Embryonic heart rate of plaintive cuckoo is lower than that of its four host species in the Southwest China

Generalist mistletoes and their hosts and potential hosts in an urban area in southwest China

Leptotrombidium imphalum is a species of chigger mites, and it can serve as a transmitting vector of scrub typhus. Southwest China is an important focus of scrub typhus. Based on the field investigation in southwest China from 2001 to 2022, this article presents the first report on the distribution and infestation of L. imphalum on rodents and other sympatric small mammals in the region. A total of 2161 L. imphalum were identified from 218 small mammal hosts in 21 of 114 survey sites. The 17 host species of L. imphalum crossed 13 genera and 5 families in 3 orders (Rodentia, Eulipotyphla, and Scandentia), indicating the low host specificity of the mite. The Asian house rat (Rattus tanezumi) was the dominant host species in the 21 sites where L. imphalum were collected, and 49.38% of mites were found on R. tanezumi. Different small mammals had different susceptibility to the infestation of L. imphalum. The prevalence (PM = 27.66%), infestation mean abundance (MA = 6 mites/per examined host), and mean intensity (MI = 21.69 mites/per infested host) for L. imphalum on the shrew gymnure (Neotetracus sinensis) were much higher than those on other host species (p < 0.05), indicating N. sinensis had a high susceptibility to the infestation of L. imphalum. The infestation indices for L. imphalum on small mammal hosts varied along different altitude and latitude gradients (p < 0.05), indicating the environmental heterogeneity of the mite infestation. Leptotrombidium imphalum exhibited an aggregated distribution among different individuals of its hosts. Besides the low host specificity of L. imphalum, the prevalence of the mite was positively correlated with the occurrence of scrub typhus, indicating the potential risk of the mite.

Urbanization not only profoundly alters landscape profiles, ecosystems and vertebrate faunal diversity but also disturbs microbial communities by increasing stochasticity, vulnerability, biotic homogenization, etc. However, because of the buffering effect of host species, microbial communities are expected to be influenced by both host species and urbanization stresses. Therefore, the impacts of urbanization on animals’ microbial symbionts could be more complex and uncertain. In this study, we quantified the urbanization degree of sampling sites and surveyed the gut and skin microbes of three amphibian host species in different sites in urban parks and nearby villages of Chengdu, Southwest China. Furthermore, a co-occurrence network analysis, the phylogenetic normalized stochasticity ratio and Sloan neutral community models were applied to infer the impact of urbanization on symbiotic microbial communities. For the three host species, urbanization increased the diversity of symbiotic microbes and the number of keystone microbial taxa. However, the negative effects of such increased diversification were evident, as the community stochasticity and co-occurrence network structure vulnerability also increased, while the network structure complexity and stability were reduced. Finally, the community stochasticity had positive associations with the network vulnerability, implying that the existence of many transient symbiotic rare microbial taxa in urban parks makes the symbiotic microbial community structure more fragile. Conclusively, urbanization increased the symbiotic microbial diversity at the cost of community stability; the results provide a new perspective for better understanding the complex triangulated environment–host–microbe relationship.

Comparing gene expressions among parasitic plants infecting different host species can have significant implications for understanding host–parasite interactions. Taxillus nigrans is a common hemiparasitic species in Southwest China that parasitizes a variety of host species. However, a lack of nucleotide sequence data to date has hindered transcriptome-level research on T. nigrans. In this study, the transcriptomes of T. nigrans individuals parasitizing four typical host species (Broussonetia papyrifera (Bpap), a broad-leaved tree species; Cryptomeria fortunei (Cfor), a coniferous tree species; Cinnamomum septentrionale (Csep), an evergreen tree species; and Ginkgo biloba (Gbil), a deciduous-coniferous tree species) were sequenced, and the expression profiles and metabolic pathways were compared among hosts. A total of greater than 400 million reads were generated in nine cDNA libraries. These were de novo assembled into 293823 transcripts with an N50 value of 1790 bp. A large number of differentially expressed genes (DEGs) were identified when comparing T. nigrans individuals on different host species: Bpap vs. Cfor (1253 DEGs), Bpap vs. Csep (864), Bpap vs. Gbil (517), Cfor vs. Csep (259), Cfor vs. Gbil (95), and Csep vs. Gbil (40). Four hundred and fifteen unigenes were common to all six pairwise comparisons; these were primarily associated with Cytochrome P450 and environmental adaptation, as determined in a KEGG enrichment analysis. Unique unigenes were also identified, specific to Bpap vs. Cfor (808 unigenes), Bpap vs. Csep (329 unigenes), Bpap vs. Gbil (87 unigenes), Cfor vs. Csep (108 unigenes), Cfor vs. Gbil (32 unigenes), and Csep vs. Gbil comparisons (23 unigenes); partial unigenes were associated with the metabolism of terpenoids and polyketides regarding plant hormone signal transduction. Weighted gene co-expression network analysis (WGCNA) revealed four modules that were associated with the hosts. These results provide a foundation for further exploration of the detailed molecular mechanisms involved in plant parasitism.

An investigation of chigger mites on the large oriental vole, Eothenomys miletus (Rodentia: Cricetidae), was conducted between 2001 and 2013 at 39 localities across southwest China, and 2463 individuals of the vole hosts were captured and examined, which is a big host sample size. From the body surface of E. miletus, 49,850 individuals of chigger mites were collected, and they were identified as comprising 175 species, 13 genera, and 3 subfamilies in 2 families (Trombiculidae and Leeuwenhoekiidae). The 175 species of chigger mites from such a single rodent species (E. miletus) within a certain region (southwest China) extremely exceeded all the species of chigger mites previously recorded from multiple species of hosts in a wide region or a whole country in some other countries, and this suggests that E. miletus has a great potential to harbor abundant species of chigger mites on its body surface. Of 175 mite species, Leptotrombidium scutellare was the most dominant species, which has been proved as one of the main vectors of scrub typhus and the potential vector of haemorrhagic fever with renal syndrome (HFRS) in China. The patchiness index (m*/m) was used to measure the spatial patterns of the dominant chigger mite species, and all the three dominant mite species (L. scutellare, Leptotrombidium sinicum, and Helenicula simena) showed aggregated distributions among the different host individuals. The coefficient of association (V) was adopted to measure the interspecies interaction between the dominant mite species and a slightly positive association existed between L. scutellare and L. sinicum (V = 0.28, P < 0.01), which implies that these two mite species can co-exist on the same species of the host, E. miletus. The tendency curve of species abundance showed that the number of chigger mite species gradually decreased with the increase of mite individuals, and this revealed that most chigger mite species were rare with very few individuals, but few dominant species had abundant individuals. The species-sample relationship indicated that the number of chigger mite species increased with the increase of the host samples. The results suggest that a big host sample size over a wide realm of geographical regions is needed in the field investigation in order to obtain a true picture of species diversity and species composition.

Many colonies of macaques (Macaca fascicularis and Macaca mulatta) are maintained in China, especially in Guangxi and Guizhou. A total of 803 fresh stool samples infected with Entamoeba were obtained from three big colonies of macaques located in southwest China. The samples were examined for the presence of five Entamoeba species using PCR. Entamoeba nuttalli, Entamoeba dispar, Entamoeba coli, and Entamoeba chattoni infections were detected, but Entamoeba histolytica infection was not. This study is the first to report on the prevalence of E. nuttalli in wild macaques from China. Eighteen E. nuttalli isolates and five E. dispar isolates were obtained by culturing the samples in Tanabe-Chiba medium. The serine-rich protein (SRP), ribosomal RNA (rRNA), hexokinase (HXK), glucose-6-phosphate isomerase (GPI), and phosphoglucomutase (PGM) genes of E. nuttalli isolates were compared with other reported isolates. The results showed clear differences among the Chinese E. nuttalli isolates and other isolates based on the SRP gene sequences. However, HXK, GPI, and PGM genes of these strains were similar to those of other isolates. The rRNA genes of E. coli and E. chattoni were also amplified and analyzed from these samples. The results suggested that host species might be a more important factor than geographic location in amebic genetic diversity.

Ectoparasitic insects and mites on Yunnan red-backed voles (Eothenomys miletus) in Dali prefecture, Yunnan Province, southwest China, were studied between 2003 and 2004. In total, 34,389 individuals of 86 species of ectoparasitic insects (seven species of fleas and five species of sucking lice) and mites (23 species of gamasid mites and 51 species of chigger mites) were collected from 916 individual hosts. The diversity of ectoparasites on this single rodent species in such a small area was much higher than in previous reports, which concerned more host species and greater geographical areas. The majority of the ectoparasites were chigger mites, which accounted for 59.3% of the parasite species and 87.4% of the individual parasites. Most voles harbored parasites with an overall prevalence (P) of 82.5% and mean abundance (MA) of 37.5 parasites per host. The dispersion coefficient (C) and patchiness index (m*/m) were used to study the spatial patterns of the seven dominant parasite species, and all seven had aggregated distributions. The species abundance distribution of the ectoparasites on the vole was fitted by Preston's lognormal distribution (R (2) = 0.82), and the total expected parasite species was estimated from this plot as 167 species. Yunnan red-backed voles harbor many ectoparasites as revealed by examination of a large host population. Future field investigations should sample large numbers of host individuals to assess ectoparasite populations.

Chiggers (chigger mites) are a group of tiny arthropods, and they are the exclusive vector of Orientia tsutsugamushi (Ot), the causative agent of scrub typhus (tsutsugamushi disease). Dehong Prefecture in Yunnan Province of southwest China is located on the China-Myanmar border and is an important focus of scrub typhus. Based on the field surveys in Dehong between 2008 and 2022, the present paper reports the infestation and ecological distribution of chiggers on the body surface of rodents and other sympatric small mammals (shrews, tree shrews, etc.) in the region for the first time. The constituent ratio (Cr), prevalence (PM), mean abundance (MA), and mean intensity (MI) were routinely calculated to reflect the infestation of small-mammal hosts with chiggers. Additionally, the species richness (S), Shannon-Wiener diversity index (H), Simpson dominance index (D), and Pielou's evenness index (E) were calculated to illustrate the chigger community structure. Preston's log-normal model was used to fit the theoretical curve of species abundance distribution, and the Chao 1 formula was used to roughly estimate the expected total species. The "corrplot" package in R software (Version 4.3.1) was used to analyze interspecific relationships, and the online drawing software was used to create a chord diagram to visualize the host-chigger associations. From 1760 small-mammal hosts, a total of 9309 chiggers were identified as belonging to 1 family, 16 genera, and 117 species, with high species diversity. The dominant chigger species were Leptotrombidium deliense, Walchia ewingi, and Gahrliepia longipedalis, with a total Cr = 47.65% (4436/9309), among which L. deliense is the most important vector of Ot in China. The overall infestation indexes (PM, MA, and MI) and community parameters (S, H, and E) of chiggers in the mountainous areas and outdoors were higher than those in the flatland areas and indoors, with an obvious environmental heterogeneity. Leptotrombidium deliense was the dominant species in the flatland and indoors, while G. longipedalis was the prevalent species in the mountainous and outdoor areas. The species abundance distribution of the chigger community conformed to log-normal distribution with the theoretical curve equation: S(R)'=28e-[0.23(R-0)]2, indicating the existence of many rare species and only a few dominant species in the community. The expected total number of chigger species was roughly estimated to be 147 species, 30 more than the 117 species actually collected, suggesting that some uncommon species may have been missed in the sampling survey. The host-parasite association analysis revealed that one host species can harbor different chigger species, and one chigger species can parasitize different host species with low host specificity. A positive or negative correlation existed among different chigger species, indicating a cooperative or competitive interspecific relationship. The species diversity of chiggers is high in Dehong on the China-Myanmar border, and a large host sample is recommended to find more uncommon species. There is an obvious environmental heterogeneity of the chigger community, with different species diversity and dominant species in different environments. The low host specificity of chiggers and the occurrence of a large number of L. deliense in Dehong, especially in flatland areas and indoors, would increase the risk of persistent transmission of scrub typhus in the region.

The last 26 years saw a rampant global epidemic of HIV-1. HIV-1 s extraordinary diversity is seeded by a high mutation rate, rapid replication, frequent recombination, and strategic placement and loss and gain of N-linked glycosylation sites. In this thesis, the genetic variation of HIV-1 was investigated with special focus on recombination and N-linked glycosylation sites. Using phylogenetic analyses, distance methods, and HIV-1 subtying tools including one called jumping profile hidden Markov model, HIV-1 recombinants dominating HIV epidemic in three different geographical regions were examined. We found that CRF13_cpx includes sections of the rare subtype J, and that breakpoint inference can be greatly improved using all available sequences within a CRF family. We confirmed that CRF02_AG, a recombinant between subtype A and G that is prevalent in West and West Central Africa, is an old recombinant. The main recombination events that generated CRF02 took place before the 1970 s, before HIV-1 had started to spread worldwide and the currently recognized subtypes had formed. Recombinants consisting of subtypes B and C are frequently found in the HIV-1 epidemic of Asia, especially in southwest China where they are associated with different drug trafficking routes. Our study suggested that CRF07 was derived from a recombination between CRF08 and subtype B. However, it is possible that the currently defined CRF07 is not the direct product of this recombination event. Lastly, we found that recent recombination between subtypes B and F in Argentina and Brazil, two epicenters in South America, has created many different, but related, recombinant forms. Taken together, it appears as if the HIV-1 epidemic is becoming more complex as it moves ahead into the future. Recombination among co-circulating forms creates new forms of HIV-1 that are now starting to dominate the epidemic in certain parts of the world. We developed methods to track N-linked glycosylation sites (sequons) in HIV-1 as they shift positions and vary in local densities. Comparing primate lentiviruses, hepatitis C virus, and influenza A viruses showed that generating and tolerating shifting sequons is a unique evolutionary avenue for HIV-1 immune evasion. In addition, we found the primate lentiviral lineages have host species - dependent levels of sequon shifting, with HIV-1 in humans the most extreme. Further, unlike influenza A hemagglutinin H3 HA1 that accumulates sequons over time, HIV does not have a net increase in the number of sites over time at the population level, indicating that variation in number and placement, not accumulation of N-linked glycosylation sites, is more critical for HIV-1 immune evasion. The studies detailed in this thesis, together with our great effort in re-subtyping > 150,000 sequences in the Los Alamos HIV sequence database, enables us to draw a more comprehensive and dynamic picture of the global HIV-1 epidemic.

BackgroundPowdery mildews (Erysiphaceae, Ascomycota) are common plant disease agents and also cause stress for forest and fruit trees worldwide as well as in Taiwan. The powdery mildew Erysiphe bulbouncinula on Koelreuteria host trees was considered an endemic species in China. While in China the host was K. paniculata and only the teleomorph stage found, the anamorph and the teleomorph were both recorded for the host in Taiwan, K. henryi. We aimed to clarify the relationship of the powdery mildews recorded under E. bulbouncinula with an apparently disjunct distribution.ResultsSpecimens of powdery mildew on K. henryi from Taiwan were characterized based on the anamorph morphology and DNA sequences. They revealed a new record of Sawadaea koelreuteriae for this host species and Taiwan and a new species of Erysiphe, E. formosana, sister to E. bulbouncinula from China.ConclusionsIn Erysiphe on Koelreuteria hosts, speciation of plant parasitic fungi seems to be correlated with disjunct host and geographic distribution possibly shaped by extinction of potential host species which are known only as fossils. Two of the three extant East Asian species of Koelreuteria are now known as hosts of specific Erysiphe species. We may predict a further not yet discovered Erysiphe species on the third East Asian species, K. bipinnata, in South and Southwest China. In the speciation in Sawadaea, the extinction events in Koelreuteria can be excluded from being involved.

Leptotrombidium rupestre, a chigger species, is a potential vector of scrub typhus. Based on field surveys in southwest China between 2001 and 2022, this paper retrospectively reports the distribution and host selection of L. rupestre in the region for the first time. A total of 4675 L. rupestre were identified from 28 species of rodents and other sympatric small mammal hosts in 23 out of 114 survey sites, and it was mainly distributed in higher latitudes (31–33° N) and altitudes (3000–3500 m), especially in western Sichuan, an important focus of scrub typhus. Among four orders of hosts, 96.15% (4495/4675) of L. rupestre were found on the order Rodentia. At species level of hosts, 40.49% of L. rupestre (Cr = 40.49%, 1893/4675) came from the vole Alexandromys oeconomus in Cricetida of Rodentia, with high prevalence (PM = 91.67%), mean abundance (MA = 157.75 chiggers/per examined vole) and mean intensity (MI = 172.09 chiggers/per infested vole), indicating an obvious host‐preference. L. rupestre was of aggregated distribution among different individuals of the hosts. The occurrence of L. rupestre in western Sichuan may increase the potential risk of the focus persistence of scrub typhus in the region. The present study enriches scientific information on this potential vector species and will contribute to the surveillance and control of scrub typhus in the future.

The Dry-Hot valleys in Southwest China are hostile environments for living organisms. The dominant plants in the valleys are drought-resistant legumes. Here, we examined the diversity and physiology of the nitrogen-fixing bacteria associated with these legumes. Thirty-three strains were isolated from the nodules of six legume species located in five valleys. Analyses of their 16S rRNA gene sequences indicated that each strain had a unique 16S rRNA gene sequence and none of the strains had a sequence identical to those reported in the GenBank. The 16S rRNA gene sequence showed little clustering based on host tree species or geographic locations. PCR fingerprinting confirmed the genetic uniqueness of these strains. Physiological tests showed that these strains were all capable of growing at 35°C or above and at hypertonic environments. All strains formed root nodules on Acacia richii, the most common legume in these valleys. The bacterial strains obtained here could help future reforestation efforts in these valleys and other environments with similar conditions. Key words: Rhizobium spp., Bradyrhizobium spp., Mesorhizobium spp., 16S rRNA, high temperature resistance, drought resistanc

Abundances and host relationships of chigger mites in Yunnan Province, China

The Bradyrhizobium-legume symbiosis is dominant in the shrubby ecosystem of the Karst region, Southwest China

ObjectiveThe present study aims to investigate the seasonal dynamics of main vectors of scrub typhus, and thereby provide scientific information for the surveillance and control of the disease.MethodsA field investigation lasting for 12 consecutive months was conducted at a fixed survey site (Waxi Village) in Binchuan County (a focus of scrub typhus), Yunnan Province of southwest China between 2019 and 2020. Based on the taxonomic identification of all collected chigger mites, the three vector chigger species of scrub typhus (Leptotrombidium deliense, L. scutellare and L. imphalum) were screened out as the object of this study. The constituent ratio (Cr), prevalence (PM), mean abundance (MA), and mean intensity (MI) were calculated to reflect the mite infestation status. The Levins’ niche breadth (Bi) and Pianka’s proportional similarity ratio (Oij) were used to calculate the ecological niche breadth and niche overlap of chiggers on different host species and temporal series.ResultsThese three vector chigger species were the dominant mites at the survey site, accounting for 60.72% of the total 115 chigger species (Cr=60.72%, 132,160/217,671). In seasonal fluctuations, L. deliense showed two peaks in summer and autumn, and the highest peak was in August of summer with highest infestation indexes (Cr=44.29%, MA=322.48, MI=422.56) on the hosts. Leptotrombidium imphalum mainly appeared in summer and autumn, and peaked in September (Cr, MA and MI) and October (PM) of early autumn. Leptotrombidium scutellare mainly appeared in November, December and January, and peaked in November of late autumn (Cr=66.09%) and December of early winter (Cr=33.83%). Leptotrombidium deliense had the widest temporal niche (Bi=0.248) and L. scutellare had the widest host niche (Bi=0.268). Leptotrombidium deliense and L. imphalum had the highest temporal niche overlap (Oij=0.715) and host niche overlap (Oij=0.986). The monthly average temperature significantly affected the seasonal fluctuation of L. scutellare.ConclusionThe three vector chigger species can parasitize a wide range of hosts with low host specificity, and their coexistence as the dominant mites at the survey site increases the potential risk of transmission and focus persistence of relevant mite-borne zoonoses. Leptotrombidium deliense and L. imphalum have similar seasonal distribution patterns (summer-autumn type) and host selection, and L. scutellare has a different type of seasonal fluctuation, autumn-winter type. The temporal and host niches of L. scutellare are very different from those of L. deliense and L. imphalum. The temperature is the most important climate factor that drives the seasonal dynamics of vector chiggers.