Trust your guts? The effect of gut section on diet composition and impact of Mus musculus on islands using metabarcoding

1. DNA metabarcoding is widely used to characterize the diet of species, and it becomes very relevant for biodiversity conservation, allowing the understanding of trophic chains and the impact of invasive species. The need for cost‐effective biodiversity monitoring methods fostered advances in this technique. One question that arises is which sample type provides a better diet representation.
2. Therefore, with this study, we intended to evaluate if there were differences in diet estimates according to the section of the gastrointestinal tract analysed and which section(s) provided the best diet representation. Additionally, we intended to infer the ecological/economic impacts of an invader as a model of the potential effects in an originally mammal‐free ecosystem.
3. We examined the gut contents of the house mouse Mus musculus introduced to Cabo Verde, considering three sections: stomach, small intestine, and large intestine. We applied a DNA‐metabarcoding approach using two genetic markers, one specific for plants and another for invertebrates.
4. We showed that this invader consumed 131 taxa (73 plants and 58 invertebrates). We obtained significant differences in the composition of two of the three sections, with a higher incidence of invertebrates in the stomach and plants in the intestines. This may be due to stomach inhibitors acting on plants and/or to faster absorption of soft‐body invertebrates compared to the plant fibers in the intestines. We verified that the impact of this invader in the ecosystem is predominantly negative, as at least 50% of the ingested items were native, endemic, or economically important taxa, and only 19% of the diet items were exotics.
5. Overall, results showed the need to analyse only two gastrointestinal tract sections to obtain robust diet data, increasing the cost‐effectiveness of the method. Furthermore, by uncovering the native taxa most frequently preyed on by mice, this DNA‐metabarcoding approach allowed us to evaluate efficiently which are at the highest risk.

     

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.

     

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.

     

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.

     

Using genomics to guide seed‐sourcing at the right taxonomical level for ecological restoration projects: The complex case of Carex bigelowii s.lat. in Norway

There is a growing demand for ecological restoration using suitable seeds following international standards or national legal demands for local seed‐sourcing. However, before selecting the appropriate geographic origin of seeds, it is vital to explore taxonomic complexity related to the focal taxa. We used ddRAD‐seq to screen genomic diversity within Carex bigelowii s.lat. focussing on Norway. This species complex is considered a candidate for seeding, but presents considerable morphological, ecological, and genetic variation. The genetic structure of 132 individuals of C. bigelowii s.lat., including Carex nigra as an outgroup, was explored using ordinations, clustering analyses, and a genetic barrier algorithm. Two highly divergent clusters were evident, supporting the recognition of two taxonomic units “C. dacica” and C. bigelowii “subsp. bigelowii”. Previously defined seed‐sourcing regions for C. bigelowii s.lat. did not consider the known taxonomic complexity, and therefore interpreted the overall genetic structure as seed‐sourcing regions, not taxa. We estimated genetic neighborhood sizes within each taxon to be 100–150 km and 300 km, respectively, indicating species‐specific delimitations of local seed‐sourcing regions. Frequent hybrids, local genetic distinctiveness, and suggested ecotypes add complexity to the discussed seed‐sourcing regions. Our results show how genomic screening of diversity and structure in a species complex can alleviate the taxonomic impediment, inform practical questions, and legal requirements related to seed‐sourcing, and together with traditional taxonomic work provide necessary information for a sound management of biodiversity.     

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.

     

Temperature but not ocean acidification affects energy metabolism and enzyme activities in the blue mussel,Mytilus edulis

1. In mosaic marine habitats, such as intertidal zones, ocean acidification (OA) is exacerbated by high variability of pH, temperature, and biological CO₂ production. The nonlinear interactions among these drivers can be context‐specific and their effect on organisms in these habitats remains largely unknown, warranting further investigation.
2. We were particularly interested in Mytilus edulis (the blue mussel) from intertidal zones of the Gulf of Maine (GOM), USA, for this study. GOM is a hot spot of global climate change (average sea surface temperature (SST) increasing by >0.2°C/year) with >60% decline in mussel population over the past 40 years.
3. Here, we utilize bioenergetic underpinnings to identify limits of stress tolerance in M. edulis from GOM exposed to warming and OA. We have measured whole‐organism oxygen consumption rates and metabolic biomarkers in mussels exposed to control and elevated temperatures (10 vs. 15°C, respectively) and current and moderately elevated P _CO2 levels (~400 vs. 800 µatm, respectively).
4. Our study demonstrates that adult M. edulis from GOM are metabolically resilient to the moderate OA scenario but responsive to warming as seen in changes in metabolic rate, energy reserves (total lipids), metabolite profiles (glucose and osmolyte dimethyl amine), and enzyme activities (carbonic anhydrase and calcium ATPase).
5. Our results are in agreement with recent literature that OA scenarios for the next 100–300 years do not affect this species, possibly as a consequence of maintaining its in vivo acid‐base balance.

     

Benefits and limitations of a new genome‐based PCR‐RFLP genotyping assay (GB‐RFLP): A SNP‐based detection method for identification of species in extremely young adaptive radiations

High‐throughput DNA sequencing technologies make it possible now to sequence entire genomes relatively easily. Complete genomic information obtained by whole‐genome resequencing (WGS) can aid in identifying and delineating species even if they are extremely young, cryptic, or morphologically difficult to discern and closely related. Yet, for taxonomic or conservation biology purposes, WGS can remain cost‐prohibitive, too time‐consuming, and often constitute a “data overkill.” Rapid and reliable identification of species (and populations) that is also cost‐effective is made possible by species‐specific markers that can be discovered by WGS. Based on WGS data, we designed a PCR restriction fragment length polymorphism (PCR‐RFLP) assay for 19 Neotropical Midas cichlid populations (Amphilophus cf. citrinellus), that includes all 13 described species of this species complex. Our work illustrates that identification of species and populations (i.e., fish from different lakes) can be greatly improved by designing genetic markers using available “high resolution” genomic information. Yet, our work also shows that even in the best‐case scenario, when whole‐genome resequencing information is available, unequivocal assignments remain challenging when species or populations diverged very recently, or gene flow persists. In summary, we provide a comprehensive workflow on how to design RFPL markers based on genome resequencing data, how to test and evaluate their reliability, and discuss the benefits and pitfalls of our approach.     

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.

     

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.

     

Functional diversity and habitat preferences of native grassland plants and ground‐dwelling invertebrates in private gardens along an urbanization gradient

Urbanization is occurring around the globe, changing environmental conditions and influencing biodiversity and ecosystem functions. Urban domestic gardens represent a small‐grained mosaic of diverse habitats for numerous species. The challenging conditions in urban gardens support species possessing certain traits, and exclude other species. Functional diversity is therefore often altered in urban gardens. By using a multi‐taxa approach focused on native grassland plants and ground‐dwelling invertebrates with overall low mobility (snails, slugs, spiders, millipedes, woodlice, ants, rove beetles), we examined the effects of urbanization (distance to city center, percentage of sealed area) and garden characteristics on functional dispersion, functional evenness, habitat preferences and body size. We conducted a field survey in 35 domestic gardens along a rural–urban gradient in Basel, Switzerland. The various groups showed different responses to urbanization. Functional dispersion of native grassland plants decreased with increasing distance to the city center, while functional dispersion of ants decreased with increasing percentage of sealed area. Functional evenness of ants increased with increasing distance to the city center and that of rove beetles decreased with increasing percentage of sealed area. Contrary to our expectation, in rove beetles, the proportion of generalists decreased with increasing percentage of sealed area in the surroundings, and the proportion of species preferring dry conditions increased with increasing distance to the city center. Body size of species increased with distance to city center for slugs, spiders, millipedes, ants, and rove beetles. Local garden characteristics had few effects on functional diversity and habitat preferences of the groups examined. Our study supports the importance of using multi‐taxa approaches when examining effects of environmental change on biodiversity. Considering only a single group may result in misleading findings for overall biodiversity. The ground‐dwelling invertebrates investigated may be affected in different ways from the more often‐studied flying pollinators or birds.     

Invasive Impatiens glandulifera: A driver of changes in native vegetation?

Biological invasions are one of the major threats to biodiversity worldwide and contribute to changing community patterns and ecosystem processes. However, it is often not obvious whether an invader is the “driver” causing ecosystem changes or a “passenger” which is facilitated by previous ecosystem changes. Causality of the impact can be demonstrated by experimental removal of the invader or introduction into a native community. Using such an experimental approach, we tested whether the impact of the invasive plant Impatiens glandulifera on native vegetation is causal, and whether the impact is habitat‐dependent. We conducted a field study comparing invaded and uninvaded plots with plots from which I. glandulifera was removed and plots where I. glandulifera was planted within two riparian habitats, alder forests and meadows. A negative impact of planting I. glandulifera and a concurrent positive effect of removal on the native vegetation indicated a causal effect of I. glandulifera on total native biomass and growth of Urtica dioica. Species α‐diversity and composition were not affected by I. glandulifera manipulations. Thus, I. glandulifera had a causal but low effect on the native vegetation. The impact depended slightly on habitat as only the effect of I. glandulifera planting on total biomass was slightly stronger in alder forests than meadows. We suggest that I. glandulifera is a “back‐seat driver” of changes, which is facilitated by previous ecosystem changes but is also a driver of further changes. Small restrictions of growth of the planted I. glandulifera and general association of I. glandulifera with disturbances indicate characteristics of a back‐seat driver. For management of I. glandulifera populations, this requires habitat restoration along with removal of the invader.     

Mixing tree species associated with arbuscular or ectotrophic mycorrhizae reveals dual mycorrhization and interactive effects on the fungal partners

1. Recent studies found that the majority of shrub and tree species are associated with both arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) fungi. However, our knowledge on how different mycorrhizal types interact with each other is still limited. We asked whether the combination of hosts with a preferred association with either AM or EM fungi increases the host tree roots’ mycorrhization rate and affects AM and EM fungal richness and community composition.
2. We established a tree diversity experiment, where five tree species of each of the two mycorrhiza types were planted in monocultures, two‐species and four‐species mixtures. We applied morphological assessment to estimate mycorrhization rates and next‐generation molecular sequencing to quantify mycobiont richness.
3. Both the morphological and molecular assessment revealed dual‐mycorrhizal colonization in 79% and 100% of the samples, respectively. OTU community composition strongly differed between AM and EM trees. While host tree species richness did not affect mycorrhization rates, we observed significant effects of mixing AM‐ and EM‐associated hosts in AM mycorrhization rate. Glomeromycota richness was larger in monotypic AM tree combinations than in AM‐EM mixtures, pointing to a dilution or suppression effect of AM by EM trees. We found a strong match between morphological quantification of AM mycorrhization rate and Glomeromycota richness.
4. Synthesis. We provide evidence that the combination of hosts differing in their preferred mycorrhiza association affects the host''s fungal community composition, thus revealing important biotic interactions among trees and their associated fungi.

     

Effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on associated soil bacterial communities: A field‐based experiment

Loss of plant biodiversity can result in reduced abundance and diversity of associated species with implications for ecosystem functioning. In ecosystems low in plant species diversity, such as Neotropical mangrove forests, it is thought that genetic diversity within the dominant plant species could play an important role in shaping associated communities. Here, we used a manipulative field experiment to study the effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on the composition and richness of associated soil bacterial communities. Using terminal restriction fragment length polymorphism (T‐RFLP) community fingerprinting, we found that bacterial community composition differed among R. mangle maternal genotypes but not with genetic diversity. Bacterial taxa richness, total soil nitrogen, and total soil carbon were not significantly affected by maternal genotypic identity or genetic diversity of R. mangle. Our findings show that genotype selection in reforestation projects could influence soil bacterial community composition. Further research is needed to determine what impact these bacterial community differences might have on ecosystem processes, such as carbon and nitrogen cycling.     

FishSizer: Software solution for efficiently measuring larval fish size

1. Length and depth of fish larvae are part of the fundamental measurements in many marine ecology studies involving early fish life history. Until now, obtaining these measurements has required intensive manual labor and the risk of inter‐ and intra‐observer variability.
2. We developed an open‐source software solution to semi‐automate the measurement process and thereby reduce both time consumption and technical variability. Using contrast‐based edge detection, the software segments images of a fish larva into “larva” and “background.” Length and depth are extracted from the “larva” segmentation while taking curvature of the larva into consideration. The graphical user interface optimizes workflow and ease of usage, thereby reducing time consumption for both training and analysis. The software allows for visual verification of all measurements.
3. A comparison of measurement methods on a set of larva images showed that this software reduces measurement time by 66%–78% relative to commonly used software.
4. Using this software instead of the commonly used manual approach has the potential to save researchers from many hours of monotonous work. No adjustment was necessary for 89% of the images regarding length (70% for depth). Hence, the only workload on most images was the visual inspection. As the visual inspection and manual dimension extraction works in the same way as currently used software, we expect no loss in accuracy.

     

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.

     

Plant history and soil history jointly influence the selection environment for plant species in a long‐term grassland biodiversity experiment

Long‐term biodiversity experiments have shown increasing strengths of biodiversity effects on plant productivity over time. However, little is known about rapid evolutionary processes in response to plant community diversity, which could contribute to explaining the strengthening positive relationship. To address this issue, we performed a transplant experiment with offspring of seeds collected from four grass species in a 14‐year‐old biodiversity experiment (Jena Experiment). We used two‐ and six‐species communities and removed the vegetation of the study plots to exclude plant–plant interactions. In a reciprocal design, we transplanted five “home” phytometers (same origin and actual environment), five “away‐same” phytometers (same species richness of origin and actual environment, but different plant composition), and five “away‐different” phytometers (different species richness of origin and actual environment) of the same species in the study plots. In the establishment year, plants transplanted in home soil produced more shoots than plants in away soil indicating that plant populations at low and high diversity developed differently over time depending on their associated soil community and/or conditions. In the second year, offspring of individuals selected at high diversity generally had a higher performance (biomass production and fitness) than offspring of individuals selected at low diversity, regardless of the transplant environment. This suggests that plants at low and high diversity showed rapid evolutionary responses measurable in their phenotype. Our findings provide first empirical evidence that loss of productivity at low diversity is not only caused by changes in abiotic and biotic conditions but also that plants respond to this by a change in their micro‐evolution. Thus, we conclude that eco‐evolutionary feedbacks of plants at low and high diversity are critical to fully understand why the positive influence of diversity on plant productivity is strengthening through time.     

Diversity and characterization of bacterial communities of five co‐occurring species at a hydrothermal vent on the Tonga Arc

Host–symbiont relationships in hydrothermal vent ecosystems, supported by chemoautotrophic bacteria as primary producers, have been extensively studied. However, the process by which densely populated co‐occurring invertebrate hosts form symbiotic relationships with bacterial symbionts remains unclear. Here, we analyzed gill‐associated symbiotic bacteria (gill symbionts) of five co‐occurring hosts, three mollusks (“Bathymodiolus” manusensis, B. brevior, and Alviniconcha strummeri) and two crustaceans (Rimicaris variabilis and Austinograea alayseae), collected together at a single vent site in the Tonga Arc. We observed both different compositions of gill symbionts and the presence of unshared operational taxonomic units (OTUs). In addition, the total number of OTUs was greater for crustacean hosts than for mollusks. The phylogenetic relationship trees of gill symbionts suggest that γ‐proteobacterial gill symbionts have coevolved with their hosts toward reinforcement of host specificity, while campylobacterial Sulfurovum species found across various hosts and habitats are opportunistic associates. Our results confirm that gill symbiont communities differ among co‐occurring vent invertebrates and indicate that hosts are closely related with their gill symbiont communities. Considering the given resources available at a single site, differentiation of gill symbionts seems to be a useful strategy for obtaining nutrition and energy while avoiding competition among both hosts and gill symbionts.     

Partitioning of beta‐diversity reveals distinct assembly mechanisms of plant and soil microbial communities in response to nitrogen enrichment

Nitrogen (N) deposition poses a serious threat to terrestrial biodiversity and alters plant and soil microbial community composition. Species turnover and nestedness reflect the underlying mechanisms of variations in community composition. However, it remains unclear how species turnover and nestedness contribute to different responses of taxonomic groups (plants and soil microbes) to N enrichment. Here, based on a 13‐year consecutive multi‐level N addition experiment in a semiarid steppe, we partitioned community β‐diversity into species turnover and nestedness components and explored how and why plant and microbial communities reorganize via these two processes following N enrichment. We found that plant, soil bacterial, and fungal β‐diversity increased, but their two components showed different patterns with increasing N input. Plant β‐diversity was mainly driven by species turnover under lower N input but by nestedness under higher N input, which may be due to a reduction in forb species, with low tolerance to soil Mn²⁺, with increasing N input. However, turnover was the main contributor to differences in soil bacterial and fungal communities with increasing N input, indicating the phenomenon of microbial taxa replacement. The turnover of bacteria increased greatly whereas that of fungi remained within a narrow range with increasing N input. We further found that the increased soil Mn²⁺ concentration was the best predictor for increasing nestedness of plant communities under higher N input, whereas increasing N availability and acidification together contributed to the turnover of bacterial communities. However, environmental factors could explain neither fungal turnover nor nestedness. Our findings reflect two different pathways of community changes in plants, soil bacteria, and fungi, as well as their distinct community assembly in response to N enrichment. Disentangling the turnover and nestedness of plant and microbial β‐diversity would have important implications for understanding plant–soil microbe interactions and seeking conservation strategies for maintaining regional diversity.