Relative importance of host environment, transmission potential and host phylogeny to the structure of parasite metacommunities

Host and parasite identity interact in scale-dependent fashion to determine parasite community structure

Understanding the ecological assembly of parasite communities is critical to characterise how changing host and environmental landscapes will alter infection dynamics and outcomes. However, studies frequently assume that (a) closely related parasite species or those with identical life-history strategies are functionally equivalent, and (b) the same factors will drive infection dynamics for a single parasite across multiple host species, oversimplifying community assembly patterns. Here, we challenge these two assumptions using a naturally occurring host-parasite system, with the mussel Anodonta anatina infected by the digenean trematode Echinoparyphium recurvatum, and the snail Viviparus viviparus infected by both E. recurvatum and Echinostoma sp. By analysing the impact of temporal parasite dispersal, host species and size, and the impact of coinfection (moving from broader environmental factors to within-host dynamics), we show that neither assumption holds true, but at different ecological scales. The assumption that closely related parasites can be functionally grouped is challenged when considering dispersal to the host (i.e. larger scales), while the assumption that the same factors will drive infection dynamics for a single parasite across multiple host species is challenged when considering within-host interspecific competition (i.e. smaller scales). Our results demonstrate that host identity, parasite identity and ecological scale require simultaneous consideration in studies of parasite community composition and transmission.

Network Analysis of Hosts and Vectors in the Multiple Transmissions of Flavivirus

Background: It is well established that infection patterns in nature can be driven by host, vector, and symbiont communities. One of the first stages in understanding how these complex systems have influenced the incidence of vector-borne diseases is to recognize what are the major vertebrate (i.e., hosts) and invertebrate (i.e., vectors) host species that propagate those microbes. Such identification opens the possibility to identify such essential species to develop targeted preventive efforts. Methods: The goal of this study, which relies on a compilation of a global database based on published literature, is to identify relevant host species in the global transmission of mosquito-borne flaviviruses, such as West Nile virus, St. Louis virus, Dengue virus, and Zika virus, which pose a concern to animal and public health. Results: The analysis of the resulting database involving 1174 vertebrate host species and 46 reported vector species allowed us to establish association networks between these species. Three host species (Mus musculus, Sapajus flavius, Sapajus libidinosus, etc.) have a much larger centrality values, suggesting that they play a key role in flavivirus community interactions. Conclusion: The methods used and the species detected as relevant in the network provide new knowledge and consistency that could aid health officials in rethinking prevention and control strategies with a focus on viral communities and their interactions. Other infectious diseases that harm animal and human health could benefit from such network techniques.

Assessing the Zooplankton Metacommunity (Branchiopoda and Copepoda) from Mediterranean Wetlands in Agricultural Landscapes

Mediterranean wetlands are suitable ecosystems for studying metacommunity theory, since they are isolated ecosystems within a land matrix with well-established limits, often with watersheds destined for agricultural uses. The zooplankton community of wetlands in agricultural landscapes is the result of processes that operate in a different multiscale context. We selected 24 ponds in Alto Guadalquivir region (SE Spain) with different local environmental variables (biological, limnological and land uses). The zooplankton community of the wetlands under study consists of a total of 60 species: 38 branchiopods and 22 copepods. This community (total, branchiopods and copepods) was analysed through two different and complementary metacommunity approaches. The pattern approach determines the species distribution along environmental gradients, and the mechanistic approach considers the involved processes, such as environmental control and dispersal limitation. The results indicated a nested metacommunity, in which five limnological variables, three land uses and six spatial variables are the main drivers that explain zooplankton distribution in these wetlands. In conclusion, species sorting and dispersal processes play a role in the structuring of the zooplankton metacommunity. This conclusion has implications for the development of adequate management policies on Mediterranean wetland protection and diversity conservation in agricultural contexts.

Predicting primate-parasite associations using exponential random graph models

Ecological associations between hosts and parasites are influenced by host exposure and susceptibility to parasites, and by parasite traits, such as transmission mode. Advances in network analysis allow us to answer questions about the causes and consequences of traits in ecological networks in ways that could not be addressed in the past. We used a network-based framework (exponential random graph models or ERGMs) to investigate the biogeographic, phylogenetic and ecological characteristics of hosts and parasites that affect the probability of interactions among nonhuman primates and their parasites. Parasites included arthropods, bacteria, fungi, protozoa, viruses and helminths. We investigated existing hypotheses, along with new predictors and an expanded host-parasite database that included 213 primate nodes, 763 parasite nodes and 2319 edges among them. Analyses also investigated phylogenetic relatedness, sampling effort and spatial overlap among hosts. In addition to supporting some previous findings, our ERGM approach demonstrated that more threatened hosts had fewer parasites, and notably, that this effect was independent of hosts also having a smaller geographic range. Despite having fewer parasites, threatened host species shared more parasites with other hosts, consistent with loss of specialist parasites and threat arising from generalist parasites that can be maintained in other, non-threatened hosts. Viruses, protozoa and helminths had broader host ranges than bacteria, or fungi, and parasites that infect non-primates had a higher probability of infecting more primate species. The value of the ERGM approach for investigating the processes structing host-parasite networks provided a more complete view on the biogeographic, phylogenetic and ecological traits that influence parasite species richness and parasite sharing among hosts. The results supported some previous analyses and revealed new associations that warrant future research, thus revealing how hosts and parasites interact to form ecological networks.

Explosive networking: The role of adaptive host radiations and ecological opportunity in a species-rich host-parasite assembly

Many species-rich ecological communities emerge from adaptive radiation events. Yet the effects of adaptive radiation on community assembly remain poorly understood. Here, we explore the well-documented radiations of African cichlid fishes and their interactions with the flatworm gill parasites Cichlidogyrus spp., including 10,529 reported infections and 477 different host-parasite combinations collected through a survey of peer-reviewed literature. We assess how evolutionary, ecological, and morphological parameters determine host-parasite meta-communities affected by adaptive radiation events through network metrics, host repertoire measures, and network link prediction. The hosts' evolutionary history mostly determined host repertoires of the parasites. Ecological and evolutionary parameters predicted host-parasite interactions. Generally, ecological opportunity and fitting have shaped cichlid-Cichlidogyrus meta-communities suggesting an invasive potential for hosts used in aquaculture. Meta-communities affected by adaptive radiations are increasingly specialised with higher environmental stability. These trends should be verified across other systems to infer generalities in the evolution of species-rich host-parasite networks.

Large-herbivore nemabiomes: patterns of parasite diversity and sharing

Amidst global shifts in the distribution and abundance of wildlife and livestock, we have only a rudimentary understanding of ungulate parasite communities and parasite-sharing patterns. We used qPCR and DNA metabarcoding of fecal samples to characterize gastrointestinal nematode (Strongylida) community composition and sharing among 17 sympatric species of wild and domestic large mammalian herbivore in central Kenya. We tested a suite of hypothesis-driven predictions about the role of host traits and phylogenetic relatedness in describing parasite infections. Host species identity explained 27-53% of individual variation in parasite prevalence, richness, community composition and phylogenetic diversity. Host and parasite phylogenies were congruent, host gut morphology predicted parasite community composition and prevalence, and hosts with low evolutionary distinctiveness were centrally positioned in the parasite-sharing network. We found no evidence that host body size, social-group size or feeding height were correlated with parasite composition. Our results highlight the interwoven evolutionary and ecological histories of large herbivores and their gastrointestinal nematodes and suggest that host identity, phylogeny and gut architecture-a phylogenetically conserved trait related to parasite habitat-are the overriding influences on parasite communities. These findings have implications for wildlife management and conservation as wild herbivores are increasingly replaced by livestock.

From island biogeography to landscape and metacommunity ecology: A macroecological perspective of bat communities

The equilibrium theory of island biogeography and its quantitative consideration of origination and extinction dynamics as they relate to island area and distance from source populations have evolved over time and enriched theory related to many disciplines in spatial ecology. Indeed, the island focus was catalytic to the emergence of landscape ecology and macroecology in the late 20th century. We integrate concepts and perspectives of island biogeography, landscape ecology, macroecology, and metacommunity ecology, and show how these disciplines have advanced the understanding of variation in abundance, biodiversity, and composition of bat communities. We leverage the well-studied bat fauna of the islands in the Caribbean to illustrate the complex interplay of ecological, biogeographical, and evolutionary processes in molding local biodiversity and system-wide structure. Thereafter, we highlight the role of habitat loss and fragmentation, which is increasing at an accelerating rate during the Anthropocene, on the structure of local bat communities and regional metacommunities across landscapes. Bat species richness increases with the amount of available habitat, often forming nested subsets along gradients of patch or island area. Similarly, the distance to and identity of sources of colonization influence the richness, composition, and metacommunity structure of islands and landscape networks.

Temporal variation of metacommunity structure in arthropod ectoparasites harboured by small mammals: the effects of scale and climatic fluctuations

We applied the elements of metacommunity structure (EMS) approach and studied the temporal dynamics of metacommunity structure in arthropod ectoparasites (fleas, gamasid mites and ixodid ticks) harboured by six small mammalian hosts sampled for three decades in the same locality in Western Siberia at three hierarchical scales (inframetacommunities, component metacommunities and a compound metacommunity). All metacommunities were positively coherent. Inframetacommunity structures varied across sampling periods in all host species. The main structural pattern in an inframetacommunity of the same host varied across sampling times but was mostly characterized by clumped species distributions (Clementsian, Gleasonian and their quasi-versions). Component metacommunities in five of the six host species were characterized by either a Clementsian or a quasi-Clementsian distribution. In four of the six host species, this pattern was driven by mite distribution. The temporal structure of compound metacommunity was characterized by a Clementsian pattern. In contrast to the majority of component metacommunities, this pattern was driven by fleas, whereas the temporal structure of gamasid mite compound metacommunities demonstrated a Gleasonian distribution. The temporal gradient in infracommunity composition was not associated with temporal changes in either air temperature or precipitation, whereas the precipitation gradient was positively correlated with the structure of component (in five host species) and compound metacommunities. In conclusion, the best-fit metacommunity structure of ectoparasites varies temporally due to temporal changes in distribution patterns that can be associated with year-to-year climatic variation, affecting both hosts and parasites.

Rodent helminths in fragmented Atlantic Forest areas in the western region of the state of Paraná

Rodents are small mammals that can be parasitized by various helminths. This study aimed to identify and describe the ecological indicators of infection in rodents captured in fragments of the Atlantic Forest in the western region of Paraná State, Brazil. Sixty-eight specimens of five rodent species were collected, necropsied, and inspected in search of helminths. The parasites were stored in 70% ethanol, morphologically identified, and counted for calculation of infection indicators. Fourteen species of helminths and one species of Crustacea were recorded: ten in Akodon montensis, four in Mus musculus, two in Thaptomys nigrita, two in Oligoryzomys nigripes, and one in Euryoryzomys russatus. The registered species of parasites were: Rodentolepis akodontis, Angiostrongylus sp., Protospirura numidica criceticola, Trichuris navonae, Syphacia alata, Syphacia criceti, Syphacia evaginata, Trichofreitasia lenti, Stilestrongylus aculeata, Stilestrongylus eta, Stilestrongylus gracielae, Stilestrongylus franciscanus, Stilestrongylus moreli, Stilestrongylus sp., and Pentastomida gen. sp. A positive correlation between the intensity of infection of T. navonae and T. lenti was observed with the body condition index of the host A. montensis. For all species, this study represents a new register of locality, and for eight of them a new host.

Historical contingency, geography and anthropogenic patterns of exposure drive the evolution of host switching in the Blastocystis species-complex

Parasites have the power to impose significant regulatory pressures on host populations, making evolutionary patterns of host switching by parasites salient to a range of contemporary ecological issues. However, relatively little is known about the colonization of new hosts by parasitic, commensal and mutualistic eukaryotes of metazoans. As ubiquitous symbionts of coelomate animals, Blastocystis spp. represent excellent candidate organisms for the study of evolutionary patterns of host switching by protists. Here, we apply a big-data phylogenetic approach using archival sequence data to assess the relative roles of several host-associated traits in shaping the evolutionary history of the Blastocystis species-complex within an ecological framework. Patterns of host usage were principally determined by geographic location and shared environments of hosts, suggesting that weight of exposure (i.e. propagule pressure) represents the primary force for colonization of new hosts within the Blastocystis species-complex. While Blastocystis lineages showed a propensity to recolonize the same host taxa, these taxa were often evolutionarily unrelated, suggesting that historical contingency and retention of previous adaptions by the parasite were more important to host switching than host phylogeny. Ultimately, our findings highlight the ability of ecological theory (i.e. ‘ecological fitting’) to explain host switching and host specificity within the Blastocystis species-complex.

Niche theory-based modeling of assembly processes of viral communities in bats

Understanding the assembly processes of symbiont communities, including viromes and microbiomes, is important for improving predictions on symbionts' biogeography and disease ecology. Here, we use phylogenetic, functional, and geographic filters to predict the similarity between symbiont communities, using as a test case the assembly process in viral communities of Mexican bats. We construct generalized linear models to predict viral community similarity, as measured by the Jaccard index, as a function of differences in host phylogeny, host functionality, and spatial co-occurrence, evaluating the models using the Akaike information criterion. Two model classes are constructed: a "known" model, where virus-host relationships are based only on data reported in Mexico, and a "potential" model, where viral reports of all the Americas are used, but then applied only to bat species that are distributed in Mexico. Although the "known" model shows only weak dependence on any of the filters, the "potential" model highlights the importance of all three filter types-phylogeny, functional traits, and co-occurrence-in the assemblage of viral communities. The differences between the "known" and "potential" models highlight the utility of modeling at different "scales" so as to compare and contrast known information at one scale to another one, where, for example, virus information associated with bats is much scarcer.

Understanding host utilization by mosquitoes: determinants, challenges and future directions

Mosquito host utilization is a key factor in the transmission of vector-borne pathogens given that it greatly influences host-vector contact rates. Blood-feeding patterns of mosquitoes are not random, as some mosquitoes feed on particular species and/or individuals more than expected by chance. Mosquitoes use a number of cues including visual, olfactory, acoustic, and thermal stimuli emitted by vertebrate hosts to locate and identify their blood meal sources. Thus, differences in the quality/intensity of the released cues may drive host selection by mosquitoes at both inter- and intra-specific levels. Such patterns of host selection by mosquitoes in space and time can be structured by factors related to mosquitoes (e.g. innate host preference, behavioural plasticity), to hosts (e.g. emission of host-seeking cues, host availability) or to both (e.g. pathogen infection). In this study, we review current evidence, from phenomena to mechanisms, of how these factors influence host utilization by mosquitoes. We also review the methodologies commonly used in this research field and identify the major challenges for future studies. To bridge the knowledge gaps, we propose improvements to strengthen traditional approaches and the use of a functional trait-based approach to infer mosquito host utilization in natural communities.

Abundance data applied to a novel model invertebrate host shed new light on parasite community assembly in nature

Understanding how environmental drivers influence the assembly of parasite communities, in addition to how parasites may interact at an infracommunity level, are fundamental requirements for the study of parasite ecology. Knowledge of how parasite communities are assembled will help to predict the risk of parasitism for hosts, and model how parasite communities may change under variable conditions. However, studies frequently rely on presence-absence data and examine multiple host species or sites, metrics which may be too coarse to characterise nuanced within-host patterns. We utilised a novel host system, the freshwater mussel Anodonta anatina, to investigate the drivers of community structure and explore parasite interactions. In addition, we aimed to highlight consistencies and inconsistencies between PA and abundance data. Our analysis incorporated 14 parasite taxa and 720 replicate infracommunities. Using Redundancy Analysis, a joint species distribution model and a Markov random field approach, we modelled the impact of both host-level and environment-level characteristics on parasite structure, as well as parasite-parasite correlations after accounting for all other factors. This approach was repeated for both the presence and abundance of all parasites. We demonstrated that the regional species pool, individual host characteristics (mussel length and gravidity) and predicted parasite-parasite interactions are all important but to varying degrees across parasite species, suggesting that applying generalities to parasite community construction is too simplistic. Furthermore, we showed that PA data fail to capture important density-dependent effects of parasite load for parasites with high abundance, and in general performs poorly for high-intensity parasites. Host and parasite traits, as well as broader environmental factors, all contribute to parasite community structure, emphasising that an integrated approach is required to study community assembly. However, care must be taken with the data used to infer patterns, as presence-absence data may lead to incorrect ecological inference.

The general architecture of black fly-parasite interactions: Parasitism in lotic systems at a continental scale

We examined the general architecture of interactions between stream-dwelling larval black flies (Diptera: Simuliidae) and their common parasites in 1736 collections across North America. Mermithid nematodes (family Mermithidae), microsporidia (phylum Microsporidia), and the fungus Coelomycidium simulii Debaisieux (phylum Blastocladiomycota) infected larval black flies. We found similar continental distributions for these three parasite taxa across North America. At least one of these taxa was represented in 42.2% of all black fly collections. Species interactions in ecological networks typically imply that each link between species is equally important. By employing quantitative measures of host susceptibilities and parasite dependencies, we provide a more complete structure for host-parasite networks. The distribution of parasite dependencies and host susceptibilities were right-skewed, with low values indicating that most dependencies (parasites) and susceptibilities (hosts) were weak. Although regression analysis between host frequency and parasite incidence were highly significant, frequency analysis suggested that the distributions of parasites differ significantly among the four most common and closely related (same subgenus) species of hosts. A highly significant pattern of nestedness in our bipartite host-parasite network indicated that specialized parasites (i.e., those that interact with few host species) tend to occur as subsets of the most common hosts.

Scale-dependent effects of host patch traits on species composition in a stickleback parasite metacommunity

A core goal of ecology is to understand the abiotic and biotic variables that regulate species distributions and community composition. A major obstacle is that the rules governing species distributions can change with spatial scale. Here, we illustrate this point using data from a spatially nested metacommunity of parasites infecting a metapopulation of threespine stickleback fish from 34 lakes on Vancouver Island, British Columbia. Like most parasite metacommunities, the composition of stickleback parasites differs among host individuals within each host population, and differs between host populations. The distribution of each parasite taxon depends, to varying degrees, on individual host traits (e.g., mass, diet) and on host-population characteristics (e.g., lake size, mean host mass, mean diet). However, in most cases in this data set, a given parasite was regulated by different factors at the host-individual and host-population scales, leading to scale-dependent patterns of parasite-species co-occurrence.

Intraspecific host variation plays a key role in virus community assembly

Infection by multiple pathogens of the same host is ubiquitous in both natural and managed habitats. While intraspecific variation in disease resistance is known to affect pathogen occurrence, how differences among host genotypes affect the assembly of pathogen communities remains untested. In our experiment using cloned replicates of naive Plantago lanceolata plants as sentinels during a seasonal virus epidemic, we find non-random co-occurrence patterns of five focal viruses. Using joint species distribution modelling, we attribute the non-random virus occurrence patterns primarily to differences among host genotypes and local population context. Our results show that intraspecific variation among host genotypes may play a large, previously unquantified role in pathogen community structure.

Eutrophication, biodiversity loss, and species invasions modify the relationship between host and parasite richness during host community assembly

Host and parasite richness are generally positively correlated, but the stability of this relationship in response to global change remains poorly understood. Rapidly changing biotic and abiotic conditions can alter host community assembly, which in turn, can alter parasite transmission. Consequently, if the relationship between host and parasite richness is sensitive to parasite transmission, then changes in host composition under various global change scenarios could strengthen or weaken the relationship between host and parasite richness. To test the hypothesis that host community assembly can alter the relationship between host and parasite richness in response to global change, we experimentally crossed host diversity (biodiversity loss) and resource supply to hosts (eutrophication), then allowed communities to assemble. As previously shown, initial host diversity and resource supply determined the trajectory of host community assembly, altering post-assembly host species richness, richness-independent host phylogenetic diversity, and colonization by exotic host species. Overall, host richness predicted parasite richness, and as predicted, this effect was moderated by exotic abundance-communities dominated by exotic species exhibited a stronger positive relationship between post-assembly host and parasite richness. Ultimately, these results suggest that, by modulating parasite transmission, community assembly can modify the relationship between host and parasite richness. These results thus provide a novel mechanism to explain how global environmental change can generate contingencies in a fundamental ecological relationship-the positive relationship between host and parasite richness.

Diversity of monogeneans and tapeworms in cypriniform fishes across two continents

Cypriniformes, which exhibit a wide geographical distribution, are the most species-rich group of freshwater fishes. Despite considerable research on their parasites, no reliable estimates of their parasite diversity on a large geographical scale are available. In the present review, we analyse species richness of two parasitic flatworm groups (monogeneans and tapeworms) reported from cypriniform fishes in the two most intensively studied parts of the Holarctic region, Europe and North America. We also review knowledge on parasite speciation and host-parasite coevolution, and emphasise the risk of parasite co-introduction resulting from transfers of cypriniforms among different continents. As parasite diversity in European cypriniforms has been more intensively explored, we predicted a lower level of knowledge on parasite diversity in North American fishes, despite North America having a higher diversity of cypriniforms than Europe. Our data revealed a higher mean species richness of monogeneans and tapeworms per cypriniform species in Europe compared with North America. We showed that species richness of both parasite taxa in both continents is strongly affected by sample size, but that fish traits also play an important role in determining monogenean and tapeworm species richness in European cyprinoids. We recorded higher host specificity for cypriniform parasites in North America, even within parasite genera shared by cypriniforms on both continents. The host range of monogeneans parasitising cyprinoids on both continents was affected by phylogeny, indicating an effect of parasite life history on host specificity. The difference in parasite host range between the two continents could potentially be explained by either the low overall level of sampling activity in North America or an underestimation of parasite diversity in Europe. We suggest that future research efforts be focussed on cypriniforms in order to obtain reliable data for robust assessments of parasite species richness and phylogenies, to assess host-parasite coevolution and to reveal fish biogeography.

Helminth metacommunity of small mammals in a Brazilian reserve: the contribution of environmental variables, host attributes and spatial variables in parasite species abundance

The role of environmental factors and landscape heterogeneity on species distribution on different spatial scales is one of the most important questions in community ecology. Variations in the environmental gradient characteristics, host attributes and spatial scales may influence the parasites distribution. The helminth metacommunity of 12 small mammal species was investigated in an Atlantic Forest reserve located in the State of Rio de Janeiro, southeast Brazil. We evaluated the influence of environmental variables, host attributes and spatial factors on the helminth metacommunity of small mammals, considering infracommunity and component community levels. Twenty-nine helminth morphospecies were recovered. The host attributes and spatial variables influenced the abundance of helminth species in the metacommunities for rodents and marsupials together, and for rodents alone at the infracommunity level. Host body mass, host diet and spatial variables at broad spatial scale (among localities) were the most important variables to explain the variation in helminth abundance. Parasite species richness influenced this variation only for the marsupial helminth metacommunity at the infracommunity level. The metacommunity showed larger turnover (parasite replacement) than nestedness (parasite loss) for their helminth species at both infracommunity and component community levels, which is associated with a high host specificity, and low helminth sharing among hosts for most species, resulting in a structured metacommunity.

Tracking the assembly of nested parasite communities: Using β-diversity to understand variation in parasite richness and composition over time and scale

Community composition is driven by a few key assembly processes: ecological selection, drift and dispersal. Nested parasite communities represent a powerful study system for understanding the relative importance of these processes and their relationship with biological scale. Quantifying β-diversity across scales and over time additionally offers mechanistic insights into the ecological processes shaping the distributions of parasites and therefore infectious disease. To examine factors driving parasite community composition, we quantified the parasite communities of 959 amphibian hosts representing two species (the Pacific chorus frog, Pseudacris regilla and the California newt, Taricha torosa) sampled over 3 months from 10 ponds in California. Using additive partitioning, we estimated how much of regional parasite richness (γ-diversity) was composed of within-host parasite richness (α-diversity) and turnover (β-diversity) at three biological scales: across host individuals, across species and across habitat patches (ponds). We also examined how β-diversity varied across time at each biological scale. Differences among ponds comprised the majority (40%) of regional parasite diversity, followed by differences among host species (23%) and among host individuals (12%). Host species supported parasite communities that were less similar than expected by null models, consistent with ecological selection, although these differences lessened through time, likely due to high dispersal rates of infectious stages. Host individuals within the same population supported more similar parasite communities than expected, suggesting that host heterogeneity did not strongly impact parasite community composition and that dispersal was high at the individual host-level. Despite the small population sizes of within-host parasite communities, drift appeared to play a minimal role in structuring community composition. Dispersal and ecological selection appear to jointly drive parasite community assembly, particularly at larger biological scales. The dispersal ability of aquatic parasites with complex life cycles differs strongly across scales, meaning that parasite communities may predictably converge at small scales where dispersal is high, but may be more stochastic and unpredictable at larger scales. Insights into assembly mechanisms within multi-host, multi-parasite systems provide opportunities for understanding how to mitigate the spread of infectious diseases within human and wildlife hosts.

Bacterial microbiota composition of Ixodes ricinus ticks: the role of environmental variation, tick characteristics and microbial interactions

Ecological factors, host characteristics and/or interactions among microbes may all shape the occurrence of microbes and the structure of microbial communities within organisms. In the past, disentangling these factors and determining their relative importance in shaping within-host microbiota communities has been hampered by analytical limitations to account for (dis)similar environmental preferences ('environmental filtering'). Here we used a joint species distribution modelling (JSDM) approach to characterize the bacterial microbiota of one of the most important disease vectors in Europe, the sheep tick Ixodes ricinus, along ecological gradients in the Swiss Alps. Although our study captured extensive environmental variation along elevational clines, the explanatory power of such large-scale ecological factors was comparably weak, suggesting that tick-specific traits and behaviours, microhabitat and -climate experienced by ticks, and interactions among microbes play an important role in shaping tick microbial communities. Indeed, when accounting for shared environmental preferences, evidence for significant patterns of positive or negative co-occurrence among microbes was found, which is indicative of competition or facilitation processes. Signals of facilitation were observed primarily among human pathogens, leading to co-infection within ticks, whereas signals of competition were observed between the tick endosymbiont Spiroplasma and human pathogens. These findings highlight the important role of small-scale ecological variation and microbe-microbe interactions in shaping tick microbial communities and the dynamics of tick-borne disease.

The effects of environment, hosts and space on compositional, phylogenetic and functional beta-diversity in two taxa of arthropod ectoparasites

We studied the effects of variation in environmental, host-associated and spatial factors on variation in compositional, phylogenetic/taxonomic and functional facets of beta-diversity in fleas and gamasid mites parasitic on small mammals and asked whether (a) the importance of these factors as drivers of beta-diversity differs among its multiple facets and (b) the effects of variation in environment, hosts and space on beta-diversity variation differ between the two ectoparasite taxa. To understand the relative effects of each group of predictors, we used a distance-based redundancy analysis and variation partitioning. The greatest portions of variation in the compositional beta-diversity of fleas were equally explained by host-associated and spatial predictors, whereas variation in host species composition contributed the most to variation in the compositional beta-diversity of mites. Variation in the phylogenetic (i.e. based on phylogenetic tree) beta-diversity of fleas was mainly due to variation in the phylogenetic composition of host communities, while the taxonomic (i.e. based on Linnean taxonomy) beta-diversity of mites was influenced by environmental variation. Unique contributions of spatial and environmental variation explained most of the variation in functional beta-diversity and its species replacement (= turnover) component (i.e. beta-diversity explained by replacement of species alone) in fleas and mites, respectively. Variation in the richness difference component (i.e. beta-diversity explained by species loss/gain alone) of functional beta-diversity was mainly affected by either variation in the functional composition of host assemblages (fleas) or its joint action with environmental variables (mites). We conclude that the pattern of the relative effects of environmental, host-associated and spatial factors on beta-diversity is context-dependent and may differ among different facets of beta-diversity, among different beta-diversity components and also among taxa dependent on biological affinities.

Viral metacommunities associated to bats and rodents at different spatial scales

One of the main goals of community ecology is to measure the relative importance of environmental filters to understand patterns of species distribution at different temporal and spatial scales. Likewise, the identification of factors that shape symbiont metacommunity structures is important in disease ecology because resulting structures drive disease transmission. We tested the hypothesis that distributions of virus species and viral families from rodents and bats are defined by shared responses to host phylogeny and host functional characteristics, shaping the viral metacommunity structures at four spatial scales (Continental, Biogeographical, Zoogeographical, and Regional). The contribution of host phylogeny and host traits to the metacommunity of viruses at each spatial scale was calculated using a redundant analysis of canonical ordering (RDA). For rodents, at American Continental scale the coherence of viral species metacommunity increased while the spatial scale decreased and Quasi-Clementsian structures were observed. This pattern suggests a restricted distribution of viruses through their hosts, while in the Big Mass (Europe, Africa, and Asia), the coherence decreased as spatial scale decreased. Viral species metacommunities associated with bats was dominated by random structures along all spatial scales. We suggest that this random pattern is a result of the presence of viruses with high occupancy range such as rabies (73%) and coronavirus (27%), that disrupt such structures. At viral family scale, viral metacommunities associated with bats showed coherent structures, with the emergence of Quasi- Clementsian and Checkerboard structures. RDA analysis indicates that the assemblage of viral diversity associated with rodents and bats responds to phylogenetic and functional characteristics, which alternate between spatial scales. Several of these variations could be subject to the spatial scale, in spite of this, we could identify patterns at macro ecological scale. The application of metacommunity theory at symbiont scales is particularly useful for large-scale ecological analysis. Understanding the rules of host-virus association can be useful to take better decisions in epidemiological surveillance, control and even predictions of viral distribution and dissemination.

Helminth metacommunity structure of wild rodents in a preserved area of the Atlantic Forest, Southeast Brazil

Abstract The helminth fauna and metacommunity structure of eight sympatric sigmodontine rodents were investigated at the Serra dos Órgãos National Park, an Atlantic Forest reserve located in the State of Rio de Janeiro, southeast Brazil. Rodents of the species Abrawayaomys ruschii, Akodon montensis, Blarinomys breviceps , Delomys dorsalis, Oligoryzomys flavescens, Oligoryzomys nigripes, Oxymycterus quaestor and Thaptomys nigrita were found infected with helminths. Akodon montensis presented the highest total helminth species richness, with six different species of helminths. The nematode Stilestrongylus lanfrediae was the most abundant and prevalent helminth species observed. The host-parasite network analysis showed little interactions among host species. Akodon montensis seems to act as a keystone-species in the rodent community. This species shared the nematodes Stilestrongylus aculeata with A. ruschii and Protospirura numidica criceticola with T. nigrita, and the cestode Rodentolepis akodontis with D. dorsalis. The congeners host species O. flavescens and O. nigripes shared the nematodes Guerrerostrongylus zetta and S. lanfrediae. The rodents B. breviceps and O. quaestor did not share any helminths with other hosts. The helminth metacommunity showed a random pattern on both infracommunity and component community levels, indicating different responses by each helminth species to the environmental gradient.

Parasites and Host Species Barriers in Animal Hybrid Zones

Species barriers are tested in hybrid zones when gene flow occurs between hybridizing species. Hybridization can erode species barriers, lead to the introgression of adaptive traits, or remain stable through time. Outcomes in hybrid zones are influenced by divergence between the hybridizing taxa, behavior, ecology, and geography. Parasites and pathogens play a major role in host fitness and appear to have varied impacts on species barriers in hybrid zones. We comprehensively reviewed the literature on parasitism in animal hybrid zones and present an evolutionary framework within which to consider parasite-hybrid interactions. Parasites most frequently show potential to contribute to species barrier breakdown in hybrid zones, but also frequently show potential to facilitate the maintenance of species barriers. Incorporating eco-immunology, parasite community theory, and spatiotemporal approaches will be important as genomic tools allow researchers to examine parasites and hybrid zones at greater resolution and in a diversity of natural habitats.

Microclimate and host body condition influence mite population growth in a wild bird-ectoparasite system

Parasite populations are never evenly distributed among the hosts they infect. Avian nest ectoparasites, such as mites, are no exception, as their distribution across the landscape is highly aggregated. It remains unclear if this pattern is driven by differences in transmission events alone, or if the environment that parasites inhabit after transmission also plays a role. Here, we experimentally examined the influence of the post-transmission microclimate, nest characteristics, and host condition on ectoparasite population growth in a bird-ectoparasite system. We infested barn swallow (Hirundo rustica erythrogaster) nests with a standardized number of Northern Fowl Mites (Ornithonyssus sylvarium) and analyzed both biotic (nestling mass, wing length, number of other arthropods present in the nest, and brood size) and abiotic (temperature, humidity, nest lining, nest dimensions, and substrate upon which the nest was built) predictors of mite population growth. Our results suggest that mite populations were most successful, in terms of growth, in nests with higher temperatures, lower humidity, few other arthropods, and hosts in good condition. We also found that nests built on wooden substrates support larger populations of mites than those constructed on metal or concrete. These findings lend insight into the factors that drive large-scale patterns of ectoparasite distributions.

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Experimental manipulations of nest mites controls for initial transmission.

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Tested the role of microclimate and host factors on mite population growth.

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Mite populations grow larger in warmer, drier nests with high body condition hosts.

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Nests on wooden substrates had more stable microclimate and larger mite populations.

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Presence of other arthropods was negatively correlated with mite population growth.

Structure of parasite communities in urban environments: the case of helminths in synanthropic rodents

Identifying patterns with sufficient predictive power is a constant challenge for ecologists to address ecological problems related to species conservation, pollution or infectious disease control. During the last years, the amounts of parasitological studies in this sense increased, but they are still scarce in urban environments. The main aim of this study was to investigate if the helminth communities of urban rodents are structured within host assembly (compound community) or they are a result of random events occurring at each individual host scale (infracommunity). A total of 203 rodents belonging to four species, Rattus rattus (Linnaeus), Rattus norvegicus (Berkenhout), Mus musculus Linnaeus and the native Oligoryzomys flavescens (Waterhouse) and captured in different landscape units of the City of Buenos Aires (industrial-residential neighbourhoods, shantytowns and parklands) were analysed. The results showed that infracommunities could be grouped according to composition and relative abundances and that they respond to the structure of the host community. Thus, the component communities defined in this study could be identified as subsets of the compound community (rodent assemblage) and infracommunities (each host) as random samples within each one. Quantitative differences among component communities were denoted by comparing the infection levels of helminths described as central species. Therefore, infracommunities of R. norvegicus and O. flavescens were the most predictable because of the high abundance of the nematodes Heterakis spumosa Schneider, 1866 and Nippostrongylus brasiliensis (Travassos, 1914), and Stilestrongylus flavescens (Sutton et Durette-Desset, 1991), respectively. Several mechanisms contribute to complexity of the structure of parasite communities, where specific parasites, definitive and intermediate hosts, and environmental and anthropogenic factors all play a role in the dynamics of the compound community.

Parasite metacommunities: Evaluating the roles of host community composition and environmental gradients in structuring symbiont communities within amphibians

Ecologists increasingly report the structures of metacommunities for free-living species, yet far less is known about the composition of symbiont communities through space and time. Understanding the drivers of symbiont community patterns has implications ranging from emerging infectious disease to managing host microbiomes. Using symbiont communities from amphibian hosts sampled from wetlands of California, USA, we quantified the effects of spatial structure, habitat filtering and host community components on symbiont occupancy and overall metacommunity structure. We built upon a statistical method to describe metacommunity structure that accounts for imperfect detection in survey data-detection error-corrected elements of metacommunity structure-by adding an analysis to identify covariates of community turnover. We applied our model to a metacommunity of eight parasite taxa observed in 3,571 Pacific chorus frogs (Pseudacris regilla) surveyed from 174 wetlands over 5 years. Symbiont metacommunity structure varied across years, showing nested structure in 3 years and random structure in 2 years. Species turnover was most consistently influenced by spatial and host community components. Occupancy generally increased in more southeastern wetlands, and snail (intermediate host) community composition had strong effects on most symbiont taxa. We have used sophisticated but accessible statistical methods to reveal that spatial components-which influence colonization-and host community composition-which mediates transmission-both drive symbiont community composition in this system. These methods allow us to associate broad patterns of community turnover to local, species-level effects, ultimately improving our understanding of spatial community dynamics.

Interhost dispersal alters microbiome assembly and can overwhelm host innate immunity in an experimental zebrafish model

The diverse collections of microorganisms associated with humans and other animals, collectively referred to as their "microbiome," are critical for host health, but the mechanisms that govern their assembly are poorly understood. This has made it difficult to identify consistent host factors that explain variation in microbiomes across hosts, despite large-scale sampling efforts. While ecological theory predicts that the movement, or dispersal, of individuals can have profound and predictable consequences on community assembly, its role in the assembly of animal-associated microbiomes remains underexplored. Here, we show that dispersal of microorganisms among hosts can contribute substantially to microbiome variation, and is able to overwhelm the effects of individual host factors, in an experimental test of ecological theory. We manipulated dispersal among wild-type and immune-deficient myd88 knockout zebrafish and observed that interhost dispersal had a large effect on the diversity and composition of intestinal microbiomes. Interhost dispersal was strong enough to overwhelm the effects of host factors, largely eliminating differences between wild-type and immune-deficient hosts, regardless of whether dispersal occurred within or between genotypes, suggesting dispersal can independently alter the ecology of microbiomes. Our observations are consistent with a predictive model that assumes metacommunity dynamics and are likely mediated by dispersal-related microbial traits. These results illustrate the importance of microbial dispersal to animal microbiomes and motivate its integration into the study of host-microbe systems.

Predicting cryptic links in host-parasite networks

Networks are a way to represent interactions among one (e.g., social networks) or more (e.g., plant-pollinator networks) classes of nodes. The ability to predict likely, but unobserved, interactions has generated a great deal of interest, and is sometimes referred to as the link prediction problem. However, most studies of link prediction have focused on social networks, and have assumed a completely censused network. In biological networks, it is unlikely that all interactions are censused, and ignoring incomplete detection of interactions may lead to biased or incorrect conclusions. Previous attempts to predict network interactions have relied on known properties of network structure, making the approach sensitive to observation errors. This is an obvious shortcoming, as networks are dynamic, and sometimes not well sampled, leading to incomplete detection of links. Here, we develop an algorithm to predict missing links based on conditional probability estimation and associated, node-level features. We validate this algorithm on simulated data, and then apply it to a desert small mammal host-parasite network. Our approach achieves high accuracy on simulated and observed data, providing a simple method to accurately predict missing links in networks without relying on prior knowledge about network structure.

Elements of metacommunity structure in Amazonian Zygoptera among streams under different spatial scales and environmental conditions

An important aspect of conservation is to understand the founding elements and characteristics of metacommunities in natural environments, and the consequences of anthropogenic disturbance on these patterns. In natural Amazonian environments, the interfluves of the major rivers play an important role in the formation of areas of endemism through the historical isolation of species and the speciation process. We evaluated elements of metacommunity structure for Zygoptera (Insecta: Odonata) sampled in 93 Amazonian streams distributed in two distinct biogeographic regions (areas of endemism). Of sampled streams, 43 were considered to have experienced negligible anthropogenic impacts, and 50 were considered impacted by anthropogenic activities. Our hypothesis was that preserved (“negligible impact”) streams would present a Clementsian pattern, forming clusters of distinct species, reflecting the biogeographic pattern of the two regions, and that anthropogenic streams would present random patterns of metacommunity, due to the loss of more sensitive species and dominance of more tolerant species, which have higher dispersal ability and environmental tolerance. In negligible impact streams, the Clementsian pattern reflected a strong biogeographic pattern, which we discuss considering the areas of endemism of Amazonian rivers. As for communities in human‐impacted streams, a biotic homogenization was evident, in which rare species were suppressed and the most common species had become hyper‐dominant. Understanding the mechanisms that trigger changes in metacommunities is an important issue for conservation, because they can help create mitigation measures for the impacts of anthropogenic activities on biological communities, and so should be expanded to studies using other taxonomic groups in both tropical and temperate systems, and, wherever possible, at multiple spatial scales.

Gastrointestinal helminth fauna of rodents from Cambodia: emphasizing the community ecology of host-parasite associations

Extensive field surveys of rodents were conducted in Cambodia from 2008 to 2014 to study the diversity and ecology of helminth infection in wild rodent populations. Gastrointestinal helminths were isolated from 14 species of rodents (569 individuals) trapped from different habitats (forest, dry land, rain-fed land and human settlements) in four provinces of Cambodia (Krong Preah Sihanouk, Mondolkiri, Pursat and Steung Treng). The average prevalence of parasitic infection was 58.5% (range, 16.0-64.7%), and 19 helminth taxa were identified in total. Trichostrongylid nematodes were the most prevalent (25.8%), followed by Raillietina sp. (14.1%), Gongylonema neoplasticum (10.7%), Syphacia muris (9.8%) and Hymenolepis diminuta (9.6%). Potential rodent-borne zoonotic helminths were also identified, and the risks of helminthiasis were discussed. The status of helminth infection and species diversity in rodents from settlements were significantly lower than in rodents from forest and peri-domesticated habitats, which indicates that habitat alteration might affect helminth infection and diversity in rodent hosts. Generalized linear models revealed that host attributes (host species and maturity) and environmental factors (habitat and geographical location) were explanatory variables for helminth infection in these rodents. Using network analyses, we showed that the oriental house rat, Rattus tanezumi, was the most central host in the rodent-helminth assemblage, based on the number of helminth taxa it shared with other rodent species. Therefore, R. tanezumi could play an important role in rodent-helminth interactions and helminth transmission to other rodent hosts.

Experimental insight into the process of parasite community assembly

Community assembly is a fundamental process that has long been a central focus in ecology. Extending community assembly theory to communities of co-infecting parasites, we used a gastrointestinal nematode removal experiment in free-ranging African buffalo to examine the community assembly patterns and processes. We first asked whether reassembled communities differ from undisturbed communities by comparing anthelmintic-treated and control hosts. Next, we examined the temporal dynamics of assembly using a cross-section of communities that reassembled for different periods of time since last experimental removal. Next, we tested for evidence of assembly processes that might drive such reassembly patterns: environmental filtering based on host traits (i.e. habitat patches), interspecific interactions, priority effects and chance dispersal from the environmental pool of infective stages (i.e. the regional species pool). On average, reassembled parasite communities had lower abundance, but were more diverse and even, and these patterns varied tightly with reassembly time. Over time, the communities within treated hosts progressively resembled controls as diversity and evenness decreased, while total abundance increased. Notably, experimental removal allowed us to attribute observed differences in abundance, diversity and evenness to the process of community assembly. During early reassembly, parasite accumulation was biased towards a subordinate species and, by excluding stochastic assembly processes (i.e. chance dispersal and priority effects), we were able to determine that early assembly is deterministic. Later in the reassembly process, we established that host traits, as well as stochastic dispersal from the environmental pool of infective stages, can affect the community composition. Overall, our results suggest that there is a high degree of resiliency and environmental dependence to the worm communities of buffalo. More generally, our data show that both deterministic and stochastic processes may play a role in the assembly of parasite communities of wild hosts, but their relative importance may vary temporally. Consequently, the best strategy for managing reassembling parasite communities may also need to shift over time.

Influence of host diet and phylogeny on parasite sharing by fish in a diverse tropical floodplain

The patterns of parasite sharing among hosts have important implications for ecosystem structure and functioning, and are influenced by several ecological and evolutionary factors associated with both hosts and parasites. Here we evaluated the influence of fish diet and phylogenetic relatedness on the pattern of infection by parasites with contrasting life history strategies in a freshwater ecosystem of key ecological importance in South America. The studied network of interactions included 52 fish species, which consumed 58 food types and were infected with 303 parasite taxa. Our results show that both diet and evolutionary history of hosts significantly explained parasite sharing; phylogenetically close fish species and/or species sharing food types tend to share more parasites. However, the effect of diet was observed only for endoparasites in contrast to ectoparasites. These results are consistent with the different life history strategies and selective pressures imposed on these groups: endoparasites are in general acquired via ingestion by their intermediate hosts, whereas ectoparasites actively seek and attach to the gills, body surface or nostrils of its sole host, thus not depending directly on its feeding habits.

Complex metacommunity structure for benthic invertebrates in a low-diversity coastal system

The majority of studies in metacommunity ecology have focused on systems other than marine benthic ecosystems, thereby providing an impetus to broaden the focus of metacommunity research to comprise marine systems. These systems are more open than many other systems and may thus exhibit relatively less discrete patterns in community structure across space. Metacommunity structure of soft-sediment benthic invertebrates was examined using a fine-grained (285 sites) data set collected during one summer across a large spatial extent (1700 km2). We applied the elements of metacommunity structure (EMS) approach, allowing multiple hypothesis of variation in community structure to be tested. We demonstrated several patterns associated with environmental variation and associated processes that could simultaneously assemble species to occur at the sites. A quasi-Clementsian pattern was observed frequently, suggesting interdependent ecological relationships among species or similar response to an underlying environmental gradient across sites. A quasi-nested clumped species loss pattern was also observed, which suggests nested habitat specialization. Species richness declined with depth (from 0.5 to 44.8 m). We argue that sensitive species may survive in shallower water, which are more stable with regard to oxygen conditions and present greater habitat complexity, in contrast to deeper waters, which may experience periodic disturbance due to hypoxia. Future studies should better integrate disturbance in terms of temporal dynamics and dispersal rates in the EMS approach. We highlight that shallow water sites may act as sources of recruitment to deeper water sites that are relatively more prone to periodic disturbances due to hypoxia. However, these shallow sites are not currently monitored and should be better prioritized in future conservation strategies in marine systems.

Why infectious disease research needs community ecology

Infectious diseases often emerge from interactions among multiple species and across nested levels of biological organization. Threats as diverse as Ebola virus, human malaria, and bat white-nose syndrome illustrate the need for a mechanistic understanding of the ecological interactions underlying emerging infections. We describe how recent advances in community ecology can be adopted to address contemporary challenges in disease research. These analytical tools can identify the factors governing complex assemblages of multiple hosts, parasites, and vectors, and reveal how processes link across scales from individual hosts to regions. They can also determine the drivers of heterogeneities among individuals, species, and regions to aid targeting of control strategies. We provide examples where these principles have enhanced disease management and illustrate how they can be further extended.

The influence of habitat fragmentation on helminth communities in rodent populations from a Brazilian Mountain Atlantic Forest

The influence of habitat structure on helminth communities of three sigomdontinae rodent species (Akodon cursor, A. montensisandOligoryzomys nigripes) was investigated in forest fragments within an agricultural landscape in south-eastern Brazil. This is a pionner study correlating the occurrence of helminth species of rodent hosts with microhabitat characteristics. Rodents were collected from 12 fragments and in a continuous conserved area. Up to 13 nematode, three cestode and two trematode species were identified, and habitat fragmentation was found to have more influence on the helminth composition ofO. nigripescompared to the other two rodent species. Fragmentation appeared to limit the development of some helminths’ life cycles, e.g. with some species such asTrichofreitasia lenti, Protospirura numidica, Cysticercus fasciolarisandAvellariasp., occurring mostly in areas with less anthropic impact. However, fragmentation did not seem to affect the life cycles of other dominant helminths, such as the trematodeCanaania obesa,the nematodesStilestrongylus lanfrediae,S. etaandS. aculeata,and the cestodeRodentolepis akodontis.The helminth community structure followed a nested pattern of distribution inA. montensisandO. nigripes.Stilestrongylus lanfrediaeseemed to be more associated with dense understorey,C. obesawith open canopy and dense understorey, andGuerrerostrongylus zettawith organic matter on the ground. Their presence in each area may be explained by aspects of their life cycles that take place in the external environment outside the host.