Host specialisation and disparate evolution of Pyrenophora teres f. teres on barley and barley grass

Background

Pathogens evolve in an arms race, frequently evolving virulence that defeats resistance genes in their hosts. Infection of multiple hosts may accelerate this virulence evolution. Theory predicts that host diversity affects pathogen diversity, with more diverse hosts expected to harbour more diverse pathogens that reproduce sexually. We tested this hypothesis by comparing the microsatellite (SSR) genetic diversity of the barley leaf pathogen Pyrenophora teres f. teres (Ptt) from barley (monoculture) and barley grass (outbreeding). We also aim to investigate host specificity and attempt to track virulence on two barley cultivars, Maritime and Keel.

Results

Genetic diversity in barley Ptt populations was higher than in populations from barley grass. Barley Ptt populations also had higher linkage disequilibrium levels, indicating less frequent sexual reproduction, consistent with the Red Queen hypothesis theory that genetically diverse hosts should select for higher levels of sexual reproduction of the pathogen. SSR analyses indicate that host-associated Ptt populations do not share genotypes and have independent evolutionary histories. Pathogenicity studies showed host specificity as host-associated Ptt isolates could not cross-infect hosts. Minimum spanning network analyses indicated two major clusters of barley Ptt. One cluster represents Maritime virulent and isolates from Western Australia (WA). Low PhiPt population differentiation between WA populations and those from Maritime and Keel, indicated a WA origin of the Maritime and Keel virulences. The main minimum spanning network cluster is represented by a panmictic population structure, represented by isolates from all over Australia.

Conclusions

Although barley Ptt populations are more diverse than barley grass Ptt populations, this may be a result of the size and number of founder Ptt populations to Australia, with larger and more barley Ptt populations introduced. More frequent sexual reproduction of Ptt on barley grass support the Red Queen Hypothesis and suggest evolutionary potential of pathogens on diverse hosts are high. Extensive gene flow of Ptt between regions in Australia is suggested to maintain a panmictic population structure, with human-mediated dispersal aiding in virulence evolution of Ptt on barley.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1446-8) contains supplementary material, which is available to authorized users.

QTL mapping of mycelial growth and aggressiveness to distinct hosts in Ceratocystis pathogens

Some species of Ceratocystis display strong host specificity, such as C. fimbriata sensu stricto that is restricted to sweet potato (Ipomoea batatas) as host. In contrast, the closely related C. manginecans, infects Acacia mangium and Mangifera indica but is not pathogenic to I. batatas. Despite the economic importance of these fungi, knowledge regarding the genetic factors that influence their pathogenicity and host specificity is limited. A recent inheritance study, based on an interspecific cross between C. fimbriata and C. manginecans and the resultant 70 F₁ progeny, confirmed that traits such as mycelial growth rate, spore production and aggressiveness on A. mangium and I. batatas are regulated by multiple genes. In the present study, a quantitative trait locus (QTL) analysis was performed to determine the genomic loci associated with these traits. All 70 progeny isolates were genotyped with SNP markers and a linkage map was constructed. The map contained 467 SNPs, distributed across nine linkage groups, with a total length of 1203 cm. Using the progeny genotypes and phenotypes, one QTL was identified on the linkage map for mycelial growth rate, one for aggressiveness to A. mangium and two for aggressiveness to I. batatas (P < 0.05). Two candidate genes, likely associated with mycelial growth rate, were identified in the QTL region. The three QTLs associated with aggressiveness to different hosts contained candidate genes involved in protein processing, detoxification and regions with effector genes and high transposable element density. The results provide a foundation for studies considering the function of genes regulating various quantitative traits in Ceratocystis.

A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family

Background

The Iridoviridae family is categorized into five genera and clustered into two subfamilies: Alphairidovirinae includes Lymphocystivirus, Ranavirus (GIV), and Megalocystivirus (TGIV), which infect vertebrate hosts and Betairidovirinae includes Iridovirus and Chloriridovirus, which infect invertebrate hosts. Clustered Iridoviridae subfamilies possess host-specific characteristics, which can be considered as exclusive features for in-silico prediction of effective epitopes for vaccine development. A voting mechanism-based linear epitope (LE) prediction system was applied to identify and endorse LE candidates with a minimum length requirement for each clustered subfamily

Results

The experimental results showed that four conserved epitopes among the Iridovirideae family, one exclusive epitope for invertebrate subfamily and two exclusive epitopes for vertebrate family were predicted. These predicted LE candidates were further validated by ELISA assays for evaluating the strength of antigenicity and cross antigenicity. The conserved LEs for Iridoviridae family reflected high antigenicity responses for the two subfamilies, while exclusive LEs reflected high antigenicity responses only for the host-specific subfamily

Conclusions

Host-specific characteristics are important features and constraints for effective epitope prediction. Our proposed voting mechanism based system provides a novel approach for in silico LE prediction prior to vaccine development, and it is especially powerful for analyzing antigen sequences with exclusive features between two clustered groups.

Long-term prevalence data reveals spillover dynamics in a multi-host (Artemia), multi-parasite (Microsporidia) community

In the study of multi-host parasites, it is often found that host species contribute asymmetrically to parasite transmission. Yet in natural populations, identifying which hosts contribute to parasite transmission and maintenance is a recurring challenge. Here, we approach this issue by taking advantage of natural variation in the composition of a host community. We studied the brine shrimps Artemia franciscana and Artemia parthenogenetica and their microsporidian parasites Anostracospora rigaudi and Enterocytospora artemiae. Previous laboratory experiments had shown that each host can transmit both parasites, but could not predict their actual contributions to the parasites' maintenance in the field. To resolve this, we gathered long-term prevalence data from a metacommunity of these species. Metacommunity patches could contain either or both of the Artemia host species, so that the presence of the hosts could be linked directly to the persistence of the parasites. First, we show that the microsporidian A. rigaudi is a spillover parasite: it was unable to persist in the absence of its maintenance host A. parthenogenetica. This result was particularly striking, as A. rigaudi displayed both high prevalence (in the field) and high infectivity (when tested in the laboratory) in both hosts. Moreover, the seasonal presence of A. parthenogenetica imposed seasonality on the rate of spillover, causing cyclical pseudo-endemics in the spillover host A. franciscana. Second, while our prevalence data was sufficient to identify E. artemiae as either a spillover or a facultative multi-host parasite, we could not distinguish between the two possibilities. This study supports the importance of studying the community context of multi-host parasites, and demonstrates that in appropriate multi-host systems, sampling across a range of conditions and host communities can lead to clear conclusions about the drivers of parasite persistence.

Uncovering Trypanosoma spp. diversity of wild mammals by the use of DNA from blood clots

Trypanosoma spp. infection in wild mammals is detected mainly through parasitological tests that usually display low sensitivity. We propose the use of DNA extracted directly from blood clots (BC), which are neglected sources of DNA for diagnosis and identification of Trypanosoma spp. This approach followed by nested PCR targeting the 18S SSU rDNA demonstrated to be sensitive and suitable to evaluate the diversity of trypanosomes infecting sylvatic mammals, including subpatent and mixed infections. Infection was detected in 95/120 (79.2%) samples from bats, carnivores and marsupials that included negative serological and hemoculture testing mammals. Thirteen Trypanosoma spp. or Molecular Operational Taxonomic Units (MOTUs) were identified, including two new MOTUs. The high diversity of trypanosomes species and MOTUs infecting bats and marsupials showed that these hosts can be considered as bio-accumulators of Trypanosoma spp., with specimens of Didelphis spp. displaying the highest trypanosome diversity. The use of blood clots allowed direct access to non-culturable parasites, mixed infections, besides bypassing the selective pressure on the parasites inherent to cultivation procedures. Trypanosoma cruzi was the species found infecting the highest number of individuals, followed by T. lainsoni. Positive PCR for T. cruzi was observed in 16 seronegative individuals and 30 individuals with negative hemocultures. Also, T. lainsoni, previously found only in rodents, showed to be capable of infecting bats and marsupials. This finding makes it clear that some species of Trypanosoma are more generalist than previously thought. Molecular diagnosis using nested PCR from DNA extracted from BC allowed the increase of the knowledge about host-spectrum and distribution of Trypanosoma spp. and allowed the identification of new MOTUs.

Local host-tick coextinction in neotropical forest fragments

Ticks are obligatory parasites with complex life cycles that often depend on larger bodied vertebrates as final hosts. These traits make them particularly sensitive to local coextinction with their host. Loss of wildlife abundance and diversity should thus lead to loss of tick abundance and diversity to the point where only generalist tick species remain. However, direct empirical tests of these hypotheses are lacking, despite their relevance to our understanding of tick-borne disease emergence in disturbed environments. Here, we compare vertebrate and tick communities across 12 forest islands and peninsulas in the Panama Canal that ranged 1000-fold in size (2.6-2811.3 ha). We used drag sampling and camera trapping to directly assess the abundance and diversity of communities of questing ticks and vertebrate hosts. We found that the abundance and species richness of ticks were positively related to those of wildlife. Specialist tick species were only present in fragments where their final hosts were found. Further, less diverse tick communities had a higher relative abundance of the generalist tick species Amblyomma oblongoguttatum, a potential vector of spotted fever group rickettsiosis. These findings support the host-parasite coextinction hypothesis, and indicate that loss of wildlife can indeed have cascading effects on tick communities. Our results also imply that opportunities for pathogen transmission via generalist ticks may be higher in habitats with degraded tick communities. If these patterns are general, then tick identities and abundances serve as useful bioindicators of ecosystem health, with low tick diversity reflecting low wildlife diversity and a potentially elevated risk of interspecific disease transmission via remaining host species and generalist ticks.

Intermediate host switches drive diversification among the largest trematode family: evidence from the Polypipapiliotrematinae n. subf. (Opecoelidae), parasites transmitted to butterflyfishes via predation of coral polyps

Podocotyloides stenometra Pritchard, 1966 (Digenea: Opecoelidae) is the only trematode known to infect anthozoan corals. It causes disease in coral polyps of the genus Porites Link (Scleractinia: Poritidae) and its life-cycle depends on ingestion of these polyps by butterflyfishes (Perciformes: Chaetodontidae). This species has been reported throughout the Indo-Pacific, from the Seychelles to the Galápagos, but no study has investigated whether multiple species are involved. Here, we recollect P. stenometra from its type-host and type-locality, in Hawaiian waters, and describe four new species from examination of 768 butterflyfishes from French Polynesia. On the basis of morphology, phylogeny and life-history, we propose Polypipapiliotrema Martin, Cutmore & Cribb n. gen. and the Polypipapiliotrematinae Martin, Cutmore & Cribb n. subf., for P. stenometra (Pritchard) n. comb., P. citerovarium Martin, Cutmore & Cribb n. sp., P. hadrometra Martin, Cutmore & Cribb n. sp., P. heniochi Martin, Cutmore & Cribb n. sp., and P. ovatheculum Martin, Cutmore & Cribb n. sp. Given the diversity uncovered here and the ubiquity, abundance and diversity of butterflyfishes on coral reefs, we predict that Polypipapiliotrema will prove to comprise a rich complex of species causing disease in corals across the Indo-Pacific. The unique life-cycle of these taxa is consistent with phylogenetic distinction of the group and provides evidence for a broader basis of diversification among the family. We argue that life-cycle specialisation, in terms of adoption of disparate second intermediate host groups, has been a key driver of the diversification and richness of the Opecoelidae, the largest of all trematode families and the group most frequently encountered in coral reef fishes.

Parvicapsula curvatura n. sp. in cultured olive flounder Paralichthys olivaceus and phylogenetic characteristics of the genus Parvicapsula

Parvicapsula curvatura n. sp. (Myxozoa; Bivalvulida) was found in the urinary bladder of olive flounder Paralichthys olivaceus cultured in a fish farm on Jeju Island, ROK. When laterally viewed, the parasite has asymmetrical curved spores that measure 9.6-11.6 µm in length. Furthermore, it has 2 subspherical polar capsules at the apex. Based on the phenotypical traits, it is most similar to P. limandae but differs in the shape of polar capsule, locality, and host specificity (family level). BLAST analysis indicated that P. curvatura was closest to P. unicornis and P. petuniae via 18S and 28S rDNA sequences, respectively. The 18S rDNA from P. curvatura was used in molecular phylogenetic analyses of Parvicapsula spp. to examine the congruence of phylogeny with spore morphology, locality, and host specificity. The results demonstrated that the spore morphotype was correlated with the phylogeny of the genus Parvicapsula, and the parasites have speciated into an oblong and semicircular spore type.

Evidence for co-invasion events: different chigger species (Actinotrichida, Trombidioidea: trombiculidae) share a host

Cases of co-invasion of various chigger species parasitizing murids and cricetids in various habitats were analysed using morphological and molecular approaches. Here we provide evidence for 25 new cases of co-parasitism of chigger mites on rodent hosts (Myodes glareolus, Apodemus flavicollis, Apodemus agrarius) accounting for 8.6% of all host-parasite associations observed in this study. The results confirm higher incidence of co-parasitism in vertebrate-associated Parasitengona mites compared to arthropod-associated ones. Among factors influencing the occurrence of co-parasitism in Trombiculidae the body constitution and year-round availability of hosts associated with lower host specificity of larvae should be considered.

Complete host specificity test plant list and associated data to assess host specificity of Archanara geminipuncta and Archanara neurica, two potential biocontrol agents for invasive Phragmites australis in North America

Introduced European genotypes of Phragmites australis are invasive and widespread in North America. Decades of management using herbicide and other means have failed to control the species and its range and populations continue to expand. Allowing continued invasion threatens native wetland biota and an endemic North American subspecies Phragmites australis americanus. The lack of conventional management to control introduced P. australis triggered research to assess host specificity of two European noctuid moths, Archanara geminipuncta and Archanara neurica. These two species are considered particularly promising potential biocontrol agents for introduced P. australis. Here we provide the complete and approved list of test plants used to assess host specificity of A. geminipuncta and A. neurica. This includes data on neonate larval acceptance and survival under no-choice conditions, and oviposition tests for all plant species tested, including for different Phragmites subspecies currently occurring in North America. We further provide temperature profiles of select cities in the temperate native European distribution of the two noctuids and those in southern US climates. We used these long-term temperature records to assess whether overwintering eggs of A. geminipuncta and A. neurica can survive under climate conditions typical for the Gulf Coast region in North America. This data article refers to "Host specificity and risk assessment of Archanarageminipuncta and Archanaraneurica, two potential biocontrol agents for invasive Phragmitesaustralis in North America Biol. Control (2018)".

Body size and ecological traits in fleas parasitic on small mammals in the Palearctic: larger species attain higher abundance

We studied the relationships between body size and (a) abundance and (b) host specificity in fleas parasitic on small mammals (rodents and shrews) in the Palearctic taking into account the confounding effect of phylogeny. We tested these relationships both across 127 flea species and within separate phylogenetic clades, predicting higher abundance and lower host specificity (in terms of the number or diversity of hosts used by a flea) in smaller species. We also tested for the relationships between body size and abundance separately for species that spend most of their lives on a host's body (the "body" fleas) and species that spend most of their lives in a host's burrow or nest (the "nest" fleas). A significant phylogenetic signal in body size was detected across all fleas, as well as in five of six separate clades. Across all fleas and in majority of phylogenetic clades, mean abundance significantly increased with an increase in body size. The same pattern was found for both the "body" and the "nest" fleas, although the slope of the relationship appeared to be steeper in the former than in the latter. Neither measure of host specificity demonstrated a significant correlation with body size regardless of the subset of flea species analysed. We explain higher abundance attained by larger flea species by higher fecundity and/or competitive advantage upon smaller species at larval stage. We conclude that the macroecological patterns reported to date in parasites are far from being universal.

Laboulbeniales (Fungi: Ascomycota) infection of bat flies (Diptera: Nycteribiidae) from Miniopterus schreibersii across Europe

BACKGROUND

Bat flies (Diptera: Nycteribiidae and Streblidae) are obligate, blood-sucking ectoparasites of bats with specialized morphology, life-cycle and ecology. Bat flies are occasionally infected by different species of Laboulbeniales (Fungi: Ascomycota), microscopic fungal ectoparasites belonging to three genera: Arthrorynchus spp. are restricted to the Eastern Hemisphere, while species of Gloeandromyces and Nycteromyces occur on Neotropical bat flies. Little is known about the distribution and host specificity of Arthrorynchus spp. on bat flies. In this study, we focused on sampling bat flies from the cave-dwelling bat species Miniopterus schreibersii. Bat and ectoparasite collection took place in Albania, Croatia, Hungary, Italy, Portugal, Slovakia, Spain and Switzerland. Flies were inspected for Laboulbeniales infections.

RESULTS

Six hundred sixty seven bat flies of five species were collected: Nycteribia latreillii, N. pedicularia, N. schmidlii, Penicillidia conspicua, and P. dufourii. Laboulbeniales infection was observed on 60 specimens (prevalence = 9%). Two Laboulbeniales species, Arthrorhynchus eucampsipodae and A. nycteribiae, were present on three bat fly species. All observations of A. eucampsipodae were on N. schmidlii, and A. nycteribiae was present on P. conspicua and P dufourii. Arthrorhynchus eucampsipodae is, for the first time, reported from Slovakia and Spain. Arthrorhynchus nycteribiae represents a new country record for Portugal and Slovakia. There were no significant differences among infection rates in different countries. Females of N. schmidlii showed a higher infection rate than males with an observable trend (P = 0.0502). No sex differences in infection rate for P. conspicua and P. dufourii were detected. Finally, thallus density was significantly lower in N. schmidlii compared to P. conspicua and P. dufourii.

CONCLUSIONS

With this study, we contribute to the knowledge of the geographical distribution and host specificity of Laboulbeniales fungi associated with ectoparasitic bat flies within Europe. We discuss parasite prevalence and host specificity in the light of our findings and the available literature. Penicillidia conspicua is unambiguously the main host species for A. nycteribiae based on our and previous findings. Differences in parasite intensity and sex-biased infections of the fungi are possible depending on the species.

Identification and characterization of new broad host-range rV5-like coliphages C203 and P206 directed against enterobacteria

We isolated and characterized two novel rV5-like lytic bacteriophages from independently collected food samples. Nucleotide sequence analysis revealed that these phages have linear double-stranded DNA genomes comprising 138,073 bp with 213 CDS and 5 tRNA genes. The two genomes contain completely identical nucleotide sequence, albeit there is a 10,718 bp-long shift in the sequence. The GC content of the phage genomes was 43.7% and they showed high general homology to rV5-like phages. The new phages were termed C203 and P206. The genome of both phages contains a unique ORF that encodes for a putative phage homing endonuclease. The phage produced clear plaques with a burst size of approx. 1000 viral particles and a latent period of 60 min. Morphological investigation indicated that the new phages are members of the family Myoviridae with an approximate head length of 85 nm, tail length of 75 nm, and a head width of 96 nm. C203 and P206 exhibit a broad and uniform host range, which included enterohemorrhagic Escherichia coli strains of serogroup O157, multi drug resistant (MDR) E. coli strains of various sero- and pathotypes, and both Shigella sonnei and S. dysenteriae strains. C203 and P206 both effectively reduced the number of living EHEC O157:H7 Sakai in experimentally inoculated minced meat. The same broad host range, the lack of any virulence related genes, the stability and its short latent period suggest that these newly found phages could be suitable candidates as a bio-control agents against food-borne pathogenic Enterobacteria.

Host specificity and species diversity of the Ostertagiinae Lopez-Neyra, 1947 in ruminants: a European perspective

Background

Nematodes of the subfamily Ostertagiinae appear to be rather specific to a species or family of hosts, but some are observed in a wide variety of hosts. The nematode Ostertagia leptospicularis draws special attention due to its presence or absence among the same host species in different European countries. Therefore, this paper focuses mainly on the host specificity among nematodes of the subfamily Ostertagiinae. The second aim of this study is to assess the possibility of treating O. leptospicularis as an Ostertagia species complex.

Methods

Data were gathered from post-mortem examinations of domestic and wild ruminants (n = 157), as well as bibliographical references (n = 96), which were pooled and discussed. The research area was limited to European countries, hence the studied ostertagiine species are limited to native ones; likewise, the host species. Special emphasis was placed on the mean abundance values that allowed a typical host or hosts for each nematode species to be specified. Correspondence analysis was performed to confirm the stated host specificity.

Results

The analysis revealed that nematodes of this subfamily tend to use ruminants from a particular subfamily as their principal host. The results indicate that Ostertagia leptospicularis, similar to Teladorsagia circumcincta, may represent a potential species complex. This nematode, as the sole member of the subfamily Ostertagiinae, occurs in almost all representatives of the Bovidae subfamily, as well as in the Cervidae.

Conclusions

Despite the stated narrow host specificity, the results obtained may suggest that O. leptospicularis is not strongly connected to any host or is comparably associated with a very wide and diverse group of hosts (Cervidae, Bovidae). The Ostertagia complex may have particular cryptic species or strains typical for any individual host or group of hosts. Such a conclusion requires further investigations on a wider scale.

Taxonomic status and epidemiology of the mesoparasitic copepod Pennella balaenoptera in cetaceans from the western Mediterranean

Pennella balaenoptera is a mesoparasitic copepod that has been reported in at least 17 cetacean species. Subtle morphological differences in the first antennae of adult females have been used to discriminate this species from P. filosa, a species infecting fishes. Other morphological traits are unreliable because of their high plasticity, and no molecular data are available to confirm the taxonomic status of P. balaenoptera as an independent species. We found no consistent morphological differences of the first antennae between P. balaenoptera and P. filosa collected from cetaceans and fish in the western Mediterranean. Molecular data on the mitochondrial cytochrome oxidase subunit I failed to show reciprocal monophyly for the 2 species, and nucleotide divergence between them was low (mean ± SD [range]: 4.1 ± 0.006% [0.5-8.9]). Thus, P. balaenoptera and P. filosa are considered conspecific. We also obtained data on infection parameters of P. balaenoptera based on 450 individuals of 6 cetacean species stranded on the Spanish Mediterranean coast between 1980 and 2017. Prevalence was significantly lowest in the most coastal species, the bottlenose dolphin Tursiops truncatus (3.6%) and highest in the most oceanic species, Cuvier's beaked whale Ziphius cavirostris (100%). This suggests that the life cycle of P. balaenoptera is primarily oceanic. Interestingly, P. filosa also occurs in the oceanic realm infecting large fishes. This ecological similarity further supports the hypothesis that P. balaenoptera and P. filosa are conspecific.

Mysteries of host switching: Diversification and host specificity in rodent-coccidia associations

Recent studies show that host switching is much more frequent than originally believed and constitutes an important driver in evolution of host-parasite associations. However, its frequency and ecological mechanisms at the population level have been rarely investigated. We address this issue by analyzing phylogeny and population genetics of an extensive sample, from a broad geographic area, for commonly occurring parasites of the genus Eimeria within the abundant rodent genera Apodemus, Microtus and Myodes, using two molecular markers. At the most basal level, we demonstrate polyphyletic arrangement, i.e. multiple origin, of the rodent-specific clusters within the Eimeria phylogeny, and strong genetic/phylogenetic structure within these lineages determined at least partially by specificities to different host groups. However, a novel and the most important observation is a repeated occurrence of host switches among closely related genetic lineages which may become rapidly fixed. Within the studied model, this phenomenon applies particularly to the switches between the eimerians from Apodemus flavicollis/Apodemus sylvaticus and Apodemus agrarius groups. We show that genetic differentiation and isolation between A. flavicollis/A. sylvaticus and A. agrarius faunas is a secondary recent event and does not reflect host-parasite coevolutionary history. Rather, it provides an example of rapid ecology-based differentiation in the parasite population.

Phytophagous larvae occurring in Central and Southeastern European oak forests as a potential host of Entomophaga maimaiga (Entomophthorales: Entomophthoraceae) - A field study

We evaluated the presence and impact of Entomophaga maimaiga on both target and non-target phytophagous larvae. All six study plots, with low gypsy moth population density, were situated in Central and Southeastern European oak forests and E. maimaiga had previously been reported from these plots. Totally, 45 of 4,045 (1.13%) collected non-target larvae died due to fungal infections. No non-target insect specimen was infected by E.maimaiga, although the presence of the pathogen could not be fully excluded in three cadavers. Out of 1,780L.dispar larvae collected, 15individuals (0.84%) were infected by E.maimaiga.

Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses

BACKGROUND

Influenza viruses are undergoing continuous and rapid evolution. The fatal influenza A/H7N9 has drawn attention since the first wave of infections in March 2013, and raised more grave concerns with its increased potential to spread among humans. Experimental studies have revealed several host and virulence markers, indicating differential host binding preferences which can help estimate the potential of causing a pandemic. Here we systematically investigate the sequence pattern and structural characteristics of novel influenza A/H7N9 using computational approaches.

RESULTS

The sequence analysis highlighted mutations in protein functional domains of influenza viruses. Molecular docking and molecular dynamics simulation revealed that the hemagglutinin (HA) of A/Taiwan/1/2017(H7N9) strain enhanced the binding with both avian and human receptor analogs, compared with the previous A/Shanghai/02/2013(H7N9) strain. The Molecular Mechanics - Poisson Boltzmann Surface Area (MM-PBSA) calculation revealed the change of residue-ligand interaction energy and detected the residues with conspicuous binding preference.

CONCLUSION

The results are novel and specific to the emerging influenza A/Taiwan/1/2017(H7N9) strain compared with A/Shanghai/02/2013(H7N9). Its enhanced ability to bind human receptor analogs, which are abundant in the human upper respiratory tract, may be responsible for the recent outbreak. Residues showing binding preference were detected, which could facilitate monitoring the circulating influenza viruses.

Ecological Complexity in Plant Virus Host Range Evolution

The host range of a plant virus is the number of species in which it can reproduce. Most studies of plant virus host range evolution have focused on the genetics of host-pathogen interactions. However, the distribution and abundance of plant viruses and their hosts do not always overlap, and these spatial and temporal discontinuities in plant virus-host interactions can result in various ecological processes that shape host range evolution. Recent work shows that the distributions of pathogenic and resistant genotypes, vectors, and other resources supporting transmission vary widely in the environment, producing both expected and unanticipated patterns. The distributions of all of these factors are influenced further by competitive effects, natural enemies, anthropogenic disturbance, the abiotic environment, and herbivory to mention some. We suggest the need for further development of approaches that (i) explicitly consider resource use and the abiotic and biotic factors that affect the strategies by which viruses exploit resources; and (ii) are sensitive across scales. Host range and habitat specificity will largely determine which phyla are most likely to be new hosts, but predicting which host and when it is likely to be infected is enormously challenging because it is unclear how environmental heterogeneity affects the interactions of viruses and hosts.

Molecular identification of Sarcocystis lutrae (Apicomplexa: Sarcocystidae) in muscles of five species of the family Mustelidae

Carnivores usually act as definitive hosts of Sarcocystis species. However, the number of reports on sarcocyst formation in musculature of predators is on the increase. In the present study, muscle samples of 68 mustelids collected in Lithuania were examined for sarcocysts of Sarcocystis species. Sarcocysts were detected in diaphragm, tongue and limb muscles of ten animals (14.7%) but were not discovered in the heart. Based on 18S rDNA, 28S rDNA, cox1 and ITS1 sequence analysis, Sarcocystis lutrae was identified in three American minks (Neovison vison), two beech martens (Martes foina), three Eurasian badgers (Meles meles), one Eurasian otter (Lutra lutra) and one European polecat (Mustela putorius). The intraspecific variability of this Sarcocystis species was determined only in ITS1 region. Based on the phylogenetic analysis, no clear separation of S. lutrae by intermediate hosts or geographical locations was established. This paper represents the first identification of S. lutrae in the American mink, the beech marten and the European polecat. Current results indicate that S. lutrae is a common species in the muscles of various European mustelids.

Comparative genomics of 151 plant-associated bacteria reveal putative mechanisms underlying specific interactions between bacteria and plant hosts

Although much work has explored how microbes can benefit plant growth, the mechanisms underlying this intriguing process remain largely unknown, especially considering the diversity of bacteria that surrounds plants. The objective of the present study was to identify bacterial genes contributing to plant-microbe associations, beneficial effects, and host specificities. For this purpose, comparative genomics investigation of 151 plant-associated bacteria was performed. A principal component analysis of seven key genomic features revealed patterns in the specific properties of these bacteria: N₂-fixing bacteria were more closely related to pathogenic ones than to beneficial bacteria. A common set of genes over-represented in these plant-associated bacteria were found to be remarkably similar in terms of (1) genetic information processing, (2) amino acid metabolism, (3) metabolism of cofactors and vitamins, (4) nucleotide metabolism, (5) human diseases, and (6) metabolism of terpenoids and polyketides. Although we did not detect a common genetic basis for these beneficial effects, further in-depth analysis revealed that each of five beneficial bacterial groups shared specific gene sets. Functional annotation showed that environmental information processing, genetic information processing and cellular processes predominated in these beneficial groups. Hypothesizing that plant-associated bacteria may have overlapping strategies to colonize their plant hosts, we successfully identified many putative genes that determine host specificities. Most of these genes were classified as transcription factors, enzymes, transporters, and chemotaxis regulators. Comparative genomics provides a powerful tool for helping to identify genes that are common among species. Genome-based views of plant-associated bacteria reveal specific interactions between bacteria and plant hosts.

Host specificity of Enterocytozoon bieneusi genotypes in Bactrian camels (Camelus bactrianus) in China

BACKGROUND

Enterocytozoon bieneusi is an obligate, intracellular fungus and is commonly reported in humans and animals. To date, there have been no reports of E. bieneusi infections in Bactrian camels (Camelus bactrianus). The present study was conducted to understand the occurrence and molecular characteristics of E. bieneusi in Bactrian camels in China.

RESULTS

Of 407 individual Bactrian camel fecal specimens, 30.0% (122) were E. bieneusi-positive by nested polymerase chain reaction (PCR) based on internal transcriber spacer (ITS) sequence analysis. A total of 14 distinct E. bieneusi ITS genotypes were obtained: eight known genotypes (genotype EbpC, EbpA, Henan-IV, BEB6, CM8, CHG16, O and WL17), and six novel genotypes (named CAM1 to CAM6). Genotype CAM1 (59.0%, 72/122) was the most predominant genotype in Bactrian camels in Xinjiang, and genotype EbpC (18.9%, 23/122) was the second-most predominant genotype. Phylogenetic analysis revealed that six known genotypes (EbpC, EbpA, WL17, Henan-IV, CM8 and O) and three novel genotypes (CAM3, CAM5 and CAM6) fell into the human-pathogenic group 1. Two known genotypes (CHG16 and BEB6) fell into the cattle host-specific group 2. The novel genotypes CAM1, CAM 2 and CAM4 cluster into group 8.

CONCLUSIONS

To our knowledge, this is the first report of E. bieneusi in Bactrian camels. The host-specific genotype CAM1 was the predominant genotype, which plays a negligible role in the zoonotic transmission of E. bieneusi. However, the second-most predominant genotype, EbpC, has greater zoonotic potential.

Inheritance of phenotypic traits in the progeny of a Ceratocystis interspecific cross

Ceratocystis fimbriata is a fungal plant pathogen that causes black rot on Ipomoea batatas. Based on inoculation studies on numerous tree species, the pathogen is known to be host specific. The closely related species, Ceratocystis manginecans, causes severe wilt on a broad range of tree hosts, including Mangifera indica, Acacia mangium and other leguminous tree species. The genetic factors underlying the pathogenicity and host specificity of Ceratocystis species have rarely been investigated. In this study, an F₁ population of 70 recombinant progeny from a cross between C. fimbriata and C. manginecans was generated and the inheritance of various phenotypic traits was investigated. Results showed that colony colour, growth rate, asexual spore production and aggressiveness to I. batatas and A. mangium are all quantitative traits with high levels of heritability. However, conidia production and aggressiveness appeared to be regulated by a small number of genes. No correlation could be found between aggressiveness and other phenotypic traits, suggesting that these are inherited independently. This is the first study to consider genetic inheritance of pathogenicity and host specificity in Ceratocystis species and the results will contribute, in future, to the identification of quantitative trait loci and candidate genes associated with the traits investigated.

Diversity of Mammomonogamus (Nematoda: Syngamidae) in large African herbivores

Four species of Mammomonogamus are known from large African herbivores. A recent study demonstrated that a single Mammomonogamus species was shared by both western lowland gorillas (Gorilla gorilla gorilla) and African forest elephants (Loxodonta cyclotis) in Central African Republic, suggesting lower species diversity than previously described in literature. We examined more than 500 fecal samples collected from sympatric African forest elephants, western lowland gorillas, and African forest buffaloes (Syncerus caffer nanus) at four study sites across Central Africa and examined them by coproscopic methods to detect Mammomonogamus eggs, which were found at three of the study sites. Subsequently, sequences of 18S rDNA, 28S rDNA, and cox1 amplified from individual eggs were analyzed. Phylogenetic analyses of both nuclear and mitochondrial DNA revealed two clades: one formed by sequences originating from Gabonese buffaloes and the other comprising gorillas and elephants. The gorilla-elephant clade was further differentiated depending on the locality. We show the existence of at least two distinct species of Mammomonogamus, M. loxodontis in elephants and gorillas and M. nasicola in buffaloes. The available information on Mammomonogamus in African herbivores is reviewed.

Blood parasite infections in a wild population of ravens (Corvus corax) in Bulgaria

BACKGROUND

Blood parasites have been studied intensely in many families of avian hosts, but corvids, a particularly cosmopolitan family, remain underexplored. Haemosporidian parasites of the common raven (Corvus corax) have not been studied, although it is the largest, most adaptable, and widespread corvid. Genetic sequence data from parasites of ravens can enhance the understanding of speciation patterns and specificity of haemosporidian parasites in corvids, and shed light how these hosts cope with parasite pressure.

METHODS

A baited cage trap was used to catch 86 ravens and a nested PCR protocol was used to amplify a 479 bp fragment of the haemosporidian cytochrome b gene from the samples. The obtained sequences were compared with the MalAvi database of all published haemosporidian lineages and a phylogenetic tree including all detected raven parasites was constructed. An examination of blood smears was performed for assessment of infection intensity.

RESULTS

Twenty blood parasite lineages were recovered from ravens caught in a wild population in Bulgaria. The prevalence of generalist Plasmodium lineages was 49%, and the prevalence of Leucocytozoon lineages was 31%. Out of 13 detected Leucocytozoon lineages six were known from different corvids, while seven others seem to be specific to ravens. A phylogenetic reconstruction suggests that Leucocytozoon lineages of ravens and other corvids are not monophyletic, with some groups appearing closely related to parasites of other host families.

CONCLUSIONS

Several different, morphologically cryptic groups of Leucocytozoon parasites appear to infect corvids. Ravens harbour both generalist corvid Leucocytozoon as well as apparently species-specific lineages. The extraordinary breeding ecology and scavenging lifestyle possibly allow ravens to evade vectors and have relatively low blood parasite prevalence compared to other corvids.

Parasite spread at the domestic animal - wildlife interface: anthropogenic habitat use, phylogeny and body mass drive risk of cat and dog flea (Ctenocephalides spp.) infestation in wild mammals

BACKGROUND

Spillover of parasites at the domestic animal - wildlife interface is a pervasive threat to animal health. Cat and dog fleas (Ctenocephalides felis and C. canis) are among the world's most invasive and economically important ectoparasites. Although both species are presumed to infest a diversity of host species across the globe, knowledge on their distributions in wildlife is poor. We built a global dataset of wild mammal host associations for cat and dog fleas, and used Bayesian hierarchical models to identify traits that predict wildlife infestation probability. We complemented this by calculating functional-phylogenetic host specificity to assess whether fleas are restricted to hosts with similar evolutionary histories, diet or habitat niches.

RESULTS

Over 130 wildlife species have been found to harbour cat fleas, representing nearly 20% of all mammal species sampled for fleas. Phylogenetic models indicate cat fleas are capable of infesting a broad diversity of wild mammal species through ecological fitting. Those that use anthropogenic habitats are at highest risk. Dog fleas, by contrast, have been recorded in 31 mammal species that are primarily restricted to certain phylogenetic clades, including canids, felids and murids. Both flea species are commonly reported infesting mammals that are feral (free-roaming cats and dogs) or introduced (red foxes, black rats and brown rats), suggesting the breakdown of barriers between wildlife and invasive reservoir species will increase spillover at the domestic animal - wildlife interface.

CONCLUSIONS

Our empirical evidence shows that cat fleas are incredibly host-generalist, likely exhibiting a host range that is among the broadest of all ectoparasites. Reducing wild species' contact rates with domestic animals across natural and anthropogenic habitats, together with mitigating impacts of invasive reservoir hosts, will be crucial for reducing invasive flea infestations in wild mammals.

Host specificity in the Giardia duodenalis species complex

Giardia duodenalis is a unicellular flagellated parasite that infects the gastrointestinal tract of a wide range of mammalian species, including humans. Investigations of protein and DNA polymorphisms revealed that G. duodenalis should be considered as a species complex, whose members, despite being morphologically indistinguishable, can be classified into eight groups, or Assemblages, separated by large genetic distances. Assemblages display various degree of host specificity, with Assemblages A and B occurring in humans and many other hosts, Assemblage C and D in canids, Assemblage E in hoofed animals, Assemblage F in cats, Assemblage G in rodents, and Assemblage H in pinnipeds. The factors determining host specificity are only partially understood, and clearly involve both the host and the parasite. Here, we review the results of in vitro and in vivo experiments, and clinical observations to highlight relevant biological and genetic differences between Assemblages, with a focus on human infection.

Taxonomy and Phylogeny of Peronospora Species (Oomycota) Parasitic to Stellaria and Pseudostellaria in Korea, with the Introduction of Peronospora casparyi sp. nov

The genus Peronospora, an obligate biotrophic group belonging to Oomycota, causes serious damage to a variety of wild and ornamental plants, as well as cultivated crops, such as beet, rose, spinach, and tobacco. To investigate the diversity of Peronospora species parasitic to Stellaria and Pseudostellaria (Caryophyllaceae) plants in Korea, we performed a morphological analysis on dried herbarium specimens and molecular phylogenetic inferences based on internal transcribed spacer rDNA and cox2 mitochondrial DNA sequences. As a result, it was confirmed that there are four species of Peronospora parasitic to specific species of Stellaria and Pseudostellaria, all of which were hitherto unrecorded in Korea: P. alsinearum (ex Stellaria media), P. stellariae-aquaticae (ex Stellaria aquatica), P. stellariae-uliginosae (ex Stellaria alsine), and P. pseudostellariae (ex Pseudostellaria palibiniana). In addition, Peronospora specimens parasitic to Pseudostellaria davidii differed morphologically from P. pseudostellariae owing to the large and ellipsoidal conidia; this morphological discrepancy was also validated by the high genetic divergence between the two species. Peronospora casparyi sp. nov. is described and illustrated here.

Host-specific Dactylogyrus parasites revealing new insights on the historical biogeography of Northwest African and Iberian cyprinid fish

Background

Host specificity in parasites represents the extent to which a parasite’s distribution is limited to certain host species. Considering host-specific parasites of primarily freshwater fish (such as gill monogeneans), their biogeographical distribution is essentially influenced by both evolutionary and ecological processes. Due to the limited capacity for historical dispersion in freshwater fish, their specific coevolving parasites may, through historical host-parasite associations, at least partially reveal the historical biogeographical routes (or historical contacts) of host species. We used Dactylogyrus spp., parasites specific to cyprinid fish, to infer potential historical contacts between Northwest African and European and Asian cyprinid faunas. Using phylogenetic reconstruction, we investigated the origin(s) of host-specific Dactylogyrus spp. parasitizing Northwest African and Iberian cyprinid species.

Results

In accordance with hypotheses on the historical biogeography of two cyprinid lineages in Northwest Africa, Barbini (Luciobarbus) and Torini (Carasobarbus), we demonstrated the multiple origins of Northwest African Dactylogyrus. Dactylogyrus spp. of Carasobarbus spp. originated from Asian cyprinids, while Dactylogyrus spp. of Luciobarbus spp. originated from European cyprinids. This indicates the historical Northern route of Dactylogyrus spp. dispersion to Northwest African Luciobarbus species rather than the Southern route, which is currently widely accepted for Luciobarbus. In addition, both Northwest African cyprinid lineages were also colonized by Dactylogyrus marocanus closely related to Dactylogyrus spp. parasitizing African Labeo spp., which suggests a single host switch from African Labeonini to Northwest African Luciobarbus. We also demonstrated the multiple origins of Dactylogyrus spp. parasitizing Iberian Luciobarbus species. One Iberian Dactylogyrus group was phylogenetically closely related to Dactylogyrus of Moroccan Carasobarbus, while the second was related to Dactylogyrus of Moroccan Luciobarbus.

Conclusions

Our study confirms the different origins of two Northwest African cyprinid lineages. It suggests several independent historical contacts between European Iberian Luciobarbus and two lineages of Northwest African cyprinids, these contacts associated with host switches of Dactylogyrus parasites.

Plasmodium reichenowi EBA-140 merozoite ligand binds to glycophorin D on chimpanzee red blood cells, shedding new light on origins of Plasmodium falciparum

Background

All symptoms of malaria are caused by the intraerythrocytic proliferation of Plasmodium merozoites. Merozoites invade erythrocytes using multiple binding ligands that recognise specific surface receptors. It has been suggested that adaptation of Plasmodium parasites to infect specific hosts is driven by changes in genes encoding Plasmodium erythrocyte-binding ligands (EBL) and reticulocyte-binding ligands (RBL). Homologs of both EBL and RBL, including the EBA-140 merozoite ligand, have been identified in P. falciparum and P. reichenowi, which infect humans and chimpanzees, respectively. The P. falciparum EBA-140 was shown to bind human glycophorin C, a minor erythrocyte sialoglycoprotein. Until now, the erythrocyte receptor for the P. reichenowi EBA-140 remained unknown.

Methods

The baculovirus expression vector system was used to obtain the recombinant EBA-140 Region II, and flow cytometry and immunoblotting methods were applied to characterise its specificity.

Results

We showed that the chimpanzee glycophorin D is the receptor for the P. reichenowi EBA-140 ligand on chimpanzee red blood cells.

Conclusions

We propose that the development of glycophorin C specificity is spurred by the P. falciparum lineage. We speculate that the P. falciparum EBA-140 evolved to hijack GPC on human erythrocytes during divergence from its ape ancestor.

The phylogenetic position of the enigmatic Balkan Aulopyge huegelii (Teleostei: Cyprinidae) from the perspective of host-specific Dactylogyrus parasites (Monogenea), with a description of Dactylogyrus omenti n. sp

BACKGROUND

The host specificity of fish parasites is considered a useful parasite characteristic with respect to understanding the biogeography of their fish hosts. Dactylogyrus Diesing, 1850 (Monogenea) includes common parasites of cyprinids exhibiting different degrees of host specificity, i.e. from strict specialism to generalism. The phylogenetic relationships and historical dispersions of several cyprinid lineages, including Aulopyge huegelii Heckel, 1843, are still unclear. Therefore, the aims of our study were to investigate (i) the Dactylogyrus spp. parasites of A. huegelii, and (ii) the phylogenetic relationships of Dactylogyrus spp. parasitizing A. huegelii as a possible tool for understanding the phylogenetic position of this fish species within the Cyprininae lineage.

RESULTS

Two species of Dactylogyrus, D. vastator Nybelin, 1924 and D. omenti n. sp., were collected from 14 specimens of A. huegelii from the Šujica River (Bosnia and Herzegovina). While D. vastator is a typical species parasitizing Carassius spp. and Cyprinus carpio L, D. omenti n. sp. is, according to phylogenetic reconstruction, closely related to Dactylogyrus species infecting European species of Barbus and Luciobarbus. The genetic distance revealed that the sequence for D. vastator from A. huegelii is identical with that for D. vastator from Barbus plebejus Bonaparte, 1839 (Italy) and Carassius gibelio (Bloch, 1782) (Croatia). Dactylogyrus omenti n. sp. was described as a species new to science.

CONCLUSIONS

Our findings support the phylogenetic position of A. huegelii within the Cyprininae lineage and suggest that A. huegelii is phylogenetically closely related to Barbus and Luciobarbus species. The morphological similarity between D. omenti n. sp. and Dactylogyrus species of Middle Eastern Barbus suggests historical contact between cyprinid species recently living in allopatry and the possible diversification of A. huegelii from a common ancestor in this area. On other hand, the genetic similarity between D. vastator ex A. huegelii and D. vastator ex C. gibelio collected in Balkan Peninsula suggests that A. huegelii was secondarily parasitized by D. vastator, originating from C. gibelio after introduction of this fish species from Asia to Europe.

in various animal groups from two French zoos

Cryptosporidium represents a major cause of gastrointestinal illness in humans and animals including domestic, wild, and in captivity animals, and more than 30 validated species of Cryptosporidium are recognized as infectious to different hosts such as mammals, birds, reptiles, amphibians, and fish. Therefore, numerous investigations have been conducted worldwide in order to shed light on the epidemiology of this parasite and to explore its potential reservoirs. Few surveys, targeting humans and animals have been carried out regarding the epidemiology of Cryptosporidium spp. in France and no data are available about the circulation of this parasite in French zoological gardens. Herein, we determined the prevalence of Cryptosporidium in animals housed in two French zoos. A total of 307 fecal samples belonging to 161 species were screened by nested PCR. Overall, Cryptosporidium DNA was detected in 1.9% of the 161 species and 1% of the total number of fecal samples tested. Additionally, three Cryptosporidium species were identified: C. galli, C. andersoni, and C. tyzzeri. To our knowledge, this is the first molecular study focused on Cryptosporidium infection in captivity animals in France. This study is of interest considering the exposure of a large number of humans and animals to this waterborne protozoan, found ubiquitously in the environment.

Population growth rate of dry bulb mite, Aceria tulipae (Acariformes: Eriophyidae), on agriculturally important plants and implications for its taxonomic status

Dry bulb mite (DBM), Aceria tulipae, is an economically important mite with a worldwide distribution and a broad host range. As a generalist, it is the most important eriophyoid mite attacking bulbous plants such as garlic, onion and tulip. To date, DBM has been recorded on host plants belonging to the families Liliaceae, Amaryllidaceae, Melanthiaceae and Asparagaceae. However, a precise understanding of DBM host range is lacking as it is largely based on casual records of mites on plants, some of which may include accidental hosts. Moreover, the possible existence of cryptic species has not been considered. In this study the hypothesis that DBM may be a complex of distinct genetic lineages or cryptic species was tested by comparing the common barcode sequence marker mtDNA COI of specimens from several populations originating from the Netherlands and Poland. The population growth rate of DBM on seven agriculturally important plant species and on various parts of the garlic plant was also experimentally assessed in the laboratory. The results did not support the first hypothesis, and indicated that DBM populations originating from Poland and the Netherlands shared essentially the same genome. In addition, they indicated that DBM reached the highest population growth rate on leek and also displayed high growth rates on garlic, chive and red onion, whereas white onion and wheat were not colonized by the mites. Answering the question of whether DBM is a single polyphagous species rather than a complex of cryptic lineages is of particular importance since the misidentification of pests may lead to ineffective control strategies. Moreover, improved knowledge of DBM host range is essential for assessing risk to crops.

Host specificity, pathogen exposure, and superinfections impact the distribution of Anaplasma phagocytophilum genotypes in ticks, roe deer, and livestock in a fragmented agricultural landscape

Anaplasma phagocytophilum is a bacterial pathogen mainly transmitted by Ixodes ricinus ticks in Europe. It infects wild mammals, livestock, and, occasionally, humans. Roe deer are considered to be the major reservoir, but the genotypes they carry differ from those that are found in livestock and humans. Here, we investigated whether roe deer were the main source of the A. phagocytophilum genotypes circulating in questing I. ricinus nymphs in a fragmented agricultural landscape in France. First, we assessed pathogen prevalence in 1837 I. ricinus nymphs (sampled along georeferenced transects) and 79 roe deer. Prevalence was dramatically different between ticks and roe deer: 1.9% versus 76%, respectively. Second, using high-throughput amplicon sequencing, we characterized the diversity of the A. phagocytophilum genotypes found in 22 infected ticks and 60 infected roe deer; the aim was to determine the frequency of co-infections. Only 22.7% of infected ticks carried genotypes associated with roe deer. This finding fits with others suggesting that cattle density is the major factor explaining infected tick density. To explore epidemiological scenarios capable of explaining these patterns, we constructed compartmental models that focused on how A. phagocytophilum exposure and infection dynamics affected pathogen prevalence in roe deer. At the exposure levels predicted by the results of this study and the literature, the high prevalence in roe deer was only seen in the model in which superinfections could occur during all infection phases and when the probability of infection post exposure was above 0.43. We then interpreted these results from the perspective of livestock and human health.

Relationships among different facets of host specificity in three taxa of haematophagous ectoparasites

Host specificity is a fundamental trait of a parasite species. Recently, multiple aspects of host specificity have been recognized, but the relationships between these facets are still poorly understood. Here, we studied pairwise relationships between basic, structural, phylogenetic and geographic host specificity in three taxa of haematophagous ectoparasitic arthropods that differ in tightness of their association with the host. We asked which metrics of host specificity are correlated within each parasite taxon and whether the patterns of the association between different facets of host specificity are similar among parasite taxa. Data on bat flies were taken from published surveys across the Neotropics while data on fleas and mites parasitic on small mammals were compiled from multiple published surveys across the Palaearctic. Basic, structural, phylogenetic and geographic specificity indices were calculated for 18 bat fly species recorded on 40 host species from 15 regions, 109 flea species recorded on 120 host species from 51 regions and 34 mite species recorded on 67 host species from 28 regions. Then, we tested for the correlation between any two measures of host specificity using model II regressions. We found that structural and basic specificity, as well as structural and geographic specificity, exhibited a positive association in all three taxa. However, basic and geographic specificity, as well as basic and phylogenetic specificity, were significantly positively associated in fleas but did not correlate in bat flies or mites. In addition, we found a significant negative association between structural and phylogenetic specificity in bat flies but no association in the remaining taxa. Moreover, geographic and phylogenetic specificity were not associated in any parasite taxon. Our results suggest that different facets of host specificity were shaped differently by natural selection in different taxa.

Plant-associated odor perception and processing in two parasitoid species with different degrees of host specificity: Implications for host location strategies

Microplitis croceipes and Cotesia marginiventris (Hymenoptera: Braconidae) are parasitoids of lepidopteran larvae with different degrees of host specificity. Both parasitoid species rely on host-related plant volatiles as odor cues to locate their herbivore hosts. To better understand mechanisms of odor processing in parasitoids, we tested responses of olfactory sensory neurons (OSNs) in the antennal sensilla placodea of female parasitoids to select plant volatiles and mixtures. The compounds tested include two green leaf volatiles (i.e., cis-3-hexenol and hexanal) and three herbivore-induced plant volatiles (i.e., cis-3-hexenyl butyrate, cis-3-hexenyl acetate and linalool). Single-sensillum recording showed that the test compounds elicited activity in large and small amplitude neurons housed in the short sensilla placodea of both parasitoid species. In general, C. marginiventris showed greater OSN responses to a low dose while M. croceipes showed greater responses to a high dose of test compounds. Binary mixtures of cis-3-hexenol and linalool inhibited OSN activity in M. croceipes, but not in C. marginiventris. These differences may have implications for odor discrimination in the two parasitoid species. In addition, anterograde neurobiotin stainings were performed to map glomerular projections of OSNs in the antennal lobe of the parasitoids. In M. croceipes, a mixture of cis-3-hexenol and linalool inhibited activity of the glomerulus activated by cis-3-hexenol alone. In C. marginiventris, a mixture of cis-3-hexenol and cis-3-hexenyl acetate showed intense labeling in their respective glomeruli, possibly suggesting a synergistic interaction. These differences in detection and coding of single compounds and mixtures may impact host location strategies in the two parasitoid species.

Phylogenetics of Australasian gall flies (Diptera: Fergusoninidae): Evolutionary patterns of host-shifting and gall morphology

This study investigated host-specificity and phylogenetic relationships in Australian galling flies, Fergusonina Malloch (Diptera: Fergusoninidae), in order to assess diversity and explore the evolutionary history of host plant affiliation and gall morphology. A DNA barcoding approach using COI data from 203 Fergusonina specimens from 5gall types on 56 host plant species indicated 85 presumptive fly species. These exhibited a high degree of host specificity; of the 40 species with multiple representatives, each fed only on a single host genus, 29 (72.5%) were strictly monophagous, and 11 (27.5%) were reared from multiple closely related hosts. COI variation within species was not correlated with either sample size or geographic distance. However variation was greater within oligophagous species, consistent with expectations of the initial stages of host-associated divergence during speciation. Phylogenetic analysis using both nuclear and mitochondrial genes revealed host genus-restricted clades but also clear evidence of multiple colonizations of both host plant genus and host species. With the exception of unilocular peagalls, evolution of gall type was somewhat constrained, but to a lesser degree than host plant association. Unilocular peagalls arose more often than any other gall type, were primarily located at the tips of the phylogeny, and did not form clades comprising more than a few species. For ecological reasons, species of this gall type are predicted to harbor substantially less genetic variation than others, possibly reducing evolutionary flexibility resulting in reduced diversification in unilocular gallers.

Host specificity, molecular phylogeny and morphological differences of Phyllodistomum pseudofolium Nybelin, 1926 and Phyllodistomum angulatum Linstow, 1907 (Trematoda: Gorgoderidae) with notes on Eurasian ruffe as final host for Phyllodistomum spp

Background

Host-specificity patterns are not well-defined for trematodes of the genus Phyllodistomum Braun, 1899. The Eurasian ruffe, Gymnocephalus cernuus L., has been recorded as a definitive host for Phyllodistomum folium (Olfers, 1816), P. angulatum Linstow, 1907 and P. megalorchis Nybelin, 1926 and as the type-host for P. pseudofolium Nybelin (1926). A wide range of other host fishes have been recorded for these species as well. All present host records have been based on light microscopy and the life-cycles of P. pseudofolium, P. angulatum and P. megalorchis are unknown. The validity of P. pseudofolium and P. megalorchis require verification. In this study, rDNA sequences generated from adult Phyllodistomum spp., as well as from larval stages developing in Pisidium amnicum Müller, were analysed to establish the real number of Phyllodistomum species utilizing G. cernuus, and to associate larvae with the corresponding adult forms.

Results

Phylogenetic analyses of adult and larval stages of Phyllodistomum spp. based on ITS2 and partial 28S rDNA data allowed the confirmation of the validity of P. pseudofolium. A macrocercous cercaria, known as Phyllodistomum sp. from P. amnicum is genetically identical to adult P. pseudofolium. Phyllodistomum megalorchis obtained from its type-host, Lota lota L., showed no genetic differences from P. angulatum parasitizing Sander lucioperca L. In our analysis, P. pseudofolium, P. angulatum and P. macrocotyle formed a highly supported clade despite the fact that these species appear to be associated with distinct patterns of first intermediate host identity and cercarial morphology. Some morphological differences between gravid specimens of P. pseudofolium and P. angulatum were observed and their SEM tegumental surface topography is described.

Conclusions

The results lead us to the perception that macroevolutionary host switching in the genus Phyllodistomum is independent of host phylogeny. This study suggests strict host-specificity (oioxeny) for P. pseudofolium using one first intermediate host species (P. amnicum) and one definitive host species (G. cernuus). Phyllodistomum megalorchis is to be regarded as a synonym of P. angulatum. The close phylogenetic relatives, P. pseudofolium and P. angulatum, can be differentiated by morphological traits, the micromorphology and tegumental surface topography of these two species is intended to provide useful data for their identification and support the use of such features as a valuable taxonomic criterion. Molecular data showed that G. cernuus is a definitive host for two species: the oioxenous P. pseudofolium and the euryxenous P. folium.

Parasite fauna of the Antarctic dragonfish Parachaenichthys charcoti (Perciformes: Bathydraconidae) and closely related Bathydraconidae from the Antarctic Peninsula, Southern Ocean

Background

As members of the Notothenioidei - the dominant fish taxon in Antarctic waters - the family Bathydraconidae includes 12 genera and 17 species. The knowledge of these species inhabiting an isolated environment is rather fragmentary, including their parasite fauna. Studies on fish hosts and their associated parasites can help gain insights into even remote ecosystems and be used to infer ecological roles in food webs; however, ecological studies on the Bathydraconidae are scarce.

Results

In this study, stomach contents and parasite fauna of the Antarctic dragonfish species Parachaenichthys charcoti (n = 47 specimens) as well as of Gerlachea australis (n = 5), Gymnodraco acuticeps (n = 9) and Racovitzia glacialis (n = 6) were examined. The parasite fauna of P. charcoti consisted of eight genera represented by 11 species, with three of them being new host records. Overall, 24 parasite genera and 26 species were found in the sampled fish, including eleven new host records.

Conclusion

Analyses revealed that the majority of the parasite species found in the different fish hosts are endemic to Antarctic waters and are characterized by a broad host range. These findings are evidence for the current lack of knowledge and the need for further parasitological studies of fish species in this unique habitat.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-017-2176-7) contains supplementary material, which is available to authorized users.

Biting midges (Ceratopogonidae) as vectors of avian trypanosomes

Background

Although avian trypanosomes are widespread parasites, the knowledge of their vectors is still incomplete. Despite biting midges (Diptera: Ceratopogonidae) are considered as potential vectors of avian trypanosomes, their role in transmission has not been satisfactorily elucidated. Our aim was to clarify the potential of biting midges to sustain the development of avian trypanosomes by testing their susceptibility to different strains of avian trypanosomes experimentally. Moreover, we screened biting midges for natural infections in the wild.

Results

Laboratory-bred biting midges Culicoides nubeculosus were highly susceptible to trypanosomes from the Trypanosoma bennetti and T. avium clades. Infection rates reached 100%, heavy infections developed in 55–87% of blood-fed females. Parasite stages from the insect gut were infective for birds. Moreover, midges could be infected after feeding on a trypanosome-positive bird. Avian trypanosomes can thus complete their cycle in birds and biting midges. Furthermore, we succeeded to find infected blood meal-free biting midges in the wild.

Conclusions

Biting midges are probable vectors of avian trypanosomes belonging to T. bennetti group. Midges are highly susceptible to artificial infections, can be infected after feeding on birds, and T. bennetti-infected biting midges (Culicoides spp.) have been found in nature. Moreover, midges can be used as model hosts producing metacyclic avian trypanosome stages infective for avian hosts.

Comparative profiling of microbial community of three economically important fishes reared in sea cages under tropical offshore environment

The present study was undertaken to evaluate the microbial composition of farmed cobia pompano and milkfish, reared in sea-cages by culture-independent methods. This study would serve as a basis for assessing the general health of fish, identifying the dominant bacterial species present in the gut for future probiotic work and in early detection of potential pathogens. High-throughput sequencing of V3-V4 hyper variable regions of 16S rDNA on Illumina MiSeq platform facilitated unravelling of composite bacterial population. Analysis of 1.3 million quality-filtered sequences revealed high microbial diversity. Characteristic marine fish gut microbes: Vibrio and Photobacterium spp. showed prevalence in cobia and pompano whereas Pelomonas and Fusobacterium spp. dominated the gut of milkfish. Pompano hindgut with 10,537 operational taxonomy units (OTUs) exhibited the highest alpha-diversity index followed by cobia (10,435) and milkfish (2799). Additionally unique and shared OTUs in each gut type were identified. Gammaproteobacteria dominated in cobia and pompano while Betaproteobacteria showed prevalence in milkfish. We obtained 96 shared OTUs among the three species though the numbers of reads were highly variable. These differences in microbiota of farmed fish reared in same environment were presumably due to differences in the gut morphology, physiological behavior and host specificity.

Did biogeographical processes shape the monogenean community of butterflyfishes in the tropical Indo-west Pacific region?

Geographical distribution of parasite species can provide insights into the evolution and diversity of parasitic communities. Biogeography of marine parasites is poorly known, especially because it requires an understanding of host-parasite interactions, information that is rare, especially over large spatial scales. Here, we have studied the biogeographical patterns of dactylogyrid parasites of chaetodontids, one of the most well-studied fish families, in the tropical Indo-west Pacific region. Dactylogyrid parasites were collected from gills of 34 butterflyfish species (n=560) at nine localities within an approximate area of 62millionkm². Thirteen dactylogyrid species were identified, with richness ranging from 6 to 12 species at individual localities. Most dactylogyrid communities were dominated by Haliotrema angelopterum or Haliotrema aurigae, for which relative abundance was negatively correlated (ρ=-0.59). Parasite richness and diversity were highest in French Polynesia and the Great Barrier Reef (Australia) and lowest in Palau. Three biogeographic regions were identified based on dactylogyrid dissimilarities: French Polynesia, characterised by the dominance of H. angelopterum, the western Pacific region dominated by H. aurigae, and Ningaloo Reef (Australia), dominated by Euryhaliotrema berenguelae. Structure of host assemblages was the main factor explaining the dissimilarity (turnover and nestedness components of the Bray-Curtis dissimilarity and overall Bray-Curtis dissimilarity) of parasite communities between localities, while environment was only significant in the turnover of parasite communities and overall dissimilarity. Spatial structure of localities explained only 10% of the turnover of parasite communities. The interaction of the three factors (host assemblages, environment and spatial structure), however, explained the highest amounts of variance of the dactylogyrid communities, indicating a strong colinearity between the factors. Our findings show that spatial arrangement of chaetodontid dactylogyrids in the tropical Indo-west Pacific is primarily characterised by the turnover of the main Haliotrema spp., which is mainly explained by the structure of host assemblages.

Parasites of parasites of bats: Laboulbeniales (Fungi: Ascomycota) on bat flies (Diptera: Nycteribiidae) in central Europe

BACKGROUND

Bat flies (Streblidae and Nycteribiidae) are among the most specialized families of the order Diptera. Members of these two related families have an obligate ectoparasitic lifestyle on bats, and they are known disease vectors for their hosts. However, bat flies have their own ectoparasites: fungi of the order Laboulbeniales. In Europe, members of the Nycteribiidae are parasitized by four species belonging to the genus Arthrorhynchus. We carried out a systematic survey of the distribution and fungus-bat fly associations of the genus in central Europe (Hungary, Romania).

RESULTS

We encountered the bat fly Nycteribia pedicularia and the fungus Arthrorhynchus eucampsipodae as new country records for Hungary. The following bat-bat fly associations are for the first time reported: Nycteribia kolenatii on Miniopterus schreibersii, Myotis blythii, Myotis capaccinii and Rhinolophus ferrumequinum; Penicillidia conspicua on Myotis daubentonii; and Phthiridium biarticulatum on Myotis capaccinii. Laboulbeniales infections were found on 45 of 1,494 screened bat flies (3.0%). We report two fungal species: Arthrorhynchus eucampsipodae on Nycteribia schmidlii, and A. nycteribiae on N. schmidlii, Penicillidia conspicua, and P. dufourii. Penicillidia conspicua was infected with Laboulbeniales most frequently (25%, n = 152), followed by N. schmidlii (3.1%, n = 159) and P. dufourii (2.0%, n = 102). Laboulbeniales seem to prefer female bat fly hosts to males. We think this might be due to a combination of factors: female bat flies have a longer life span, while during pregnancy female bat flies are significantly larger than males and accumulate an excess of fat reserves. Finally, ribosomal DNA sequences for A. nycteribiae are presented.

CONCLUSIONS

We screened ectoparasitic bat flies from Hungary and Romania for the presence of ectoparasitic Laboulbeniales fungi. Arthrorhynchus eucampsipodae and A. nycteribiae were found on three species of bat flies. This study extends geographical and host ranges of both bat flies and Laboulbeniales fungi. The sequence data generated in this work contribute to molecular phylogenetic studies of the order Laboulbeniales. Our survey shows a complex network of bats, bat flies and Laboulbeniales fungi, of which the hyperparasitic fungi are rare and species-poor. Their host insects, on the other hand, are relatively abundant and diverse.

First record of three African trichodinids (Ciliophora: Peritrichida) in cultured Nile tilapia (Oreochromis niloticus) in Saudi Arabia with re-evaluation of their host specificity

Saudi Arabia has a developing aquaculture industry that farms primarily tilapia. Although trichodinids are presumably the most usually encountered protozoan parasites in these cultured fish, they have rarely been studied in this context, and there is no data on the species that might infect cultured tilapia in Saudi Arabia. The present study was therefore carried out as a general survey to investigate the occurrence and identify the species of trichodinids that can infect cultured tilapia (Oreochromis niloticus) in Saudi Arabia. A total of 500 tilapia fish were collected from fish farms in Riyadh city and examined in order to determine the species of trichodinids present in the positive specimens. Three species of trichodinids (Trichodina maritinkae, T. centrostrigeata and T. frenata) were isolated and described as new records in Saudi Arabia. These trichodinids were found simultaneously in the same fish with overall prevalence of 20% (100/500). The identification and characterization of these three species are documented based on Riyadh specimens, for the first time. Additionally, the present paper confirms the existence of T. frenata for the second time globally and establishes this trichodinid as a new parasite for O. niloticus. T. maritinkae is highly specific to clariids, and previously, it has not been reported from any fish species other than clariids. The present work also confirmed that T. centrostrigeata can also infest cichlid fish. The list of host records of these species is expanded and their host specificity re-evaluated based on the results of this study in addition to the previously published data. We conclude that there is a need for further study of the impacts of these Trichodina spp. on Saudi Arabian fishery sector.

Root endophytic fungal communities associated with pitch pine, switchgrass, and rosette grass in the pine barrens ecosystem

Almost all plants in nature harbour fungi in their roots but the knowledge on distribution and the underlying principles of assemblage is still poorly developed for the root-associated fungi. In this study we analysed the root endophytic fungal communities associated with switchgrass, rosette grass, and pitch pine in the acidic, oligotrophic pine barrens ecosystem. A total of 434 fungal isolates were obtained from 600 root segments of 60 plant samples. DNA barcoding and morphological analyses identified 92 fungal species, which belong to 39 genera in six classes. Compared to other ecosystems, the pine barrens has a higher proportion of Leotiomycetes. The fungal community associated with pitch pine was significantly different from those associated with the grasses, while less difference was found between those associated with the two grasses. Our results suggest that edaphic factors and host specificity play a role in shaping root endophytic fungal community. This study also corroborates our previous finding that plant roots in the pine barrens are a rich reservoir of novel fungi.

An assessment of ectomycorrhizal fungal communities in Tasmanian temperate high-altitude Eucalyptus delegatensis forest reveals a dominance of the Cortinariaceae

Fungal diversity of Australian eucalypt forests remains underexplored. We investigated the ectomycorrhizal (EcM) fungal community characteristics of declining temperate eucalypt forests in Tasmania. Within this context, we explored the diversity of EcM fungi of two forest types in the northern highlands in the east and west of the island. We hypothesised that EcM fungal community richness and composition would differ between forest type but that the Cortinariaceae would be the dominant family irrespective of forest type. We proposed that EcM richness would be greater in the wet sclerophyll forest than the dry sclerophyll forest type. Using both sporocarps and EcM fungi from root tips amplified by PCR and sequenced in the rDNA ITS region, 175 EcM operational taxonomic units were identified of which 97 belonged to the Cortinariaceae. The Cortinariaceae were the most diverse family, in both the above and below ground communities. Three distinct fungal assemblages occurred within the wet and dry sclerophyll forest types and two geographic regions that were studied, although this pattern did not remain when only the root tip data were analysed. EcM sporocarp richness was unusually higher than root tip richness and EcM richness did not significantly differ among forest types. The results are discussed in relation to the importance of the Cortinariaceae and the drivers of EcM fungal community composition within these forests.

PCR-activated cell sorting as a general, cultivation-free method for high-throughput identification and enrichment of virus hosts

Characterizing virus-host relationships is critical for understanding the impact of a virus on an ecosystem, but is challenging with existing techniques, particularly for uncultivable species. We present a general, cultivation-free approach for identifying phage-associated bacterial cells. Using PCR-activated cell sorting, we interrogate millions of individual bacteria for the presence of specific phage nucleic acids. If the nucleic acids are present, the bacteria are recovered via sorting and their genomes analyzed. This allows targeted recovery of all possible host species in a diverse population associated with a specific phage, and can be easily targeted to identify the hosts of different phages by modifying the PCR primers used for detection. Moreover, this technique allows quantification of free phage particles, as benchmarked against the "gold standard" of virus enumeration, the plaque assay.

Cyprinid herpesvirus 3 and its evolutionary future as a biological control agent for carp in Australia

Biological invasions are a major threat to global biodiversity. Australia has experienced many invasive species, with the common carp (Cyprinus carpio L.) a prominent example. Cyprinid herpesvirus 3 (CyHV-3) has been proposed as a biological control (biocontrol) agent for invasive carp in Australia. Safety and efficacy are critical factors in assessing the suitability of biocontrol agents, and extensive host-specificity testing suggests that CyHV-3 is safe. Efficacy depends on the relationship between virus transmissibility and virulence. Based on observations from natural outbreaks, as well as the biology of virus-host interactions, we hypothesize that (i) close contact between carp provides the most efficient transmission of virus, (ii) transmission occurs at regular aggregations of carp that favour recrudescence of latent virus, and (iii) the initially high virulence of CyHV-3 will decline following its release in Australia. We also suggest that the evolution of carp resistance to CyHV-3 will likely necessitate the future release of progressively more virulent strains of CyHV-3, and/or an additional broad-scale measure(s) to complement the effect of the virus. If the release of CyHV-3 does go ahead, longitudinal studies are required to track the evolution of a virus-host relationship from its inception, and particularly the complex interplay between transmission, virulence and host resistance.

Geographical, landscape and host associations of Trypanosoma cruzi DTUs and lineages

Background

The evolutionary history and ecological associations of Trypanosoma cruzi, the need to identify genetic markers that can distinguish parasite subpopulations, and understanding the parasite’s evolutionary and selective processes have been the subject of a significant number of publications since 1998, the year when the first DNA sequence analysis for the species was published.

Methods

The current analysis systematizes and re-analyzes this original research, focusing on critical methodological and analytical variables and results that have given rise to interpretations of putative patterns of genetic diversity and diversification of T. cruzi lineages, discrete typing units (DTUs), and populations, and their associations with hosts, vectors, and geographical distribution that have been interpreted as evidence for parasite subpopulation specificities.

Results

Few studies use hypothesis-driven or quantitative analysis for T. cruzi phylogeny (16/58 studies) or phylogeography (10/13). Among these, only one phylogenetic and five phylogeographic studies analyzed molecular markers directly from tissues (i.e. not from isolates). Analysis of T. cruzi DTU or lineage niche and its geographical projection demonstrate extensive sympatry among all clades across the continent and no significant niche differences among DTUs. DTU beta-diversity was high, indicating diverse host assemblages across regions, while host dissimilarity was principally due to host species turnover and to a much lesser degree to nestedness. DTU-host order specificities appear related to trophic or microenvironmental interactions.

Conclusions

More rigorous study designs and analyses will be required to discern evolutionary processes and the impact of landscape modification on population dynamics and risk for T. cruzi transmission to humans.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1918-2) contains supplementary material, which is available to authorized users.

Novel application of species richness estimators to predict the host range of parasites

Host range is a critical life history trait of parasites, influencing prevalence, virulence and ultimately determining their distributional extent. Current approaches to measure host range are sensitive to sampling effort, the number of known hosts increasing with more records. Here, we develop a novel application of results-based stopping rules to determine how many hosts should be sampled to yield stable estimates of the number of primary hosts within regions, then use species richness estimation to predict host ranges of parasites across their distributional ranges. We selected three mistletoe species (hemiparasitic plants in the Loranthaceae) to evaluate our approach: a strict host specialist (Amyema lucasii, dependent on a single host species), an intermediate species (Amyema quandang, dependent on hosts in one genus) and a generalist (Lysiana exocarpi, dependent on many genera across multiple families), comparing results from geographically-stratified surveys against known host lists derived from herbarium specimens. The results-based stopping rule (stop sampling bioregion once observed host richness exceeds 80% of the host richness predicted using the Abundance-based Coverage Estimator) worked well for most bioregions studied, being satisfied after three to six sampling plots (each representing 25 host trees) but was unreliable in those bioregions with high host richness or high proportions of rare hosts. Although generating stable predictions of host range with minimal variation among six estimators trialled, distribution-wide estimates fell well short of the number of hosts known from herbarium records. This mismatch, coupled with the discovery of nine previously unrecorded mistletoe-host combinations, further demonstrates the limited ecological relevance of simple host-parasite lists. By collecting estimates of host range of constrained completeness, our approach maximises sampling efficiency while generating comparable estimates of the number of primary hosts, with broad applicability to many host-parasite systems.