Measuring continuous compositional change using decline and decay in zeta diversity

Effects of livestock on arthropod biodiversity in Iberian holm oak savannas revealed by metabarcoding

Increasing food production while avoiding negative impacts on biodiversity constitutes one of the main challenges of our time. Traditional silvopastoral systems like Iberian oak savannas ("dehesas") set an example, where free-range livestock has been reared for centuries while preserving a high natural value. Nevertheless, factors decreasing productivity need to be addressed, one being acorn losses provoked by pest insects. An increased and focalized grazing by livestock on infested acorns would kill the larvae inside and decrease pest numbers, but increased livestock densities could have undesired side effects on ground arthropod communities as a whole. We designed an experimental setup including areas under trees with livestock exclosures of different ages (short-term: 1-year exclusion, long-term: 10-year exclusion), along with controls (continuous grazing), using DNA metabarcoding (mitochondrial markers COI and 16S) to rapidly assess arthropod communities' composition. Livestock removal quickly increased grass cover and arthropod taxonomic richness and diversity, which was already higher in short-term (1-year exclosures) than beneath the canopies of control trees. Interestingly, arthropod diversity was not highest at long-term exclosures (≥10 years), although their community composition was the most distinct. Also, regardless of treatment, we found that functional diversity strongly correlated with the vegetation structure, being higher at trees beneath which there was higher grass cover and taller herbs. Overall, the taxonomic diversity peak at short term exclosures would support the intermediate disturbance hypothesis, which relates it with the higher microhabitat heterogeneity at moderately disturbed areas. Thus, we propose a rotatory livestock management in dehesas: plots with increased grazing should co-exist with temporal short-term exclosures. Ideally, a few long-term excluded areas should be also kept for the singularity of their arthropod communities. This strategy would make possible the combination of biological pest control and arthropod conservation in Iberian dehesas.

Dissimilarity in flea and host assemblages and their interaction networks along a spatial distance gradient: different patterns revealed by different network dissimilarity metrics

We investigated the distance-decay pattern (an increase in dissimilarity with increasing geographic distance) in regional assemblages of fleas and their small mammalian hosts, as well as their interaction networks, in four biogeographic realms. Dissimilarity of assemblages (βtotal) was partitioned into species richness differences (βrich) and species replacement (βrepl) components. Dissimilarity of networks was assessed using two metrics: (a) whole network dissimilarity (βWN) partitioned into species replacement (βST) and interaction rewiring (βOS) components and (b) D statistics, measuring dissimilarity in the pure structure of the networks, without using information on species identities and calculated for hosts-shared-by-fleas networks (Dh) and fleas-shared-by-hosts networks (Df). We asked whether the distance-decay pattern (a) occurs among interactor assemblages or their interaction networks; (b) depends on the network dissimilarity metric used; and (c) differs between realms. The βtotal and βrepl of flea and host assemblages increased with distance in all realms except for host assemblages in the Afrotropics. βrich for flea and host assemblages increased with distance in the Nearctic only. In networks, βWN and βST demonstrated a distance-decay pattern, whereas βOS was mainly spatially invariant except in the Neotropics. Correlations of Dh or Df and geographic distance were mostly non-significant. We conclude that investigations of dissimilarity in interaction networks should include both types of dissimilarity metrics (those that consider partner identities and those that consider the pure structure of networks). This will allow elucidating the predictability of some facets of network dissimilarity and the unpredictability of other facets.

Investigating the relationship between microbial network features of giant kelp "seedbank" cultures and subsequent farm performance

Microbial inoculants can increase the yield of cultivated crops and are successful in independent trials; however, efficacy drops in large-scale applications due to insufficient consideration of microbial community dynamics. The structure of microbiomes, in addition to the impact of individual taxa, is an important factor to consider when designing growth-promoting inoculants. Here, we investigate the microbial network and community assembly patterns of Macrocystis pyrifera gametophyte germplasm cultures (collectively referred to as a "seedbank") used to cultivate an offshore farm in Santa Barbara, California, and identify network features associated with increased biomass of mature sporophytes. We found that [1] several network features, such as clustering coefficient and edge ratios, significantly vary with biomass outcomes; [2] gametophytes that become low- or high-biomass sporophytes have different hub taxa; and [3] microbial community assembly of gametophyte germplasm cultures is niche-driven. Overall, this study describes microbial community dynamics in M. pyrifera germplasm cultures and ultimately supports the development of early life stage inoculants that can be used on seaweed cultivars to increase biomass yield.

Core taxa underpin soil microbial community turnover during secondary succession

Understanding the processes that underpin the community assembly of bacteria is a key challenge in microbial ecology. We studied soil bacterial communities across a large-scale successional gradient of managed and abandoned grasslands paired with mature forest sites to disentangle drivers of community turnover and assembly. Diversity partitioning and phylogenetic null-modelling showed that bacterial communities in grasslands remain compositionally stable following abandonment and secondary succession but they differ markedly from fully afforested sites. Zeta diversity analyses revealed the persistence of core microbial taxa that both reflected and differed from whole-scale community turnover patterns. Differences in soil pH and C:N were the main drivers of community turnover between paired grassland and forest sites and the variability of pH within successional stages was a key factor related to the relative dominance of deterministic assembly processes. Our results indicate that grassland microbiomes could be compositionally resilient to abandonment and secondary succession and that the major changes in microbial communities between grasslands and forests occur fairly late in the succession when trees have established as the dominant vegetation. We also show that core taxa may show contrasting responses to management and abandonment in grasslands.

Tree communities and functional traits determine herbivore compositional turnover

There are many factors known to drive species turnover, although the mechanisms by which these operate are less clear. Based on comprehensive datasets from the largest tree diversity experiment worldwide (BEF-China), we used shared herbivore species (zeta diversity) and multi-site generalized dissimilarity modelling to investigate the patterns and determinants of species turnover of Lepidoptera herbivores among study plots across a gradient in tree species richness. We found that zeta diversity declined sharply with an increasing number of study plots, with complete changes in caterpillar species composition observed even at the fine spatial scale of our study. Plant community characteristics rather than abiotic factors were found to play key roles in driving caterpillar compositional turnover, although these effects varied with an increasing number of study plots considered, due to the varying contributions of rare and common species to compositional turnover. Our study reveals details of the impact of phylogeny- and trait-mediated processes of trees on herbivore compositional turnover, which has implications for forest management and conservation and shows potential avenues for maintenance of heterogeneity in herbivore communities.

Zooplankton community turnover in response to a novel TiO2-coated nano-formulation of carbendazim and its constituents

Novel nanomaterial-based pesticide formulations are increasingly perceived as promising aids in the transition to more efficient agricultural production systems. The current understanding of potential unintended (eco)toxicological impacts of nano-formulated pesticides is scarce, in particular with regard to (non-target) aquatic organisms and ecosystems. The present study reports the results of a long-term freshwater mesocosm experiment which assessed responses of individual zooplankton taxa and communities to a novel TiO2-coated nano-formulation of the fungicide carbendazim. Population- and community trends were assessed and compared in response to the nano-formulation and its constituents applied individually (i.e. nano-sized TiO2, carbendazim) and in combination (i.e. nano-sized TiO2 & carbendazim). Minimal differences were observed between effects induced by the nano-formulation and its active ingredient (i.e. carbendazim) when applied at equivalent nominal test concentrations (4 μg L-1). Nano-sized TiO2 was found to affect zooplankton community trends when applied separately at environmentally realistic concentrations (20 μg L-1 nominal test concentration). However, when nano-sized TiO2 was applied in combination with carbendazim, nano-sized TiO2 was found not to alter effects on community trends induced by carbendazim. The findings of the current study provide an extensive and timely addition to the current body of work available on non-target impacts of nano-formulated pesticides.

Uncovering the determinants of biodiversity hotspots in China: Evidence from the drivers of multiple diversity metrics on insect assemblages and implications for conservation

Understanding large-scale biodiversity patterns and underlying mechanisms during the formation process is essential for guiding conservation efforts. However, previous studies on the identification and formation mechanism of diversity hotspots in China were often limited to a single (alpha) diversity metric, while multiple (beta or zeta) diversity has rarely been used for exploring drivers and conservation actions. Here, a comprehensive species distribution dataset consisting of representative families of three insect orders was compiled to explore biodiversity hotspots based on different algorithms. Furthermore, to assess the effects of environmental factors on hotspots, we fitted generalized additive mixed-effects models (GAMMs) for species richness, generalized dissimilarity models (GDMs) and multi-site generalized dissimilarity modeling (MS-GDM) for the total beta and zeta diversity. Our results showed that biodiversity hotspots were mainly concentrated in central and southern China, especially in mountainous areas with complex topography, which indicated the insects' affinity to montane environments. Further analyses based on multiple models showed that water-energy factors exerted the strongest explanatory power for the insect assemblage diversity in hotspots of both alpha and beta (or zeta) levels. Additionally, anthropogenic factors also exerted a significant effect on hotspots, and this effect was higher for beta diversity than for alpha diversity. Overall, our study elucidates a comprehensive analysis of the identification and underlying mechanism of biodiversity hotspots in China. Despite several limitations, we still believe that our findings can provide some new insights for conservation efforts in Chinese hotspots.

Stronger Geographic Limitations Shape a Rapid Turnover and Potentially Highly Connected Network of Core Bacteria on Microplastics

Core microbiota is shared microbial taxa within the same habitat, which is important for understanding the stable and consistent components of the complex microbial assembly. However, information on the microplastic core bacteria from the river ecosystems is poor. Here, we investigated the composition and function of microplastic core bacteria from the Three Gorges Reservoir area along the approximate 662 km of the Yangtze River via full-length 16S rRNA gene sequencing, compared with those in water, sediment, and soil. The results showed that the spatial turnover of bacterial communities in four habitats supported deterministic processes dominated by niche differentiation, which shaped their core bacteria. The composition and function of microplastic core bacteria were significantly different from those in the other three habitats. Rhodobacteraceae was the main component of microplastic core bacteria, while the main component of core bacteria in water, sediment, and soil were Burkholderiaceae (21.90%), Burkholderiaceae (5.01%), Nitrosomonadaceae (4.61%), respectively. Furthermore, microplastic core bacteria had stronger geographic limitations along the Yangtze River in the Three Gorges Reservoir area. Stronger geographic limitations shaped the rapid community turnover and a potentially more connected network for the microplastic core bacteria than water, sediment, and soil. More importantly, microplastic core bacteria had strong potential functions of drug resistance and could cause risks to ecosystems and human health. Microplastic core bacteria were mainly influenced by sediment core bacteria, although the bacteria colonizing on microplastics could be from all the contact environments and original sources. These findings provide important insights into the composition, function, and association of microplastic core bacteria with their surrounding environment.

Zeta diversity patterns in metabarcoded lotic algal assemblages as a tool for bioassessment

Assessments of the ecological health of algal assemblages in streams typically focus on measures of their local diversity and classify individuals by morphotaxonomy. Such assemblages are often connected through various ecological processes, such as dispersal, and may be more accurately assessed as components of regional-, rather than local-scale assemblages. With recent declines in the costs of sequencing and computation, it has also become increasingly feasible to use metabarcoding to more accurately classify algal species and perform regional-scale bioassessments. Recently, zeta diversity has been explored as a novel method of constructing regional bioassessments for groups of streams. Here, we model the use of zeta diversity to investigate whether stream health can be determined by the landscape diversity of algal assemblages. We also compare the use of DNA metabarcoding and morphotaxonomy classifications in these zeta diversity-based bioassessments of regional stream health. From 96 stream samples in California, we used various orders of zeta diversity to construct models of biotic integrity for multiple assemblages of diatoms, as well as hybrid assemblages of diatoms in combination with soft-bodied algae, using taxonomy data generated with both DNA sequencing as well as traditional morphotaxonomic approaches. We compared our ability to evaluate the ecological health of streams with the performance of multiple algal indices of biological condition. Our zeta diversity-based models of regional biotic integrity were more strongly correlated with existing indices for algal assemblages classified using metabarcoding compared to morphotaxonomy. Metabarcoding for diatoms and hybrid algal assemblages involved rbcL and 18S V9 primers, respectively. Importantly, we also found that these algal assemblages, independent of the classification method, are more likely to be assembled under a process of niche differentiation rather than stochastically. Taken together, these results suggest the potential for zeta diversity patterns of algal assemblages classified using metabarcoding to inform stream bioassessments.

Two dominant forms of multisite similarity decline - Their origins and interpretation

The number of species shared by two or more sites is a fundamental measure of spatial variation in species composition. As more sites are included in the comparison of species composition, the average number of species shared across them declines, with a rate increasingly dependent on only the most widespread species. In over 80% of empirical communities, models of decline in shared species across multiple sites (multisite similarity decline) follow one of two distinct forms. An exponential form is assumed to reflect stochastic assembly and a power law form niche-based sorting, yet these explanations are largely untested, and little is known of how the two forms arise in nature. Using simulations, we first show that the distribution of the most widespread species largely differentiates the two forms, with the power law increasingly favored where such species occupy more than ~75% of sites. We reasoned the less cosmopolitan distribution of widespread species within exponential communities would manifest as differences in community biodiversity properties, specifically more aggregated within-species distributions, less even relative abundance distributions, and weaker between-species spatial associations. We tested and largely confirmed these relationships using 80 empirical datasets, suggesting that the form of multisite similarity decline offers a basis to predict how landscape-scale loss or gain of widespread species is reflected in different local-scale community structures. Such understanding could, for example, be used to predict changes in local-scale competitive interactions following shifts in widespread species' distributions. We propose multiple explanations for the origin of exponential decline, including high among-site abiotic variation, sampling of highly specialized (narrow niche width) taxa, and strong dispersal limitation. We recommend these are evaluated as alternative hypotheses to stochastic assembly.

Drivers of compositional turnover of narrow-ranged versus widespread naturalised woody plants in South Africa

Introduction

Alien trees and shrubs have become increasingly common invaders globally and have caused major negative impacts to ecosystems and society. Non-native woody plant species make up the majority of legislated invasive alien taxa in South Africa and contribute substantially to recorded negative impacts. It is of management interest to elucidate the macroecological processes that mediate the assembly of alien taxa, as this is expected to be associated with anthropogenic factors (e.g., human activity, introduction events, pathways of propagule dispersal mediated by humans) and bioclimatic factors (such as diurnal temperature range and precipitation gradients). These analyses require large species-occurrence datasets with comprehensive sampling across broad environmental conditions. Efforts of citizen scientists produce large numbers of occurrence records in a consistent manner which may be utilised for scientific investigations.

Methods

Research Grade occurrence data on naturalised plants of South Africa were extracted from the citizen scientist platform iNaturalist. Sampling bias was mitigated using statistical modelling of background points estimated from a Target Group of species which identifies well sampled communities. The drivers of assembly for alien plants at different range sizes were identified using multi-site generalised dissimilarity modelling (MS-GDM) of zeta diversity. The predicted compositional similarity between all cells was computed based on the subset of identified well sampled communities and using generalised dissimilarity modelling (GDM). From this, alien bioregions were identified using a k-means cluster analysis.

Results and Discussion

Bioclimatic factors significantly influenced community turnover in inland areas with large diurnal temperature ranges, and in areas with high precipitation. Communities separated by large geographical distances had significantly different compositions, indicating little contribution of long-range propagule movement by humans, and the presence of localised introduction hubs within the country which harbour unique species compositions. Analyses also showed a significant contribution of road density to turnover, which may be moderated by the habitat service provided by road verges. The same is true for natural dispersal via rivers in arid areas. The distribution of naturalised tree and shrub species is geographically clustered and forms six alien bioregions that are distinct from the South African biomes defined by native species distributionanalysis.

The species composition of local flea assemblages at a small scale in two South American regions is predominantly driven by niche-based mechanisms

We applied a step-down factor analysis (SDFA) and multi-site generalised dissimilarity modelling (MS-GDM) to local flea communities harboured by small mammals (i.e., collected at small sampling sites over a short time period) in two South American regions (Patagonia and the Northwestern Argentina) with the aim of understanding whether these communities were assembled via niche-based or dispersal-based processes. The SDFA allows us to determine whether clusters of flea assemblages across different types of climates, vegetation and soils can be distinguished (suggesting niche-based assembly). MS-GDM allows us to determine whether a substantial proportion of the variation in flea species turnover is explained by specific climate-associated, vegetation-associated and soil-associated variables (indicating niche-based assembly) or host turnover (indicating dispersal-based assembly). Mapping of assemblages on climate, vegetation and soil maps, according to their loadings on axis 1 or axis 2 of the SDFA, did not provide clear-cut results. Clusters of similar loadings could be recognized within some, but not other, climate, vegetation and soil types. However, MS-GDM demonstrated that the effect of environmental variables (especially air temperature) on flea compositional turnover was much stronger than that of host turnover, indicating the predominance of niche-based processes in local community assembly. A comparison of our results with those on the mechanisms that drive species assembly in regional communities allows us to conclude that local and regional communities result from the joint action of niche-based and dispersal-based processes, with the former more important at a smaller spatial scale and the latter at a larger spatial scale.

Spatial turnover of core and occasional bacterial taxa in the plastisphere from a plateau river, China

Plastic surfaces in the environment are a comparatively new niche for microbial colonization, also known as the "plastisphere". However, our understanding of the core and occasional bacterial taxa in the plastisphere is limited. Here, environmental plastic, water, and sediment samples were collected from 10 sites in a plateau river (Lhasa River, China) in September of 2019. The composition and spatial turnover of core and occasional bacterial taxa in the plastisphere were revealed via 16S rRNA gene sequencing and compared with water and sediment. The results indicated that deterministic processes dominated the habitat specialization that shaped the formation of core and occasional taxa in the plastisphere, water, and sediment of the Lhasa River because the decline in zeta diversity in the plastisphere, water, and sediment was more fitted to a power-law form rather than an exponential form. Proteobacteria (65.9%), Bacteroidetes (16.0%), and Cyanobacteria (11.7%) dominated the plastic core taxa. Core taxa rather than occasional taxa in the plastisphere had a lower (21.7%) proportion of OTUs and a higher (81.7%) proportion of average relative abundance than water and sediment, which were dominant in plastic bacterial communities. The spatial turnover of core and occasional bacterial taxa in the plastisphere was governed by abiotic as well as biotic factors. Specifically, the spatial turnover of core taxa in the plastisphere with high connectivity but low functional redundancy was easily affected by geographical distance, altitude, and heavy metals. Furthermore, strong drug resistance was found in the spatially persistent core taxa in the plastisphere. This study provides empirical support for the spatial turnover (species variation) and potential ecological mechanisms of bacterial communities in the plastisphere from river ecosystems.

Fungal Diversity in Two Wastewater Treatment Plants in North Italy

In urban wastewater treatment plants, bacteria lead the biological component of the depuration process, but the microbial community is also rich in fungi (mainly molds, yeasts and pseudo-yeasts), whose taxonomical diversity and relative frequency depend on several factors, e.g., quality of wastewater input, climate, seasonality, and depuration stage. By joining morphological and molecular identification, we investigated the fungal diversity in two different plants for the urban wastewater treatment in the suburbs of the two major cities in Lombardia, the core of industrial and commercial activities in Italy. This study presents a comparison of the fungal diversity across the depuration stages by applying the concepts of α-, β- and ζ-diversity. Eurotiales (mainly with Aspergillus and Penicillium), Trichosporonales (Trichosporon sensu lato), Saccharomycetales (mainly with Geotrichum) and Hypocreales (mainly with Fusarium and Trichoderma) are the most represented fungal orders and genera in all the stages and both the plants. The two plants show different trends in α-, β- and ζ-diversity, despite the fact that they all share a crash during the secondary sedimentation and turnover across the depuration stages. This study provides an insight on which taxa potentially contribute to each depuration stage and/or keep viable propagules in sludges after the collection from the external environment.

Host genetics, phenotype and geography structure the microbiome of a foundational seaweed

Interactions between hosts and their microbiota are vital to the functioning and resilience of macro-organisms. Critically, for hosts that play foundational roles in communities, understanding what drives host-microbiota interactions is essential for informing ecosystem restoration and conservation. We investigated the relative influence of host traits and the surrounding environment on microbial communities associated with the foundational seaweed Phyllospora comosa. We quantified 16 morphological and functional phenotypic traits, including host genetics (using 354 single nucleotide polymorphisms) and surface-associated microbial communities (using 16S rRNA gene amplicon sequencing) from 160 individuals sampled from eight sites spanning Phyllospora's entire latitudinal distribution (1,300 km). Combined, these factors explained 54% of the overall variation in Phyllospora's associated microbial community structure, much of which was related to the local environment (~32%). We found that putative "core" microbial taxa (i.e., present on all Phyllospora individuals sampled) exhibited slightly higher associations with host traits when compared to "variable" taxa (not present on all individuals). We identified several key genetic loci and phenotypic traits in Phyllospora that were strongly related to multiple microbial amplicon sequence variants, including taxa with known associations to seaweed defence, disease and tissue degradation. This information on how host-associated microbial communities vary with host traits and the environment enhances our current understanding of how "holobionts" (hosts plus their microbiota) are structured. Such understanding can be used to inform management strategies of these important and vulnerable habitats.

Impact of marine protected areas on temporal stability of fish species diversity

Preserving biodiversity over time is a pressing challenge for conservation science. A key goal of marine protected areas (MPAs) is to maintain stability in species composition, via reduced turnover, to support ecosystem function. Yet, this stability is rarely measured directly under different levels of protection. Rather, evaluations of MPA efficacy generally consist of static measures of abundance, species richness, and biomass, and rare measures of turnover are limited to short-term studies involving pairwise (beta diversity) comparisons. Zeta diversity is a recently developed metric of turnover that allows for measurement of compositional similarity across multiple assemblages and thus provides more comprehensive estimates of turnover. We evaluated the effectiveness of MPAs at preserving fish zeta diversity across a network of marine reserves over 10 years in Batemans Marine Park, Australia. Snorkel transect surveys were conducted across multiple replicated and spatially interspersed sites to record fish species occurrence through time. Protection provided by MPAs conferred greater stability in fish species turnover. Marine protected areas had significantly shallower decline in zeta diversity compared with partially protected and unprotected areas. The retention of harvested species was four to six times greater in MPAs compared with partially protected and unprotected areas, and the stabilizing effects of protection were observable within 4 years of park implementation. Conversely, partial protection offered little to no improvement in stability, compared with unprotected areas. These findings support the efficacy of MPAs for preserving temporal fish diversity stability. The implementation of MPAs helps stabilize fish diversity and may, therefore, support biodiversity resilience under ongoing environmental change.

Rare, common, alien and native species follow different rules in an understory plant community

Biological invasions are a leading threat to biodiversity globally. Increasingly, ecosystems experience multiple introductions, which can have significant effects on patterns of diversity. The way these communities assemble will depend partly on whether rare and common alien species respond to environmental predictors in the same manner as rare and common native species, but this is not well understood. To examine this question across four national parks in south-eastern Australia, we sampled the understory plant community of eucalypt-dominated dry forest subject to multiple plant introductions. The drivers of diversity and turnover in alien and native species of contrasting frequency of occurrence (low, intermediate, and high) were each tested individually. We found alien species diversity and turnover were both strongly associated with abiotic conditions (e.g., soil pH), while distance had little influence because of the greater extent of occurrence and more homogeneous composition of common aliens. In contrast, native species diversity was not associated with abiotic conditions and their turnover was as strongly influenced by distance as by abiotic conditions. In both alien and native species, however, the most important predictors of turnover changed with frequency of occurrence. Although local coexistence appears to be facilitated by life history trade-offs, species richness of aliens and natives was negatively correlated and native species might face greater competition in areas with more neutral soils (e.g., pH > ~5.5) where alien richness and relative frequency were both highest. We conclude that diversity and turnover in the generally more widespread alien species are mainly driven by species sorting along an environmental gradient associated with pH and nutrient availability, whereas turnover of native species is driven by more neutral processes associated with dispersal limitation. We show alien and native plant species respond to different environmental factors, as do rare and common species within each component.

Environmental drivers of sympatric mammalian species compositional turnover in giant panda nature reserves: Implications for conservation

The charismatic giant panda (Ailuropoda melanoleuca) is an iconic species of wildlife conservation worldwide. As the most effective measure to protect giant pandas and their habitats, China has established 67 giant panda nature reserves (GPNR) during the last five decades, which also bring benefits to many sympatric medium- and large-bodied mammals (MLM). To better inform the planning of the GPNR network with the view of preserving regional MLM diversity, we investigated the zeta diversity (a novel index to measure species compositional turnover considering the contributions of both rare and common species) patterns (i.e. zeta decline and retention rate curve) of MLMs across 40 GPNRs. The effects of species' body mass and conservation status on the zeta diversity patterns were tested. Further, we applied the multi-site generalized dissimilarity modelling (MS-GDM) framework to explore the impacts of environmental and geographic distances on MLM turnover. The results indicated that there are a core set of 17 MLM species sympatric with the giant panda in the GPNRs. Species' body mass can affect the patterns of zeta decline and retention rate curves, and the number of large-bodied species shared by multiple GPNRs is higher than that of medium-bodied species across zeta orders. The MS-GDM revealed the important roles of difference in habitat heterogeneity and spatial distance between GPNRs in driving MLM turnover. Consequently, we advocate maintaining and increasing the diversity of (natural) habitats in GPNRs to protect giant panda's sympatric MLM diversity. The government should consider optimizing the GPNR network (e.g. incorporating multiple small GPNRs into one single large reserve) to capture the most turnover of MLMs, and the newly-established Giant Panda National Park is relevant to fulfilling this long-term goal.

Climate-induced forest dieback drives compositional changes in insect communities that are more pronounced for rare species

Species richness, abundance and biomass of insects have recently undergone marked declines in Europe. We metabarcoded 211 Malaise-trap samples to investigate whether drought-induced forest dieback and subsequent salvage logging had an impact on ca. 3000 species of flying insects in silver fir Pyrenean forests. While forest dieback had no measurable impact on species richness, there were significant changes in community composition that were consistent with those observed during natural forest succession. Importantly, most observed changes were driven by rare species. Variation was explained primarily by canopy openness at the local scale, and the tree-related microhabitat diversity and deadwood amount at landscape scales. The levels of salvage logging in our study did not explain compositional changes. We conclude that forest dieback drives changes in species assemblages that mimic natural forest succession, and markedly increases the risk of catastrophic loss of rare species through homogenization of environmental conditions.

A multi-site method to capture turnover in rare to common interactions in bipartite species networks

Ecological network structure is maintained by a generalist core of common species. However, rare species contribute substantially to both the species and functional diversity of networks. Capturing changes in species composition and interactions, measured as turnover, is central to understanding the contribution of rare and common species and their interactions. Due to a large contribution of rare interactions, the pairwise metrics used to quantify interaction turnover are, however, sensitive to compositional change in the interactions of, often rare, peripheral specialists rather than common generalists in the network. Here we expand on pairwise interaction turnover using a multi-site metric that enables quantifying turnover in rare to common interactions (in terms of occurrence of interactions). The metric further separates this turnover into interaction turnover due to species turnover and interaction rewiring. We demonstrate the application and value of this method using a host-parasitoid system sampled along gradients of environmental modification. In the study system, both the type and amount of habitat needed to maintain interaction composition depended on the properties of the interactions considered, that is, from rare to common. The analyses further revealed the potential of host switching to prevent or delay species loss, and thereby buffer the system from perturbation. Multi-site interaction turnover provides a comprehensive measure of network change that can, for example, detect ecological thresholds to habitat loss for rare to common interactions. Accurate description of turnover in common, in addition to rare, species and their interactions is particularly relevant for understanding how network structure and function can be maintained.

Rarity facets of biodiversity: Integrating Zeta diversity and Dark diversity to understand the nature of commonness and rarity

Measuring commonness and rarity is pivotal to ecology and conservation. Zeta diversity, the average number of species shared by multiple sets of assemblages, and Dark diversity, the number of species that could occur in an assemblage but are missing, have been recently proposed to capture two aspects of the commonness-rarity spectrum. Despite a shared focus on commonness and rarity, thus far, Zeta and Dark diversities have been assessed separately. Here, we review these two frameworks and suggest their integration into a unified paradigm of the "rarity facets of biodiversity." This can be achieved by partitioning Alpha and Beta diversities into five components (the Zeta, Eta, Theta, Iota, and Kappa rarity facets) defined based on the commonness and rarity of species. Each facet is assessed in traditional and multiassemblage fashions to bridge conceptual differences between Dark diversity and Zeta diversity. We discuss applications of the rarity facets including comparing the taxonomic, functional, and phylogenetic diversity of rare and common species, or measuring species' prevalence in different facets as a metric of species rarity. The rarity facets integrate two emergent paradigms in biodiversity science to better understand the ecology of commonness and rarity, an important endeavor in a time of widespread changes in biodiversity across the Earth.

Understanding the metabolome and metagenome as extended phenotypes: The next frontier in macroalgae domestication and improvement

"Omics" techniques (including genomics, transcriptomics, metabolomics, proteomics, and metagenomics) have been employed with huge success in the improvement of agricultural crops. As marine aquaculture of macroalgae expands globally, biologists are working to domesticate species of macroalgae by applying these techniques tested in agriculture to wild macroalgae species. Metabolomics has revealed metabolites and pathways that influence agriculturally relevant traits in crops, allowing for informed crop crossing schemes and genomic improvement strategies that would be pivotal to inform selection on macroalgae for domestication. Advances in metagenomics have improved understanding of host-symbiont interactions and the potential for microbial organisms to improve crop outcomes. There is much room in the field of macroalgal biology for further research toward improvement of macroalgae cultivars in aquaculture using metabolomic and metagenomic analyses. To this end, this review discusses the application and necessary expansion of the omics tool kit for macroalgae domestication as we move to enhance seaweed farming worldwide.

The surface bacterial community of an Australian kelp shows cross-continental variation and relative stability within regions

Epiphytic microbial communities often have a close relationship with their eukaryotic host, assisting with defence, health, disease prevention and nutrient transfer. Shifts in the structure of microbial communities could therefore have negative effects on the individual host and indirectly impact the surrounding ecosystem, particularly for major habitat-forming hosts, such as kelps in temperate rocky shores. Thus, an understanding of the structure and dynamics of host-associated microbial communities is essential for monitoring and assessing ecosystem changes. Here, samples were taken from the ecologically important kelp, Ecklonia radiata, over a 17-month period, from six different sites in two distinct geographic regions (East and West coasts of Australia), separated by ∼3,300 kms, to understand variation in the kelp bacterial community and its potential environmental drivers. Differences were observed between kelp bacterial communities between the largely disconnected geographical regions. In contrast, within each region and over time the bacterial communities were considerably more stable, despite substantial seasonal changes in environmental conditions.

Measuring change in biological communities: multivariate analysis approaches for temporal datasets with low sample size

Effective and robust ways to describe, quantify, analyse, and test for change in the structure of biological communities over time are essential if ecological research is to contribute substantively towards understanding and managing responses to ongoing environmental changes. Structural changes reflect population dynamics, changes in biomass and relative abundances of taxa, and colonisation and extinction events observed in samples collected through time. Most previous studies of temporal changes in the multivariate datasets that characterise biological communities are based on short time series that are not amenable to data-hungry methods such as multivariate generalised linear models. Here, we present a roadmap for the analysis of temporal change in short-time-series, multivariate, ecological datasets. We discuss appropriate methods and important considerations for using them such as sample size, assumptions, and statistical power. We illustrate these methods with four case-studies analysed using the R data analysis environment.

Termite Assemblage and Damage on Tree Trunks in Fast-Growing Teak Plantations of Different Age: A Case Study in West Java, Indonesia

We conducted surveys of termite assemblages and tree trunks damaged by termites in teakwood (Tectona grandis L.f.) plantations. The surveys were conducted in five-, six-, and nine-year-old plantations. We used a standardized belt-transect to collect termites and build tree inventories. Data of collected termites at the genus and functional-group levels and termites' diversity between plantations were compared with their attack rate. The results showed that four genera of soil recycler termites belonging to groups IIf and III were present across the plantations. Distribution analysis suggested that termite communities might develop from a stochastic distribution to a nonrandom co-occurrence distribution over time. Diversity analysis showed an increased nestedness-resultant diversity contribution to the total dissimilarity over time. Observed attacks on tree trunks were superficial and limited to the outer bark, with group IIf as the main contributor. Furthermore, the level of damage done by termites to tree trunks was positively correlated with increases in the group IIf occupancy area and overgrown understory vegetation. Plantation management by maintaining an adequate understory might suppress termite attacks on fast-growing teakwood, although in the case of our study, termite attacks are inevitable when termites from group IIf were already present.

Trait positions for elevated invasiveness in adaptive ecological networks

Our ability to predict the outcome of invasion declines rapidly as non-native species progress through intertwined ecological barriers to establish and spread in recipient ecosystems. This is largely due to the lack of systemic knowledge on key processes at play as species establish self-sustaining populations within the invaded range. To address this knowledge gap, we present a mathematical model that captures the eco-evolutionary dynamics of native and non-native species interacting within an ecological network. The model is derived from continuous-trait evolutionary game theory (i.e., Adaptive Dynamics) and its associated concept of invasion fitness which depicts dynamic demographic performance that is both trait mediated and density dependent. Our approach allows us to explore how multiple resident and non-native species coevolve to reshape invasion performance, or more precisely invasiveness, over trait space. The model clarifies the role of specific traits in enabling non-native species to occupy realised opportunistic niches. It also elucidates the direction and speed of both ecological and evolutionary dynamics of residing species (natives or non-natives) in the recipient network under different levels of propagule pressure. The versatility of the model is demonstrated using four examples that correspond to the invasion of (i) a horizontal competitive community; (ii) a bipartite mutualistic network; (iii) a bipartite antagonistic network; and (iv) a multi-trophic food web. We identified a cohesive trait strategy that enables the success and establishment of non-native species to possess high invasiveness. Specifically, we find that a non-native species can achieve high levels of invasiveness by possessing traits that overlap with those of its facilitators (and mutualists), which enhances the benefits accrued from positive interactions, and by possessing traits outside the range of those of antagonists, which mitigates the costs accrued from negative interactions. This ‘central-to-reap, edge-to-elude’ trait strategy therefore describes the strategic trait positions of non-native species to invade an ecological network. This model provides a theoretical platform for exploring invasion strategies in complex adaptive ecological networks.

Multiple stressor effects on alpha, beta and zeta diversity of riverine fish

We examined the effects of regional scale land use and local scale environmental and biotic stressors on alpha, beta and zeta diversities of native fish communities in wadeable streams and non-wadeable rivers in the Danube basin, Hungary. Relationships among land use and local scale environmental and biotic stressors were weak both in streams and rivers, suggesting that these stressors act relatively independently. Alpha diversity decreased strongly with increasing local scale environmental stressor intensity in rivers. On the contrary, its response to stressors was more obscure in streams, where the best-fit statistical model indicated the importance of the interaction between land use, local scale environmental and biotic stressors, while the secondly ranked model highlighted the negative impact of local scale environmental stressors. Analysis of variance using distance matrices provided evidence that stressors alone and in interactions explained compositional differences of pairs of study sites (beta diversity). Considering the degree of overall degradation, both local (alpha) and among-site (beta and zeta) diversity indices responded to increasing stressor intensity, generally negatively. Riverine fish communities showed higher degrees of similarity (lower beta and higher zeta) than stream fish communities. They also showed increasing similarity (i.e. homogenization) with increasing overall stressor intensity, unlike stream fish communities, which showed no relationship with overall stressor intensity. Our results suggest that the relationships between land use and local scale environmental and biotic stressors can be complex and so do their effects on biodiversity. While stressor specific indices can provide information on the role of specific stressors in some cases, the examination of overall stressor effects is needed to assess realistically the effects of anthropogenic disturbances on native fish diversity. Diversity indices that quantify among-site changes in species composition, such as measures of beta and zeta diversity, can be fruitful for better understanding the role of multiple stressors in structuring ecological communities.

Compositional turnover in ecto- and endoparasite assemblages of an African bat, Miniopterus natalensis (Chiroptera, Miniopteridae): effects of hierarchical scale and host sex

We studied the compositional turnover in infracommunities and component communities of ecto- and endoparasites infesting a bat, Miniopterus natalensis (Chiroptera, Miniopteridae), across seven sampling sites using the zeta diversity metric (measuring similarity between multiple communities) and calculating zeta decline and retention rate (both scales) and zeta decay (component communities). We asked whether the patterns of zeta diversity differ between (a) infracommunities and component communities; (b) ecto- and endoparasites and (c) subsets of communities infecting male and female bats. The pattern of compositional turnover differed between infracommunities and component communities in endoparasites only. The shape of zeta decline for infracommunities indicated that there were approximately equal probabilities of ecto- and endoparasitic species to occur on/in any bat individual within a site. The shape of zeta decline for component communities suggested the stochasticity of ectoparasite turnover, whereas the turnover of endoparasites was driven by niche-based processes. Compositional turnover in component communities of ectoparasites was more spatially dependent than that of endoparasites. Spatial independence of compositional turnover in endoparasites was due to subcommunities harboured by female bats. We conclude that the patterns of compositional turnover in infracommunities were similar in ecto- and endoparasites, whereas the patterns of turnover in component communities differed between these groups.

Soil Bacterial Communities Exhibit Strong Biogeographic Patterns at Fine Taxonomic Resolution

Bacteria have been inferred to exhibit relatively weak biogeographic patterns. To what extent such findings reflect true biological phenomena or methodological artifacts remains unclear. Here, we addressed this question by analyzing the turnover of soil bacterial communities from three data sets. We applied three methodological innovations: (i) design of a hierarchical sampling scheme to disentangle environmental from spatial factors driving turnover; (ii) resolution of 16S rRNA gene amplicon sequence variants to enable higher-resolution community profiling; and (iii) application of the new metric zeta diversity to analyze multisite turnover and drivers. At fine taxonomic resolution, rapid compositional turnover was observed across multiple spatial scales. Turnover was overwhelmingly driven by deterministic processes and influenced by the rare biosphere. The communities also exhibited strong distance decay patterns and taxon-area relationships, with z values within the interquartile range reported for macroorganisms. These biogeographical patterns were weakened upon applying two standard approaches to process community sequencing data: clustering sequences at 97% identity threshold and/or filtering the rare biosphere (sequences lower than 0.05% relative abundance). Comparable findings were made across local, regional, and global data sets and when using shotgun metagenomic markers. Altogether, these findings suggest that bacteria exhibit strong biogeographic patterns, but these signals can be obscured by methodological limitations. We advocate various innovations, including using zeta diversity, to advance the study of microbial biogeography.IMPORTANCE It is commonly thought that bacterial distributions show lower spatial variation than for multicellular organisms. In this article, we present evidence that these inferences are artifacts caused by methodological limitations. Through leveraging innovations in sampling design, sequence processing, and diversity analysis, we provide multifaceted evidence that bacterial communities in fact exhibit strong distribution patterns. This is driven by selection due to factors such as local soil characteristics. Altogether, these findings suggest that the processes underpinning diversity patterns are more unified across all domains of life than previously thought, which has broad implications for the understanding and management of soil biodiversity.

Spatial and temporal turnover of parasite species and parasite-host interactions: a case study with fleas and gamasid mites parasitic on small mammals

We studied patterns of ectoparasite species turnover and pairwise ectoparasite-host interactions across space and time in fleas and mites harboured by small mammals using a novel metric, zeta diversity (similarity between multiple communities). We asked whether the zeta diversity of parasites and their interactions with hosts follow a similar spatial or temporal trend. We found substantial differences in some (zeta decline and retention rate) but not in other (zeta decay) spatial patterns of zeta diversity between species and interactions, whereas the differences between the patterns of the temporal species versus interaction zeta diversity occurred to a much lesser extent. In particular, the parametric form of zeta decline suggested that the distribution of ectoparasite species across localities is driven mainly by niche-based processes, whereas the spatial distribution of flea-host and mite-host interactions is predominantly stochastic. We also found much stronger variation in the number of shared species and interactions over space than over time. Parasite community composition, in terms of species, appeared to be much more temporally stable than that in terms of parasite-host interactions. The parametric form of temporal zeta decline indicated that both parasite communities and parasite-host networks are assembled over time via niche-based processes.

Patterns of zeta diversity in ectoparasite communities harboured by small mammals at three hierarchical scales: taxon-invariance and scale-dependence

We studied compositional turnover in communities of fleas and mites harboured by small mammals using zeta diversity metric (similarity between multiple communities) and asked whether the patterns of zeta diversity decline with an increase in the number of communities differ between taxa and hierarchical scales [infracommunities (parasite assemblages on individual hosts), component communities (parasite assemblages harboured by host populations), and compound communities (all parasite species in a locality)]. The average number of shared species declined with an increasing number of communities (zeta order). It attained zero at higher orders in infracommunities of both taxa with the shape of the zeta decline being best fitted by the negative exponential function, and the retention rate curves being modal. In contrast, zeta diversity values for compound communities of mites and fleas did not attain zero at higher zeta orders, and the form of the zeta decline was best fitted by the power-law function, whereas the retention rate curves were asymptotic. In component communities, the form of zeta decline was best fitted by either exponential or power-law function in dependence of whether communities were considered within a host across localities or across hosts within a locality and whether ubiquitous species were taken into account. Our main conclusions are that (a) the rules governing compositional turnover in parasite communities for the lowest and the highest hierarchical scales are taxon-invariant but scale-dependent and (b) species composition of infracommunities is mainly driven by stochastic assembly processed, whereas that of compound communities is mainly driven by niche-based processes.

Drivers of compositional turnover are related to species' commonness in flea assemblages from four biogeographic realms: zeta diversity and multi-site generalised dissimilarity modelling

We investigated drivers of species turnover in fleas parasitic on small mammals in four biogeographic realms using novel methodology (zeta diversity, and Multi-Site Generalised Dissimilarity Modelling). We asked whether (i) flea turnover was better explained by host turnover or environmental variables; (ii) different factors drive the turnover of rare and widespread fleas; (iii) the factors affecting the turnover of rare or widespread fleas differ between realms; and (iv) environmental variables drive flea turnover directly or via their effects on hosts. Dissimilarity in host species composition was the most important factor affecting flea turnover in all realms. In the Afrotropics, the Nearctic, and the Neotropics, this was true mainly for rare species, whereas the zeta diversity of the Palearctic hosts exerted a strong effect on the turnover of both rare and widespread fleas. Dissimilarity in temperature contributed the most to the turnover of rare fleas in the Neotropics and the Palearctic, whereas the turnover of widespread species in these realms was strongly affected by dissimilarity in precipitation. In the Nearctic, dissimilarity in precipitation or temperature mostly affected the turnover of rare fleas or common species, respectively. In the Afrotropics, dissimilarity in the Normalised Difference Vegetation Index and temperature affected the turnover of all species, independently of their level of commonness, while dissimilarity in rainfall was important for the turnover of rare fleas. The responses of flea assemblages to environmental factors represented a combination of direct responses and responses mediated via effects on host turnover. We conclude that host turnover is a more important factor than environmental dissimilarity in its effect on flea species turnover. However, the relative effects of host composition and environment, as well as those of temperature, precipitation and the amount of vegetation, on flea turnover differ (i) between realms and (ii) between rare and common fleas.

Patterns and drivers of species richness and turnover of neo-endemic and palaeo-endemic vascular plants in a Mediterranean hotspot: the case of Crete, Greece

Background

Exploring species richness and turnover patterns and their drivers can provide new insights into underlying mechanisms shaping community assembly, with significant implications for biodiversity conservation. Here, we explored diversity patterns of non-endemic, neo-endemic and palaeo-endemic vascular plants in Crete, Greece, a Mediterranean hotspot of plant richness and endemism. We evaluated the relationship between α-diversity and environmental (bioclimatic variables, topography), and anthropogenic variables by Generalized Additive Models, after accounting for spatial autocorrelation. Then, we quantified turnover using the novel concept of zeta diversity (the number of shared species by multiple sites), a framework which allows to explore the full spectrum of compositional turnover, the contribution of rare and widespread species to observed patterns and the underlying processes shaping them. Finally, we explored the abiotic and biotic effects, i.e. how well one category of species (non-endemics, palaeo-endemics, neo-endemics) predicts the patterns of the other categories, on zeta diversity by multi-site Generalized Dissimilarity Modelling.

Results

We found a strong correlation between neo-endemic and palaeo-endemic α-diversity, with climate, topography, and human impact driving species richness. Zeta diversity analysis revealed a sharper decrease of shared palaeo-endemic species, followed by neo-endemics, and then by non-endemics with the number of sites considered to estimate compositional turnover. Perhaps, the narrow distributions of palaeo-endemics as relict species and often habitat specialists, thus persisting locally, and of neo-endemics that may have not reached yet their potential geographical range, resulted in the observed zeta diversity decline pattern. Deterministic processes controlled species turnover of rare non-endemic and neo-endemic species, while deterministic and stochastic processes contributed similarly to palaeo-endemic turnover. However, stochasticity dominates in the case of widespread species in all occasions. The environmental and anthropogenic variables were poor predictors of compositional turnover, especially of widespread species. However, the non-endemic species composition was correlated to rare palaeo-endemics and neo-endemics, highlighting the importance of biotic effects in driving turnover patterns.

Conclusions

It seems that centers of neo-endemism of vascular plants coincide with centers of palaeo-endemism in Crete, but species richness and species turnover are shaped by different drivers.