Nucleotide and dinucleotide preference of segmented viruses are shaped more by segment: In case study of tomato spotted wilt virus.

Several studies have showed that the nucleotide and dinucleotide composition of viruses possibly follows their host species or protein coding region. Nevertheless, the influence of viral segment on viral nucleotide and dinucleotide composition is still unknown. Here, we explored through tomato spotted wilt virus (TSWV), a segmented virus that seriously threatens the production of tomatoes all over the world. Through nucleotide composition analysis, we found the same over-representation of A across all viral segments at the first and second codon position, but it exhibited distinct in segments at the third codon position. Interestingly, the protein coding regions which encoded by the same or different segments exhibit obvious distinct nucleotide preference. Then, we found that the dinucleotides UpG and CpU were overrepresented and the dinucleotides UpA, CpG and GpU were underrepresented, not only in the complete genomic sequences, but also in different segments, protein coding regions and host species. Notably, 100% of the data investigated here were predicted to the correct viral segment and protein coding region, despite the fact that only 67% of the data analyzed here were predicted to the correct viral host species. In conclusion, in case study of TSWV, nucleotide composition and dinucleotide preference of segment viruses are more strongly dependent on segment and protein coding region than on host species. This research provides a novel perspective on the molecular evolutionary mechanisms of TSWV and provides reference for future research on genetic diversity of segmented viruses.

TMPRSS2-mediated SARS-CoV-2 uptake boosts innate immune activation, enhances cytopathology, and drives convergent virus evolution.

The accessory protease transmembrane protease serine 2 (TMPRSS2) enhances severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uptake into ACE2-expressing cells, although how increased entry impacts downstream viral and host processes remains unclear. To investigate this in more detail, we performed infection assays in engineered cells promoting ACE2-mediated entry with and without TMPRSS2 coexpression. Electron microscopy and inhibitor experiments indicated TMPRSS2-mediated cell entry was associated with increased virion internalization into endosomes, and partially dependent upon clathrin-mediated endocytosis. TMPRSS2 increased panvariant uptake efficiency and enhanced early rates of virus replication, transcription, and secretion, with variant-specific profiles observed. On the host side, transcriptional profiling confirmed the magnitude of infection-induced antiviral and proinflammatory responses were linked to uptake efficiency, with TMPRSS2-assisted entry boosting early antiviral responses. In addition, TMPRSS2-enhanced infections increased rates of cytopathology, apoptosis, and necrosis and modulated virus secretion kinetics in a variant-specific manner. On the virus side, convergent signatures of cell-uptake-dependent innate immune induction were recorded in viral genomes, manifesting as switches in dominant coupled Nsp3 residues whose frequencies were correlated to the magnitude of the cellular response to infection. Experimentally, we demonstrated that selected Nsp3 mutations conferred enhanced interferon antagonism. More broadly, we show that TMPRSS2 orthologues from evolutionarily diverse mammals facilitate panvariant enhancement of cell uptake. In summary, our study uncovers previously unreported associations, linking cell entry efficiency to innate immune activation kinetics, cell death rates, virus secretion dynamics, and convergent selection of viral mutations. These data expand our understanding of TMPRSS2's role in the SARS-CoV-2 life cycle and confirm its broader significance in zoonotic reservoirs and animal models.

Morpho-physiological studies of sandalwood-host interaction under individual and interactive water and salt stress.

To find out the possibilities of growing white sandalwood in sub-tropical regions of India where farmers facing the problem of water deficit and salinity stress, a RBD experiment was conducted. Sandalwood grown alone and with five selected hosts (Alternanthera sp., Neem, Shisham, Dek and Agarwood) on the basis of prior study under water deficit, salinity stress and combined water deficit and salinity stress. Sandalwood plants were harvested after 180 days of imposing stress treatments. Morphological traits (plant height, collar diameter, shoot fresh and dry biomass) showed significant reduction under water deficit and salinity stress, which were further aggravated under combined water deficit and salinity stress. Studied plant water traits, ionic balance and gas exchange attributes were also reduced by these stresses. While among studied host, Shisham and Dek identified as the best host species under water deficit, salinity and interactive stress by maintaining ion homeostasis, osmotic adjustments and plant water regulation. Results depicted that sandalwood plants cultivated alone were not able to survive under salinity and combined stress conditions and showed poor growth under water deficit and control conditions. Different indices were also calculated based on morpho-physiological and ionic traits and also indicated that sandalwood grown with Dalbergia sissoo and Melia dubia showed higher drought, salt and stress tolerance potential, which made sandalwood adaptable under these stresses. Therefore, the present study signifies the importance of host especially D. sissoo and M. dubia which might be excellent long-term host species for sandalwood cultivation under sub-tropical conditions to thrive under changing environments.

Host Plant Modulated Physio-Biochemical Process Enhances Adaptive Response of Sandalwood (Santalum album L.) under Salinity Stress.

Salinity is one of the most significant abiotic stress that affects the growth and development of high-value tree species, including sandalwood, which can also be managed effectively on saline soils with the help of suitable host species. Therefore, the current investigation was conducted to understand the physiological processes and antioxidant mechanisms in sandalwood along the different salinity gradients to explore the host species that could support sandalwood growth in salt-affected agro-ecosystems. Sandalwood seedlings were grown with ten diverse host species with saline water irrigation gradients (ECiw~3, 6, and 9 dS m-1) and control (ECiw~0.82 dS m-1). Experimental findings indicate a decline in the chlorophyll content (13-33%), relative water content (3-23%), photosynthetic (27-61%) and transpiration rate (23-66%), water and osmotic potential (up to 137%), and ion dynamics (up to 61%) with increasing salinity levels. Conversely, the carotenoid content (23-43%), antioxidant activity (up to 285%), and membrane injury (82-205%) were enhanced with increasing salinity stress. Specifically, among the hosts, Dalbergia sissoo and Melia dubia showed a minimum reduction in chlorophyll content, relative water content, and plant water relation and gas exchange parameters of sandalwood plants. Surprisingly, most of the host tree species maintained K+/Na+ of sandalwood up to moderate water salinity of ECiw~6 dS m-1; however, a further increase in water salinity decreased the K+/Na+ ratio of sandalwood by many-fold. Salinity stress also enhanced the antioxidative enzyme activity, although the maximum increase was noted with host plants M. dubia, followed by D. sissoo and Azadirachta indica. Overall, the investigation concluded that sandalwood with the host D. sissoo can be successfully grown in nurseries using saline irrigation water and, with the host M. dubia, it can be grown using good quality irrigation water.

Avian Influenza A Viruses Modulate the Cellular Cytoskeleton during Infection of Mammalian Hosts.

Influenza is one of the most prevalent causes of death worldwide. Influenza A viruses (IAVs) naturally infect various avian and mammalian hosts, causing seasonal epidemics and periodic pandemics with high morbidity and mortality. The recent SARS-CoV-2 pandemic showed how an animal virus strain could unpredictably acquire the ability to infect humans with high infection transmissibility. Importantly, highly pathogenic avian influenza A viruses (AIVs) may cause human infections with exceptionally high mortality. Because these latter infections pose a pandemic potential, analyzing the ecology and evolution features of host expansion helps to identify new broad-range therapeutic strategies. Although IAVs are the prototypic example of molecular strategies that capitalize on their coding potential, the outcome of infection depends strictly on the complex interactions between viral and host cell factors. Most of the studies have focused on the influenza virus, while the contribution of host factors remains largely unknown. Therefore, a comprehensive understanding of mammals' host response to AIV infection is crucial. This review sheds light on the involvement of the cellular cytoskeleton during the highly pathogenic AIV infection of mammalian hosts, allowing a better understanding of its modulatory role, which may be relevant to therapeutic interventions for fatal disease prevention and pandemic management.

The functional role of Daphnia in the host-pathogen interaction of crayfish and the crayfish plague disease agent (Aphanomyces astaci).

Pathogen spores have been recognized as prey with implications for resource dynamics, energy transfer and disease transmission. In aquatic ecosystems, filter-feeders are able to consume such motile forms of pathogens that can cause severe disease in susceptible hosts. The interactions between European crayfish and the crayfish plague pathogen Aphanomyces astaci are of particular conservation interest. In this study, we aim to evaluate the ecological interactions between Ap. astaci, its host Astacus astacus and individuals of the genus Daphnia, filter-feeding planktonic crustaceans. Our focus was on the consumption of the motile zoospores by Daphnia individuals, but we also considered the potential of Daphnia as non-target hosts. We conducted a series of infection and life-history experiments with Ap. astaci, three Daphnia species (D. magna, D. galeata, and D. pulex) and the noble crayfish As. astacus. We did not observe any lethal effects in the infection experiments involving Ap. astaci and Daphnia. Only D. pulex showed differences in some life-history traits. The feeding experiment using the motile zoospores of Ap. astaci as alternative food source or as supplement to different amounts of algal food revealed their nutritional value: D. magna individuals survived, grew, and reproduced on a zoospore diet alone. When zoospores were supplemented to the regular algal diet, all life-history parameters have been significantly improved. However, this successful consumption of zoospores did not result in a reduced mortality of the susceptible crayfish As. astacus during the infection experiment. Nevertheless, the pathogen load of Ap. astaci in the tissues of As. astacus was significantly reduced as a consequence of the feeding activity of Daphnia. Our results indicate that an abundant filter-feeding community can reduce the amount of infective zoospores in the water body and thus be beneficial to susceptible crayfish hosts, potentially acting as a general buffer against zoospore-transmitted diseases in lentic waters.

Diversity of parasitoid wasps (Insecta, Hymenoptera) in oilseed rape fields in Serbia.

Background: Oilseed rape is an important crop grown worldwide and used for various purposes, including oil extraction and animal feed. In Europe, there are six major pest species and several other minor pests that can significantly affect oilseed rape production, requiring growers to effectively control them in order to ensure crop yield. The host-parasitoid complexes of these pests have been studied in detail and recorded mainly in western, central and northern Europe. As an abundant source of pollen and nectar, oilseed rape may also be attractive to other parasitoids that do not have direct trophic interactions with oilseed rape pest species. The aim of this study is to fill the knowledge gap regarding the wider parasitoid community in oilseed rape fields, particularly in southern Europe. New information: During the two-year study, a total of 3135 specimens of primary and secondary parasitoids were sampled, of which 2855 were found in oilseed rape fields and 280 in semi-natural habitats. We found 153 taxa, of which 119 were found in oilseed rape fields and 87 in semi-natural habitats. We identified 31 genera (33 species) as parasitoids of oilseed rape pests, 54 genera (97 species) parasitising non-pest species and 10 genera (23 species) as possible parasitoids of oilseed rape pests. This study shows that the parasitoid community in oilseed rape fields is very diverse and that includes parasitoids of both oilseed rape pest and non-pest species.

The Role of Some Free-Ranging Animals in the Transmission of Multi-Host Species of Cryptosporidium Spp.

Background: We aimed to characterize Cryptosporidium spp. in rats, cats, pigeons, and crows. Methods: Fifty-five animal origin Cryptosporidium spp. genome were identified, genotyped and confirmed by nested PCR and of RFLP-PCR analysis as well as sequenced based on 18s rRNA and gp60 genes in Tehran (2012-2019). Finally, the phylogenetic analysis was performed by MEGA software (version 7). Results: By the molecular method, Cryptosporidium spp. were detected in 24 (15.2%), 15 (15%), 2 (2%) and 13 (13%) cases of wild rats, cat, pigeon, and crow, respectively. Among the identified species by the RFLP pattern, most isolates were identified as C. parvum (24/157) 17.8% in rats, (15/100) 15% in cats, (13/100) 13%in crew and (2/100) 2% in pigeons; and the rest of the cases were C. muris and C. felis. The results of sequencing did not prove the existence of C. parvum, C. felis, C. muris, and rat genotype. Subtyping of C. parvum was indicated that the dominant subtype family belongs to the IId family and the subtype A20G1 was the most common subtype detected in all hosts while A19G1 was detected in one isolate of cat and pigeon. Conclusion: Free-ranging animals are infected by species/subtype of Cryptosporidium, which can infect humans. This shows by itself the hygienic importance of the free-ranging animals in urban ecosystems. In the transmission of human cryptosporidiosis, the multi-host Cryptosporidium species such as C. parvum, C. felis, and C. muris can be transferred potentially from these animals to humans.

A framework for community curation of interspecies interactions literature.

The quantity and complexity of data being generated and published in biology has increased substantially, but few methods exist for capturing knowledge about phenotypes derived from molecular interactions between diverse groups of species, in such a way that is amenable to data-driven biology and research. To improve access to this knowledge, we have constructed a framework for the curation of the scientific literature studying interspecies interactions, using data curated for the Pathogen-Host Interactions database (PHI-base) as a case study. The framework provides a curation tool, phenotype ontology, and controlled vocabularies to curate pathogen-host interaction data, at the level of the host, pathogen, strain, gene, and genotype. The concept of a multispecies genotype, the 'metagenotype,' is introduced to facilitate capturing changes in the disease-causing abilities of pathogens, and host resistance or susceptibility, observed by gene alterations. We report on this framework and describe PHI-Canto, a community curation tool for use by publication authors.

The increasingly vast amount of data being produced in research communities can be difficult to manage, making it challenging for both humans and computers to organise and connect information from different sources. Currently, software tools that allow authors to curate peer-reviewed life science publications are designed solely for single species, or closely related species that do not interact. Although most research communities are striving to make their data FAIR (Findable, Accessible, Interoperable and Reusable), it is particularly difficult to curate detailed information based on interactions between two or more species (interspecies), such as pathogen-host interactions. As a result, there was a lack of tools to support multi-species interaction databases, leading to a reliance on labour-intensive curation methods. To address this problem, Cuzick et al. used the Pathogen-Host Interactions database (PHI-base), which curates knowledge from the text, tables and figures published in over 200 journals, as a case study. A framework was developed that could capture the many observable traits (phenotype annotations) for interactions and link them directly to the combination of genotypes involved in those interactions across multiple scales ­ ranging from microscopic to macroscopic. This demonstrated that it was possible to build a framework of software tools to enable curation of interactions between species in more detail than had been done before. Cuzick et al. developed an online tool called PHI-Canto that allows any researcher to curate published pathogen-host interactions between almost any known species. An ontology ­ a collection of concepts and their relations ­ was created to describe the outcomes of pathogen-host interactions in a standardised way. Additionally, a new concept called the 'metagenotype' was developed which represents the combination of a pathogen and a host genotype and can be easily annotated with the phenotypes arising from each interaction. The newly curated multi-species FAIR data on pathogen-host interactions will enable researchers in different disciplines to compare and contrast interactions across species and scales. Ultimately, this will assist the development of new approaches to reduce the impact of pathogens on humans, livestock, crops and ecosystems with the aim of decreasing disease while increasing food security and biodiversity. The framework is potentially adoptable by any research community investigating interactions between species and could be adapted to explore other harmful and beneficial interspecies interactions.

Continuous surveillance of potentially zoonotic avian pathogens detects contemporaneous occurrence of highly pathogenic avian influenza viruses (HPAIV H5) and flaviviruses (USUV, WNV) in several wild and captive birds.

Three avian viral pathogens circulate in Germany with particular importance for animal disease surveillance due to their zoonotic potential, their impact on wild bird populations and/or poultry farms: Highly pathogenic (HP) avian influenza virus (AIV) of subtype H5 (HPAIV H5), Usutu virus (USUV), and West Nile virus (WNV). Whereas HPAIV H5 has been mainly related to epizootic outbreaks in winter, the arthropod-borne viruses USUV and WNV have been detected more frequently during summer months corresponding to peak mosquito activity. Since 2021, tendencies of a potentially year-round, i.e. enzootic, status of HPAIV in Germany have raised concerns that Orthomyxoviruses (AIV) and Flaviviruses (USUV, WNV) may not only circulate in the same region, but also at the same time and in the same avian host range. In search of a host species group suitable for a combined surveillance approach for all mentioned pathogens, we retrospectively screened and summarized case reports, mainly provided by the respective German National Reference Laboratories (NRLs) from 2006 to 2021. Our dataset revealed an overlap of reported infections among nine avian genera. We identified raptors as a particularly affected host group, as the genera Accipiter, Bubo, Buteo, Falco, and Strix represented five of the nine genera, and highlighted their role in passive surveillance. This study may provide a basis for broader, pan-European studies that could deepen our understanding of reservoir and vector species, as HPAIV, USUV, and WNV are expected to further become established and/or spread in Europe in the future and thus improved surveillance measures are of high importance.

Rearing Host Dependency of Ovariole Number and Body Size in Campoletis chlorideae Uchida (Hymenoptera: Ichneumonidae).

Campoletis chlorideae has great biocontrol potential against some major noctuid pests. In order to achieve the commercial development and utilization of C. chlorideae, this study focused on the effect of rearing host species and larval instars on the ovariole number and body size of this wasp. Firstly, the morphology of the reproductive system and ovarioles of female wasps were observed. The number of ovarioles displayed great variability and asymmetry between bilateral ovaries. Moreover, the effect of four host species on ovariole number and body size of C. chlorideae were studied. The wasps had a larger ovariole number and body size when reared in Helicoverpa armigera. Additionally, the ovariole number and body size were larger when reared in the third instar larvae than in the first or second instar larvae of H. armigera. There was a strong positive correlation between the ovariole number and body size of C. chlorideae. The ovariole number and body size of the wasp could be improved under optimized artificial rearing conditions. According to these results, body size combined with ovariole number can be used as an important index to evaluate the quality of C. chlorideae. This study provides important clues for the development and application of biocontrol using C. chlorideae.

Co-Surveillance of Rotaviruses in Humans and Domestic Animals in Central Uganda Reveals Circulation of Wide Genotype Diversity in the Animals.

Rotavirus genotypes are species specific. However, interspecies transmission is reported to result in the emergence of new genotypes. A cross-sectional study of 242 households with 281 cattle, 418 goats, 438 pigs, and 258 humans in Uganda was undertaken between 2013 and 2014. The study aimed to determine the prevalence and genotypes of rotaviruses across co-habiting host species, as well as potential cross-species transmission. Rotavirus infection in humans and animals was determined using NSP3 targeted RT-PCR and ProSpecT Rotavirus ELISA tests, respectively. Genotyping of rotavirus-positive samples was by G- and P-genotype specific primers in nested RT-PCR assays while genotyping of VP4 and VP7 proteins for the non-typeable human positive sample was done by Sanger sequencing. Mixed effect logistic regression was used to determine the factors associated with rotavirus infection in animals. The prevalence of rotavirus was 4.1% (95% CI: 3.0-5.5%) among the domestic animals and 0.8% (95% CI: 0.4-1.5%) in humans. The genotypes in human samples were G9P[8] and P[4]. In animals, six G-genotypes, G3(2.5%), G8(10%), G9(10%), G11(26.8%), G10(35%), and G12(42.5%), and nine P-genotypes, P[1](2.4%), P[4](4.9%), P[5](7.3%), P[6](14.6%), P[7](7.3%), P[8](9.8%), P[9](9.8%), P[10](12.2%), and P[11](17.1%), were identified. Animals aged 2 to 18 months were less likely to have rotavirus infection in comparison with animals below 2 months of age. No inter-host species transmission was identified.

Risk factors for Lyme disease: A scale-dependent effect of host species diversity and a consistent negative effect of host phylogenetic diversity.

Biodiversity can influence disease risk. One example of a diversity-disease relationship is the dilution effect, which suggests higher host species diversity (often indexed by species richness) reduces disease risk. While numerous studies support the dilution effect, its generality remains controversial. Most studies of diversity-disease relationships have overlooked the potential importance of phylogenetic diversity. Furthermore, most studies have tested diversity-disease relationships at one spatial scale, even though such relationships are likely scale dependent. Using Lyme disease as a model system, we investigated the effects of host species richness and phylogenetic relatedness on the number of reported Lyme disease cases in humans in the U.S.A. at two spatial scales (the county level and the state level) using piecewise structural equation modelling. We also accounted for relevant climatic and habitat-related factors and tested their correlations with the number of Lyme disease cases. We found that species assemblages with more related species (i.e., host species in the order Rodentia) were associated with more Lyme disease cases in humans. Host species richness correlated negatively with the number of Lyme disease cases at the state level (i.e., a dilution effect), a pattern that might be explained by the higher number of reservoir-incompetent species at high levels of species richness at this larger spatial scale. In contrast, a positive correlation was found between species richness and the number of Lyme disease cases at the county level, where a higher proportion of rodent species was associated with higher levels of species richness, potentially amplifying the disease risk. Our results highlight that analyse at a single spatial scale can miss some impacts of biodiversity on human health. Thus, multi-scale analyses with consideration of host phylogenetic diversity are critical for improving our understanding of diversity-disease relationships.

Potential host range of Cotesia vanessae (Hymenoptera: Braconidae), a parasitoid new to North America and a possible biological control agent of noctuid pest species.

The likelihood of parasitoids establishing in new geographic regions depends upon the availability of suitable host species. Identifying these hosts and the degree of their suitability is particularly important when they include species that are economically important as pests. In laboratory studies, we examined the suitability of 47 species of Lepidoptera as potential hosts of a parthenogenetic strain of the gregarious parasitoid Cotesia vanessae (Hymenoptera: Braconidae). Previously known from Eurasia and northern Africa, the first known recovery of C. vanessae in North America was in 2009. C. vanessae completed development in 34 species, of which three were known hosts (Noctuidae) and 31 (30 Noctuidae, 1 Nymphalidae) were not. Many of these noctuid species are economic pests. Parasitoid fitness was generally highest on species of Plusiinae (Noctuidae), measured as either percentage of successful parasitism, developmental time, or number and mass of F1 progeny. Closely related species were generally similar in their suitability as hosts. In some cases, parasitoid eggs or larvae were killed by the immune system of the parasitized host, but the host eventually failed to excrete food waste, did not pupate, and ultimately died. Such cases reached up to 100% mortality depending upon the lepidopteran species. The suitability of many species of noctuid pests as hosts for C. vanessae suggests that this parasitoid will become established widely throughout North America and may help to suppress populations of some pest species.

RNA Sequencing Reveals the Potential Adaptation Mechanism to Different Hosts of Grapholita molesta.

Grapholita molesta is an important fruit tree worldwide pest which feeds on hosts extensively and does serious harm. In this paper, the growth and development parameters and protease activities of G. molesta fed on different hosts were compared. Using Illumina RNA sequencing technology, 18 midgut samples from five different hosts (apple, pear, plum, peach and peach shoots) and artificial diet were sequenced and compared with the reference genome, resulting in 15269 genes and 2785 predicted new genes. From 15 comparative combinations, DEGs were found from 286 to 4187 in each group, with up-regulated genes from 107 to 2395 and down-regulated genes from 83 to 2665. KEGG pathway analysis showed that DEGs were associated with amino acid metabolism, starch and sucrose metabolism, carbohydrate metabolism, and hydrolase activity. A total of 31 co-expression gene modules of different hosts were identified by WGCNA. qRT-PCR showed that the expression pattern of the trypsin gene was consistent with RNA sequencing. In this study, growth and development parameters, protease activity, DEGs, enrichment analysis and qRT-PCR were combined to reveal the adaptation process to different hosts of G. molesta in many aspects. The results of this study provide a basis for further exploration of the molecular mechanism of host adaptation of G. molesta.

Investigation of Gut Bacterial Communities of Asian Citrus Psyllid (Diaphorina citri) Reared on Different Host Plants.

Diaphorina citri Kuwayama (Hemiptera: Liviidae) can cause severe damage to citrus plants, as it transmits Candidatus Liberibacter spp., a causative agent of Huanglongbing disease. Symbiotic bacteria play vital roles in the ecology and biology of herbivore hosts, thereby affecting host growth and adaptation. In our research, the effects of Rutaceous plants (i.e., Citrus reticulata cv. Shatangju, Citrus poonensis cv. Ponkan, Murraya paniculata (orange jasmine), Citrus limon (lemon), and Citrus sinensis (navel orange)) on the gut microbiota (GM) and microbial diversity of D. citri adults were investigated by 16S rRNA high-throughput sequencing. It was found that Proteobacteria dominated the GM communities. The gut microbe diversity was the highest in the ponkan-feeding population, and the lowest in the Shatangju-feeding population. The NMDS analysis revealed that there were obvious differences in the GM communities among the different hosts. PICRUSt function prediction indicated significant differences in host function, and those pathways were crucial for maintaining population reproduction, growth, development, and adaptation to environmental stress in D. citri. Our study sheds new light on the interactions between symbionts, herbivores, and host plants and expands our knowledge on host adaptation related to GM in D. citri.

Host Species Influence the Gut Microbiota of Endemic Cold-Water Fish in Upper Yangtze River.

The fish gut microbiome plays an important role in nutrition absorption and energy metabolism. Studying the gut microbes of cold-water fish is important to understand the dietary adaptation strategies in extreme environments. In this study, the gut samples of Schizothorax wangchiachii (SW, herbivorous), Schizothorax kozlovi (SK, omnivorous), and Percocypris pingi (PP, carnivorous) in the upper Yangtze River were collected, and we sequenced 16S rRNA amplicon to study the potential relationship between gut microbes and host species. The results showed that gut microbial composition and diversity were significantly different between the three cold-water fishes. These fishes had different key taxa in their gut microbes, including bacteria involved in the breakdown of food (e.g., Cetobacterium, Aeromonas, and Clostridium sensu stricto 10). The highest alpha diversity indices (e.g., Chao 1 index) were identified in the herbivore (SW), followed by the carnivore (PP), and the lowest in the omnivore (SK). Non-metric multidimensional scaling (NMDS) results revealed that the gut microbial community of these species was different between host species. The neutral community model (NCM) showed that the microbial community structure of SW was shaped by stochastic processes, and the highest species dispersal was found in SW, followed by PP, and the lowest in SK. The results of niche breadth agreed with these findings. Our results demonstrated that host species influenced the gut microbiome composition, diversity, and microbial community assembly processes of the three cold-water fishes. These findings implied that the variation of gut microbiome composition and function plays a key role in digesting and absorbing nutrients from different foods in cold-water fish.

Accommodating sampling location uncertainty in continuous phylogeography.

Phylogeographic inference of the dispersal history of viral lineages offers key opportunities to tackle epidemiological questions about the spread of fast-evolving pathogens across human, animal and plant populations. In continuous space, i.e. when locations are specified by longitude and latitude, these reconstructions are however often limited by the availability or accessibility of precise sampling locations required for such spatially explicit analyses. We here review the different approaches that can be considered when genomic sequences are associated with a geographic area of sampling instead of precise coordinates. In particular, we describe and compare the approaches to define homogeneous and heterogeneous prior ranges of sampling coordinates.

Phyllosphere bacterial and fungal communities vary with host species identity, plant traits and seasonality in a subtropical forest.

BACKGROUND: Phyllosphere microbes play important roles in host plant performance and fitness. Recent studies have suggested that tropical and temperate forests harbor diverse phyllosphere bacterial and fungal communities and their assembly is driven by host species identity and plant traits. However, no study has yet examined how seasonality (e.g. dry vs. wet seasons) influences phyllosphere microbial community assembly in natural forests. In addition, in subtropical forests characterized as the transitional zonal vegetation type from tropical to temperate forests, how tree phyllosphere microbial communities are assembled remains unknown. In this study, we quantified bacterial and fungal community structure and diversity on the leaves of 45 tree species with varying phylogenetic identities and importance values within a 20-ha lower subtropical evergreen broad-leaved forest plot in dry and wet seasons. We explored if and how the microbial community assembly varies with host species identity, plant traits and seasonality. RESULTS: Phyllosphere microbial communities in the subtropical forest are more abundant and diverse than those in tropical and temperate forests, and the tree species share a "core microbiome" in either bacteria or fungi. Variations in phyllosphere bacterial and fungal community assembly are explained more by host species identity than by seasonality. There is a strong clustering of the phyllosphere microbial assemblage amongst trees by seasonality, and the seasonality effects are more pronounced on bacterial than fungal community assembly. Host traits have different effects on community compositions and diversities of both bacteria and fungi, and among them calcium concentration and importance value are the most powerful explaining variables for bacteria and fungi, respectively. There are significant evolutionary associations between host species and phyllosphere microbiome. CONCLUSIONS: Our results suggest that subtropical tree phyllosphere microbial communities vary with host species identity, plant traits and seasonality. Host species identity, compared to seasonality, has greater effects on phyllosphere microbial community assembly, and such effects differ between bacterial and fungal communities. These findings advance our understanding of the patterns and drivers of phyllosphere microbial community assembly in zonal forests at a global scale.

Similar gut bacteria composition in Apriona germari on two preferred host plants.

Apriona germari is one of the most serious wood-boring pests that cause damage to economic and landscaping trees and has adapted to a wide range of plants as diet. Gut bacteria play an important role in biology and ecology of herbivores, especially in growth and adaptation. To investigate how plant hosts shape A. germari gut microbiota, A. germari larvae were collected from Populus tomentosa and Malus pumilal, and gut microbiomes were sequenced based on 16S rDNA high-throughput sequencing technology. A total of 853,424 high-quality reads were obtained and clustered into 196 operational taxonomic units under a 97% similarity cutoff, which were annotated into 8 phyla, 10 classes, 21 orders, 34 families, 59 genera, and 39 species. Gibbsiella was the most dominant genus of intestinal bacteria, followed by Enterobacter and Acinetobacter. No significant difference was observed in larvae gut bacterial richness and diversity of A. germari collected from two hosts, though alpha diversity showed that the richness of gut bacteria in A. germari larvae collected on P. tomentosa was slightly higher than that in A. germari on M. pumilal, and beta diversity showed little difference between two host plants. The functional abundance analysis of the detected bacteria revealed fermentation, chemoheterotrophy, symbionts, and nitrate relative functions that highly possibly support wood-boring beetles to feed on woody tissues. Our study provided a theoretical basis for investigating the function of intestinal symbiosis bacteria of A. germari.