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1. Experimental work increasingly suggests that non-random pathogen associations can affect the spread or severity of disease. Yet due to difficulties distinguishing and interpreting co-infections, evidence for the presence and directionality of pathogen co-occurrences in wildlife is rudimentary. 2. We provide empirical evidence for pathogen co-occurrences by analysing infection matrices for avian malaria (Haemoproteus and Plasmodium spp.) and parasitic filarial nematodes (microfilariae) in wild birds (New Caledonian Zosterops spp.). 3. Using visual and genus-specific molecular parasite screening, we identified high levels of co-infections that would have been missed using PCR alone. Avian malaria lineages were assigned to species level using morphological descriptions. We estimated parasite co-occurrence probabilities, while accounting for environmental predictors, in a hierarchical multivariate logistic regression. 4. Co-infections occurred in 36% of infected birds. We identified both positively and negatively correlated parasite co-occurrence probabilities when accounting for host, habitat and island effects. Two of three pairwise avian malaria co-occurrences were strongly negative, despite each malaria parasite occurring across all islands and habitats. Birds with microfilariae had elevated heterophil to lymphocyte ratios and were all co-infected with avian malaria, consistent with evidence that host immune modulation by parasitic nematodes facilitates malaria co-infections. Importantly, co-occurrence patterns with microfilariae varied in direction among avian malaria species; two malaria parasites correlated positively but a third correlated negatively with microfilariae. 5. We show that wildlife co-infections are frequent, possibly affecting infection rates through competition or facilitation. We argue that combining multiple diagnostic screening methods with multivariate logistic regression offers a platform to disentangle impacts of environmental factors and parasite co-occurrences on wildlife disease.

Biogeography has traditionally focused on the spatial distribution and abundance of species. Both are driven by the way species interact with one another, but only recently community ecologists realized the need to document their spatial and temporal variation. Here, we call for an integrated approach, adopting the view that community structure is best represented as a network of ecological interactions, and show how it translates to biogeography questions. We propose that the ecological niche should encompass the effect of the environment on species distribution (the Grinnellian dimension of the niche) and on the ecological interactions among them (the Eltonian dimension). Starting from this concept, we develop a quantitative theory to explain turnover of interactions in space and time – i.e. a novel approach to interaction distribution modeling. We apply this framework to host–parasite interactions across Europe and find that two aspects of the environment (temperature and precipitation) exert a strong imprint on species co‐occurrence, but not on species interactions. Even where species co‐occur, interaction proves to be stochastic rather than deterministic, adding to variation in realized network structure. We also find that a large majority of host‐parasite pairs are never found together, thus precluding any inferences regarding their probability to interact. This first attempt to explain variation of network structure at large spatial scales opens new perspectives at the interface of species distribution modeling and community ecology.

We applied a novel framework based on network theory and a concept of modularity that estimates congruence between trait-based ( = functional) co-occurrence networks, thus allowing the inference of co-occurrence patterns and the determination of the predominant mechanism of community assembly. The aim was to investigate the relationships between species co-occurrence and trait similarity in flea communities at various scales (compound communities: across regions within a biogeographic realm or across sampling sites within a geographic region; component communities: across sampling sites within a geographic region; and infracommunities: within a sampling site). We found that compound communities within biogeographic realms were assembled via environmental or host-associated filtering. In contrast, functional and spatial/host-associated co-occurrence networks, at the scale of regional compound communities, mostly indicated either stochastic processes or the lack of dominance of any deterministic process. Analyses of congruence between functional and either spatial (for component communities) or host-associated (for infracommunities) co-occurrence networks demonstrated that assembly rules in these communities varied among host species. In component communities, stochastic processes prevailed, whereas environmental filtering was indicated in 4 and limiting similarity/competition in 9 of 31 communities. Limiting similarity/competition processes dominated in infracommunities, followed by stochastic mechanisms. We conclude that assembly processes in parasite communities are scale-dependent, with different mechanisms acting at different scales.

Ticks prefer specific feeding sites on a host that are influenced by host–tick and tick–tick interactions. This study focused on the spatiotemporal distribution of ticks in Hokkaido sika deer, an important tick host in Hokkaido, Japan. Tick sampling was performed on the sika deer in the Shiretoko National Park between June and October 2022. Ticks were collected from 9 different body parts of the deer to compare their attachment site preferences. Interspecific and intraspecific relationships among ticks were examined using co-occurrence analysis. The collected ticks were nymphal and adult stages of 4 species: Ixodes ovatus , Ixodes persulcatus , Haemaphysalis japonica and Haemaphysalis megaspinosa . Seasonal variations in tick burden were observed, with I. persulcatus and I. ovatus peaking in June and declining towards October; H. japonica showing low numbers in July and August and increasing from September; and H. megaspinosa appearing from September onwards with little variation. Attachment site preferences varied among species, with a significant preference for the pinna in I. ovatus and I. persulcatus . Haemaphysalis japonica was mainly found on the body and legs between June and August, and shifted to the pinna from September. Haemaphysalis megaspinosa showed a general preference for areas other than the legs. Co-occurrence analysis revealed positive, negative and random co-occurrence patterns among the tick species. Ticks of the same genus and species exhibited positive co-occurrence patterns; I. ovatus showed negative co-occurrence patterns with Haemaphysalis spp. This study revealed the unique attachment site preferences and distinct seasonal distributions of tick species in the Hokkaido sika deer.

Strongylid nematodes represent a major health and performance concern for equids globally. However, the epidemiology of strongylid infections in horse populations remains largely unexplored in Thailand. This study investigated the prevalence of strongylid parasites and the associated risk factors in domesticated horses in Thailand. Additionally, the study utilized ITS-2 rDNA metabarcoding to characterize the diversity and co-occurrence patterns of strongylid species. Of the 408 horses examined, 50.98% tested positive for strongyle infection, with an average intensity of 445.67 ± 639.58 eggs. Notably, only 25.74% exhibited fecal egg counts of ≥ 200 eggs per gram (EPG), highlighting the need for targeted deworming protocols. Significantly higher EPG values were observed in yearling horses ( p  = 0.001) and those kept in outdoor pastures ( p  = 0.0001). Metabarcoding identified 15 strongylid species, with Cylicostephanus longibursatus being the most abundant (mean relative abundance: 37.30%, SD = 31.16%). No Strongylus species were detected. Alpha diversity analysis revealed no significant differences in species richness and evenness across horse groups, while beta diversity analysis showed significant dissimilarities ( p  = 0.004), primarily driven by Cylicostephanus longibursatus , Cyathostomum pateratum , and Cylicostephanus calicatus , which contributed to over 60% of the variation. Species co-occurrence patterns were largely random, with a limited number of positive ( n  = 5) and negative ( n  = 2) species pair associations. These findings provide essential insights into the current state of strongylid infections in Thai horses and offer a foundation for future research and management strategies.

Background: Equine strongyles encompass more than 64 species of nematode worms that are responsible for growth retardation and the death of animals. The factors underpinning variation in the structure of the equine strongyle community remain unknown. Methods: Using horse-based strongyle community data collected after horse deworming (48 horses in Poland, 197 horses in Ukraine), we regressed species richness and the Gini-Simpson index upon the horse’s age, faecal egg count, sex and operation of origin. Using the Ukrainian observations, we applied a hierarchical diversity partitioning framework to estimate how communities were remodelled across operations, age groups and horses. Lastly, strongyle species counts collected after necropsy (46 horses in France, 150 in Australia) were considered for analysis of their co-occurrences across intestinal compartments using a joint species distribution modelling approach.Results: First, inter-operation variation accounted for > 45% of the variance in species richness or the Gini-Simpson index (which relates to species dominance in communities). Species richness decreased with horse’s age ( P = 0.01) and showed a mild increase with parasite egg excretion ( P < 0.1), but the Gini-Simpson index was neither associated with parasite egg excretion ( P = 0.8) nor with horse age ( P = 0.37). Second, within-host diversity represented half of the overall diversity across Ukrainian operations. While this is expected to erase species diversity across communities, community dissimilarity between horse age classes was the second most important contributor to overall diversity (25.8%). Third, analysis of species abundance data quantified at necropsy defined a network of positive co-occurrences between the four most prevalent strongyle genera. This pattern was common to necropsies performed in France and Australia. Conclusions: Taken together, these results show a pattern of β-diversity maintenance across age classes combined with positive co-occurrences that might be grounded by priority effects between the major species.

Bat flies (Streblidae) are diverse, obligate blood-feeding insects and probably the most conspicuous ectoparasites of bats. They show preferences for specific body regions on their host bat, which are reflected in behavioural characteristics. In this study, we corroborate the categorization of bat flies into three ecomorphological groups, focusing only on differences in hind leg morphology. As no detailed phylogeny of bat flies is available, it remains uncertain whether these morphological differences reflect the evolutionary history of bat flies or show convergent adaptations for the host habitat type. We show that the division of the host bat into three distinct habitats contributes to the avoidance of interspecific competition of bat fly species. Finally, we found evidence for density-dependent competition between species belonging to the same ecomorphological group.

Meloidogyne graminicola, also known as the rice root-knot nematode, is one of the most damaging plant-parasitic nematode, especially on rice. This obligate soilbome parasite induces the formation of galls that disturb the root morphology and physiology. Its impact on the root microbiome is still not well described. Here, we conducted a survey in Northern Vietnam where we collected infected (with galls) and non-infected root tips from the same plants in three naturally infested fields. Using a metabarcoding approach, we discovered that M. graminicola infection caused modifications of the root bacterial community composition and network structure. Interestingly, we observed in infected roots a higher diversity and species richness (+24% observed ESVs) as well as a denser and more complex co-occurrence network (+44% nodes and +136% links). We identified enriched taxa that include several hubs, which could serve as potential indicators or biocontrol agents of the nematode infection. Moreover, the community of infected roots is more specific suggesting changes in the functional capabilities to survive in the gall environment. We thus describe the signature of the gall microbiome (the 'gallobiome, with shifting abundances and enrichments that lead to a strong restructuration of the root microbiome.

Ginseng is a profitable crop worldwide; however, the ginseng replanting problem (GRP) is a major threat to its production. Soil amendment is a non-chemical method that is gaining popularity for alleviating continuous cropping obstacles, such as GRP. However, the impact of soil amendment with either cow dung or canola on GRP reduction and the associated soil microbiota remains unclear. In the present study, we evaluated the effect of soil amendment with cow dung, canola seed powder, and without amendment (control), on the survival of ginseng seedling transplants, the soil bacterial and fungal communities, and their associated metabolic functions. The results showed that cow dung increased ginseng seedling survival rate by 100 percent and had a remarkable positive effect on ginseng plant growth compared to control, whereas canola did not. Cow dung improved soil nutritional status in terms of pH, electrical conductivity, NO 3 − , total carbon, total phosphorus, and available phosphorus. The amplicon sequencing results using Illumina MiSeq showed that canola had the strongest negative effect in reducing soil bacterial and fungal diversity. On the other hand, cow dung stimulated beneficial soil microbes, including Bacillus , Rhodanobacter , Streptomyces , and Chaetomium , while suppressing Acidobacteriota. Community-level physiological profiling analysis using Biolog Ecoplates containing 31 different carbon sources showed that cow dung soil had a different metabolic activity with higher utilization rates of carbohydrates and polymer carbon sources, mainly Tween 40 and beta-methyl-d-glucoside. These carbon sources were most highly associated with Bacillota. Furthermore, predicted ecological function analyses of bacterial and fungal communities showed that cow dung had a higher predicted function of fermentation and fewer functions related to plant pathogens and fungal parasites, signifying its potential to enhance soil suppressiveness. Co-occurrence network analysis based on random matrix theory (RMT) revealed that cow dung transformed the soil microbial network into a highly connected and complex network. This study is the first to report the alleviation of GRP using cow dung as a soil amendment, and the study contributes significantly to our understanding of how the soil microbiota and metabolic alterations via cow dung can aid in GRP alleviation.

Background Hosts and their parasites are under reciprocal selection, leading to coevolution. However, parasites depend not only on a host, but also on the host’s environment. In addition, a single host species is rarely infested by a single species of parasite and often supports multiple species (i.e., multi-infestation). Although the arms race between a parasite and its host has been well studied, few data are available on how environmental conditions may influence the process leading to multiple infestations. In this study, we examine whether: (1) environmental factors including altitude, temperature, vegetation cover, human disturbance, and grazing by livestock affect the prevalence of two types of ectoparasites, mites and ticks, on their host (the common lizard, Zootoca vivipara ) and (2) competition is evident between mites and ticks. Results We found the probability of mite infestation increased with altitude and vegetation cover, but decreased with human disturbance and presence of livestock. In contrast, the probability of tick infestation was inversely associated with the same factors. Individuals with low body condition and males had higher mite loads. However, this pattern was not evident for tick loads. The results from a structural equation model revealed that mites and ticks indirectly and negatively affected each other’s infestation probability through an interaction involving the environmental context. We detected a direct negative association between mites and ticks only when considering estimates of parasite load. This suggests that both mites and ticks could attach to the same host, but once they start to accumulate, only one of them takes advantage. Conclusion The environment of hosts has a strong effect on infestation probabilities and parasite loads of mites and ticks. Autecological differences between mites and ticks, as indicated by their opposing patterns along environmental gradients, may explain the pattern of weak contemporary interspecific competition. Our findings emphasize the importance of including environmental factors and the natural history of each parasite species in studies of host–parasite coevolution.