured such as the negative relationship between FD and elevation found in Mediterranean mountains and the negative relationship between FD and TD found in both Spanish mountain ranges (independently of their different climates). A remarkable finding of this study is that ecological factors such as soil total nitrogen and elevation indirectly alter the relationships between the diversity facets. Our results suggest that diversity facets are simultaneously affected by different ecological and biogeographical/evolutionary processes, resulting in some general trends but also in parallel idiosyncratic patterns. Our findings highlight that although FD stand out by its explanatory power of community processes, TD and PD provide a complementary and necessary view that should not be disregarded in the attempt to globally explain community assembly processes.

Alpine vegetation dataset from three contrasting mountain ranges differing in climate and evolutionary history.

Vegetation above treeline constitutes one of the most vulnerable ecosystems to climate warming and other drivers of Global Change. Given the panorama of such an uncertain future facing these plant communities, it is critical to know how they respond to environmental changes and improve the knowledge on the potential impacts of climate change on their distribution. Recently, with the impressive development of trait-based approaches, relevant progress has been made to better understand the relationships between environmental conditions and plant communities. In this data paper, we describe data on abundances of 327 alpine plant species across 430 subplots of 2.4 m × 2.4 m in three mountain ranges (Sierra de Guadarrama and Pyrenees in Spain, and the Central Andes in Chile). We provide data on different environmental variables that represent variation in abiotic conditions and operate at different spatial scales (e.g., climatic, topographic and soil conditions). Data on six plant functional traits are also shown, which were measured on ten individuals of each species, following standard protocols. We provided the dataset as tables in the supplementary material. This information could be used to analyse the relationship between the alpine vegetation and changes in environmental conditions, and ultimately, to understand ecosystem functioning and guide conservation strategies of theses threatened and valuable ecosystems.

Estimating belowground plant abundance with DNA metabarcoding.

Most work on plant community ecology has been performed above ground, neglecting the processes that occur in the soil. DNA metabarcoding, in which multiple species are computationally identified in bulk samples, can help to overcome the logistical limitations involved in sampling plant communities belowground. However, a major limitation of this methodology is the quantification of species' abundances based on the percentage of sequences assigned to each taxon. Using root tissues of five dominant species in a semi-arid Mediterranean shrubland (Bupleurum fruticescens, Helianthemum cinereum, Linum suffruticosum, Stipa pennata and Thymus vulgaris), we built pairwise mixtures of relative abundance (20%, 50% and 80% biomass), and implemented two methods (linear model fits and correction indices) to improve estimates of root biomass. We validated both methods with multispecies mixtures that simulate field-collected samples. For all species, we found a positive and highly significant relationship between the percentage of sequences and biomass in the mixtures (R2  = .44-.66), but the equations for each species (slope and intercept) differed among them, and two species were consistently over- and under-estimated. The correction indices greatly improved the estimates of biomass percentage for all five species in the multispecies mixtures, and reduced the overall error from 17% to 6%. Our results show that, through the use of post-sequencing quantification methods on mock communities, DNA metabarcoding can be effectively used to determine not only species' presence but also their relative abundance in field samples of root mixtures. Importantly, knowledge of these aspects will allow us to study key, yet poorly understood, belowground processes.

Determinants of high mountain plant diversity in the Chilean Andes: From regional to local spatial scales.

Mountains are considered excellent natural laboratories for studying the determinants of plant diversity at contrasting spatial scales. To gain insights into how plant diversity is structured at different spatial scales, we surveyed high mountain plant communities in the Chilean Andes where man-driven perturbations are rare. This was done along elevational gradients located at different latitudes taking into account factors that act at fine scales, including abiotic (potential solar radiation and soil quality) and biotic (species interactions) factors, and considering multiple spatial scales. Species richness, inverse of Simpson's concentration (Dequiv), beta-diversity and plant cover were estimated using the percentage of cover per species recorded in 34 sites in the different regions with contrasted climates. Overall, plant species richness, Dequiv and plant cover were lower in sites located at higher latitudes. We found a unimodal relationship between species richness and elevation and this pattern was constant independently of the regional climatic conditions. Soil quality decreased the beta-diversity among the plots in each massif and increased the richness, the Dequiv and cover. Segregated patterns of species co-occurrence were related to increases in richness, Dequiv and plant cover at finer scales. Our results showed that elevation patterns of alpine plant diversity remained constant along the regions although the mechanisms underlying these diversity patterns may differ among climatic regions. They also suggested that the patterns of plant diversity in alpine ecosystems respond to a series of factors (abiotic and biotic) that act jointly at different spatial scale determining the assemblages of local communities, but their importance can only be assessed using a multi-scale spatial approach.

Winter is coming: plant freezing resistance as a key functional trait for the assembly of annual Mediterranean communities.

Background and Aims: In Mediterranean annual plants, germination mainly occurs during the autumn and only those seedlings that survive winter freezing can flower and produce seedlings in spring. Surprisingly, the effect of freezing events as an abiotic determinant of these communities remains unexplored. The present study aimed to investigate how freezing events affect annual Mediterranean communities and whether their functional structure as related to freezing resistance is linked to the main biotic and abiotic determinants of these communities. Methods: In 120 plots located on a semi-arid Mediterranean steppe (Spain), the community functional structure related to the lethal temperature causing 50 % frost damage (LT50 trait) in seedlings was estimated and summarized as the community-weighted mean (CWM-LT50) and its functional diversity (FD-LT50). Plots were stratified according to distance to rabbit shelters and latrines as a proxy for rabbit density, proximity to Stipa tenacissima and spring water availability, where annual species abundance was recorded in all plots over three consecutive years. Key Results: Annual species were able to resist a threshold temperature of -4 °C and most had LT50 values around the absolute minimum temperature (-9.5 °C) in the three years. Higher rabbit densities led to lower CWM-LT50 and higher FD-LT50 values. Plots close to Stipa tussocks had higher CWM-LT50 values whereas water availability had no effects. Conclusions: High freezing resistance was extended among winter annual species, suggesting the presence of an association between historical environmental filtering and low winter temperatures. However, the community functional structure related to freezing resistance remained variable among scenarios with differences in herbivory pressure and distance to perennial vegetation. The trends observed indicate that traits that allow plants to deal with herbivory may also promote freezing resistance, and that tussocks can act as nurses via microclimatic amelioration of harsher winter conditions.

Summer Freezing Resistance: A Critical Filter for Plant Community Assemblies in Mediterranean High Mountains.

Assessing freezing community response and whether freezing resistance is related to other functional traits is essential for understanding alpine community assemblages, particularly in Mediterranean environments where plants are exposed to freezing temperatures and summer droughts. Thus, we characterized the leaf freezing resistance of 42 plant species in 38 plots at Sierra de Guadarrama (Spain) by measuring their ice nucleation temperature, freezing point (FP), and low-temperature damage (LT50), as well as determining their freezing resistance mechanisms (i.e., tolerance or avoidance). The community response to freezing was estimated for each plot as community weighted means (CWMs) and functional diversity (FD), and we assessed their relative importance with altitude. We established the relationships between freezing resistance, growth forms, and four key plant functional traits (i.e., plant height, specific leaf area, leaf dry matter content (LDMC), and seed mass). There was a wide range of freezing resistance responses and more than in other alpine habitats. At the community level, the CWMs of FP and LT50 responded negatively to altitude, whereas the FD of both traits increased with altitude. The proportion of freezing-tolerant species also increased with altitude. The ranges of FP and LT50 varied among growth forms, and only leaf dry matter content was negatively correlated with freezing-resistance traits. Summer freezing events represent important abiotic filters for assemblies of Mediterranean high mountain communities, as suggested by the CWMs. However, a concomitant summer drought constraint may also explain the high freezing resistance of species that thrive in these areas and the lower FD of freezing resistance traits at lower altitudes. Leaves with high dry matter contents may maintain turgor at lower water potential and enhance drought tolerance in parallel to freezing resistance. This adaptation to drought seems to be a general prerequisite for plants found in xeric mountains.

Individual species affect plant traits structure in their surroundings: evidence of functional mechanisms of assembly.

Evaluating community assembly through the use of functional traits is a promising tool for testing predictions arising from Niche and Coexistence theories. Although interactions among neighboring species and their inter-specific differences are known drivers of coexistence with a strong spatial signal, assessing the role of individual species on the functional structure of the community at different spatial scales remains a challenge. Here, we ask whether individual species exert a measurable effect on the spatial organization of different functional traits in local assemblages. We first propose and compute two functions that describe different aspects of functional trait organization around individual species at multiple scales: individual weighted mean area relationship and individual functional diversity area relationship. Secondly, we develop a conceptual model on the relationship and simultaneous variation of these two metrics, providing five alternative scenarios in response to the ability of some target species to modify its neighbor environment and the possible assembly mechanisms involved. Our results show that some species influence the spatial structure of specific functional traits, but their effects were always restricted to the finest spatial scales. In the basis of our conceptual model, the observed patterns point to two main mechanisms driving the functional structure of the community at the fine scale, "biotic" filtering meditated by individual species and resource partitioning driven by indirect facilitation rather than by competitive mechanisms.

Plant trait variation along an altitudinal gradient in mediterranean high mountain grasslands: controlling the species turnover effect.

Assessing changes in plant functional traits along gradients is useful for understanding the assembly of communities and their response to global and local environmental drivers. However, these changes may reflect the effects of species composition (i.e. composition turnover), species abundance (i.e. species interaction), and intra-specific trait variability (i.e. species plasticity). In order to determine the relevance of the latter, trait variation can be assessed under minimal effects of composition turnover. Nine sampling sites were established along an altitudinal gradient in a Mediterranean high mountain grassland community with low composition turnover (Madrid, Spain; 1940 m-2419 m). Nine functional traits were also measured for ten individuals of around ten plant species at each site, for a total of eleven species across all sites. The relative importance of different sources of variability (within/between site and intra-/inter-specific functional diversity) and trait variation at species and community level along the considered gradients were explored. We found a weak individual species response to altitude and other environmental variables although in some cases, individuals were smaller and leaves were thicker at higher elevations. This lack of species response was most likely due to greater within- than between-site species variation. At the community level, inter-specific functional diversity was generally greater than the intra-specific component except for traits linked to leaf element content (leaf carbon content, leaf nitrogen content, δ13C and δ15N). Inter-specific functional diversity decreased with lower altitude for four leaf traits (specific leaf area, leaf dry matter content, δ13C and δ15N), suggesting trait convergence between species at lower elevations, where water shortage may have a stronger environmental filtering effect than colder temperatures at higher altitudes. Our results suggest that, within a vegetation type encompassing various environmental gradients, both, changes in species abundance and intra-specific trait variability adjust for the community functional response to environmental changes.

Maintaining distances with the engineer: patterns of coexistence in plant communities beyond the patch-bare dichotomy.

Two-phase plant communities with an engineer conforming conspicuous patches and affecting the performance and patterns of coexisting species are the norm under stressful conditions. To unveil the mechanisms governing coexistence in these communities at multiple spatial scales, we have developed a new point-raster approach of spatial pattern analysis, which was applied to a Mediterranean high mountain grassland to show how Festuca curvifolia patches affect the local distribution of coexisting species. We recorded 22 111 individuals of 17 plant perennial species. Most coexisting species were negatively associated with F. curvifolia clumps. Nevertheless, bivariate nearest-neighbor analyses revealed that the majority of coexisting species were confined at relatively short distances from F. curvifolia borders (between 0-2 cm and up to 8 cm in some cases). Our study suggests the existence of a fine-scale effect of F. curvifolia for most species promoting coexistence through a mechanism we call 'facilitation in the halo'. Most coexisting species are displaced to an interphase area between patches, where two opposite forces reach equilibrium: attenuated severe conditions by proximity to the F. curvifolia canopy (nutrient-rich islands) and competitive exclusion mitigated by avoiding direct contact with F. curvifolia.