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Integrative population genetics and metagenomics reveals urbanization increases pathogen loads and decreases connectivity in a wild bee
Abstract
As urbanization continues to increase, it is expected that two-thirds of the human population will reside in cities by 2050. Urbanization fragments and degrades natural landscapes, threatening wildlife including economically important species such as bees. In this study, we employ whole genome sequencing to characterize the population genetics, metagenome and microbiome, and environmental stressors of a common wild bee, Ceratina calcarata. Population genomic analyses revealed the presence of low genetic diversity and elevated levels of inbreeding. Through analyses of isolation by distance, resistance, and environment across urban landscapes, we found that green spaces including shrubs and scrub were the most optimal pathways for bee dispersal, and conservation efforts should focus on preserving these land traits to maintain high connectivity across sites for wild bees. Metagenomic analyses revealed landscape sites exhibiting urban heat island effects, such as high temperatures and development but low precipitation and green space, had the highest taxa alpha diversity across all domains even when isolating for potential pathogens. Notably, the integration of population and metagenomic data showed that reduced connectivity in urban areas is not only correlated with lower relatedness among individuals but is also associated with increased pathogen diversity, exposing vulnerable urban bees to more pathogens. Overall, our combined population and metagenomic approach found significant environmental variation in bee microbiomes and nutritional resources even in the absence of genetic differentiation, as well as enabled the potential early detection of stressors to bee health.
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Bees and their microbes interact in complex networks in which bees form symbiotic relationships with their bacteria and fungi. Microbial composition and abundance affect bee health through nutrition, immunity, and fitness. In ever-expanding urban landscapes, land use development changes bee habitats and floral resource availability, thus altering the sources of microbes that wild bees need to establish their microbiome. Here, we implement metabarcoding of the bacterial 16S and fungal ITS regions to characterize the diversity and composition of the microbiome in 58 small carpenter bees, Ceratina calcarata, across urban land use gradients (study area 6,425 km2). By categorizing land use development, green space, precipitation, and temperature variables as indicators of habitat across the city, we found that land use variables can predict microbial diversity. Microbial composition was also found to vary across urban land use gradients, with certain microbes such as Acinetobacter and Apilactobacillus overrepresented in less urban locations and Penicillium more abundant in developed areas. Environmental features may also lead to differences in microbe interactions, as co-occurrences between bacteria and fungi varied across percent land use development, exemplified by the correlation between Methylobacterium and Sphingomonas being more prevalent in areas of higher urban development. Surrounding landscapes change the microbial landscape in wild bees and alter the relationships they have with their microbiome. As such, urban centres should consider the impact of growing cities on their pollinators’ health and protect wild bees from the effects of anthropogenic activities.
The importance of the holobiont has been studied across many bee species, but less is known about the changes in the microbiome throughout the course of development, particularly in subsocial bees. This study used 16S rRNA and ITS amplicon sequencing of pollen provisions and individuals of the small carpenter bee, Ceratina calcarata, across stages of development to characterize the composition and diversity of bacteria and fungi in the microbiome. Pollen provisions and larval stages showed similar beta diversity, but differences in taxa composition. There was no significant decrease in diversity during the transition between larval and pupal stages that was expected post defecation. However, there were unexpected and progressive declines in diversity as development progressed from the early to late pupal stages and again from the callow to adult stages. Bees across all stages lacked members of the Lactobacillus (now Apilactobacillus) genus, which has been shown in other studies to be part of the core bacterial community in C. calcarata and all bees. Three correlations between bacteria and fungi were found, suggesting common beneficial bacteria may protect the bees from prevalent fungal pathogens. Low alpha diversity, particularly in the later stages of development through adulthood, is concerning as the microbiome plays an important role in maintaining wild bee health. Developmental stages of the small carpenter bee Ceratina calcarata. Eggs are provisioned on a pollen ball and larvae consume pollen until pupation. Pupae develop into callow adults and this study tracks the developmental microbiome of this bee.
Environmental heterogeneity resulting from human-modified landscapes can increase intraspecific trait variation. However, less known is whether such phenotypic variation is driven by plastic or adaptive responses to local environments. Here, we study five bumble bee (Apidae: Bombus) species across an urban gradient in the greater Saint Louis, Missouri region in the North American Midwest and ask: (1) Can urban environments induce intraspecific spatial structuring of body size, an ecologically consequential functional trait? And, if so, (2) is this body size structure the result of plasticity or adaptation? We additionally estimate genetic diversity, inbreeding, and colony density of these species - three factors that affect extinction risk. Using ≥ 10 polymorphic microsatellite loci per species and measurements of body size, we find that two of these species (Bombus impatiens, Bombus pensylvanicus) exhibit body size clines across the urban gradient, despite a lack of population genetic structure. We also reaffirm reports of low genetic diversity in B. pensylvanicus and find evidence that Bombus griseocollis, a species thought to be thriving in North America, is inbred in the greater Saint Louis region. Collectively, our results have implications for conservation in urban environments and suggest that plasticity can cause phenotypic clines across human-modified landscapes.
Including probiotics in honeybee nutrition represents a promising solution for mitigating diseases, and recent evidence suggests that various microbes possess mechanisms that can bioremediate
environmental pollutants. Thus, the use of probiotics capable of degrading pesticides used in modern agriculture would help to both reduce colony losses due to the exposure of foragers to these toxic molecules and improve honeybee health and wellbeing globally. We conducted in vitro experiments to isolate and identify probiotic candidates from bacterial isolates of the honeybee gut (i.e., endogenous strains) according to their ability to (i) grow in contact with three sublethal concentrations of the pesticide clothianidin (0.15, 1 and 10 ppb) and (ii) degrade clothianidin at 0.15 ppb. The isolated bacterial strains were indeed able to grow in contact with the three sublethal
concentrations of clothianidin. Bacterial growth rate differed significantly depending on the probiotic candidate and the clothianidin concentration used. Clothianidin was degraded by seven endogenous honeybee gut bacteria, namely Edwardsiella sp., two Serratia sp., Rahnella sp., Pantoea sp., Hafnia sp. and Enterobacter sp., measured within 72 h under in vitro conditions. Our findings highlight that endogenous bacterial strains may constitute the base material from which to develop a promising probiotic strategy to mitigate the toxic effects of clothianidin exposure on honeybee colony health.
Honeybees are essential pollinators supporting global agricultural economies and food supplies. Recent honeybee decline has been linked to several factors, while pathogen infection is considered one of the most significant contributing factors.
The potential of the gut microbiome as a driver of individual cognitive differences in natural populations of animals remains unexplored. Here, using metagenomic sequencing of individual bumblebee hindguts, we find a positive correlation between the abundance of Lactobacillus Firm-5 cluster and memory retention on a visual discrimination task. Supplementation with the Firm-5 species Lactobacillus apis , but not other non-Firm-5 bacterial species, enhances bees’ memory. Untargeted metabolomics after L. apis supplementation show increased LPA (14:0) glycerophospholipid in the haemolymph. Oral administration of the LPA increases long-term memory significantly. Based on our findings and metagenomic/metabolomic analyses, we propose a molecular pathway for this gut-brain interaction. Our results provide insights into proximate and ultimate causes of cognitive differences in natural bumblebee populations.
Aim: Understanding how the landscape influences gene flow is important in explaining biodiversity, especially when co-distributed taxa across heterogeneous landscapes exhibit species-specific habitat associations. Here, we test predictions about the effects of forest-type on population connectivity in two sympatric species of spiny rats that differ in their forest associations. Specifically, we evaluate the hypothesis that seasonal floodplain forests (várzea) provide linear connectivity, facilitating gene flow among individuals , while non-flooded forests (terra-firme) may diminish the functional connectivity.
Location: Western Amazon, South America. Taxon: Proechimys simonsi (non-flooded forests, terra-firme) and Proechimys steerei (seasonal floodplain forests, várzea).
Methods: We analyse about 13,000 single nucleotide polymorphisms along with characterizations of landscape heterogeneity for two forest types to test for differences in the functional connectivity. Influence of the landscape and environmental variables are quantified using maximum-likelihood population effect models to identify the relative importance of variables in explaining the gene flow.
Results: There are significant differences in functional connectivity between species. However, the genomic data does not support the conventional hypotheses of higher con-nectivity for inhabitants of várzea than those of terra-firme. Stronger genetic structure in P. steerei than P. simonsi based on isolation by distance models suggests reduced gene flow in species associated with várzea forests. Isolation by resistance reinforces that wetland habitats inhibit and promote the functional connectivity in P. simonsi and P. steerei, respectively, although large distances along the rivers can prevent gene flow in P. steerei.
Main conclusion: Interpreting differences between connectivity in taxa apparent from genetic analyses through the lens of a single dimension of Amazonian heterogeneity-that is, forest type-may be an oversimplification. Our statistical modelling and fit of the data to different models points to specific environmental and habitat differences between the ecological divergent spiny rat species that may contribute to differences in the genetic structure of these sympatric taxa.
KEYWORDS: isolation by resistance, landscape genetics, MLPE mixed models, phylogeography, RADseq, terra-firme, várzea
Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows for: (i) de novo gene prediction from raw contigs, (ii) built-in pairwise orthology prediction, (iii) fast protein domain discovery, and (iv) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de.
Insect-pollinated legumes are rich in plant-based proteins making them a vital constituent of sustainable healthy diets for people and livestock. Furthermore, they deliver or support a range of ecosystem services that underpin agricultural production and their prevalence in agricultural landscapes is likely to increase. Under typical implementation and management, the value of legumes to pollinators has, however, been questioned. Through exploring a range of legume crops, grown as monocultures and mixtures, this study aims to identify multifunctional legume cropping systems that optimise forage availability for a diversity of wild pollinators whilst delivering a wide range of agronomic and environmental benefits. This study innovatively explores legume mixtures concurrently with monocultures of the component species using replicated small-plot field trials established in two geographical locations. Observational plots assessed the richness and abundance of floral resources, and wild pollinators (i.e. bumblebees and hoverflies) throughout the peak flowering period. Densely flowering, highly profitable legumes (e.g. Trifolium incarnatum and Trifolium mixes) supported abundant and rich pollinator assemblages. The functional makeup of floral visitors was strongly influenced by flower structure and hoverflies, with their shorter proboscises, were largely constrained to legumes with shallower corolla and open weed species. Floral richness was not a key driver of pollinator assemblages; however, clear intra-specific differences were observed in flowering phenology. Combining functionally distinct legumes with respect to flower structure and phenology, will support a wider suite of pollinating insects and help stabilise the temporal availability of forage. For highly competitive legumes (e.g. Vicia faba and Vicia sativa), planting in discrete patches is recommended to reduce the risk of less competitive species failing in mixtures. Legumes can provide valuable forage for pollinators; however, they fail to meet all resource requirements. They should therefore be used in combination with agri-environmental measures targeted to promote early-season forage (e.g. hedgerows and farm woodlands), open flowers for hoverflies, saprophytic hoverfly larval resources (e.g. ditches and ponds) and nesting habitats (e.g. undisturbed field margins).
In light of bee declines, the importance of pollination services from managed and native bees to our agriculture and economy is of great political, scientific and public interest. Viruses, first observed in honeybees, have been documented in bumblebees and the prevalence and load of some RNA viruses have been associated with managed honeybees. Shared flowers may be the bridge across which viruses pass between bees but no study has yet demonstrated that bumblebees can pick up viruses while foraging on contaminated flowers.
Here, through a series of mechanistic laboratory experiments and mathematical modelling, we ask whether viruses can be transmitted between bee genera on shared flowers and how transmission can be effectively mitigated.
We demonstrated that deformed wing virus (DWV) can be transmitted from infected honeybees to bumblebees through the use of shared red clover. We were also able to show that the route may work in reverse and bumblebees could contribute to the spread as well.
Our model showed that reducing vector‐mediated transmission in honeybee colonies could potentially lead to a far greater reduction in bumblebee infection than simply reducing the number of honeybees. Additionally, we identified a dilution effect, whereby increasing floral abundance reduced transmission.
Synthesis and applications . In this study, we showed that DWV may be spread between bee genera through the shared use of flowers. Through mathematical simulation, we identified two practical management options for reducing spread. The combination of treating honeybees effectively for the Varroa mite, a known vector of DWV, and increasing floral abundance where honeybees and native pollinators share the landscape were shown to reduce the spread of DWV within bee communities in simulations.
Regression analysis makes up a large part of supervised machine learning, and consists of the prediction of a continuous independent target from a set of other predictor variables. The difference between binary classification and regression is in the target range: in binary classification, the target can have only two values (usually encoded as 0 and 1), while in regression the target can have multiple values. Even if regression analysis has been employed in a huge number of machine learning studies, no consensus has been reached on a single, unified, standard metric to assess the results of the regression itself. Many studies employ the mean square error (MSE) and its rooted variant (RMSE), or the mean absolute error (MAE) and its percentage variant (MAPE). Although useful, these rates share a common drawback: since their values can range between zero and +infinity, a single value of them does not say much about the performance of the regression with respect to the distribution of the ground truth elements. In this study, we focus on two rates that actually generate a high score only if the majority of the elements of a ground truth group has been correctly predicted: the coefficient of determination (also known as R -squared or R ² ) and the symmetric mean absolute percentage error (SMAPE). After showing their mathematical properties, we report a comparison between R ² and SMAPE in several use cases and in two real medical scenarios. Our results demonstrate that the coefficient of determination ( R -squared) is more informative and truthful than SMAPE, and does not have the interpretability limitations of MSE, RMSE, MAE and MAPE. We therefore suggest the usage of R -squared as standard metric to evaluate regression analyses in any scientific domain.
An hour precipitation dataset of 42 automatic weather stations is developed and applied to analyze the temporal and spatial characteristics of light precipitation in urban areas of Beijing City during 2007–2017. The stations are classified into three groups, including 18 sites in central urban area (4th Ring-Road, RR), 10 sites in peri-urban area (4th–5th RR), and 14 sites in suburban area (5th–6th RR). Light precipitation is defined as hourly rainfall of 0.1–0.3 mm. Analysis shows that light precipitation occurred in urban area the whole day, with the peak value in 0600 LST and minimum value in 1600 LST; monthly variation of light precipitation frequency (LPF) was characterized by the highest value in summer and the lowest value in winter; remarkable differences are found for the various urbanized areas, with the annual and seasonal mean LPF being generally small in central urban area and gradually increasing toward suburban area; the hourly mean LPFs during morning and nighttime are higher in summer than those in other seasons in each of the urban areas; relative humidity, aerosol, and wind speed might have been the major influential factors for the observed temporal and spatial pattern of light precipitation.
Multiple global change pressures, and their interplay, cause plant-pollinator extinctions and modify species assemblages and interactions. This may alter the risks of pathogen host shifts, intra- or interspecific pathogen spread, and emergence of novel population or community epidemics. Flowers are hubs for pathogen transmission. Consequently, the structure of plant-pollinator interaction networks may be pivotal in pathogen host shifts and modulating disease dynamics. Traits of plants, pollinators, and pathogens may also govern the interspecific spread of pathogens. Pathogen spillover-spillback between managed and wild pollinators risks driving the evolution of virulence and community epidemics. Understanding this interplay between host-pathogen dynamics and global change will be crucial to predicting impacts on pollinators and pollination underpinning ecosystems and human wellbeing.
Background
Microbiomes play vital roles in plant health and performance, and the development of plant beneficial microbiomes can be steered by organic fertilizer inputs. Especially well-studied are fertilizer-induced changes on bacteria and fungi and how changes in these groups alter plant performance. However, impacts on protist communities, including their trophic interactions within the microbiome and consequences on plant performance remain largely unknown. Here, we tracked the entire microbiome, including bacteria, fungi, and protists, over six growing seasons of cucumber under different fertilization regimes (conventional, organic, and Trichoderma bio-organic fertilization) and linked microbial data to plant yield to identify plant growth-promoting microbes.
Results
Yields were higher in the (bio-)organic fertilization treatments. Soil abiotic conditions were altered by the fertilization regime, with the prominent effects coming from the (bio-)organic fertilization treatments. Those treatments also led to the pronounced shifts in protistan communities, especially microbivorous cercozoan protists. We found positive correlations of these protists with plant yield and the density of potentially plant-beneficial microorganisms. We further explored the mechanistic ramifications of these relationships via greenhouse experiments, showing that cercozoan protists can positively impact plant growth, potentially via interactions with plant-beneficial microorganisms including Trichoderma, the biological agent delivered by the bio-fertilizer.
Conclusions
We show that protists may play central roles in stimulating plant performance through microbiome interactions. Future agricultural practices might aim to specifically enhance plant beneficial protists or apply those protists as novel, sustainable biofertilizers.
The conservation field is experiencing a rapid increase in the amount, variety, and quality of spatial data that can help us understand species movement and landscape connectivity patterns. As interest grows in more dynamic representations of movement potential, modelers are often limited by the capacity of their analytic tools to handle these datasets. Technology developments in software and high-performance computing are rapidly emerging in many fields, but uptake within conservation may lag, as our tools or our choice of computing language can constrain our ability to keep pace. We recently updated Circuitscape, a widely used connectivity analysis tool developed by Brad McRae and Viral Shah, by implementing it in Julia, a high-performance computing language. In this initial re-code (Circuitscape 5.0) and later updates, we improved computational efficiency and parallelism, achieving major speed improvements, and enabling assessments across larger extents or with higher resolution data. Here, we reflect on the benefits to conservation of strengthening collaborations with computer scientists, and extract examples from a collection of 572 Circuitscape applications to illustrate how through a decade of repeated investment in the software, applications have been many, varied, and increasingly dynamic. Beyond empowering continued innovations in dynamic connectivity, we expect that faster run times will play an important role in facilitating co-production of connectivity assessments with stakeholders, increasing the likelihood that connectivity science will be incorporated in land use decisions.
Key insights on needs in urban regional governance - Global urbanization (the increasing concentration in urban settlements of the increasing world population), is a driver and accelerator of shifts in diversity, new cross-scale interactions, decoupling from ecological processes, increasing risk and exposure to shocks. Responding to the challenges of urbanization demands fresh commitments to a city–regional perspective in ways that are explictly embedded in the Anthopocene bio- techno- and noospheres, to extend existing understanding of the city–nature nexus and regional scale. Three key dimensions of cities that constrain or enable constructive, cross scale responses to disturbances and extreme events include 1) shifting diversity, 2) shifting connectivity and modularity, and 3) shifting complexity. These three dimensions are characteristic of current urban processes and offer potential intervention points for local to global action.
Increasing evidence suggests the microbiome plays an important role in bee ecology and health. However, the relationship between bees and their bacterial symbionts has only been explored in a handful of species. We characterized the microbiome across the life cycle of solitary, ground-nesting alkali bees ( Nomia melanderi ). We find that feeding status is a major determinant of microbiome composition. The microbiome of feeding larvae was similar to that of pollen provisions, but the microbiome of post-feeding larvae (pre-pupae) was similar to that of the brood cell walls and newly-emerged females. Feeding larvae and pollen provisions had the lowest beta diversity, suggesting the composition of larval diet is highly uniform. Comparisons between lab-reared, newly-emerged, and nesting adult females suggest that the hindgut bacterial community is largely shaped by the external environment. However, we also identified taxa that are likely acquired in the nest or which increase or decrease in relative abundance with age. Although Lactobacillus micheneri was highly prevalent in pollen provisions, it was only detected in one lab-reared female, suggesting it is primarily acquired from environmental sources. These results provide the foundation for future research on metagenomic function and development of probiotics for these native pollinators.
Urbanization is a major anthropogenic driver of decline for ecologically and economically important taxa including bees. Despite their generally negative impact on pollinators, cities can display a surprising degree of biodiversity compared to other landscapes. The pollinating communities found within these environments, however, tend to be filtered by interacting local and landscape features that comprise the urban matrix. Landscape and local features exert variable influence on pollinators within and across taxa, which ultimately affects community composition in such a way that contributes to functional trait homogenization and reduced phylogenetic diversity. Although previous results are not easily generalizable, bees and pollinators displaying functional trait characteristics such as polylectic diet, cavity-nesting behavior, and later emergence appear most abundant across different examined cities. To preserve particularly vulnerable species, most notably specialists that have become underrepresented within city communities, green spaces like parks and urban gardens have been examined as potential refuges. Such spaces are scattered across the urban matrix and vary in pollinator resource availability. Therefore, ensuring such spaces are optimized for pollinators is imperative. This review examines how urban features affect pollinators in addition to ways these green spaces can be manipulated to promote greater pollinator abundance and diversity.
Knowledge about the impacts of urban heat islands (UHI) and associated thermal gradients on vegetation seasonality (i.e. phenology) is vital for understanding spatial patterns in vegetation ecosystem functions. However, in contrast to temperate cites, there is little evidence to show how UHI influences landscape phenological processes in the tropics. In this study, we examined vegetation phenological responses to urban form, distance from the city centre and surface temperatures, in the tropical city of Kampala, Uganda. Estimates of vegetation growing season length and land surface temperature were derived from MODIS satellite imagery for multiple years (2013–2015) and urban form was characterised using the Local Climate Zone (LCZ) classification. We showed that growing season length increased along the urban–rural gradient (p < 0.001) and was longest in the least built-up LCZ class (p < 0.001). Growing season length was significantly reduced as land surface temperature increased (p < 0.001). These findings contrast with results reported for temperate cities, where higher temperatures are often associated with longer vegetation growing seasons. Our findings suggest that enhanced surface temperatures associated with UHI are a limiting factor to season length in the urban tropics. Urban planners in tropical cities should therefore account for vegetation sensitivity to UHI when developing targeted management strategies aiming to optimise the benefits accrued from vegetation.
Incongruence among phylogenetic results has become a common occurrence in analyses of genome-scale data sets. Incongruence originates from uncertainty in underlying evolutionary processes (e.g. incomplete lineage sorting) and from difficulties in determining the best analytical approaches for each situation. To overcome these difficulties, more studies are needed that identify incongruences and demonstrate practical ways to confidently resolve them. Here we present results of a phylogenomic study based on the analysis 197 taxa and 2,526 Ultraconserved Element (UCE) loci. We investigate evolutionary relationships of Eucerinae, a diverse subfamily of apid bees (relatives of honey bees and bumble bees) with more than 1,200 species. We sampled representatives of all tribes within the group and more than 80% of genera, including two mysterious South American genera, Chilimalopsis and Teratognatha. Initial analysis of the UCE data revealed two conflicting hypotheses for relationships among tribes. To resolve the incongruence, we tested concatenation and species tree approaches and used a variety of additional strategies including locus filtering, partitioned gene-trees searches, and gene-based topological tests. We show that within-locus partitioning improves gene-tree and subsequent species-tree estimation, and that this approach, confidently resolves the incongruence observed in our data set. After exploring our proposed analytical strategy on eucerine bees, we validated its efficacy to resolve hard phylogenetic problems by implementing it on a published UCE data set of Adephaga (Insecta: Coleoptera). Our results provide a robust phylogenetic hypothesis for Eucerinae and demonstrate a practical strategy for resolving incongruence in other phylogenomic data sets.
Widespread antibiotic usage in apiculture contributes substantially to the global dissemination of antimicrobial resistance and has the potential to negatively influence bacterial symbionts of honey bees (Apis mellifera). Here, we show that routine antibiotic administration with oxytetracycline selectively increased tetB (efflux pump resistance gene) abundance in the gut microbiota of adult workers while concurrently depleting several key symbionts known to regulate immune function and nutrient metabolism such as Frischella perrera and Lactobacillus Firm-5 strains. These microbial changes were functionally characterized by decreased capped brood counts (marker of hive nutritional status and productivity) and reduced antimicrobial capacity of adult hemolymph (indicator of immune competence). Importantly, combination therapy with three immunostimulatory Lactobacillus strains could mitigate antibiotic-associated microbiota dysbiosis and immune deficits in adult workers, as well as maximize the intended benefit of oxytetracycline by suppressing larval pathogen loads to near-undetectable levels. We conclude that microbial-based therapeutics may offer a simple but effective solution to reduce honey bee disease burden, environmental xenobiotic exposure, and spread of antimicrobial resistance.
Urbanisation is a global phenomenon with major effects on species, the structure of community functional traits and ecological interactions. Body size is a key species trait linked to metabolism, life‐history and dispersal as well as a major determinant of ecological networks. Here, using a well‐replicated urban‐rural sampling design in Central Europe, we investigate the direction of change of body size in response to urbanisation in three common bumblebee species, Bombus lapidarius , Bombus pascuorum and Bombus terrestris , and potential knock‐on effects on pollination service provision. We found foragers of B. terrestris to be larger in cities and the body size of all species to be positively correlated with road density (albeit at different, species‐specific scales); these are expected consequences of habitat fragmentation resulting from urbanisation. High ambient temperature at sampling was associated with both a small body size and an increase in variation of body size in all three species. At the community level, the community‐weighted mean body size and its variation increased with urbanisation. Urbanisation had an indirect positive effect on pollination services through its effects not only on flower visitation rate but also on community‐weighted mean body size and its variation. We discuss the eco‐evolutionary implications of the effect of urbanisation on body size, and the relevance of these findings for the key ecosystem service of pollination.
Bees collect pollen from flowers for their offspring, and by doing so contribute critical pollination services for our crops and ecosystems. Unlike many managed bee species, wild bees are thought to obtain much of their microbiome from the environment. However, we know surprisingly little about what plant species bees visit and the microbes associated with the collected pollen. Here, we addressed the hypothesis that the pollen and microbial components of bee diets would change across the range of the bee, by amplicon sequencing pollen provisions of a widespread small carpenter bee, Ceratina calcarata, across three populations. Ceratina calcarata was found to use a diversity of floral resources across its range, but the bacterial genera associated with pollen provisions were very consistent. Acinetobacter, Erwinia, Lactobacillus, Sodalis, Sphingomonas and Wolbachia were among the top ten bacterial genera across all sites. Ceratina calcarata uses both raspberry (Rubus) and sumac (Rhus) stems as nesting substrates, however nests within these plants showed no preference for host plant pollen. Significant correlations in plant and bacterial co-occurrence differed between sites, indicating that many of the most common bacterial genera have either regional or transitory floral associations. This range-wide study suggests microbes present in brood provisions are conserved within a bee species, rather than mediated by climate or pollen composition. Moving forward, this has important implications for how these core bacteria affect larval health and whether these functions vary across space and diet. These data increase our understanding of how pollinators interact with and adjust to their changing environment.
Abstract Human activity continues to impact global ecosystems, often by altering the habitat suitability, persistence, and movement of native species. It is thus critical to examine the population genetic structure of key ecosystemservice providers across human‐altered landscapes to provide insight into the forces that limit wildlife persistence and movement across multiple spatial scales. While some studies have documented declines of bee pollinators as a result of human‐mediated habitat alteration, others suggest that some bee species may benefit from altered land use due to increased food or nesting resource availability; however, detailed population and dispersal studies have been lacking. We investigated the population genetic structure of the Eastern carpenter bee, Xylocopa virginica, across 14 sites spanning more than 450 km, including dense urban areas and intensive agricultural habitat. X. virginica is a large bee which constructs nests in natural and human‐associated wooden substrates, and is hypothesized to disperse broadly across urbanizing areas. Using 10 microsatellite loci, we detected significant genetic isolation by geographic distance and significant isolation by land use, where urban and cultivated landscapes were most conducive to gene flow. This is one of the first population genetic analyses to provide evidence of enhanced insect dispersal in human‐altered areas as compared to semi‐natural landscapes. We found moderate levels of regional‐scale population structure across the study system (GʹST = 0.146) and substantial co‐ancestry between the sampling regions, where co‐ancestry patterns align with major human transportation corridors, suggesting that human‐mediated movement may be influencing regional dispersal processes. Additionally, we found a signature of strong site‐level philopatry where our analyses revealed significant levels of high genetic relatedness at very fine scales (
Pollinator reductions can leave communities less diverse and potentially at increased risk of infectious diseases. Species-rich plant and bee communities have high species turnover, making the study of disease dynamics challenging. To address how temporal dynamics shape parasite prevalence in plant and bee communities, we screened >5,000 bees and flowers over an entire growing season for five common bee microparasites (Nosema ceranae, Nosema bombi, Crithidia bombi, Crithidia expoeki and neogregarines). Over 110 bee species and 89 flower species were screened, revealing that 42% of bee species (12.2% individual bees) and 70% of flower species (8.7% individual flowers) had at least one parasite in or on them, respectively. Some common flowers (for example, Lychnis flos-cuculi) harboured multiple parasite species whilst others (for example, Lythrum salicaria) had few. Significant temporal variation of parasite prevalence in bees was linked to bee diversity, bee and flower abundance and community composition. Specifically, we found that bee communities had the highest prevalence late in the season, when social bees (Bombus spp. and Apis mellifera) were dominant and bee diversity was lowest. Conversely, prevalence on flowers was lowest late in the season when floral abundance was highest. Thus turnover in the bee community impacted community-wide prevalence, and turnover in the plant community impacted when parasite transmission was likely to occur at flowers. These results imply that efforts to improve bee health will benefit from the promotion of high floral numbers to reduce transmission risk, maintaining bee diversity to dilute parasites and monitoring the abundance of dominant competent hosts.
Cities are uniquely complex systems regulated by interactions and feedbacks between natural and social processes. Characteristics of human society – including culture, economics, technology, and politics – underlie social patterns and activity, creating a heterogeneous environment that can influence and be influenced by both ecological and evolutionary processes. Increasing interest in urban ecology and evolutionary biology has coincided with growing interest in eco‐evolutionary dynamics, which encompasses the interactions and reciprocal feedbacks between evolution and ecology. Research on both urban evolutionary biology and eco‐evolutionary dynamics frequently focuses on contemporary evolution of species that have potentially substantial ecological – and even social – significance. Still, little research fully integrates urban evolutionary biology and eco‐evolutionary dynamics, and rarely do researchers in either of these fields fully consider the role of human social patterns and processes. Because cities are fundamentally regulated by human activities, are inherently interconnected, and are frequently undergoing social and economic transformation, they represent an opportunity for ecologists and evolutionary biologists to study urban “socio‐eco‐evolutionary dynamics.” Through this new framework, we encourage researchers of urban ecology and evolution to fully integrate human social drivers and feedbacks to increase understanding and conservation of ecosystems, their functions, and their contributions to people within and outside cities.
Along with agricultural intensification, urbanization is often implicated in bee declines worldwide. While the vast majority of studies investigate how bee assemblages respond to urbanization across different spatial scales, very few attempts have used a temporal comparison to evaluate the impact of urbanization. The city of Curitiba in southern Brazil is unique for having long-term data of bees, and thus is a good model for studying urban temporal changes. The main goal of this study is to investigate how a ground-nesting assemblage responded to six decades of urban growth in Curitiba. In this time lapse the city population grew from 140 thousand to almost 2 million inhabitants. We demonstrate a 94% decline in nest abundance, a 35% decline in species richness, and a 24% decline in phylogenetic diversity from 1955 (T1) to 2018 (T2). Temporal beta diversity values between T1 and T2 were very high and most sampling sites were dominated by losses in nest abundance. All sampling sites changed similarly with losses in nesting substrates (i.e. exposed soil) and a substantial increase in surrounding impervious surface. This study exhibits how depletion of nesting substrates combined with increases in urban cover can affect pollinators, a concerning scenario as most bees nest in friable soil and thus are strongly susceptible to urbanization. We emphasize that urban planning policies to protect ground-nesting bees are essential to preserve the important ecological service of pollination in cities.
Wild bees encounter environmental microbes while foraging. While environmental context affects bee diversity, little is known about it how affects the wild bee microbiome. We used field surveys in 17 urban gardens to examine whether and how variation in local and landscape habitat features shapes the microbiome of the solitary Blue Orchard Bee, Osmia lignaria. We installed O. lignaria cocoons at each site, allowed bees to emerge and forage, then collected them. We measured local features of gardens using vegetation transects and landscape features with GIS. We found that in microbiome composition between bee individuals varied by environmental features such as natural habitat, floral resources, and bee species richness. We also found that environmental features were associated with the abundance of bacterial groups important for bee health, such as Lactobacillus. Our study highlights complex interactions between environment context, bee species diversity, and the bee-associated microbes.
Since its migration from the Asian honey bee (Apis cerana) to the European honey bee (Apis mellifera), the ectoparasitic mite Varroa destructor has emerged as a major issue for beekeeping worldwide. Due to a short history of coevolution, the host–parasite relationship between A. mellifera and V. destructor is unbalanced, with honey bees suffering infestation effects at the individual, colony and population levels. Several control solutions have been developed to tackle the colony and production losses due to Varroa, but the burden caused by the mite in combination with other biotic and abiotic factors continues to increase, weakening the beekeeping industry. In this synthetic review, we highlight the main advances made between 2015 and 2020 on V. destructor biology and its impact on the health of the honey bee, A. mellifera. We also describe the main control solutions that are currently available to fight the mite and place a special focus on new methodological developments, which point to integrated pest management strategies for the control of Varroa in honey bee colonies.
The parasitic mite, Varroa destructor, has shaken the beekeeping and pollination industries since its spread from its native host, the Asian honey bee (Apis cerana), to the naïve European honey bee (Apis mellifera) used commercially for pollination and honey production around the globe. Varroa is the greatest threat to honey bee health. Worrying observations include increasing acaricide resistance in the varroa population and sinking economic treatment thresholds, suggesting that the mites or their vectored viruses are becoming more virulent. Highly infested weak colonies facilitate mite dispersal and disease transmission to stronger and healthier colonies. Here, we review recent developments in the biology, pathology, and management of varroa, and integrate older knowledge that is less well known.
A growing body of research indicates that cities can support diverse bee communities. However, urbanization may disproportionately benefit exotic bees, potentially to the detriment of native species. We examined the influence of urbanization on exotic and native bees using two datasets from Michigan, USA. We found that urbanization positively influenced exotic—but not native—bee abundance and richness, and that this association could not be explained by proximity to international ports of entry, prevalence of exotic flora or urban warming. We found a negative relationship between native and exotic bee abundance at sites with high total bee abundance, suggesting that exotic bees may negatively affect native bee populations. These effects were not driven by the numerically dominant exotic honeybee, but rather by other exotic bees. Our findings complicate the emerging paradigm of cities as key sites for pollinator conservation.
Bees acquire carbohydrates from nectar and lipids; and amino acids from pollen, which also contains polysaccharides including cellulose, hemicellulose, and pectin. These potential energy sources could be degraded and fermented through microbial enzymatic activity, resulting in short chain fatty acids available to hosts. However, the contributions of individual microbiota members to polysaccharide digestion have remained unclear. Through analysis of bacterial isolate genomes and a metagenome of the honey bee gut microbiota, we identify that Bifidobacterium and Gilliamella are the principal degraders of hemicellulose and pectin. Both Bifidobacterium and Gilliamella show extensive strain-level diversity in gene repertoires linked to polysaccharide digestion. Strains from honey bees possess more such genes than strains from bumble bees. In Bifidobacterium , genes encoding carbohydrate-active enzymes are colocated within loci devoted to polysaccharide utilization, as in Bacteroides from the human gut. Carbohydrate-active enzyme-encoding gene expressions are up-regulated in response to particular hemicelluloses both in vitro and in vivo. Metabolomic analyses document that bees experimentally colonized by different strains generate distinctive gut metabolomic profiles, with enrichment for specific monosaccharides, corresponding to predictions from genomic data. The other 3 core gut species clusters ( Snodgrassella and 2 Lactobacillus clusters) possess few or no genes for polysaccharide digestion. Together, these findings indicate that strain composition within individual hosts determines the metabolic capabilities and potentially affects host nutrition. Furthermore, the niche specialization revealed by our study may promote overall community stability in the gut microbiomes of bees.
Teeming within pollen provisions are diverse communities of symbiotic microbes, which provide a variety of benefits to bees. Microbes themselves may represent a major dietary resource for developing bee larvae. Despite their apparent importance in sustaining bee health, evidence linking pollen-borne microbes to larval health is currently lacking. We examined the effects of microbe-deficient diets on the fitness of larval mason bees. In a series of diet manipulations, microbe-rich maternally collected pollen provisions were replaced with increasing fractions of sterilized, microbe-deficient pollen provisions before being fed to developing larvae. Convergent findings from amino acid and fatty acid trophic biomarker analyses revealed that larvae derived a substantial amount of nutrition from microbial prey and occupied a significantly higher trophic position than that of strict herbivores. Larvae feeding on increasingly sterile diets experienced significant adverse effects on growth rates, biomass and survivorship. When completely deprived of pollen-borne microbes, larvae consistently exhibited marked decline in fitness. We conclude that microbes associated with aged pollen provisions are central to bee health, not only as nutritional mutualists, but also as a major dietary component. In an era of global bee decline, the conservation of such bee-microbe interactions may represent an important facet of pollinator protection strategies.
Urbanization is one of the most significant land cover transformations, and while
climate alteration is one of its most cited ecological consequences we have very
limited knowledge on its effect on species’ thermal responses. We investigated whether
changes in environmental thermal variability caused by urbanization influence thermal
tolerance in honey bees (Apis mellifera) in a semi-arid city in central Mexico. Ambient
environmental temperature and honey bee thermal tolerance were compared in urban
and rural sites. Ambient temperature variability decreased with urbanization due to
significantly higher nighttime temperatures in urban compared to rural sites and not
from differences in maximum daily temperatures. Honey bee thermal tolerance breadth
[critical thermal maxima (CTmax)—critical thermal minima (CTmin)] was narrower for
urban bees as a result of differences in cold tolerance, with urban individuals having
significantly higher CTmin than rural individuals, and CTmax not differing among urban
and rural individuals. Honey bee body size was not correlated to thermal tolerance, and
body size did not differ between urban and rural individuals. We found that honey bees’
cold tolerance is modified through acclimation. Our results show that differences in
thermal variability along small spatial scales such as urban-rural gradients can influence
species’ thermal tolerance breadths.
Infectious diseases are a primary driver of bee decline worldwide, but limited understanding of how pathogens are transmitted hampers effective management. Flowers have been implicated as hubs of bee disease transmission, but we know little about how interspecific floral variation affects transmission dynamics. Using bumblebees ( Bombus impatiens), a trypanosomatid pathogen ( Crithidia bombi) and three plant species varying in floral morphology, we assessed how host infection and plant species affect pathogen deposition on flowers, and plant species and flower parts impact pathogen survival and acquisition at flowers. We found that host infection with Crithidia increased defaecation rates on flowers, and that bees deposited faeces onto bracts of Lobelia siphilitica and Lythrum salicaria more frequently than onto Monarda didyma bracts . Among flower parts, bracts were associated with the lowest pathogen survival but highest resulting infection intensity in bee hosts. Additionally, we found that Crithidia survival across flower parts was reduced with sun exposure. These results suggest that efficiency of pathogen transmission depends on where deposition occurs and the timing and place of acquisition, which varies among plant species and environmental conditions. This information could be used for development of wildflower mixes that maximize forage while minimizing disease spread.
Habitat degradation and climate change are currently threatening wild pollinators, compromising their ability to provide pollination services to wild and cultivated plants. Landscape genomics offers powerful tools to assess the influence of landscape modifications on genetic diversity and functional connectivity, and identify adaptations to local environmental conditions that could facilitate future bee survival. Here we assessed range‐wide patterns of genetic structure, genetic diversity, gene flow and local adaptation in the stingless bee Melipona subnitida, a tropical pollinator of key biological and economic importance inhabiting one of the driest and hottest regions of South America. Our results reveal four genetic clusters across the species’ full distribution range. All populations were found to be under a mutation‐drift equilibrium and genetic diversity was not influenced by the amount of reminiscent natural habitats. However, genetic relatedness was spatially autocorrelated and isolation by landscape resistance explained range‐wide relatedness patterns better than isolation by geographic distance, contradicting earlier findings for stingless bees. Specifically, gene flow was enhanced by increased thermal stability, higher forest cover, lower elevations, and less corrugated terrains. Finally, we detected genomic signatures of adaptation to temperature, precipitation and forest cover, spatially distributed in latitudinal and altitudinal patterns. Taken together, our findings shed important light on the life history of M. subnitida, and highlight the role of regions with large thermal fluctuations, deforested areas and mountain ranges as dispersal barriers. Conservation actions such as restricting long‐distance colony transportation, preserving local adaptations, and improving the connectivity between highlands and lowlands, are likely to assure future pollination services.
1. Urban areas can host speciose bee communities due partially to the species-rich combination of both native and alien plant species found in these landscapes. However, in intensively-constructed zones, it could be expected to record a low plant diversity used by bees because of the high proportion of paved surfaces in these areas.
2. We investigated the influence of urbanisation on the cavity-nesting bee-plant community and interaction network structures in a medium-sized city. The floral diversity used by nesting females in cell provisioning was retrieved from the pollen content obtained from trap-nests collected in 11 sites located in an urban landscape gradient.
3. Eighty pollen types belonging to 20 families were identified in the 155 pollen samples analysed. At least seven alien plant species were identified in samples from all sampling points. The landscape analysis revealed a positive influence of the proportion of green areas on the pollen type richness, although the null model was also selected as best model. Likewise, all network metrics but connectance were not influenced by any of the landscape variables.
4. Our findings demonstrated that notwithstanding the sampling sites the floral diversity used by bees and the alien pollen type richness were similar. Likewise, the bee-plant networks were modular, asymmetric, and highly specialised. The positive adaptation that cavity-nesting bee species present in urban environments and the presence of bee species that can explore a diverse flora may indicate that the local variation in the landscape had little influence on their interactions with plants.
Invasive bee species have negative impacts on native bee species and are a source of conservation concern. The invasion of bee species is mediated by the abiotic environment, biotic communities, and propagule pressure of the invader. Each of these factors is further affected by management, which can amplify the magnitude of the impact on native bee species. The ecological traits and behavior of invasive bees also play a role in whether and to what degree they compete with or otherwise negatively affect native bee species. The magnitude of impact of an invasive bee species relates both to its population size in the introduced habitat and the degree of overlap between its resources and the resources native bees require.
For a number of years, the decline of honeybee (Apis mellifera) in North America and Europe has been the subject of much debate. Among the many factors proposed by hundreds of studies to explain this phenomenon is the hypothesis that agricultural activities using pesticides contribute to the weakness of bee colonies. Moreover, while urban beekeeping is presently booming in several cities, we do not know if this environment is more beneficial for bees than the typical, rural area. In the summer of 2018, we sampled honeybees (foragers and larvae) in rural (Laurentians) and urban (city of Montreal) areas and compared them using the following biomarkers: carotenoids, retinoids, α-tocopherol, metallothionein-like proteins (MTLPs), lipid peroxidation, triglycerides, acetylcholinesterase activity (AChE) and proteins. Pesticides, pharmaceuticals and personal care products (PPCPs) and metals were also quantified in honeybees’ tissues. Our result revealed that, globally, urban foragers had higher levels of insecticides and PPCPs and that metals were in greater concentrations in urban larvae. Compared to rural foragers, urban foragers had higher concentrations of MTLPs, triglycerides, protein and AChE activity. The multifactorial analysis confirmed that insecticides, some metals and PPCPs were the most influential components in the contaminant‒biomarker relationships for both foragers and larvae.
Stingless bees (Meliponini) are a monophyletic group of eusocial insects inhabiting tropical and subtropical regions. These insects represent the most abundant and diversified group of corbiculate bees. Meliponini mostly rely on fermentation by symbiont microbes to preserve honey and transform pollen in stored food. Bee nests harbor diverse microbiota that includes bacteria, yeasts, filamentous fungi, and viruses. These microorganisms may interact with the bees through symbiotic relationships, or they may act as food for the insects, or produce biomolecules that aid in the biotransformation of bee products, such as honey and bee bread. Certain microbial species can also produce antimicrobial compounds that inhibit opportunistic bee pathogens.
Anthropogenic activities are rapidly changing the environment, and species that do not respond face a higher risk of extinction. Species may respond to environmental changes by modifying their behaviors, shifting their distributions, or changing their morphology. Recent morphological responses are often measured by changes in body size. Changes in body size are often attributed to climate change, but may instead be due to differences in available resources associated with changes in local land-use. The effects of temperature and land-use can be uncoupled in populations of the small carpenter bee Ceratina
calcarata, which have experienced changes in agricultural and urban cover independent of climate change. We studied how the morphology of this bee has changed over the past
18 years (1902–2019) in relation to climate change and the past 45 years (1974–2019) in relation to agricultural and urban cover. Over this time, summer temperatures increased. We found that male and female size decreased with increasing temperature. Male size also decreased with agricultural expansion. Female size, however, increased with agricultural expansion. These results suggest that rising temperatures correlate with a decrease in female body size, while, opposite to predicted, agricultural land-use may select for increased female body size. These opposing pressures act concurrently and may result in bee extirpation from agricultural habitats if selection for large sizes is unsustainable as temperatures continue to increase. Furthermore, this study emphasizes the need to consider multiple environmental stressors when examining the effects of climate change due to their interactions.
• As native bee populations decrease, there is a need to better understand their nutritional requirements to sustain healthy pollinator populations. A common native bee to eastern North America is the small carpenter bee, Ceratina calcarata. Previous studies have shown that the primary pollen sources for C. calcarata consist of clover and rose.
• The aim of this study is to compare the effects of diet composition on body size, development and survival. Artificial pollen diets were created using five different ratios of commercially available clover and rose pollen.
• Diets containing higher ratios of clover pollen produced larger individuals with increased survival rates and faster development times. To examine this further, the macronutrient profiles of clover and rose pollen were characterised comparing: protein, sugar, fatty acid, and amino acid content. Results indicated that rose pollen contained significantly higher protein and sugar content, while clover pollen had higher concentrations of essential amino acids. These are crucial to bee health and development, which helps to explain the increased survivorship observed on high clover diet treatments.
• Taken together, these results show that clover pollen provides a higher quality diet for larval development and survival of the native small carpenter bee. This research indicates that diet has a significant effect on the health of the native pollinator community and more research is needed to further explore the balance between pollen quality and availability, including essential macronutrients and the availability of these floral sources for wild bees.
Bacteria act in the most diverse roles in nature, being responsible for the pathogenicity, and also for the benefits mainly to plants. Of the benefits to living organisms, some groups of bacteria help in plant development, increasing absorption capacity of the plants, and solubilizing phosphate and biological nitrogen fixation (BNF) from the atmosphere.
The group of bacteria of the genus Clostridium are both attached to the benefits to living organisms as well as acting as “villains” of those. The genus Clostridium is composed of rod-shaped, Gram-positive, mesophilic, anaerobic, and oxygen-tolerant bacteria living in soils, water, living organisms, and other ecological niches.
While the genus is represented by approximately 235 species and subspecies, few are representative of the beneficial effects on plants. In this way, the Clostridium sp. has been used in the production of bio-fertilizers to promote vegetal growth. Promoting growth through BNF, the species C. pasteurianum (old C. pastorianum) is representative, which plays an important role being the first free-living bacteria fixer isolated. There are also reports of the occurrence of phosphate solubilization, making it available to plants.
This promotion effect on plant growth was observed in beet, barley, wheat, red radish, tomato, cucumber, rice and in Trifolium repens.
Apart from the beneficial effects, the genus Clostridium can present bacteria that cause deleterious effects, producing toxins, which cause diseases in plants, animals, and even humans.
However, there are still bacteria that can be used in the industrial processing as well as in the production of cellulose degradation, biofuels, biohydrogen, acetone, and biobutanol, considering the genus with great potential in obtaining productive gains in the crops and in the increase of industrial profitability, reducing the impacts on the environment and consequently a favorable agroecological role.
Bee hotels are increasingly set up by land managers in public parks to promote wild bee populations. However, we have very little evidence of the usefulness of bee hotels as tools to help the conservation of wild bees within cities. In this study, we installed 96 bee hotels in public parks of Marseille (France) for a year and followed their use as a nesting substrate by the local fauna. The most abundant species that emerged from bee hotels was the exotic bee species Megachile sculpturalis, representing 40% of all individuals. Moreover, we only detected four native bee species all belonging to the Osmia genus. More worryingly, we found a negative correlation between the occurrence of M. sculpturalis in bee hotels and the presence of native bees. One hypothesis to explain this result might be linked to the described territorial and aggressive behaviour of M. sculpturalis toward the nests built by the native fauna. This study raises the question about the usefulness of bee hotels for the conservation of native bees especially within cities harbouring high abundance of exotic bees. We provide here concrete advices to land managers to build bee hotels that can both host native bees and prevent the installation of M. sculpturalis.
Since 2012, a new pathogenic syndrome has frequently been observed in many areas of kiwifruit cultivation in Italy. Main symptoms include an initial withering of the leaves followed by a total and sudden collapse of plants, mainly occurring during summer. The withered leaves fall down and the main and secondary feeder roots appear rotten, sometimes showing a reddish‐brown discoloration. The disease, that affects both the green and yellow‐fleshed cultivars, has been called kiwifruit vine decline and it is locally known as “moria”. The syndrome has been found consistently associated with soil waterlogging, which frequently occurs either after the traditional agronomical practice to irrigate orchards through surface irrigation or after very heavy rainfall. So far, the role played by bacteria in this syndrome has not been investigated. In the present study, Clostridium spp. were isolated from both rotten roots and soils obtained from Italian kiwifruit orchards affected by the syndrome, indicating for the first time that anaerobic bacteria are able to cause damage to woody crops. C. bifermentans and C. subterminale incited symptoms to kiwifruit in both in vivo and in vitro pathogenicity tests. Soil waterlogging seems to potentially favour colonization of kiwifruit roots by anaerobic bacteria, probably because saturation of the soil can facilitate proliferation and persistence of these bacteria during long periods of the vegetative growth of the crop. The occurrence of anaerobic bacteria does not exclude the possibility that other microorganisms can play additional/synergic role(s) in causing the kiwifruit vine decline.
Changes in land use and management intensification, especially in agriculture, have led to alarming declines in bee populations and the important ecological services they provide. Little is known how wild bee communities respond to these landscape changes at the phylogenetic level. Phylogenetic diversity was found to be correlated to functional trait diversity, since the former reflects a species evolutionary history while the later reflects the traits a species has accumulated. Here we use a mix of traditional measures of biodiversity and phylogenetic methods to examine differences in wild bee assemblages at six landscapes associated with grazing pressure and different management schemes. We found that grazing pressure strongly influences bee abundance, species richness and functional trait diversity while management intensity has little effect. Interestingly, wild bee phylogenetic diversity was not highly affected by land use, management, or grazing pressure as landscapes retained high levels of phylogenetic evenness. We additionally found evidence of phylogenetic signaling of examined traits. Our findings reveal that wild bee communities can maintain functional trait diversity even with low abundance and species richness. Furthermore, our study supports the notion that trait conservation through evolutionary lineages may only occur for some traits.
Accumulating reports of global bee declines have drawn much attention to the bee microbiota and its importance. Most research has focused on social bees, while solitary species have received scant attention despite their enormous biodiversity, ecological importance, and agroeconomic value. We review insights from several recent studies on diversity, function, and drivers of the solitary-bee microbiota, and compare these factors with those relevant to the social-bee microbiota. Despite basic similarities, the social-bee model, with host-specific core microbiota and social transmission, is not representative of the vast majority of bee species. The solitary-bee microbiota exhibits greater variability and biodiversity, with a strong impact of environmental acquisition routes. Our synthesis identifies outstanding questions that will build understanding of these interactions, responses to environmental threats, and consequences for health.