Agent‐based modeling of the effects of forest dynamics,selective logging,and fragment size on epiphyte communities

1. Forest canopies play a crucial role in structuring communities of vascular epiphytes by providing substrate for colonization, by locally varying microclimate, and by causing epiphyte mortality due to branch or tree fall. However, as field studies in the three‐dimensional habitat of epiphytes are generally challenging, our understanding of how forest structure and dynamics influence the structure and dynamics of epiphyte communities is scarce.
2. Mechanistic models can improve our understanding of epiphyte community dynamics. We present such a model that couples dispersal, growth, and mortality of individual epiphytes with substrate dynamics, obtained from a three‐dimensional functional–structural forest model, allowing the study of forest–epiphyte interactions. After validating the epiphyte model with independent field data, we performed several theoretical simulation experiments to assess how (a) differences in natural forest dynamics, (b) selective logging, and (c) forest fragmentation could influence the long‐term dynamics of epiphyte communities.
3. The proportion of arboreal substrate occupied by epiphytes (i.e., saturation level) was tightly linked with forest dynamics and increased with decreasing forest turnover rates. While species richness was, in general, negatively correlated with forest turnover rates, low species numbers in forests with very‐low‐turnover rates were due to competitive exclusion when epiphyte communities became saturated. Logging had a negative impact on epiphyte communities, potentially leading to a near‐complete extirpation of epiphytes when the simulated target diameters fell below a threshold. Fragment size had no effect on epiphyte abundance and saturation level but correlated positively with species numbers.
4. Synthesis: The presented model is a first step toward studying the dynamic forest–epiphyte interactions in an agent‐based modeling framework. Our study suggests forest dynamics as key factor in controlling epiphyte communities. Thus, both natural and human‐induced changes in forest dynamics, for example, increased mortality rates or the loss of large trees, pose challenges for epiphyte conservation.

     

Location,but not defensive genotype,determines ectomycorrhizal community composition in Scots pine (Pinus sylvestris L.) seedlings

1. For successful colonization of host roots, ectomycorrhizal (EM) fungi must overcome host defense systems, and defensive phenotypes have previously been shown to affect the community composition of EM fungi associated with hosts. Secondary metabolites, such as terpenes, form a core part of these defense systems, but it is not yet understood whether variation in these constitutive defenses can result in variation in the colonization of hosts by specific fungal species.
2. We planted seedlings from twelve maternal families of Scots pine (Pinus sylvestris) of known terpene genotype reciprocally in the field in each of six sites. After 3 months, we characterized the mycorrhizal fungal community of each seedling using a combination of morphological categorization and molecular barcoding, and assessed the terpene chemodiversity for a subset of the seedlings. We examined whether parental genotype or terpene chemodiversity affected the diversity or composition of a seedling''s mycorrhizal community.
3. While we found that terpene chemodiversity was highly heritable, we found no evidence that parental defensive genotype or a seedling''s terpene chemodiversity affected associations with EM fungi. Instead, we found that the location of seedlings, both within and among sites, was the only determinant of the diversity and makeup of EM communities.
4. These results show that while EM community composition varies within Scotland at both large and small scales, variation in constitutive defensive compounds does not determine the EM communities of closely cohabiting pine seedlings. Patchy distributions of EM fungi at small scales may render any genetic variation in associations with different species unrealizable in field conditions. The case for selection on traits mediating associations with specific fungal species may thus be overstated, at least in seedlings.

     

The influence of competing root symbionts on below‐ground plant resource allocation

1. Plants typically interact with multiple above‐ and below‐ground organisms simultaneously, with their symbiotic relationships spanning a continuum ranging from mutualism, such as with arbuscular mycorrhizal fungi (AMF), to parasitism, including symbioses with plant‐parasitic nematodes (PPN).
2. Although research is revealing the patterns of plant resource allocation to mutualistic AMF partners under different host and environmental constraints, the root ecosystem, with multiple competing symbionts, is often ignored. Such competition is likely to heavily influence resource allocation to symbionts.
3. Here, we outline and discuss the competition between AMF and PPN for the finite supply of host plant resources, highlighting the need for a more holistic understanding of the influence of below‐ground interactions on plant resource allocation. Based on recent developments in our understanding of other symbiotic systems such as legume–rhizobia and AMF‐aphid‐plant, we propose hypotheses for the distribution of plant resources between contrasting below‐ground symbionts and how such competition may affect the host.
4. We identify relevant knowledge gaps at the physiological and molecular scales which, if resolved, will improve our understanding of the true ecological significance and potential future exploitation of AMF‐PPN‐plant interactions in order to optimize plant growth. To resolve these outstanding knowledge gaps, we propose the application of well‐established methods in isotope tracing and nutrient budgeting to monitor the movement of nutrients between symbionts. By combining these approaches with novel time of arrival experiments and experimental systems involving multiple plant hosts interlinked by common mycelial networks, it may be possible to reveal the impact of multiple, simultaneous colonizations by competing symbionts on carbon and nutrient flows across ecologically important scales.

     

Intraspecific trait variability and community assembly in hawkmoths (Lepidoptera: Sphingidae) across an elevational gradient in the eastern Himalayas,India

1. We investigated some aspects of hawkmoth community assembly at 13 elevations along a 200‐ to 2770‐m transect in the eastern Himalayas, a little studied biodiversity hot spot of global importance. We measured the morphological traits of body mass, wing loading, and wing aspect ratio of 3,301 free‐ranging individuals of 76 species without having to collect or even constrain them. We used these trait measurements and T‐statistic metrics to assess the strength of intracommunity (“internal") and extra‐community (“external”) filters which determine the composition of communities vis‐a‐vis the regional pool of species.
2. The trait distribution of constituent species turned out to be nonrandom subsets of the community‐trait distribution, providing strong evidence for internal filtering in all elevational communities. The external filter metric was more ambiguous. However, the elevational dependence of many metrics including that of the internal filter provided evidence for external (i.e., environmental) filtering. On average, a species occupied as much as 50%–75% of the total community‐trait space, yet the T‐statistic metric for internal filter was sufficiently sensitive to detect a strong nonrandom structure in the trait distribution.
3. We suggest that the change in T‐statistic metrics along the environmental gradient may provide more clues to the process of community assembly than previously envisaged. A large, smoothly varying and well‐sampled environmental span would make it easier to discern them. Developing T‐statistics for combined analysis of multiple traits will perhaps provide a more accurate picture of internal/filtering and niche complementarity. Moths are a hyperdiverse taxon and a very important component of many ecosystems. Our technique for accurately measuring body and wing dimensions of free‐ranging moths can generate trait database for a large number of individuals in a time‐ and resource‐efficient manner for a variety of community assembly studies using this important taxon.

     

Nitrogen Uptake by Trees and Mycorrhizal Fungi in a Successional Northern Temperate Forest: Insights from Multiple Isotopic Methods

Forest succession may cause changes in nitrogen (N) availability, vegetation and fungal community composition that affect N uptake by trees and their mycorrhizal symbionts. Understanding how these changes affect the functioning of the mycorrhizal symbiosis is of interest to ecosystem ecology because of the fundamental roles mycorrhizae play in providing nutrition to trees and structuring forest ecosystems. We investigated changes in tree and mycorrhizal fungal community composition, the availability and uptake of N by trees and mycorrhizal fungi in a forest undergoing a successional transition (age-related loss of early successional tree taxa). In this system, 82–96% of mycorrhizal hyphae were ectomycorrhizal (EM). As biomass production of arbuscular mycorrhizal (AM) trees increased, AM hyphae comprised a significantly greater proportion of total fungal hyphae, and the EM contribution to the N requirement of EM-associated tree taxa declined from greater than 75% to less than 60%. Increasing N availability was associated with lower EM hyphal foraging and ¹⁵N tracer uptake, yet the EM-associated later-successional species Quercus rubra was nonetheless a stronger competitor for ¹⁵N than AM-associated Acer rubrum, likely due to the more extensive nature of the persistent EM hyphal network. These results indicate that successional increases in N availability and co-dominance by AM-associated trees have increased the importance of AM fungi in the mycorrhizal community, while down-regulating EM N acquisition and transfer processes. This work advances understanding of linkages between tree and fungal community composition, and indicates that successional changes in N availability may affect competition between tree taxa with divergent resource acquisition strategies.     

Remotely sensed between‐individual functional trait variation in a temperate forest

1. Trait‐based ecology holds the promise to explain how plant communities work, for example, how functional diversity may support community productivity. However, so far it has been difficult to combine field‐based approaches assessing traits at the level of plant individuals with limited spatial coverage and approaches using remote sensing (RS) with complete spatial coverage but assessing traits at the level of vegetation pixels rather than individuals. By delineating all individual‐tree crowns within a temperate forest site and then assigning RS‐derived trait measures to these trees, we combine the two approaches, allowing us to use general linear models to estimate the influence of taxonomic or environmental variation on between‐ and within‐species variation across contiguous space.
2. We used airborne imaging spectroscopy and laser scanning to collect individual‐tree RS data from a mixed conifer‐angiosperm forest on a mountain slope extending over 5.5 ha and covering large environmental gradients in elevation as well as light and soil conditions. We derived three biochemical (leaf chlorophyll, carotenoids, and water content) and three architectural traits (plant area index, foliage‐height diversity, and canopy height), which had previously been used to characterize plant function, from the RS data. We then quantified the contributions of taxonomic and environmental variation and their interaction to trait variation and partitioned the remaining within‐species trait variation into smaller‐scale spatial and residual variation. We also investigated the correlation between functional trait and phylogenetic distances at the between‐species level. The forest consisted of 13 tree species of which eight occurred in sufficient abundance for quantitative analysis.
3. On average, taxonomic variation between species accounted for more than 15% of trait variation in biochemical traits but only around 5% (still highly significant) in architectural traits. Biochemical trait distances among species also showed a stronger correlation with phylogenetic distances than did architectural trait distances. Light and soil conditions together with elevation explained slightly more variation than taxonomy across all traits, but in particular increased plant area index (light) and reduced canopy height (elevation). Except for foliage‐height diversity, all traits were affected by significant interactions between taxonomic and environmental variation, the different responses of the eight species to the within‐site environmental gradients potentially contributing to the coexistence of the eight abundant species.
4. We conclude that with high‐resolution RS data it is possible to delineate individual‐tree crowns within a forest and thus assess functional traits derived from RS data at individual level. With this precondition fulfilled, it is then possible to apply tools commonly used in field‐based trait ecology to partition trait variation among individuals into taxonomic and potentially even genetic variation, environmental variation, and interactions between the two. The method proposed here presents a promising way of assessing individual‐based trait information with complete spatial coverage and thus allowing analysis of functional diversity at different scales. This information can help to better understand processes shaping community structure, productivity, and stability of forests.

     

Plant phylogeny drives arboreal caterpillar assemblages across the Holarctic

1. Assemblages of insect herbivores are structured by plant traits such as nutrient content, secondary metabolites, physical traits, and phenology. Many of these traits are phylogenetically conserved, implying a decrease in trait similarity with increasing phylogenetic distance of the host plant taxa. Thus, a metric of phylogenetic distances and relationships can be considered a proxy for phylogenetically conserved plant traits and used to predict variation in herbivorous insect assemblages among co‐occurring plant species.
2. Using a Holarctic dataset of exposed‐feeding and shelter‐building caterpillars, we aimed at showing how phylogenetic relationships among host plants explain compositional changes and characteristics of herbivore assemblages.
3. Our plant–caterpillar network data derived from plot‐based samplings at three different continents included >28,000 individual caterpillar–plant interactions. We tested whether increasing phylogenetic distance of the host plants leads to a decrease in caterpillar assemblage overlap. We further investigated to what degree phylogenetic isolation of a host tree species within the local community explains abundance, density, richness, and mean specialization of its associated caterpillar assemblage.
4. The overlap of caterpillar assemblages decreased with increasing phylogenetic distance among the host tree species. Phylogenetic isolation of a host plant within the local plant community was correlated with lower richness and mean specialization of the associated caterpillar assemblages. Phylogenetic isolation had no effect on caterpillar abundance or density. The effects of plant phylogeny were consistent across exposed‐feeding and shelter‐building caterpillars.
5. Our study reveals that distance metrics obtained from host plant phylogeny are useful predictors to explain compositional turnover among hosts and host‐specific variations in richness and mean specialization of associated insect herbivore assemblages in temperate broadleaf forests. As phylogenetic information of plant communities is becoming increasingly available, further large‐scale studies are needed to investigate to what degree plant phylogeny structures herbivore assemblages in other biomes and ecosystems.

     

Modeling mycorrhizal fungi dispersal by the mycophagous swamp wallaby (Wallabia bicolor)

Despite the importance of mammal‐fungal interactions, tools to estimate the mammal‐assisted dispersal distances of fungi are lacking. Many mammals actively consume fungal fruiting bodies, the spores of which remain viable after passage through their digestive tract. Many of these fungi form symbiotic relationships with trees and provide an array of other key ecosystem functions. We present a flexible, general model to predict the distance a mycophagous mammal would disperse fungal spores. We modeled the probability of spore dispersal by combining animal movement data from GPS telemetry with data on spore gut‐retention time. We test this model using an exemplar generalist mycophagist, the swamp wallaby (Wallabia bicolor). We show that swamp wallabies disperse fungal spores hundreds of meters—and occasionally up to 1,265 m—from the point of consumption, distances that are ecologically significant for many mycorrhizal fungi. In addition to highlighting the ecological importance of swamp wallabies as dispersers of mycorrhizal fungi in eastern Australia, our simple modeling approach provides a novel and effective way of empirically describing spore dispersal by a mycophagous animal. This approach is applicable to the study of other animal‐fungi interactions in other ecosystems.     

Rewilding with invertebrates and microbes to restore ecosystems: Present trends and future directions

1. Restoration ecology has historically focused on reconstructing communities of highly visible taxa while less visible taxa, such as invertebrates and microbes, are ignored. This is problematic as invertebrates and microbes make up the vast bulk of biodiversity and drive many key ecosystem processes, yet they are rarely actively reintroduced following restoration, potentially limiting ecosystem function and biodiversity in these areas.
2. In this review, we discuss the current (limited) incorporation of invertebrates and microbes in restoration and rewilding projects. We argue that these groups should be actively rewilded during restoration to improve biodiversity, ecosystem function outcomes, and highlight how they can be used to greater effect in the future. For example, invertebrates and microbes are easily manipulated, meaning whole communities can potentially be rewilded through habitat transplants in a practice that we refer to as “whole‐of‐community” rewilding.
3. We provide a framework for whole‐of‐community rewilding and describe empirical case studies as practical applications of this under‐researched restoration tool that land managers can use to improve restoration outcomes.
4. We hope this new perspective on whole‐of‐community restoration will promote applied research into restoration that incorporates all biota, irrespective of size, while also enabling a better understanding of fundamental ecological theory, such as colonization and competition trade‐offs. This may be a necessary consideration as invertebrates that are important in providing ecosystem services are declining globally; targeting invertebrate communities during restoration may be crucial in stemming this decline.

     

Ectomycorrhizal fungi and past high CO2 atmospheres enhance mineral weathering through increased below-ground carbon-energy fluxes

Field studies indicate an intensification of mineral weathering with advancement from arbuscular mycorrhizal (AM) to later-evolving ectomycorrhizal (EM) fungal partners of gymnosperm and angiosperm trees. We test the hypothesis that this intensification is driven by increasing photosynthate carbon allocation to mycorrhizal mycelial networks using ¹⁴CO₂-tracer experiments with representative tree–fungus mycorrhizal partnerships. Trees were grown in either a simulated past CO₂ atmosphere (1500 ppm)—under which EM fungi evolved—or near-current CO₂ (450 ppm). We report a direct linkage between photosynthate-energy fluxes from trees to EM and AM mycorrhizal mycelium and rates of calcium silicate weathering. Calcium dissolution rates halved for both AM and EM trees as CO₂ fell from 1500 to 450 ppm, but silicate weathering by AM trees at high CO₂ approached rates for EM trees at near-current CO₂. Our findings provide mechanistic insights into the involvement of EM-associating forest trees in strengthening biological feedbacks on the geochemical carbon cycle that regulate atmospheric CO₂ over millions of years.     

Underwater photogrammetry for close‐range 3D imaging of dry‐sensitive objects: The case study of cephalopod beaks

• Technical advances in 3D imaging have contributed to quantifying and understanding biological variability and complexity. However, small, dry‐sensitive objects are not easy to reconstruct using common and easily available techniques such as photogrammetry, surface scanning, or micro‐CT scanning. Here, we use cephalopod beaks as an example as their size, thickness, transparency, and dry‐sensitive nature make them particularly challenging. We developed a new, underwater, photogrammetry protocol in order to add these types of biological structures to the panel of photogrammetric possibilities.
• We used a camera with a macrophotography mode in a waterproof housing fixed in a tank with clear water. The beak was painted and fixed on a colored rotating support. Three angles of view, two acquisitions, and around 300 pictures per specimen were taken in order to reconstruct a full 3D model. These models were compared with others obtained with micro‐CT scanning to verify their accuracy.
• The models can be obtained quickly and cheaply compared with micro‐CT scanning and have sufficient precision for quantitative interspecific morphological analyses. Our work shows that underwater photogrammetry is a fast, noninvasive, efficient, and accurate way to reconstruct 3D models of dry‐sensitive objects while conserving their shape. While the reconstruction of the shape is accurate, some internal parts cannot be reconstructed with photogrammetry as they are not visible. In contrast, these structures are visible using reconstructions based on micro‐CT scanning. The mean difference between both methods is very small (10⁻⁵ to 10⁻⁴ mm) and is significantly lower than differences between meshes of different individuals.
• This photogrammetry protocol is portable, easy‐to‐use, fast, and reproducible. Micro‐CT scanning, in contrast, is time‐consuming, expensive, and nonportable. This protocol can be applied to reconstruct the 3D shape of many other dry‐sensitive objects such as shells of shellfish, cartilage, plants, and other chitinous materials.

     

Age‐specific habitat preference,carrying capacity,and landscape structure determine the response of population spatial variability to fishing‐driven age truncation

1. Understanding the mechanisms underlying spatial variability of exploited fish is critical for the sustainable management of fish stocks. Empirical studies suggest that size‐selective fishing can elevate fish population spatial variability (i.e., more heterogeneous distribution) through age truncation, making the population less resilient to changing environment. However, species differ in how their spatial variability responds to age truncation and the underlying mechanisms remain unclear.
2. We hypothesize that age‐specific habitat preference, together with environmental carrying capacity and landscape structure, determines the response of population spatial variability to fishing‐induced age truncation. To test these hypotheses, we design an individual‐based model of an age‐structured fish population on a two‐dimensional landscape under size‐selective fishing. Individual fish reproduces and survives, and moves between habitats according to age‐specific habitat preference and density‐dependent habitat selection.
3. Population spatial variability elevates with increasing age truncation, and the response is stronger for populations with stronger age‐specific habitat preference. On a gradient landscape, reducing carrying capacity elevates the relative importance of density dependence in habitat selection, which weakens the response of spatial variability to age truncation for populations with strong age‐specific habitat preference. On a fragmented landscape, both populations with strong and weak age‐specific habitat preferences are restricted at local optimal habitats, and reducing carrying capacity weakens the responses of spatial variability to age truncation for both populations.
4. Synthesis and applications. We demonstrate that to track and predict the changes in population spatial variability under exploitation, it is essential to consider the interactive effects of age‐specific habitat preference, carrying capacity, and landscape structure. To improve spatial management in fisheries, it is crucial to enhance empirical and theoretical developments in the methodology to quantify age‐specific habitat preference of marine fish, and to understand how climatic change influences carrying capacity and landscape continuity.

     

Relieving efforts in palm‐tree tissue sampling for population genetics analyses

1. The young leaves are the main source of nucleic acids for population genetic studies in palm‐trees; however, the access to this tissue may be limited by specific features of each species. Using root tissues as an alternative source of nucleic acids could facilitate the sampling in large populations.
2. This study tests root tissue viability as an alternative nucleic acid source (root versus. leaf) and explores different protocols (tissue storage and DNA extraction methods) to obtain high‐quality DNA samples.
3. The results showed no significant differences in DNA concentration (603.7 vs. 599.1 ng/μl) and quality ratios (A260/280:2.1 vs. 1.9, and A260/230:2.1 vs. 2.0) for the comparisons of tissue source (leaf vs. root) and DNA extraction method (manual vs. kit). For tissue storage method, DNA concentration was significantly higher for root tissues stored in 70% and 90% alcohol solutions (692.8 and 822.6 ng/μl, respectively) versus those obtained from leaf tissue (603.7 ng/μl); however, for the quality parameters, no differences were found.
4. Results showed the effective potential of using root tissue as an alternative source for nucleic acids, which could facilitate population sampling of palm‐tree species for future studies, and this methodological alternative could be applied to other plant systems with similar sampling challenges.

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Interacting forces of predation and fishing affect species’ maturation size

1. Fishing is a strong selective force and is supposed to select for earlier maturation at smaller body size. However, the extent to which fishing‐induced evolution is shaping ecosystems remains debated. This is in part because it is challenging to disentangle fishing from other selective forces (e.g., size‐structured predation and cannibalism) in complex ecosystems undergoing rapid change.
2. Changes in maturation size from fishing and predation have previously been explored with multi‐species physiologically structured models but assumed separation of ecological and evolutionary timescales. To assess the eco‐evolutionary impact of fishing and predation at the same timescale, we developed a stochastic physiologically size‐structured food‐web model, where new phenotypes are introduced randomly through time enabling dynamic simulation of species'' relative maturation sizes under different types of selection pressures.
3. Using the model, we carried out a fully factorial in silico experiment to assess how maturation size would change in the absence and presence of both fishing and predation (including cannibalism). We carried out ten replicate stochastic simulations exposed to all combinations of fishing and predation in a model community of nine interacting fish species ranging in their maximum sizes from 10 g to 100 kg. We visualized and statistically analyzed the results using linear models.
4. The effects of fishing on maturation size depended on whether or not predation was enabled and differed substantially across species. Fishing consistently reduced the maturation sizes of two largest species whether or not predation was enabled and this decrease was seen even at low fishing intensities (F = 0.2 per year). In contrast, the maturation sizes of the three smallest species evolved to become smaller through time but this happened regardless of the levels of predation or fishing. For the four medium‐size species, the effect of fishing was highly variable with more species showing significant and larger fishing effects in the presence of predation.
5. Ultimately our results suggest that the interactive effects of predation and fishing can have marked effects on species'' maturation sizes, but that, at least for the largest species, predation does not counterbalance the evolutionary effect of fishing. Our model also produced relative maturation sizes that are broadly consistent with empirical estimates for many fish species.

     

Looking for the needle in a downsized haystack: Whole‐exome sequencing unravels genomic signals of climatic adaptation in Douglas‐fir (Pseudotsuga menziesii)

1. Conifers often occur along steep gradients of diverse climates throughout their natural ranges, which is expected to result in spatially varying selection to local climate conditions. However, signals of climatic adaptation can often be confounded, because unraveled clines covary with signals caused by neutral evolutionary processes such as gene flow and genetic drift. Consequently, our understanding of how selection and gene flow have shaped phenotypic and genotypic differentiation in trees is still limited.
2. A 40‐year‐old common garden experiment comprising 16 Douglas‐fir (Pseudotsuga menziesii) provenances from a north‐to‐south gradient of approx. 1,000 km was analyzed, and genomic information was obtained from exome capture, which resulted in an initial genomic dataset of >90,000 single nucleotide polymorphisms. We used a restrictive and conservative filtering approach, which permitted us to include only SNPs and individuals in environmental association analysis (EAA) that were free of potentially confounding effects (LD, relatedness among trees, heterozygosity deficiency, and deviations from Hardy–Weinberg proportions). We used four conceptually different genome scan methods based on F_ST outlier detection and gene–environment association in order to disentangle truly adaptive SNPs from neutral SNPs.
3. We found that a relatively small proportion of the exome showed a truly adaptive signal (0.01%–0.17%) when population substructuring and multiple testing was accounted for. Nevertheless, the unraveled SNP candidates showed significant relationships with climate at provenance origins, which strongly suggests that they have featured adaptation in Douglas‐fir along a climatic gradient. Two SNPs were independently found by three of the employed algorithms, and one of them is in close proximity to an annotated gene involved in circadian clock control and photoperiodism as was similarly found in Populus balsamifera.

Synthesis. We conclude that despite neutral evolutionary processes, phenotypic and genomic signals of adaptation to climate are responsible for differentiation, which in particular explain disparity between the well‐known coastal and interior varieties of Douglas‐fir.     

Rhizosphere soil bacterial communities and nitrogen cycling affected by deciduous and evergreen tree species

Deciduous and evergreen trees differ in their responses to drought and nitrogen (N) demand. Whether or not these functional types affect the role of the bacterial community in the N cycle during drought remains uncertain. Two deciduous tree species (Alnus cremastogyne, an N₂‐fixing species, and Liquidambar formosana) and two evergreen trees (Cunninghamia lanceolata and Pinus massoniana) were used to assess factors in controlling rhizosphere soil bacterial community and N cycling functions. Photosynthetic rates and biomass production of plants, 16S rRNA sequencing and N‐cycling‐related genes of rhizosphere soil were measured. The relative abundance of the phyla Actinobacteria and Firmicutes was higher, and that of Proteobacteria, Acidobacteria, and Gemmatimondaetes was lower in rhizosphere soil of deciduous trees than that of evergreen. Beta‐diversity of bacterial community also significantly differed between the two types of trees. Deciduous trees showed significantly higher net photosynthetic rates and biomass production than evergreen species both at well water condition and short‐term drought. Root biomass was the most important factor in driving soil bacterial community and N‐cycling functions than total biomass and aboveground biomass. Furthermore, 44 bacteria genera with a decreasing response and 46 taxa showed an increased response along the root biomass gradient. Regarding N‐cycle‐related functional genes, copy numbers of ammonia‐oxidizing bacteria (AOB) and autotrophic ammonia‐oxidizing archaea (AOA), N₂ fixation gene (nifH), and denitrification genes (nirK, nirS) were significantly higher in the soil of deciduous trees than in that of the evergreen. Structural equation models explained 50.2%, 47.6%, 48.6%, 49.4%, and 37.3% of the variability in copy numbers of nifH, AOB, AOA, nirK, and nirS, respectively, and revealed that root biomass had significant positive effects on copy numbers of all N‐cycle functional genes. In conclusion, root biomass played key roles in affecting bacterial community structure and soil N cycling. Our findings have important implications for our understanding of plants control over bacterial community and N‐cycling function in artificial forest ecosystems.     

Weather variation affects the dispersal of grasshoppers beyond their elevational ranges

1. Understanding how abiotic conditions influence dispersal patterns of organisms is important for understanding the degree to which species can track and persist in the face of changing climate.
2. The goal of this study was to understand how weather conditions influence the dispersal pattern of multiple nonmigratory grasshopper species from lower elevation grassland habitats in which they complete their life‐cycles to higher elevations that extend beyond their range limits.
3. Using over a decade of weekly spring to late‐summer field survey data along an elevational gradient, we explored how abundance and richness of dispersing grasshoppers were influenced by temperature, precipitation, and wind speed and direction. We also examined how changes in population sizes at lower elevations might influence these patterns.
4. We observed that the abundance of dispersing grasshoppers along the gradient declined 4‐fold from the foothills to the subalpine and increased with warmer conditions and when wind flow patterns were mild or in the downslope direction. Thirty‐eight unique grasshopper species from lowland sites were detected as dispersers across the survey years, and warmer years and weak upslope wind conditions also increased the richness of these grasshoppers. The pattern of grasshoppers along the gradient was not sex biased. The positive effect of temperature on dispersal rates was likely explained by an increase in dispersal propensity rather than by an increase in the density of grasshoppers at low elevation sites.
5. The results of this study support the hypothesis that the dispersal patterns of organisms are influenced by changing climatic conditions themselves and as such, that this context‐dependent dispersal response should be considered when modeling and forecasting the ability of species to respond to climate change.

     

Evolution of trees and mycorrhizal fungi intensifies silicate mineral weathering

Forested ecosystems diversified more than 350 Ma to become major engines of continental silicate weathering, regulating the Earth''s atmospheric carbon dioxide concentration by driving calcium export into ocean carbonates. Our field experiments with mature trees demonstrate intensification of this weathering engine as tree lineages diversified in concert with their symbiotic mycorrhizal fungi. Preferential hyphal colonization of the calcium silicate-bearing rock, basalt, progressively increased with advancement from arbuscular mycorrhizal (AM) to later, independently evolved ectomycorrhizal (EM) fungi, and from gymnosperm to angiosperm hosts with both fungal groups. This led to ‘trenching’ of silicate mineral surfaces by AM and EM fungi, with EM gymnosperms and angiosperms releasing calcium from basalt at twice the rate of AM gymnosperms. Our findings indicate mycorrhiza-driven weathering may have originated hundreds of millions of years earlier than previously recognized and subsequently intensified with the evolution of trees and mycorrhizas to affect the Earth''s long-term CO₂ and climate history.     

Meta‐analysis shows that environmental DNA outperforms traditional surveys,but warrants better reporting standards

1. Decades of environmental DNA (eDNA) method application, spanning a wide variety of taxa and habitats, has advanced our understanding of eDNA and underlined its value as a tool for conservation practitioners. The general consensus is that eDNA methods are more accurate and cost‐effective than traditional survey methods. However, they are formally approved for just a few species globally (e.g., Bighead Carp, Silver Carp, Great Crested Newt). We conducted a meta‐analysis of studies that directly compare eDNA with traditional surveys to evaluate the assertion that eDNA methods are consistently “better.”
2. Environmental DNA publications for multiple species or single macro‐organism detection were identified using the Web of Science, by searching “eDNA” and “environmental DNA” across papers published between 1970 and 2020. The methods used, focal taxa, habitats surveyed, and quantitative and categorical results were collated and analyzed to determine whether and under what circumstances eDNA outperforms traditional surveys.
3. Results show that eDNA methods are cheaper, more sensitive, and detect more species than traditional methods. This is, however, taxa‐dependent, with amphibians having the highest potential for detection by eDNA survey. Perhaps most strikingly, of the 535 papers reviewed just 49 quantified the probability of detection for both eDNA and traditional survey methods and studies were three times more likely to give qualitative statements of performance.
4. Synthesis and applications: The results of this meta‐analysis demonstrate that where there is a direct comparison, eDNA surveys of macro‐organisms are more accurate and efficient than traditional surveys. This conclusion, however, is based on just a fraction of available eDNA papers as most do not offer this granularity. We recommend that conclusions are substantiated with comparable and quantitative data. Where a direct comparison has not been made, we caution against the use of qualitative statements about relative performance. This consistency and rigor will simplify how the eDNA research community tracks methods‐based advances and will also provide greater clarity for conservation practitioners. To this end suggest reporting standards for eDNA studies.

     

High‐throughput sequencing on preservative ethanol is effective at jointly examining infraspecific and taxonomic diversity,although bioinformatics pipelines do not perform equally

1. High‐throughput sequencing of amplicons (HTSA) has been proposed as an effective approach to evaluate taxonomic and genetic diversity at the same time. However, there are still uncertainties as to how the results produced by different bioinformatics treatments impact the conclusions drawn on biodiversity and population genetics indices.
2. We evaluated the ability of six bioinformatics pipelines to recover taxonomic and genetic diversity from HTSA data obtained from controlled assemblages. To that end, 20 assemblages were produced using 354 colonies of Botrylloides spp., sampled in the wild in ten marinas around Brittany (France). We used DNA extracted from preservative ethanol (ebDNA) after various time of storage (3, 6, and 12 months), and from a bulk of preserved specimens (bulkDNA). DNA was amplified with primers designed for targeting this ascidian genus. Results obtained from HTSA data were compared with Sanger sequencing on individual zooids (i.e., individual barcoding).
3. Species identification and relative abundance determined with HTSA data from either ebDNA or bulkDNA were similar to those obtained with traditional individual barcoding. However, after 12 months of storage, the correlation between HTSA and individual‐based data was lower than after shorter durations. The six bioinformatics pipelines were able to depict accurately the genetic diversity using standard population genetics indices (H_S and F_ST), despite producing false positives and missing rare haplotypes. However, they did not perform equally and dada2 was the only pipeline able to retrieve all expected haplotypes.
4. This study showed that ebDNA is a nondestructive alternative for both species identification and haplotype recovery, providing storage does not last more than 6 months before DNA extraction. Choosing the bioinformatics pipeline is a matter of compromise, aiming to retrieve all true haplotypes while avoiding false positives. We here recommend to process HTSA data using dada2, including a chimera‐removal step. Even if the possibility to use multiplexed primer sets deserves further investigation to expand the taxonomic coverage in future similar studies, we showed that primers targeting a particular genus allowed to reliably analyze this genus within a complex community.