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Permafrost active layer soils are harsh environments with thaw/freeze cycles and sub-zero temperatures, harboring diverse microorganisms. However, the distribution patterns, assembly mechanism, and driving forces of soil microeukaryotes in permafrost remain largely unknown. In this study, we investigated microeukaryotes in permafrost active layer across the Qinghai-Tibet Plateau (QTP) using 18S rRNA gene sequencing. The results showed that the microbial eukaryotic communities were dominated by Nematozoa, Ciliophora, Ascomycota, Cercozoa, Arthropoda, and Basidiomycota in terms of relative abundance and operational taxonomic unit (OTU) richness. Nematozoa had the highest relative abundance, while Ciliophora had the highest OTU richness. These phyla had strong interactions between each other. Their alpha diversity and community structure were differently influenced by the factors associated to location, climate, and soil properties, particularly the soil properties. Significant but weak distance-decay relationships with different slopes were established for the communities of these dominant phyla, except for Basidiomycota. According to the null model, community assemblies of Nematozoa and Cercozoa were dominated by heterogeneous selection, Ciliophora and Ascomycota were dominated by dispersal limitation, while Arthropoda and Basidiomycota were highly dominated by non-dominant processes. The assembly mechanisms can be jointly explained by biotic interactions, organism treats, and environmental influences. Modules in the co-occurrence network of the microeukaryotes were composed by members from different taxonomic groups. These modules also had interactions and responded to different environmental factors, within which, soil properties had strong influences on these modules. The results suggested the importance of biological interactions and soil properties in structuring microbial eukaryotic communities in permafrost active layer soil across the QTP., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Permafrost thaw create widespread thermokarst landscapes. As a result, distinct habitats are provided to harbor different bacterial communities in degraded permafrost soil (PBCs), thermokarst lake sediment (SBCs), and lake water (WBCs), driving carbon metabolism differentially. In this study, we investigated functional diversity and redundancy, and carbon metabolism potentials of PBCs, SBCs, and WBCs in thermokarst landscapes across the Qinghai-Tibet Plateau. The results showed that PBCs and SBCs had higher taxonomic and functional alpha diversity than WBCs, while WBCs had lower functional redundancy. WBCs had the highest beta diversity followed by SBCs and PBCs, suggesting strong determination of taxonomic variations on functional differences. Community assembly processes also had significant influences on beta diversity, especially for SBCs. Metabolism pathways of carbohydrate metabolism, methane metabolism, and carbon fixation were enriched differentially in PBCs, SBCs, and WBCs, suggesting different C fate in distinct habitats. Carbohydrate metabolism data suggested that PBCs might have stronger potentials to mineralize a greater diversity of organic carbon substrate than SBCs and WBCs, promoting degradation of organic carbon stocks in degraded permafrost soils. Methane metabolism data showed that SBCs had a stronger methanogenesis potential followed by PBCs and WBCs, while PBCs had a stronger methane oxidation potential. High abundance of genes involving in formaldehyde assimilation might suggested that a large proportion of produced methane might be assimilated by methanotrophs in the thermokarst landscapes. Both aerobic and anaerobic carbon fixation pathways were enriched in PBCs. The results added our understanding of functional properties and biogeochemical carbon cycles in thermokarst landscapes, improving our abilities in accurate modeling of carbon dynamics and the ultimate fate of permafrost carbon in a warming world., Competing Interests: Declaration of competing interest The authors declare no competing interests., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Background: Clonorchiasis is a serious food-borne parasitic disease caused by Clonorchis sinensis infection. C. sinensis , a major fish-borne trematode, is a known causative agent of cholangiocarcinoma. The risk factors for C. sinensis infection include individual eating behaviors and environmental factors. In this study, we evaluated the C. sinensis infection rate and the associated risk factors among residents in Binyang County, Guangxi, China. Methods: In 2016 and 2017, five villages from Binyang, Guangxi were selected by multistage cluster random sampling for a cross-sectional study. A modified Kato-Katz thick smear method was used to examine C. sinensis eggs in fecal samples in triplicate (three smears for each sample). Both uni-variate and multi-variate logistic regression analyses were carried out to identify the risk factors for C. sinensis infection. Results: A total of 1,977 fecal samples were collected from villagers in the investigated areas. The overall infection rates of C. sinensis in Binyang County was 20.49% (405/1,977). The mean age of participants was 39.42 ± 23.48 (range: 3-89 years old), and the highest infection rate (33.72%) was seen in the age group of 40-49 years old, followed by those aged 50-59 (31.83%). Multi-variate logistic regression analysis showed that higher infection rates were significantly associated with males ( aOR = 6.51, 95% CI = 4.67-9.08), Zhuang ( aOR = 2.41, 95% CI = 1.62-3.59), ages ( aOR = 33.51, 95% CI = 10.13-110.86), frequency of raw fresh fish consumption ( aOR = 14.56, 95% CI = 9.80-21.63), and close contact with cats and dogs ( aOR = 1.53, 95% CI = 1.02-2.30). Occupations and education levels showed no significant association with C. sinensis infection ( P > 0.05). Conclusions: High levels of C. sinensis infection were observed among residents in Binyang County, Guangxi. Intervention strategies should be strengthened among the investigated population at high risk, such as males, Zhuang and older individuals, especially those who frequently eat raw fresh fish. In addition, the individuals contacting with cats and/or dogs were observed to have significantly higher infection rate of C. sinensis than those having no contact with cats and dogs. The association between contacting with cats and/or dogs and C. sinensis infection needs to be explored and confirmed in the future study by more epidemiological investigations of human C. sinensis infection from different areas., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Xu, Jiang, Yin, Cao, Shen and Cao.)

Schistosoma japonicum infection causes pathological injury to the host. Multiple studies have shown that intestinal helminth infection causes dysbiosis for the gut microbial community and impacts host immunology. However, the effect of acute S. japonicum infection on the gut microbiome structure (abundance and diversity) is still unclear. We collected fecal samples from healthy and infected patients from a single hospital in Hunan Province, China. The bacterial community was analyzed using 16S ribosomal RNA gene sequencing of the V4 hypervariable region using the HiSeq platform. Compared with healthy subjects, infected patients exhibited an increase in relative abundance of the TM7 phylum. At the genus level, there were seven differentially abundant genera between groups. The most significant finding was a Bacteroides enterotype in patients with acute schistosomiasis. These results suggest that S. japonicum infection has a significant effect on microbiome composition characterized by a higher abundance of the TM7 phylum and development of a Bacteroides enterotype., (© Y. Jiang et al., published by EDP Sciences, 2021.)

Cystic echinococcosis is a worldwide chronic zoonotic disease that threatens human health and animal husbandry. Exosome-like vesicles (ELVs) have emerged recently as mediators in the parasite-parasite intercommunication and parasite-host interactions. Exosome-like vesicles from parasites can transfer non-coding RNAs (ncRNAs) into host cells to regulate their gene expression; however, the ncRNAs profiles of the ELVs from Echinococcus granulosus remain unknown. Here, we isolated protoscolece (PSC)-ELVs and hydatid fluid (HF)-ELVs from the culture medium for E. granulosus PSCs in vitro and the HF of fertile sheep cysts, respectively. The microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) profiles of the two types of ELVs were analyzed using high-throughput sequencing, and their functions were predicted using Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis. In PSC-ELVs and HF-ELVs, 118 and 58 miRNAs were identified, respectively, among which 53 miRNAs were present in both ELVs, whereas 65 and 5 miRNAs were unique to PSC-ELVs and HF-ELVs, respectively; 2,361 and 1,254 lncRNAs were identified in PSC-ELVs and HF-ELVs, respectively, among which 1,004 lncRNAs were present in both ELVs, whereas 1,357 and 250 lncRNAs were unique to PSC-ELVs and HF-ELVs, respectively. Intriguingly, the spilled PSCs from cysts excrete ELVs with higher numbers of and higher expression levels of miRNAs and circRNAs than HF-ELVs. The miRNA sequencing data were validated by quantitative reverse transcription-polymerase chain reaction. Furthermore, the target lncRNAs and mRNAs regulated by the 20 most abundant miRNAs were screened, and a ceRNA regulatory network containing 5 miRNAs, 41 lncRNAs, and 23 mRNAs was constructed, which provided new ideas and the molecular basis for further clarification of the function and mechanism of E. granulosus ELVs ncRNAs in the parasite-host interactions. Egr-miR-125-5p and egr-miR-10a-5p, sharing identical seed sites with host miRNAs, were predicted to mediate inflammatory response, collagen catabolic process, and mitogen-activated protein kinase cascade during parasite infections. In conclusion, for the first time, we identified the ncRNAs profiles in PSC-ELVs and HF-ELVs that might be involved in host immunity and pathogenesis, and enriched the ncRNAs data of E. granulosus . These results provided valuable resources for further analysis of the regulatory potential of ncRNAs, especially miRNAs, in both types of ELVs at the parasite-host interface., (Copyright © 2020 Zhang, Gong, Cao, Yin, Zhang, Cao and Shen.)

Background: Enterocytozoon bieneusi is the most frequently detected microsporidian species in humans and animals. Currently, to the best of our knowledge, no information on E. bieneusi infection in Himalayan marmots (Marmota himalayana) and Alashan ground squirrels (Spermophilus alashanicus) is available worldwide. The aim of the present study was to understand the occurrence and genetic characterizations of E. bieneusi in Himalayan marmots and Alashan ground squirrels in the Qinghai-Tibetan Plateau area (QTPA), Gansu Province, China., Methods: A total of 498 intestinal contents were collected from 399 Himalayan marmots and 99 Alashan ground squirrels in QTPA. These samples were screened for the presence of E. bieneusi by using nested polymerase chain reaction and sequencing of the internal transcribed spacer (ITS) region of the ribosomal RNA (rRNA) gene. The ITS-positive sequences were aligned and phylogenetically analyzed to determine the genotypes of E. bieneusi., Results: The average infection rate of E. bieneusi was 10.0% (50/498), with 11.8% (47/399) in Himalayan marmots and 3.0% (3/99) in Alashan ground squirrels. A total of 7 distinct E. bieneusi genotypes were confirmed: 1 known genotype, YAK1 (n = 18) and 6 novel genotypes, named as ZY37 (n = 27), HN39 (n = 1), HN96 (n = 1), SN45 (n = 1), XH47 (n = 1) and ZY83 (n = 1). All the genotypes obtained in the present study were classified into group 1., Conclusions: To our knowledge, this is the first report of E. bieneusi in Himalayan marmots and Alashan ground squirrels in China. The identification of genotype YAK1 in the two rodent species expanded the host range of this genotype. All the seven genotypes were clustered into zoonotic group 1, suggesting that these animal species can be potential epidemiological vectors of zoonotic microsporidiosis caused by E. bieneusi and pose a threat to ecological security. It is necessary to strengthen management practices and surveillance in the investigated areas to reduce the risk of E. bieneusi infection from the two rodent species to humans.

Background: Cystic echinococcosis is a chronic disease caused by infection with the larvae of Echinococcus granulosus. The parasite's ability to establish persistent infection is partly due to its evolving immune evasion strategies. One strategy may involve the protective effect of arginase, which impedes the control of pathogens or tumors, whereas it remains largely unknown during E. granulosus infection. Here, we analyzed whether arginase was produced in peritoneal cells and assessed its role in immunosuppression in mice infected with protoscoleces of E. granulosus., Methods: BALB/c mice injected with protoscoleces of E. granulosus were used to evaluate the expression of arginase (ARG) in mRNA and protein levels. The profiles of ARG-1 expression in peritoneal cells and CD3ζ expression in T cells from spleens were assessed at different time points (3, 6, 9 and 12 months post-infection) by flow cytometry. In vitro, peritoneal cells were co-cultured with purified T cells in a transwell system, and the levels of CD3ζ re-expression were compared by flow cytometry. Meanwhile, the changes of L-arginine and its related metabolites in serum were tested., Results: Compared to the control group, the peritoneal cells from infected mice showed higher levels of ARG-1 mRNA and protein, unchanged ARG-2 and iNOS. Enhanced ARG-1 expression was present in SSC low CD11b + F4/80 + , CD11b + CD11c + , CD11b + Gr-1 + Ly-6C + Ly-6G - , CD11b + Gr-1 + Ly-6C - Ly-6G + , CD11b + Gr-1 + and CD11b + Ly-6G + cells. The proportion of cells and the proportion of ARG-1 expression in corresponding cells exhibited a rising trend along with the extension of infection time, except for fluctuations in SSC low CD11b + F4/80 + and CD11b + CD11c + cells at 12 months post-infection, whereas the expression of CD3ζ chain in CD4 + and CD8 + T cells showed a descending trend. Purified T cells showed declined re-expression of CD3ζ when co-cultured with peritoneal cells from infected mice, and CD3ζ was regenerated by supplement of L-arginine or arginase inhibitor BEC, rather than NOS inhibitor L-NMMA or catalase. Meanwhile, the concentrations of L-arginine, L-citrulline and NO decreased, and those of L-ornithine and urea increased in serum post-infection., Conclusions: Our findings demonstrated that ARG-1 expression is enhanced in multiple myeloid cells from peritoneum and promotes immune evasion of E. granulosus in mice by inhibiting the expression of T cell receptor CD3ζ chain and antagonism against iNOS.

Cryptosporidium spp., Giardia spp. and microsporidia are important intestinal protozoa responsible for diarrhea in humans and other mammals. China is a major chicken-raising country, and studies on these protozoa in chickens have important public health significance. Here, we investigated the prevalence and genetic characterization of these parasites in chickens from Ezhou City, Hubei Province, China. In total, 206 stool specimens were collected from chickens in four villages of Ezhou between July 2014 and February 2015. Genomic DNA of each specimen was tested by nested PCR based on the Cryptosporidium small subunit rRNA gene, the Giardia intestinalis triose phosphate isomerase gene, and the internal transcribed spacer of the Enterocytozoon bieneusi rRNA gene, respectively. The public health significance of G. intestinalis and E. bieneusi identified in our study was evaluated via phylogenetic analysis. The infection rates were determined to be 2.43% (5/206), 8.25% (17/206), and 1.94% (4/206) for Cryptosporidium, G. intestinalis , and E. bieneusi , respectively. One sample showed coinfection with G. intestinalis and E. bieneusi . Meanwhile, sequence analysis of the PCR-positive samples showed that the Cryptosporidium was C. baileyi, G. intestinalis was assemblage C, and E. bieneusi was genotype D and novel genotype EZ0008. This is the first report of zoonotic G. intestinalis assemblage C in chickens in the world, and the first report of zoonotic E. bieneusi genotype D in chickens in China. These findings indicate new transmission dynamics and molecular epizootiology., (Copyright © 2020 Cao, Xu, Jiang, Liu, Yuan, Sun, Cao and Shen.)

Clonorchiasis is an infectious disease caused by helminths of Clonorchis sinensis ( C. sinensis ). The adult parasite mainly inhabits the bile duct and gall bladder, and results in various complications to the hepatobiliary system. The amount of bile secreted into the intestine is reduced in cases of C. sinensis infection, which may alter the pH of the gut and decrease the amount of surfactant protein D released from the gallbladder. However, the impact of parasitic infection on the human gut microbiome remains unclear. To this end, we examined the gut microbiota composition in 47 modified Kato-Katz thick smear-positive (egg-positive) volunteers and 42 healthy controls from five rural communities. Subjects were grouped into four sub-populations based on age and infection status. High-throughput 16S rRNA gene sequencing revealed significant changes in alpha diversity between EP1 and EN1. The beta diversity showed alterations between C. sinensis -infected subjects and healthy controls. In C. sinensis infected patients, we found the significant reduction of certain taxa, such as Bacteroides and anti-inflammatory Bifidobacterium ( P < 0.05). Bacteroides , a predominant gut bacteria in healthy populations, was negatively correlated with the number of C. sinensis eggs per gram (EPG, r = -0.37, P adjust < 0.01 in 20-60 years old group; r = -0.64, P adjust = 0.04 in the 60+ years old group). What's more, the reduction in the abundance of Bifidobacterium , a common probiotic, was decreased particularly in the 60 + years old group ( r = -0.50, P = 0.04). The abundance of Dorea , a potentially pro-inflammatory microbe, was higher in infected subjects than in healthy individuals ( P < 0.05). Variovorax was a unique bacteria that was only detected in infected subjects. These results clearly demonstrate the significant influence of C. sinensis infection on the human gut microbiota and provided new insights into the control, prevention, diagnosis, and clinical study of clonorchiasis through the human gut microbiota.

Background: Cystic echinococcosis is a worldwide chronic zoonotic disease caused by infection with the larval stage of Echinococcus granulosus. Previously, we found significant accumulation of myeloid-derived suppressor cells (MDSCs) in E. granulosus infection mouse models and that they play a key role in immunosuppressing T lymphocytes. Here, we compared the long non-coding RNA (lncRNA) and mRNA expression patterns between the splenic monocytic MDSCs (M-MDSCs) of E. granulosus protoscoleces-infected mice and normal mice using microarray analysis., Methods: LncRNA functions were predicted using Gene Ontology enrichment and the Kyoto Encyclopedia of Genes and Genomes pathway analysis. Cis- and trans-regulation analyses revealed potential relationships between the lncRNAs and their target genes or related transcription factors., Results: We found that 649 lncRNAs were differentially expressed (fold change ≥ 2, P < 0.05): 582 lncRNAs were upregulated and 67 lncRNAs were downregulated; respectively, 28 upregulated mRNAs and 1043 downregulated mRNAs were differentially expressed. The microarray data was validated by quantitative reverse transcription-PCR. The results indicated that mRNAs co-expressed with the lncRNAs are mainly involved in regulating the actin cytoskeleton, Salmonella infection, leishmaniasis, and the vascular endothelial growth factor (VEGF) signaling pathway. The lncRNA NONMMUT021591 was predicted to cis-regulate the retinoblastoma gene (Rb1), whose expression is associated with abnormal M-MDSCs differentiation. We found that 372 lncRNAs were predicted to interact with 60 transcription factors; among these, C/EBPβ (CCAAT/enhancer binding protein beta) was previously demonstrated to be a transcription factor of MDSCs., Conclusions: Our study identified dysregulated lncRNAs in the M-MDSCs of E. granulosus infection mouse models; they might be involved in M-MDSC-derived immunosuppression in related diseases.

Desert riparian forests are the main body of natural oases in the lower reaches of inland rivers; its growth and distribution are closely related to water use sources. However, how does the desert riparian forest obtains a stable water source and which water sources it uses to effectively avoid or overcome water stress to survive? This paper describes an analysis of the water sources, using the stable oxygen isotope technique and the linear mixed model of the isotopic values and of desert riparian Populus euphratica forests growing at sites with different groundwater depths and conditions. The results showed that the main water source of Populus euphratica changes from water in a single soil layer or groundwater to deep subsoil water and groundwater as the depth of groundwater increases. This appears to be an adaptive selection to arid and water-deficient conditions and is a primary reason for the long-term survival of P. euphratica in the desert riparian forest of an extremely arid region. Water contributions from the various soil layers and from groundwater differed and the desert riparian P. euphratica forests in different habitats had dissimilar water use strategies.