Symbiont plasticity as a driver of plant success.

We discuss which plant species are likely to become winners, that is achieve the highest global abundance, in changing landscapes, and whether plant-associated microbes play a determining role. Reduction and fragmentation of natural habitats in historic landscapes have led to the emergence of patchy, hybrid landscapes, and novel landscapes where anthropogenic ecosystems prevail. In patchy landscapes, species with broad niches are favoured. Plasticity in the degree of association with symbiotic microbes may contribute to broader plant niches and optimization of symbiosis costs and benefits, by downregulating symbiosis when it is unnecessary and upregulating it when it is beneficial. Plasticity can also be expressed as the switch from one type of mutualism to another, for example from nutritive to defensive mutualism with increasing soil fertility and the associated increase in parasite load. Upon dispersal, wide mutualistic partner receptivity is another facet of symbiont plasticity that becomes beneficial, because plants are not limited by the availability of specialist partners when arriving at new locations. Thus, under conditions of global change, symbiont plasticity allows plants to optimize the activity of mutualistic relationships, potentially allowing them to become winners by maximizing geographic occupancy and local abundance.

Spatial and evolutionary predictability of phytochemical diversity.

To cope with environmental challenges, plants produce a wide diversity of phytochemicals, which are also the source of numerous medicines. Despite decades of research in chemical ecology, we still lack an understanding of the organization of plant chemical diversity across species and ecosystems. To address this challenge, we hypothesized that molecular diversity is not only related to species diversity, but also constrained by trophic, climatic, and topographical factors. We screened the metabolome of 416 vascular plant species encompassing the entire alpine elevation range and four alpine bioclimatic regions in order to characterize their phytochemical diversity. We show that by coupling phylogenetic information, topographic, edaphic, and climatic variables, we predict phytochemical diversity, and its inherent composition, of plant communities throughout landscape. Spatial mapping of phytochemical diversity further revealed that plant assemblages found in low to midelevation habitats, with more alkaline soils, possessed greater phytochemical diversity, whereas alpine habitats possessed higher phytochemical endemism. Altogether, we present a general tool that can be used for predicting hotspots of phytochemical diversity in the landscape, independently of plant species taxonomic identity. Such an approach offers promising perspectives in both drug discovery programs and conservation efforts worldwide.

Estimation of annual soil CO2 efflux under the erosion and deposition conditions by measuring and modeling its respiration rate in southern China.

Soil respiration (Rs) is a crucial ecological process of carbon (C) cycling in the terrestrial ecosystems, and soil erosion has a significant impact on its C budget and balance. However, the variations of Rs rate and their CO2 efflux induced by erosion are currently poorly understood. To this end, four landscape positions (top, up, middle and toe) with different erosional and depositional characteristics were selected on a typical eroded slope in southern China to conduct field experiments, aiming to explore the effects of erosion and deposition on Rs among various sites. From March 2021 to February 2022, the in-situ Rs were measured using an automated soil respiration system, together with soil temperature at 5 cm depth (Ts5) and water content at 10 cm depth (SWC10). We initially constructed various Rs models across a one-year period, based on its relationships with Ts5 and SWC10. Subsequently, the seasonal changes of Rs at different erosional sites were simulated by the optimum models, and their annual CO2 fluxes were further estimated. The results showed that Rs rates at all sites displayed a bimodal seasonal pattern, with the highest values in May and August. And the measured Rs of the eroding and depositional sites were 0.05-7.71 and 1.47-13.03 µmol m-2 s-1, respectively. Also, remarkably higher Ts5 and SWC10 were observed in depositional sites versus the eroding sites (P < 0.05). Additionally, Rs rates at all sites were positively correlated with SOC and Ts5, but negatively correlated with SWC10. Herein, Rs models to single- and double-variable were established at different positions, and we found that the fitted R2 and AIC differed on various sites, primarily in erosional and depositional sites. Furthermore, through the best-fitting models (higher R2 and lowest AIC) we screened, the average Rs values of 3.03 and 4.46 µmol m-2 s-1 were quantitatively estimated for the eroding and depositional sites, respectively. Finally, it could be further assessed that the mean annual soil CO2-C efflux of eroded site (1104.14 g m-2) was significantly lower than that of depositional site (1629.46 g m-2). These findings highlighted the effect of erosion and deposition on Rs, which will facilitate a better understanding of C cycling in terrestrial ecosystems.

The impact of large-scale ecological restoration projects on trade-offs/synergies and clusters of ecosystem services.

Understanding the relationships between ecosystem services (ES) and the factors driving their changes over long periods and multiple scales is key for landscape managers in decision-making. However, the widespread implementation of restoration programs has led to significant ES changes, with trade-offs across space and time that have been little explored empirically, making it challenging to provide effective experience for managers. We quantified changes and interactions among five ES across various stages of the Grain-to-Green Program in the eastern Loess Plateau, examining these dynamics at threefold spatial scales. We observed notable increases in soil retention and Net Ecosystem Production but declines in habitat quality and Landscape aesthetics under afforestation. Over time, and with more integrated restoration strategies, synergies between ES pairs weakened, and non-correlations (even trade-offs) increased. To avoid unnecessary trade-offs, we recommend incorporating socio-ecological factors driving ES changes and ES bundles, informed by empirical experience, into proactive spatial planning and environmental management strategies for multi-ES objectives. The temporal lags and spatial trade-offs highlighted by this study offer crucial insights for large-scale restoration programs worldwide.

Exploring the interrelations and driving factors among typical ecosystem services in the Yangtze river economic Belt, China.

Exploring the spatiotemporal characteristics of ecosystem services (ESs) and their drivers is crucial for managers to develop significant scientific policies that further sustainable development. We used the Yangtze River Economic Belt (YREB) to explore the trends, hotspots, and drivers of water yield (WY), soil conservation (SC), carbon sequestration (CS), and food supply (FS) between 2000 and 2020. Similarly, we analyzed relationships among ESs and drivers of the multiple ecosystem services landscape index (MESLI). We used the self-organizing map method to obtain the types and distribution of the ES bundles, revealing the bundles, trade-offs, and synergies among ESs. The four ESs had an increasing trend, with CS having the highest increase; ES hotspot analysis showed differences among upper, middle, and lower reaches. Constraint lines among ESs and drivers were diverse; the corresponding SC and WY reached thresholds when CS values were 1477.81 and 460.5 t km-2, respectively. When FS values were 67.34 and 86.17 × 104 Yuan·km-2, CS and WY reached their thresholds. All critical drivers of the four ESs were natural factors. The thresholds that the MESLI reached with driver status were 1000 mm (evapotranspiration), 2121 mm (precipitation), 2.42° (slope), 1.46% (soil organic matter), 36.08% (sand), 30.75% (proportion of non-agricultural population), 18.57% (cropland proportion), 1.05 × 104 persons·km-2 (population density), and 84.84% (proportion of non-agricultural industries in total gross domestic product), respectively. FS, water supply, and ecological conservation bundles changed over the 20 years, and trade-offs and synergies among ESs within bundles differed. We revealed the complexity of ESs from multiple perspectives, which will enable the development of ecosystem management and conservation recommendations for the YREB and large-scale economic zones worldwide.

Evolutionary patterns and influencing factors of relationships among ecosystem services in the hilly red soil region of Southern China.

As a crucial ecological protection area in China, the Southern hilly red soil region is characterized by uneven spatial and temporal distribution of ecological landscape elements, unpredictable and changeable interrelationships between them, diversified driving factors, and lack of comprehensive consideration of ecosystem services. In order to better understand the interaction between ecosystem services, restore regional ecology, and promote sustainable development, the evolution law and influencing mechanism of ecosystem services and their driving factors are quantitatively analyzed in the study. Based on simulations of different ecosystem services from 2000 to 2020, their spatial and temporal changes and the contributions of main drivers are quantified, their trade-offs and synergies are analyzed, and the changing rules under the influence of natural factors and socioeconomic factors are explored. The results show that (1) the crop production significantly increases in the southwest and north regions, the habitat quality decreases in urban and coastal areas, and the soil retention and water yield show an increasing trend from west to east. (2) Land use/cover is the main driver of carbon storage and habitat quality variation, and precipitation is an important driver of water yield spatial variation. (3) The crop production and the other four ecosystem services show a trade-offs relationship, and the relationship between supporting services and regulating services is the synergetic. (4) The altitude weakens the synergistic relationship between soil retention and habitat quality/carbon storage, while it enhances the synergistic relationship between soil retention and water yield. Driven by precipitation factors, ecosystem services related to water yield have significant differences in the change. The population density enhances the trade-offs of crop production and soil retention, as well as the synergistic relationship between soil retention and habitat quality/carbon storage. In different land use/cover (LULC), the influence of urban land on ecosystem services relationship change is more obvious. Overall, this study can provide scientific bases and policy suggestions for ecosystem protection/restoration in the red soil region of Southern China, which has an important theoretical and practical significance.

Community assembly of comammox Nitrospira in coastal wetlands across southeastern China.

Complete ammonia oxidizers (comammox Nitrospira) are ubiquitous in coastal wetland sediments and play an important role in nitrification. Our study examined the impact of habitat modifications on comammox Nitrospira communities in coastal wetland sediments across tropical and subtropical regions of southeastern China. Samples were collected from 21 coastal wetlands in five provinces where native mudflats were invaded by Spartina alterniflora and subsequently converted to aquaculture ponds. The results showed that comammox Nitrospira abundances were mainly influenced by sediment grain size rather than by habitat modifications. Compared to S. alterniflora marshes and native mudflats, aquaculture pond sediments had lower comammox Nitrospira diversity, lower clade A.1 abundance, and higher clade A.2 abundance. Sulfate concentration was the most important factor controlling the diversity of comammox Nitrospira. The response of comammox Nitrospira community to habitat change varied significantly by location, and environmental variables accounted for only 11.2% of the variations in community structure across all sites. In all three habitat types, dispersal limitation largely controlled the comammox Nitrospira community assembly process, indicating the stochastic nature of these sediment communities in coastal wetlands. IMPORTANCE Comammox Nitrospira have recently gained attention for their potential role in nitrification and nitrous oxide (N2O) emissions in soil and sediment. However, their distribution and assembly in impacted coastal wetland are poorly understood, particularly on a large spatial scale. Our study provides novel evidence that the effects of habitat modification on comammox Nitrospira communities are dependent on the location of the wetland. We also found that the assembly of comammox Nitrospira communities in coastal wetlands was mainly governed by stochastic processes. Nevertheless, sediment grain size and sulfate concentration were identified as key variables affecting comammox Nitrospira abundance and diversity in coastal sediments. These findings are significant as they advance our understanding of the environmental adaptation of comammox Nitrospira and how future landscape modifications may impact their abundance and diversity in coastal wetlands.

Functional substitutability of native herbivores by livestock for soil carbon stock is mediated by microbial decomposers.

Grazing by large mammalian herbivores impacts climate as it can favor the size and stability of a large carbon (C) pool in the soils of grazing ecosystems. As native herbivores in the world's grasslands, steppes, and savannas are progressively being displaced by livestock, it is important to ask whether livestock can emulate the functional roles of their native counterparts. While livestock and native herbivores can have remarkable similarity in their traits, they can differ greatly in their impacts on vegetation composition which can affect soil-C. It is uncertain how these similarities and differences impact soil-C via their influence on microbial decomposers. We test competing alternative hypotheses with a replicated, long-term, landscape-level, grazing-exclusion experiment to ask whether livestock in the Trans-Himalayan ecosystem of northern India can match decadal-scale (2005-2016) soil-C stocks under native herbivores. We evaluate multiple lines of evidence from 17 variables that influence soil-C (quantity and quality of C-input from plants, microbial biomass and metabolism, microbial community composition, eDNA, veterinary antibiotics in soil), and assess their inter-relationships. Livestock and native herbivores differed in their effects on several soil microbial processes. Microbial carbon use efficiency (CUE) was 19% lower in soils under livestock. Compared to native herbivores, areas used by livestock contained 1.5 kg C m-2 less soil-C. Structural equation models showed that alongside the effects arising from plants, livestock alter soil microbial communities which is detrimental for CUE, and ultimately also for soil-C. Supporting evidence pointed toward a link between veterinary antibiotics used on livestock, microbial communities, and soil-C. Overcoming the challenges of sequestering antibiotics to minimize their potential impacts on climate, alongside microbial rewilding under livestock, may reconcile the conflicting demands from food-security and ecosystem services. Conservation of native herbivores and alternative management of livestock is crucial for soil-C stewardship to envision and achieve natural climate solutions.

Modeling impacts of saltwater intrusion on methane and nitrous oxide emissions in tidal forested wetlands.

Emissions of methane (CH4 ) and nitrous oxide (N2 O) from soils to the atmosphere can offset the benefits of carbon sequestration for climate change mitigation. While past study has suggested that both CH4 and N2 O emissions from tidal freshwater forested wetlands (TFFW) are generally low, the impacts of coastal droughts and drought-induced saltwater intrusion on CH4 and N2 O emissions remain unclear. In this study, a process-driven biogeochemistry model, Tidal Freshwater Wetland DeNitrification-DeComposition (TFW-DNDC), was applied to examine the responses of CH4 and N2 O emissions to episodic drought-induced saltwater intrusion in TFFW along the Waccamaw River and Savannah River, USA. These sites encompass landscape gradients of both surface and porewater salinity as influenced by Atlantic Ocean tides superimposed on periodic droughts. Surprisingly, CH4 and N2 O emission responsiveness to coastal droughts and drought-induced saltwater intrusion varied greatly between river systems and among local geomorphologic settings. This reflected the complexity of wetland CH4 and N2 O emissions and suggests that simple linkages to salinity may not always be relevant, as non-linear relationships dominated our simulations. Along the Savannah River, N2 O emissions in the moderate-oligohaline tidal forest site tended to increase dramatically under the drought condition, while CH4 emission decreased. For the Waccamaw River, emissions of both CH4 and N2 O in the moderate-oligohaline tidal forest site tended to decrease under the drought condition, but the capacity of the moderate-oligohaline tidal forest to serve as a carbon sink was substantially reduced due to significant declines in net primary productivity and soil organic carbon sequestration rates as salinity killed the dominant freshwater vegetation. These changes in fluxes of CH4 and N2 O reflect crucial synergistic effects of soil salinity and water level on C and N dynamics in TFFW due to drought-induced seawater intrusion.

Integrating demographic niches and black spruce range expansion at subarctic treelines.

When investigating relationships between species' niches and distributions, niches can be divided demographically, resulting in unique niches for different life stages. This approach can identify changing substrate requirements throughout a species' life cycle. Using non-metric multidimensional scaling, we quantified microsite conditions associated with successful recruitment in the tundra landscape and successful seed production amongst adult trees of black spruce (Picea mariana) at subarctic treeline in Yukon, Canada to assess how life stage-specific requirements may impact the distribution of this widespread boreal tree species. Treeline ecotones in this region showed high heterogeneity in tundra microsites available for establishment. Black spruce exhibited changing microsite associations from germination to reproductive maturity, which were mainly driven by changes in plant community and soil moisture. These associations limit the microsites where individuals can establish and reproduce to a subset available within the heterogeneous landscape. Overall, we suggest that (1) substrates suitable for early recruitment are limited at the range edge; and (2) reproductive adults have a narrow niche, limiting successful seed production in adults and forming sink populations where suitable conditions are limited. Our multivariate assessment of microsite suitability can provide valuable insights into the spatial distribution of a species throughout its life cycle and identify life stage-specific constraints to range expansion.

The Golden Goal of Soil Management: Disease-Suppressive Soils.

Disease-suppressive soils encompass specific plant-pathogen-microbial interactions and represent a rare example of an agroecosystem where soil conditions and microbiome together prevent the pathogen from causing disease. Such soils have the potential to serve as a model for characterizing soil pathogen-related aspects of soil health, but the mechanisms driving the establishment of suppressive soils vary and are often poorly characterized. Yet, they can serve as a resource for identifying markers for beneficial activities of soil microorganisms concerning pathogen prevention. Many recent studies have focused on the nature of disease-suppressive soils, but it has remained difficult to predict where and when they will occur. This review outlines current knowledge on the distribution of these soils, soil manipulations leading to pathogen suppression, and markers including bacterial and fungal diversity, enzymes, and secondary metabolites. The importance to consider soil legacy in research on the principles that define suppressive soils is also highlighted. The goal is to extend the context in which we understand, study, and use disease-suppressive soils by evaluating the relationships in which they occur and function. Finally, we suggest that disease-suppressive soils are critical not only for the development of indicators of soil health, but also for the exploration of general ecological principles about the surrounding landscape, effects of deeper layers of the soil profile, little studied soil organisms, and their interactions for future use in modern agriculture.

The dynamic relationships between landscape structure and ecosystem services: An empirical analysis from the Wuhan metropolitan area, China.

Environmental managers have been striving to optimize landscape structure to achieve a sustained supply of ecosystem services (ESs). However, we still lack a full understanding of the relationships between landscape structure and ESs due to the absence of thorough investigations on the variability of these relationships in space and time. To fill this critical gap, we assessed landscape structure alongside four important ESs (agricultural production (AP), carbon sequestration (CS), soil conservation (SC), and water retention (WR)) in the Wuhan metropolitan area (WMA), and then analyzed the spatiotemporal impacts of landscape structure on ESs from 2000 to 2020 using Geographically and Temporally Weighted Regression. The results show only AP maintained a stable growth trend over the past two decades, while the other ESs fluctuated considerably with a noticeable decline in SC and WR. The importance of landscape structure in influencing ESs varies by time and place, depending on the local landscape composition and configuration. In general, landscape composition has a stronger and less temporally stable impact on ESs compared to configuration. Furthermore, increases in landscape diversity, as measured through Shannon's diversity index, and the percentage of woodlands were found to contribute to the simultaneous benefits of multiple ESs, but in most cases the effects of landscape structure on different ESs were different or even opposite, suggesting that trade-offs are critical in landscape management. The findings highlight the complex response of ESs to dramatically changing landscapes in the WMA and can guide decision-makers in precise spatial arrangement and temporal adjustments to improve current landscape management.

Coupling strength of human-natural systems mediates the response of ecosystem services to land use change.

Addressing the dynamics of human-natural systems (HNS) driven by land use change (LC) is a key challenge for the sustainable development of ecosystem services (ES). However, how changes to the HNS coupling relationships affect ES is rarely reported. We used network analysis methods to construct an HNS correlation network in the Loess Plateau based on the correlation between the main components of HNS, such as ES, human factors, landscape pattern, vegetation cover, climate change and geomorphic characteristics, and quantitatively described the HNS coupling relationships through key network attributes. We analyzed the variation in HNS network attributes and their relationships with ES along an LC intensity gradient. The results show that carbon storage and soil conservation in the Loess Plateau increased by 0.56% and 0.26%, respectively, during the study period, while the habitat quality and water yield decreased by 0.11% and 0.18%, respectively. An increase in LC intensity reduces connectivity and density in the HNS network, which results in looser connections among HNS components. Importantly, we found that HNS network attributes explained 85% of ES variation across different LC intensity gradients and that connectivity and density had the strongest explanatory power. This means that LC mainly affects ES dynamics by changing the coupling strength of HNS. Our research offers a new perspective for linking LC-HNS-ES, which will help guide practitioners toward establishing and maintaining the sustainability of human well-being amidst changing HNS.

Assessment of soil- and water-related ecosystem services with coupling the factors of climate and land-use change (Example of the Nitra region, Slovakia).

Climate and land use change can profoundly impact the provision of ecosystem services (ES) over time, particularly in the landscape of open fields along with growing urbanization and rising demand for space, food and energy. Policymakers are keen on knowing the combined effects of climate and land use change on ESs as a critical issue in human well-being. However, deep knowledge of how to identify these relationships is still lacking. This research aims to undertake a comprehensive assessment of soil- and water-related ES, and improvement in understanding how they are affected by climate and land use change. We applied the Integrated Valuation of Ecosystem Services and Trade-offs model for four ES (soil retention, nutrient delivery ratio, carbon storage, and water yield) for the years 2000 and 2018 in the Nitra region, Slovakia. We investigated the spatial and temporal changes in ES provision and determined the hotspots and coldspots of multiple ES. We found that soil retention, water yield, and carbon storage display a rising trend while the nutrient delivery ratio showed a decreasing trend over the past 18 years. Although all the mentioned services mainly attributed to land use change, the relative contribution of climate change was not deniable. Forests in the north and east and distributed urbanization and agriculture are the hotspots and coldspots for all ESs, respectively. Our results, in terms of determining the relative importance of land use and climate change and identifying the sensitive areas of ES provision, provide a scientific basis for ecosystem conservation and management priority setting at the local and regional levels.

Spatial and temporal dynamics of base flow in semi-arid montane watersheds and the effects of landscape patterns and topography.

Base flow (BF) is harder to predict than other hydrological signatures. The lack of hydrologically relevant information or adequately broad spectrum of typically selected catchment attributes (particularly landscape and topography) hinders the explanatory power. Our goals were to identify the most influential controls on base flow spatially and temporally and to elucidate the response relationships. Base flow in 19 semi-arid sub-watersheds was separated by digital filtering. One hundred and fourteen sub-watershed attributes were related to base flow using random forest regression. The main results were as follows: (1) Annual BF significantly declined since 1999 due to decreased precipitation, increased air temperature, afforestation, urban expansion, and increasing water consumption. Annual base flow index (BFI), varying between 0.319 and 0.695, showed less noticeable temporal trends. (2) Precipitation (P) and underlying carbonate rocks primarily controlled the spatial variation of annual BF and total flow (TF), with the impacts being positive. Landscape was less influential. After the abrupt runoff decline, landscape composition rather than configuration exerted greater impacts on spatial BF and TF, and the importance of forest increased, whereas landscape configuration was decisive for BFI during the whole observation period. The absence of significant links between landscape configuration and water quantity may result from a scale issue. Concave profile curvatures were found to be topographic variables more important than slopes. The impact of soil was the least. This study would benefit the selection of catchment attributes and spatial extents to quantify these attributes in building BF predicting models in future studies.

Tyroviruses are a new group of temperate phages that infect Bacillus species in soil environments worldwide.

BACKGROUND: Bacteriophages are widely considered to be highly abundant and genetically diverse, with their role in the evolution and virulence of many pathogens becoming increasingly clear. Less attention has been paid on phages preying on Bacillus, despite the potential for some of its members, such as Bacillus anthracis, to cause serious human disease. RESULTS: We have isolated five phages infecting the causative agent of anthrax, Bacillus anthracis. Using modern phylogenetic approaches we place these five new Bacillus phages, as well as 21 similar phage genomes retrieved from publicly available databases and metagenomic datasets into the Tyrovirus group, a newly proposed group named so due to the conservation of three distinct tyrosine recombinases. Genomic analysis of these large phages (~ 160-170 kb) reveals their DNA packaging mechanism and genomic features contributing to virion morphogenesis, host cell lysis and phage DNA replication processes. Analysis of the three tyrosine recombinases suggest Tyroviruses undergo a prophage lifecycle that may involve both host integration and plasmid stages. Further we show that Tyroviruses rely on divergent invasion mechanisms, with a subset requiring host S-layer for infection. CONCLUSIONS: Ultimately, we expand upon our understanding on the classification, phylogeny, and genomic organisation of a new and substantial phage group that prey on critically relevant Bacillus species. In an era characterised by a rapidly evolving landscape of phage genomics the deposition of future Tyroviruses will allow the further unravelling of the global spread and evolutionary history of these Bacillus phages.

The nuanced nature of mesic refugia in arid landscapes: a tale of two peas.

BACKGROUND AND AIMS: Understanding how genetic diversity is distributed and maintained within species is a central tenet of evolutionary and conservation biology, yet is understudied in arid regions of the globe. In temperate, glaciated environments, high genetic diversity in plant species is frequently found in refugial areas, which are often associated with southern non-glaciated landscapes. In arid, unglaciated environments, landscape features providing mesic conditions are likely to be refugia, although our understanding needs more refinement in these biomes. We test whether refugia and nuclear diversity hotspots occur in high-elevation, topographically complex areas for co-distributed shrubs (Petalostylis labicheoides and Indigofera monophylla; Fabaceae) in the ancient, arid Pilbara bioregion of north-western Australia. METHODS: We conducted extensive sampling of the Pilbara (>1400 individuals from 62 widespread populations) to detect patterns in nuclear diversity and structure based on 13-16 microsatellite loci. Evidence of historical refugia was investigated based on patterns of diversity in three non-coding chloroplast (cp) sequence regions for approx. 240 individuals per species. Haplotype relationships were defined with median-joining networks and maximum likelihood phylogenetic trees. KEY RESULTS: We found cpDNA evidence for a high-elevation refugium in P. labicheoides but not for I. monophylla that instead exhibited extraordinary haplotype diversity and evidence for persistence across a widespread area. Nuclear diversity hotspots occurred in, but were not exclusive to, high-elevation locations and extended to adjacent, low-elevation riparian areas in both species. CONCLUSIONS: Phylogeographic refugia in arid environments may occur in high-elevation areas for some species but not all, and may be influenced by species-specific traits: a mesic montane refugium in P. labicheoides could be related to its preference for growth in water-gaining areas, while a lack of such evidence in I. monophylla could be related to maintenance of cpDNA diversity in a large soil seed bank and dynamic evolutionary history. Mesic environments created by the intersection of topographically complex landscapes with riparian zones can be contemporary reservoirs of genetic diversity in arid landscapes.

Ecological resilience of physical plant-soil feedback to chronic deer herbivory: Slow, partial, but functional recovery.

Ecological resilience to ungulate overbrowsing is an important issue in forest ecosystems. After chronic herbivory, the recovery rate of understory vegetation and its related functions can be slow even with decreasing grazing intensity; thus, detecting elasticity during alternative successional trajectories is fundamental to understanding state perturbations. In this context, we focused on physical plant-soil feedback (functional interactions between plant growth and soil physical conditions) and evaluated elasticity and recovery processes according to deer density. The effects of 40 years of chronic herbivory by sika deer (average density 14.7 individuals km-2 ) on the recovery of understory plant communities and associated changes in soil physical properties in headwater catchments were assessed. Using 8 years of catchment-wide exclusion (fenced) and reduction (only culled; average 4.3 individuals km-2 ) treatments, plot sampling was conducted in 2010 (before treatment) and 2018 (after treatment). The recovery of vegetation and soil physical properties were evaluated, and functional plant-soil relationships and spatial variability were assessed to detect recovery processes during alternative successional trajectory. Woody species increased only under the exclusion treatment and the average soil bulk density was lower than that under reduction treatments. Soil bulk density was negatively correlated with root biomass in the fenced catchment, and root biomass was positively associated with woody species richness. Reduced soil bulk density (~0.5 g cm-3 ) was observed with greater root biomass and woody species richness on upper hillslopes in the deer-excluded catchment where plant coverage was minimal. Successional failure under the reduction treatment suggested slow recovery with a depressed threshold according to deer density, indicating a clockwise hysteretic response to deer density. Unlike plant coverage during the earlier period of overbrowsing, woody species root development led the recovery of functional physical plant-soil feedback; however, this was probably limited by the higher soil erosion rate in riparian areas and an under-developed herb layer. Our results highlight an alternative recovery trajectory of physical plant-soil feedback driven by an alternative plant element (woody roots) to recovery trajectory with increasing plant cover. However, riparian erosion and herb layer would still suppress recovery. Therefore, recovery might be slower at the landscape scale.

Functional traits mediate individualistic species-environment distributions at broad spatial scales while fine-scale species associations remain unpredictable.

PREMISE: Numerous processes influence plant distributions and co-occurrence patterns, including ecological sorting, limiting similarity, and stochastic effects. To discriminate among these processes and determine the spatial scales at which they operate, we investigated how functional traits and phylogenetic relatedness influence the distribution of temperate forest herbs. METHODS: We surveyed understory plant communities across 257 forest stands in Wisconsin and Michigan (USA) and applied Bayesian phylogenetic linear mixed-effects models (PGLMMs) to quantify how functional traits and phylogenetic relatedness influence the environmental distribution of 139 herbaceous plant species along broad edaphic, climatic, and light gradients. These models also allowed us to test how functional and phylogenetic similarity affect species co-occurrence within microsites. RESULTS: Leaf height, specific leaf area, and seed mass all influenced individualistic plant distributions along landscape-scale gradients in soil texture, soil fertility, light availability, and climate. In contrast, phylogenetic relationships did not consistently predict species-environment relationships. Neither functionally similar nor phylogenetically related herbs segregated among microsites within forest stands. CONCLUSIONS: Trait-mediated ecological sorting appears to drive temperate-forest community assembly, generating individualistic plant distributions along regional environmental gradients. This finding links classic studies in plant ecology and prior research in plant physiological ecology to current trait-based approaches in community ecology. However, our results fail to support the common assumption that limiting similarity governs local plant co-occurrences. Strong ecological sorting among forest stands coupled with stochastic fine-scale interactions among species appear to weaken deterministic, niche-based assembly processes at local scales.

Liana functional assembly along the hydrological gradient in Central Amazonia.

Soil hydrology, nutrient availability, and forest disturbance determine the variation of tropical tree species composition locally. However, most habitat filtering is explained by tree species' hydraulic traits along the hydrological gradient. We asked whether these patterns apply to lianas. At the community level, we investigated whether hydrological gradient, soil fertility, and forest disturbance explain liana species composition and whether liana species-environment relationships are mediated by leaf and stem wood functional traits. We sampled liana species composition in 18 1-ha plots across a 64 km2 landscape in Central Amazonia and measured eleven leaf and stem wood traits across 115 liana species in 2000 individuals. We correlated liana species composition, summarized using PCoA with the functional composition summarized using principal coordinate analysis (PCA), employing species mean values of traits at the plot level. We tested the relationship between ordination axes and environmental gradients. Liana species composition was highly correlated with functional composition. Taxonomic (PCoA) and functional (PCA) compositions were strongly associated with the hydrological gradient, with a slight influence from forest disturbance on functional composition. Species in valley areas had larger stomata size and higher proportions of self-supporting xylem than in plateaus. Liana species on plateaus invest more in fast-growing leaves (higher SLA), although they show a higher wood density. Our study reveals that lianas use different functional solutions in dealing with each end of the hydrological gradient and that the relationships among habitat preferences and traits explain lianas species distributions less directly than previously found in trees.