Hierarchical metacommunity structure of fungal endophytes.

The ecological and evolutionary processes shaping community structure and functions of microbial symbionts are known to be scale-dependent. Nonetheless, understanding how the relative importance of these processes changes across spatial scales, and deciphering the hierarchical metacommunity structure of fungal endophytes has proven challenging. We investigated metacommunities of endophytic fungi within leaves of an invasive plant (Alternanthera philoxeroides) across wide latitudinal transects both in its native (Argentina) and introduced (China) ranges to test whether metacommunities of fungal endophytes were structured by different drivers at different spatial scales. We found Clementsian structures with seven discrete compartments (distinctive groups of fungal species with coincident distribution ranges), which coincided with the distribution of major watersheds. Metacommunity compartments were explicitly demarcated at three spatial scales, that is, the between-continent, between-compartment, and within-compartment scales. At larger spatial scales, local environmental conditions (climate, soil, and host plant traits) were replaced by other geographical factors as principal determinants of metacommunity structure of fungal endophytes and community diversity-function relationships. Our results reveal novel insights into the scale dependency of diversity and functions of fungal endophytes, which are likely similar for plant symbionts. These findings can potentially improve our understanding of the global patterns of fungal diversity.

Rapid evolution of latitudinal clines in growth and defence of an invasive weed.

Re-establishment of heritable latitudinal clines in growth-related traits has been recognised as evidence for adaptive evolution in invasive plants. However, less information is known about latitudinal clines in defence and joint clinal evolution of growth and defence in invasive plants. We planted 14 native Argentinean populations and 14 introduced Chinese populations of Alternanthera philoxeroides in replicate common gardens in China. We investigated the latitudinal clines of traits related to growth and defence, and plasticity of these traits in relation to experiment site and soil nitrogen. We found that chemical defence decreased with latitude in introduced populations but increased with latitude in native populations. For growth rate, latitudinal clines were positive in introduced populations but nonexistent in native populations. There were also parallel positive latitudinal clines in total/shoot biomass and specific leaf area. Experiment site affected the occurrence or magnitude of latitudinal clines in growth rate, branch intensity and triterpenoid saponins concentration. Introduced populations were more plastic to experiment site and soil nitrogen than native populations. We provide evidence for rapid evolution of clines in growth and defence in an invasive plant. Altered herbivory gradients and trade-off between growth and defence may explain nonparallel clines between the native and introduced ranges.

Meta-transcriptomic analysis of companion animal infectomes reveals their diversity and potential roles in animal and human disease.

Companion animals such as cats and dogs harbor diverse microbial communities that can potentially impact human health due to close and frequent contact. To better characterize their total infectomes and assess zoonotic risks, we characterized the overall infectomes of companion animals (cats and dogs) and evaluated their potential zoonotic risks. Meta-transcriptomic analyses were performed on 239 samples from cats and dogs collected across China, identifying 24 viral species, 270 bacterial genera, and two fungal genera. Differences in the overall microbiome and infectome composition were compared across different animal species (cats or dogs), sampling sites (rectal or oropharyngeal), and health status (healthy or diseased). Diversity analyses revealed that viral abundance was generally higher in diseased animals compared to healthy ones, while differences in microbial composition were mainly driven by sampling site, followed by animal species and health status. Disease association analyses validated the pathogenicity of known pathogens and suggested potential pathogenic roles of previously undescribed bacteria and newly discovered viruses. Cross-species transmission analyses identified seven pathogens shared between cats and dogs, such as alphacoronavirus 1, which was detected in both oropharyngeal and rectal swabs albeit with differential pathogenicity. Further analyses showed that some viruses, like alphacoronavirus 1, harbored multiple lineages exhibiting distinct pathogenicity, tissue, or host preferences. Ultimately, a systematic evolutionary screening identified 27 potential zoonotic pathogens in this sample set, with far more bacterial than viral species, implying potential health threats to humans. Overall, our meta-transcriptomic analysis reveals a landscape of actively transcribing microorganisms in major companion animals, highlighting key pathogens, those with the potential for cross-species transmission, and possible zoonotic threats. IMPORTANCE: This study provides a comprehensive characterization of the entire community of infectious microbes (viruses, bacteria, and fungi) in companion animals like cats and dogs, termed the "infectome." By analyzing hundreds of samples from across China, the researchers identified numerous known and novel pathogens, including 27 potential zoonotic agents that could pose health risks to both animals and humans. Notably, some of these zoonotic pathogens were detected even in apparently healthy pets, highlighting the importance of surveillance. The study also revealed key microbial factors associated with respiratory and gastrointestinal diseases in pets, as well as potential cross-species transmission events between cats and dogs. Overall, this work sheds light on the complex microbial landscapes of companion animals and their potential impacts on animal and human health, underscoring the need for monitoring and management of these infectious agents.

Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity.

Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Here, using a meta-transcriptomic approach, we determined the viromes of 2,438 individual mosquitoes (81 species), spanning ~4,000 km along latitudes and longitudes in China. From these data we identified 393 viral species associated with mosquitoes, including 7 (putative) species of arthropod-borne viruses (that is, arboviruses). We identified potential mosquito species and geographic hotspots of viral diversity and arbovirus occurrence, and demonstrated that the composition of individual mosquito viromes was strongly associated with host phylogeny. Our data revealed a large number of viruses shared among mosquito species or genera, enhancing our understanding of the host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, perhaps reflecting long-distance mosquito dispersal. Together, these results greatly expand the known mosquito virome, linked viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the biogeography and diversity of viruses in insect vectors.

Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential.

Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within individual bats, and hence the frequency of virus co-infection and spillover among them. We characterize the mammal-associated viruses in 149 individual bats sampled from Yunnan province, China, using an unbiased meta-transcriptomics approach. This reveals a high frequency of virus co-infection (simultaneous infection of bat individuals by multiple viral species) and spillover among the animals studied, which may in turn facilitate virus recombination and reassortment. Of note, we identify five viral species that are likely to be pathogenic to humans or livestock, based on phylogenetic relatedness to known pathogens or in vitro receptor binding assays. This includes a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV and SARS-CoV-2. In vitro assays indicate that this recombinant virus can utilize the human ACE2 receptor such that it is likely to be of increased emergence risk. Our study highlights the common occurrence of co-infection and spillover of bat viruses and their implications for virus emergence.

Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses.

Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Using a meta-transcriptomic approach, we analysed the virome of 2,438 individual mosquitos (79 species), spanning ~4000 km along latitudes and longitudes in China. From these data we identified 393 core viral species associated with mosquitos, including seven (putative) arbovirus species. We identified potential species and geographic hotspots of viral richness and arbovirus occurrence, and demonstrated that host phylogeny had a strong impact on the composition of individual mosquito viromes. Our data revealed a large number of viruses shared among mosquito species or genera, expanding our knowledge of host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, possibly facilitated by long-distance mosquito migrations. Together, our results greatly expand the known mosquito virome, linked the viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the ecology of viruses of insect vectors.

Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses.

Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within bats at the level of individual animals, and hence the frequency of virus co-infection and inter-species transmission. Using an unbiased meta-transcriptomics approach we characterised the mammalian associated viruses present in 149 individual bats sampled from Yunnan province, China. This revealed a high frequency of virus co-infection and species spillover among the animals studied, with 12 viruses shared among different bat species, which in turn facilitates virus recombination and reassortment. Of note, we identified five viral species that are likely to be pathogenic to humans or livestock, including a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV-2 and SARS-CoV, with only five amino acid differences between its receptor-binding domain sequence and that of the earliest sequences of SARS-CoV-2. Functional analysis predicts that this recombinant coronavirus can utilize the human ACE2 receptor such that it is likely to be of high zoonotic risk. Our study highlights the common occurrence of inter-species transmission and co-infection of bat viruses, as well as their implications for virus emergence.

Plant invasion alters latitudinal pattern of plant-defense syndromes.

The relationship between herbivory and latitude may differ between native and introduced populations of invasive plants, which can generate latitudinal heterogeneity in the strength of enemy release. However, still little is known about how latitudinal heterogeneity in herbivore pressure influences latitudinal variation in defense phenotypes of invasive plants. We tested how latitudinal patterns in multi-variate defense syndromes differed between native (Argentinian) and introduced (Chinese) populations of the invasive herb Alternanthera philoxeroides. In addition, to better understand the drivers underlying latitudinal patterns, we also tested whether associations of defense syndromes with climate and herbivory differed between native and introduced ranges. We found that native plant populations clustered into three main defense syndromes associated with latitude. In contrast, we only found two defense syndromes in the introduced range. One matched the high-latitude syndrome from the native range, but was distributed at both the northern and southern range limits in the introduced range. The other was unique to the introduced range and occurred at mid-latitudes. Climatic conditions were associated with variation in syndromes in the native range, and climatic conditions and herbivory were associated with variation in syndromes in the introduced range. Together, our results demonstrate that plants may under the new environmental conditions in the introduced range show latitudinal patterns of defense syndromes that are different from those in their native range. This emphasizes that geographical dependence of population differentiation should be explicitly considered in studies on the evolution of defense in invasive plants.