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IntroductionSoil fungal communities play a crucial role in maintaining the ecological functions of alpine forest soil ecosystems. However, it is currently unclear how the distribution patterns of fungal communities in different soil layers of alpine forests will change along the elevational gradients.Material and methodsTherefore, Illumina MiSeq sequencing technology was employed to investigate fungal communities in three soil layers (0–10, 10–20, and 20–30 cm) along an elevational gradient (3500 m to 4300 m) at Sygera Mountains, located in Bayi District, Nyingchi City, Tibet.Results and discussionThe results indicated that: 1) Soil depth had a greater impact on fungal diversity than elevation, demonstrating a significant reduction in fungal diversity with increased soil depth but showing no significant difference with elevation changes in all soil layers. Within the 0–10 cm soil layer, both Basidiomycota and Ascomycota co-dominate the microbial community. However, as the soil depth increases to 10–20 and 20–30 cm soil layers, the Basidiomycota predominantly dominates. 2) Deterministic processes were dominant in the assembly mechanism of the 0–10 cm fungal community and remained unchanged with increasing elevation. By contrast, the assembly mechanisms of the 10–20 and 20–30 cm fungal communities shifted from deterministic to stochastic processes as elevation increased. 3) The network complexity of the 0–10 cm fungal community gradually increased with elevation, while that of the 10–20 and 20–30 cm fungal communities exhibited a decreasing trend. Compared to the 0–10 cm soil layer, more changes in the relative abundance of fungal biomarkers occurred in the 10–20 and 20–30 cm soil layers, indicating that the fungal communities at these depths are more sensitive to climate changes. Among the key factors driving these alterations, soil temperature and moisture soil water content stood out as pivotal in shaping the assembly mechanisms and network complexity of fungal communities. This study contributes to the understanding of soil fungal community patterns and drivers along elevational gradients in alpine ecosystems and provides important scientific evidence for predicting the functional responses of soil microbial ecosystems in alpine forests.

As a common foodborne pathogen, infection with L. monocytogenes poses a significant threat to human life and health. The objective of this study was to employ comparative genomics to unveil the biodiversity and evolutionary characteristics of L. monocytogenes strains from different regions, screening for potential target genes and mining novel target genes, thus providing significant reference value for the specific molecular detection and therapeutic targets of L. monocytogenes strains. Pan-genomic analysis revealed that L. monocytogenes from different regions have open genomes, providing a solid genetic basis for adaptation to different environments. These strains contain numerous virulence genes that contribute to their high pathogenicity. They also exhibit relatively high resistance to phosphonic acid, glycopeptide, lincosamide, and peptide antibiotics. The results of mobile genetic elements indicate that, despite being located in different geographical locations, there is a certain degree of similarity in bacterial genome evolution and adaptation to specific environmental pressures. The potential target genes identified through pan-genomics are primarily associated with the fundamental life activities and infection invasion of L. monocytogenes, including known targets such as inlB, which can be utilized for molecular detection and therapeutic purposes. After screening a large number of potential target genes, we further screened them using hub gene selection methods to mining novel target genes. The present study employed eight different hub gene screening methods, ultimately identifying ten highly connected hub genes (bglF_1, davD, menE_1, tilS, dapX, iolC, gshAB, cysG, trpA, and hisC), which play crucial roles in the pathogenesis of L. monocytogenes. The results of pan-genomic analysis showed that L. monocytogenes from different regions exhibit high similarity in bacterial genome evolution. The PCR results demonstrated the excellent specificity of the bglF_1 and davD genes for L. monocytogenes. Therefore, the bglF_1 and davD genes hold promise as specific molecular detection and therapeutic targets for L. monocytogenes strains from different regions.

Fusarium crown rot (FCR) is one of the most important soilborne diseases affecting wheat production. To investigate the diversity of the pathogens causing this disease, 199 diseased wheat samples were collected from 13 cities in Shandong province. In total, 468 isolates were obtained, and from these isolates, 11 Fusarium species were identified based on phylogenetic analyses with the translation elongation factor-1α (TEF-1α), RNA polymerase II largest subunit (RPB1), and RNA polymerase II second largest subunit (RPB2) gene sequences. Of these Fusarium isolates, 283 were identified as Fusarium pseudograminearum and the remaining isolates were identified as Fusarium graminearum (n = 113), Fusarium sinensis (n = 28), Fusarium acuminatum (n = 18), Fusarium incarnatum (n = 13), Fusarium ipomoeae (n = 5), Fusarium flocciferum (n = 3), Fusarium proliferatum (n = 2), Fusarium asiaticum (n = 1), Fusarium culmorum (n = 1), and Fusarium oxysporum (n = 1), suggesting that F. pseudograminearum is the dominant pathogen of FCR of wheat in Shandong province. Pathogenicity tests demonstrated that all 11 Fusarium species could cause typical symptoms of FCR on wheat seedlings. The results of the study indicate that a greater diversity of Fusarium species can cause FCR of wheat in Shandong province than that has been previously reported. This is the first report in the world of Fusarium incarnatum, Fusarium ipomoeae, and Fusarium flocciferum as pathogens causing FCR in wheat.

Pathogenic invasion of Trichoderma pleuroticola profoundly altered microflora in the Auricularia cornea crop production system, impacting diversity and composition in both artificial bed-log and fruiting bodies. A more complex ecological network between the diseased and healthy bodies. Researchers still have poor knowledge about how the important agricultural relationship between the composition of the microbiome of the artificial bed-log and the fruiting bodies is infected by the pathogenic invasive microbes T. pleuroticola, but this knowledge is crucial if we want to use or improve it. Here, we investigated 8 groups (48 biological samples) across 5 growth stages of the A. cornea production system using metagenomic technology. Diseased and healthy fruiting bodies exhibited distinct microbial compositions, while core members in artificial bed-logs remained stable. Core microbiota analysis highlighted Pseudomonas and Pandoraea bacterial genera, as well as Sarocladium, Cephalotrichum, Aspergillus, and Mortierella fungal genera as biomarker species after the bodies were treated with the pathogenic invasive microbes T. pleuroticola. In diseased bodies, these core members upregulated pathways including polymyxin resistance, L-arginine degradation II, superpathway of L-arginine and L-ornithine degradation, glucose degradation (oxidative), glucose and glucose-1-phosphate degradation, promoting fruit spoilage. Our data confirm that T. pleuroticola plays an important role in the early stages of disease development in the A. cornea crop generation system. The exposed volatile core microbiome may play an important role in accelerating T. pleuroticola-induced decay of fruiting bodies.

Color variations in cultivated edible mushrooms present novel and potentially valuable alternatives to the research and cultivation industries. We collected, identified, and domesticated a white strain of Auricularia cornea and a white strain of Auricularia heimuer from China. However, due to an unstable phenotype and stricter requirements on environment and management technology, the production and utilization of Auricularia heimuer cv. Bai Muer make slow progress. Outcrossing is an essential means to broaden the intraspecific genetic resources to expand the gene pool and compensate for the limitations of related species hybridization. In this study, interspecies hybridization between Auricularia cornea cv. Yu Muer and Auricularia heimuer cv. Bai Muer was conducted using polyethylene glycol (PEG)-induced double-inactivated protoplast fusion. Apart from the functional complementation of double-inactivated protoplasts, the hybrids were characterized by colony morphology, antagonistic test, primordial morphology, and polymerase chain reaction (PCR) fingerprinting. The results suggested that the hybrids and their parents showed significant differences in their colony morphology. Moreover, positive barrage reactions were observed between each parent and hybrid. Inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) profile analysis of fusants and parents depicted that fusants contained polymorphic bands, which indicated the rearrangement and deletion of deoxyribonucleic acid (DNA) in the fusants. Yellowish-white primordia were obtained from two hybrids. Protoplast fusion may reinforce the genetic potential and provide an ideal alternative for breeding albino Auricularia.

Green mold disease, caused by Trichoderma spp., is one of the most devastating diseases of mushrooms in China. The application of fungicides remains one of the important control methods among the integrated pest management tools for disease management in mushroom farms. This study aimed to identify Trichoderma spp., isolated from G. sichuanense fruiting bodies displaying green mold symptoms collected from mushroom farms in Zhejiang, Hubei, and Jilin Province, China, and evaluate their in vitro sensitivity to six fungicides. A total of 47 isolates were obtained and classified into nine Trichoderma spp. namely, T. asperellum, T. citrinoviride, T. ganodermatiderum, T. guizhouense, T. hamatum, T. harzianum, T. koningiopsis, T. paratroviride, and T. virens, through morphological characteristics and phylogenetic analysis of concatenated sequences of translation elongation factor 1-alpha (TEF) and DNA-dependent RNA polymerase II subunit (RPB2) genes. The pathogenicity test was repeated two times, and re-isolation of the nine Trichoderma spp. from the fruiting bodies of G. sichuanense fulfilled Koch’s postulates. Prochloraz manganese showed the best performance against most species. This research contributes to our understanding of green mold disease, reveals the phylogenetic relationships among Trichoderma species, and expands our knowledge of Trichoderma species diversity associated with green mold disease in G. sichuanense.

Biological seed dressing is a cost-effective means to protect plant roots from pathogens. Trichoderma is generally considered as one of the most common biological seed dressings. However, there is still a dearth of information on the effects of Trichoderma on microbial community of rhizosphere soil. High-throughput sequencing was used to analyze the effects of Trichoderma viride and a chemical fungicide on microbial community of soybean rhizosphere soil. The results showed that both T. viride and chemical fungicide could significantly reduce the disease index of soybean (15.11% for Trichoderma and 17.33% for Chemical), while no significant difference was observed between them. Both T. viride and chemical fungicide could affect the structure of rhizosphere microbial community, they increased the β-diversity of microbial community and significantly reduce the relative abundance of Saprotroph-Symbiotroph. Chemical fungicide could reduce the complexity and stability of co-occurrence network. However, T. viride is beneficial for maintaining network stability and increasing network complexity. There were 31 bacterial genera and 21 fungal genera significantly correlated with the disease index. Furthermore, several potential plant pathogenic microorganisms were also positively correlated with disease index, such as Fusarium, Aspergillus, Conocybe, Naganishia, and Monocillium. From this work, T. viride may be used as a substitute for chemical fungicide to control soybean root rot and be more friendly to soil microecology.

Boletaceae, the largest family in Boletales, has been attracted by mycologists in the world due to its diverse morphology and complex history of evolution. Although considerable work has been done in the past decades, novel taxa are continually described. The current study aimed to introduce three new taxa and one new record of Boletaceae from China. The morphological descriptions, color photographs, phylogenetic trees to show the positions of the taxa, and comparisons with allied taxa are provided. The new genus Hemilanmaoa is unique in the Pulveroboletus group, and Hemilanmaoa retistipitatus was introduced as the type species. It can be distinguished by its bluing basidioma when injured, a decurrent hymenophore, a stipe covered with distinct reticulations, and a fertile stipitipellis. Porphyrellus pseudocyaneotinctus is characterized by its pileipellis consisting of broadly concatenated cells and thin-walled caulocystidia in Porphyrellus. In Phylloporus, Phylloporus biyangensis can be distinguished by its hymenophores that change to blue when injured and yellow basal mycelium. Lanmaoa angustispora, as a new record, is first reported in Northern China. Internal transcribed spacer (ITS), 28S rDNA (28S), translation elongation factor 1-alpha (tef1-α), RNA polymerase II subunit 1 (rpb1), and RNA polymerase II subunit 2 (rpb2) were employed to execute phylogenetic analyses.

As one of the important sources of human nutrition, Brassicaceae vegetables are widely grown worldwide. Black rot caused by Xanthomonas campestris pv. campestris (Xcc) seriously affects the quality and yield of Brassicaceae vegetables. Therefore, it is important to study control methods of Xcc for Brassicaceae vegetable production. This paper reviews the physical, chemical, and biological control methods of Xcc in Brassicaceae vegetables developed in recent years, and the underlying mechanisms of control methods are also discussed. Based on our current knowledge, future research directions for Xcc control are also proposed. This review also provides a reference basis for the control of Xcc in the field cultivation of Brassicaceae vegetables.

Gymnopus sect. Impudicae is a poorly studied group around the world. However, it is well known for its pungent smell—a total of five species from China belonging to sect. Impudicae were recorded, and included four species new to science—G. epiphyllus, G. cystidiosus, G. subdensilamellatus, and G. subpolyphyllus—which were delimited and proposed based on morphological and molecular evidences, and one new record from Henan, Jiangxi, and Gansu Province, China—G. densilamellatus. Detailed descriptions and illustrations were presented as well as comparisons to similar species. Phylogenetic analysis inferred from the ITS and nLSU dataset supported the Gymnopus as a monophyletic genus which was defined by Oliveira et al., and the novel species grouped as separate lineages within it. A Key to the reported species of Gymnopus sect. Impudicae is also provided.

Echovirus 30 (E30) causes various diseases, such as viral encephalitis; aseptic meningitis; hand, foot, and mouth diseases; and acute flaccid paralysis. Related neurological infections are most concerning. However, the molecular mechanisms of E30 pathogenesis are not fully understood. There is a growing research interest in E30 as a cause of neurological disease. The aim of this study was to describe E30 infection, especially the changes in differential factor expressions after infection, in human glioma (U251) cells and mice brains using transcriptome sequencing analysis. Clear changes in the gene expression of factors associated with the defense response to viruses, inflammation-related signaling pathways, and neurological complication-related pathways were observed. Our results suggest that after E30 infection, the genes related to immune response were induced in the human glioma cells and mice brains, whereas genes functioning in the development and function of neural tissue were inhibited. Overall, this study successfully established E30 infection of U251 and mouse brain tissue, profiled the infection-induced changes in cellular and organizational transcriptomes, and revealed the molecular level changes during E30 infection.

Since December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the world and has had a devastating impact on health and economy. The biochemical characterization of SARS-CoV-2 proteins is important for drug design and development. In this study, we discovered that the SARS-CoV-2 nucleocapsid protein can melt double-stranded DNA (dsDNA) in the 5′-3′ direction, similar to SARS-CoV-2 nonstructural protein 13. However, the unwinding activity of SARS-CoV-2 nucleocapsid protein was found to be more than 22 times weaker than that of SARS-CoV-2 nonstructural protein 13, and the melting process was independent of nucleoside triphosphates and Mg2+. Interestingly, at low concentrations, the SARS-CoV-2 nucleocapsid protein exhibited a stronger annealing activity than SARS-CoV-2 nonstructural protein 13; however, at high concentrations, it promoted the melting of dsDNA. These findings have deepened our understanding of the SARS-CoV-2 nucleocapsid protein and will help provide novel insights into antiviral drug development.

Pseudomonas fluorescens 2P24 is a plant root-associated bacterium that suppresses several soilborne plant diseases due to its production of the antibiotic 2,4-diacetylphloroglucinol (2,4-DAPG). The biosynthesis of 2,4-DAPG is controlled by many regulatory elements, including the global regulator of the Gac/Rsm regulon and the pathway-specific repressor PhlF. In this work, a novel genetic element grxD, which encodes the monothiol glutaredoxin GrxD, was identified and characterized in the production of 2,4-DAPG in P. fluorescens 2P24. Our data showed that the mutation of grxD remarkably decreased 2,4-DAPG production. GrxD lost its ability to alter the production of 2,4-DAPG when the active-site CGFS motif of GrxD was mutated by site-directed mutagenesis. Further studies showed that the RsmA and RsmE proteins were essential for the GrxD-mediated regulation of 2,4-DAPG and exoprotease production. In addition, our data revealed that the deletion of grxD increased the expression of phlF, which negatively regulated the production of 2,4-DAPG. In addition, the grxD mutant was severely impaired in the biocontrol effect against the bacterial wilt of tomato. Overall, our results indicated that the monothiol glutaredoxin GrxD is involved in the production of 2,4-DAPG of P. fluorescens by influencing the Gac/Rsm global signaling pathway and transcriptional regulator PhlF and is essential for the biocontrol properties.

A two-way relationship between diabetes and periodontitis has been discussed recently. Periodontitis microbiota might affect the immune homeostasis of diabetes, but the molecular mechanism of their interactions is still not clear. The aims of this study were to clarify the possible immune regulatory effects of periodontitis microbiota on diabetes and the correlation between immunomodulation and ectopic colonization. A model of germ-free mice with streptozotocin-induced type 1 diabetes mellitus (T1D), which was orally inoculated with mixed saliva samples for 2 weeks, was used in this study. Those mice were randomly divided into two groups, namely, SP (where the T1D mice were orally inoculated with mixed saliva samples from periodontitis patients) and SH (where the T1D mice were orally inoculated with mixed saliva samples from healthy subjects). Ectopic colonization of saliva microbiota was assessed using culture-dependent method and Sanger sequencing, and the composition of gut microbiota was analyzed using 16S rRNA gene sequencing. Changes in 15 types of immune cells and six cytokines either from the small intestine or spleen were detected by multicolor flow cytometry. The correlation between gut microbiota and immune cells was evaluated by redundancy analysis. Although periodontitis microbiota minorly colonized the lungs, spleens, and blood system, they predominantly colonized the gut, which was mainly invaded by Klebsiella. SH and SP differed in beta diversity of the gut bacterial community. Compared to SH, microbial alteration in small intestine occurred with an increase of Lacticaseibacillus, Bacillus, Agathobacter, Bacteroides, and a decrease of Raoultella in SP. More types of immune cells were disordered in the spleen than in the small intestine by periodontitis microbiota, mainly with a dramatical increase in the proportion of macrophages, plasmacytoid dendritic cells (pDCs), monocytes, group 3 innate lymphoid cells, CD4-CD8- T cells and Th17 cells, as well as a decline of αβT cells in SP. Cytokines of IFNγ, IL17, and IL22 produced by CD4 + T cells as well as IL22 produced by ILCs of small intestine rose in numbers, and the intestinal and splenic pDCs were positively regulated by gut bacterial community in SP. In conclusion, periodontitis microbiota invasion leads to ectopic colonization of the extra-oral sites and immune cells infiltration, which might cause local or systemic inflammation. Those cells are considered to act as a “bridge” between T1D and periodontitis.

Trichinellosis is a serious zoonotic parasitic disease caused by Trichinella spiralis (T. spiralis) that causes considerable economic losses for the global pig breeding and food industries. As such, there is an urgent need for a vaccine that can prevent T. spiralis infection. Previous studies have reported that recombinant invasive Lactococcus lactis (LL) expressing Staphylococcus aureus fibronectin binding protein A (LL-FnBPA+) can transfer DNA vaccines directly to dendritic cells (DCs) across an epithelial cell monolayer, leading to significantly higher amounts of heterologous protein expression compared to non-invasive Lactococcus lactis. In this study, the invasive bacterium Lactiplantibacillus plantarum (L. plantarum) expressing FnBPA was used as a carrier to deliver a novel oral DNA vaccine consisting of T. spiralis adult putative serine protease (Ts-ADpsp) and murine interleukin (IL)-4 DNA to mouse intestinal epithelial cells. Experimental mice were orally immunized 3 times at 10-day intervals. At 10 days after the last vaccination, mice were challenged with 350 T. spiralis infective larvae by oral inoculation. Immunization with invasive L. plantarum harboring pValac-Ts-ADpsp/pSIP409-FnBPA induced the production of anti-Ts-ADpsp-specific IgG of serum, type 1 and 2 helper T cell cytokines of mesenteric lymph node (MLN) and spleen, secreted (s) IgA of intestinal lavage, and decreased T. spiralis burden and intestinal damage compared to immunization with non-invasive L. plantarum expressing Ts-ADpsp (pValac-Ts-ADpsp/pSIP409). Thus, invasive L. plantarum expressing FnBPA and IL-4 stimulates both mucosal and cellular immune response to protect against T. spiralis infection, highlighting its therapeutic potential as an effective DNA vaccine for trichinellosis.

Truffles (Tuber spp.) are edible ectomycorrhizal fungi with high economic value. Bacteria in ectomycorrhizosphere soils are considered to be associated with the nutrient uptake of truffles and hosts. Whether Tuber spp. inoculation can affect the growth of Quercus aliena, the ectomycorrhizosphere soil, and the rhizosphere nirK and nirS-denitrifier communities at the ectomycorrhizae formation stage is still unclear. Therefore, we inoculated Q. aliena with the black truffles Tuber melanosporum and Tuber indicum, determined the physiological activity and morphological indices of Q. aliena seedlings, analyzed the physicochemical properties of ectomycorrhizosphere soils, and applied DNA sequencing to assess the nirK and nirS- denitrifier community structure in ectomycorrhizosphere soils. Peroxidase activity was higher in the seedlings inoculated with T. melanosporum than in the T. indicum inoculation and uninoculated control treatments. The available phosphorus contents were lower and nitrate contents were higher in those with truffle inoculation, and T. melanosporum treatment differed more from the control than the T. indicum treatment. The richness of the nirK-community was highest in the T. indicum treatment and lowest in the uninoculated treatment. The differences in nirK-community composition across treatments were not statistically significant, but the nirS communities were different. The nirS-type bacteria correlated with three environmental factors (pH, available phosphorus, and nitrate contents), whereas the nirK-type bacteria were only associated with the nitrate contents. Generally, this work revealed that inoculation with Tuber spp. would change a few nutrient contents and richness of nirK-type bacteria and had little effects on growth of Q. aliena seedlings in the initial stage of inoculation. The results of this study may provide in-depth insights into the relationships between Tuber spp. and hosts, which should be taken into account when developing truffle production methods.

The current study was to investigate the modulatory effects of total dietary fiber (TDF) levels on cecal morphology and the response of microbiota to maintain gut health for duck growth. A total of 192 14-day-old male white Pekin ducks were randomly allocated to three dietary groups and fed diets, containing 12.4, 14.7, and 16.2% TDF, respectively, until 35 days under the quantitative feed intake. Each dietary group consisted of eight replicate cages of eight birds. The results revealed that 14.7 and 16.2% TDF groups significantly promoted growth performance and improved villus height, the ratio of villus to crypt, muscle layer thickness, and goblet cells per villus of cecum in ducks. qPCR results showed that the transcriptional expression of Claudin-1, Muc2, IGF-1, and SLC16A1 was significantly upregulated in cecum in 14.7 and 16.2% TDF groups. Meanwhile, the concentration of IGF-1 in circulating was significantly increased in 14.7 and 16.2% TDF groups while that of DAO was significantly decreased in 16.2% TDF group. Furthermore, the concentrations of butyrate, isobutyrate, valerate, and isovalerate in cecum were conspicuously improved in 14.7 and 16.2% TDF groups while that of propionate was significantly decreased. In addition, the concentrations of butyrate, isobutyrate, valerate, and isovalerate in cecum presented negative correlations with the concentration of DAO in circulating. 16S rRNA gene sequencing results showed that the 14.7% TDF group importantly elevated the microbial richness. Simultaneously, butyrate-producing bacteria like the family Lachnospiraceae, Oscillospiraceae, and Erysipelatoclostridiaceae were enriched as biomarkers in the 16.2% TDF group. Correlation network analysis revealed that the associations between specific bacteria and short-chain fatty acids (SCFAs) induced by different TDF levels, and the correlations among bacteria were also witnessed. For example, the genus Monoglobus and CHKCI002 showed a positive correlation with butyrate, and there was a positively coexistent association between Monoglobus and CHKCI002. In summary, these data revealed that increasing the TDF level could enhance the cecal morphology and drive cecal species-specific of SCFAs in ducks.

The current study was to investigate the effects of total dietary fiber (TDF) on growth performance, cecal structure, cecal microbial community, and short-chain fatty acids (SCFAs) profiles in the cecum of growing White Pekin ducks. A total of 108 male Pekin ducks of 14-days-old were randomly allocated and fed diets containing 12.4, 14.7, and 16.2% TDF for 35 days. Each dietary treatment consisted of six replicates with six birds each. The results showed that 14.7 and 16.2% TDF treatments promoted growth performance relative to 12.4% TDF treatments (P < 0.05). A total of 14.7 and 16.2% TDF treatments significantly elevated villus height, the ratio of villus height to crypt depth and muscle layer thickness of cecum, and lowered crypt depth compared with 12.4% TDF treatment (P < 0.05). Simultaneously, 14.7 and 16.2% TDF treatments up-regulated Claudin-1 mRNA expression of barrier genes in the cecum compared with 12.4% TDF (P < 0.05). Butyrate-producing bacteria like Oscillopiraceae affiliating to the phyla Firmicutes were observed as a biomarker in the 16.2% TDF. Higher concentration of butyrate in the cecum was obtained in the 14.7% TDF compared with 12.4 and 16.2% TDF (P < 0.05). The concentrations of isobutyrate, valerate, and isovalerate in the cecum were significantly increased in the 16.2% TDF compared with 12.4 and 14.7% TDF (P < 0.05). Meanwhile, the abundance of genus UCG-005 and Enterococcus was positive correlations with isobutyrate and valerate (P < 0.05). However, the concentration of propionate in the cecum significantly decreased in 14.7 and 16.2% TDF treatments relative to 12.4% TDF treatments (P < 0.05). In summary, increasing TDF levels improved growth performance, cecal histomorphology, and barrier function of meat ducks and it might be mediated by the changes of microbiota communities, especially bloom of SCFAs-producing bacteria, which facilitated the interaction between intestinal mucosa and microbiota.

Adaptive laboratory evolution (ALE) experiments are a serviceable method for the industrial utilization of the microalgae, which can improve the phenotype, performance, and stability of microalgae to obtain strains containing beneficial mutations. In this article, we reviewed the research into the microalgae ALE test and assessed the improvement of microalgae growth, tolerance, metabolism, and substrate utilization by ALE. In addition, the principles of ALE and the key factors of experimental design, as well as the issues and drawbacks of the microalgae ALE method were discussed. In general, improving the efficiency of ALE and verifying the stability of ALE resulting strains are the primary problems that need to be solved in future research, making it a promising method for the application of microalgae biotechnology.

In the present study, the mitogenome of Tuber calosporum was assembled and analyzed. The mitogenome of T. calosporum comprises 15 conserved protein-coding genes, two rRNA genes, and 14 tRNAs, with a total size of 287,403 bp. Fifty-eight introns with 170 intronic open reading frames were detected in the T. calosporum mitogenome. The intronic region occupied 69.41% of the T. calosporum mitogenome, which contributed to the T. calosporum mitogenome significantly expand relative to most fungal species. Comparative mitogenomic analysis revealed large-scale gene rearrangements occurred in the mitogenome of T. calosporum, involving gene relocations and position exchanges. The mitogenome of T. calosporum was found to have lost several tRNA genes encoding for cysteine, aspartate, histidine, etc. In addition, a pair of fragments with a total length of 32.91 kb in both the nuclear and mitochondrial genomes of T. calosporum was detected, indicating possible gene transfer events. A total of 12.83% intragenomic duplications were detected in the T. calosporum mitogenome. Phylogenetic analysis based on mitochondrial gene datasets obtained well-supported tree topologies, indicating that mitochondrial genes could be reliable molecular markers for phylogenetic analyses of Ascomycota. This study served as the first report on mitogenome in the family Tuberaceae, thereby laying the groundwork for our understanding of the evolution, phylogeny, and population genetics of these important ectomycorrhizal fungi.

In recent years, rapidly increasing trade and travel across the China–Kazakhstan border has increased the potential risk of the introduction and exportation of vectors and their related diseases. The Ebinur Lake Nature Reserve is located in Xinjiang Uygur Autonomous Region, near the China–Kazakhstan border, with a suitable ecosystem for mosquito breeding. In our previous work, a novel Orthobunyavirus species named Ebinur Lake virus (EBIV) was isolated in the reserve. To gain insights into the potential risk of EBIV in this region, we conducted a study that aimed to clearly outline EBIV’s biological characteristics and its human seroprevalence in this region. Phylogenetically, the analysis of all three segments of EBIV demonstrated that it belongs to the genus Orthobunyavirus, which is clustered in the Bunyamwera serogroup. EBIV replicated efficiently and caused cytopathic effects (CPEs) in vertebrate cells. The survival rates of the EBIV-challenged mice were 0 and 20% when inoculated with viral concentrations ≥104 or 102 plaque-forming units, respectively. For EBIV-infected mice, internal bleeding and pathological changes were observed. In addition, the overall immunoglobulin M (IgM) antibody [1:4 by immunofluorescence assay (IFA)], immunoglobulin G (IgG) antibody (1:10 by IFA), and neutralizing antibody [90% plaque reduction neutralization test (PRNT)] prevalence was 8.05, 12.3, and 0.95%, respectively, in the studied residents. In summary, EBIV is a new member of the Bunyamwera serogroup and is able to competently infect cells derived from mosquitoes, rodents, monkeys, or humans. Furthermore, EBIV caused severe disease and even death in challenged Kunming mice, and the antibodies against EBIV have been detected in local residents, indicating that the virus is a potential animal or human pathogen.

Truffles are ascomycetous ectomycorrhizal fungi that have elevated status in the culinary field due to their unique aroma and taste as well as their nutritional value and potential biological activities. Tuber melanosporum, T. indicum, T. panzhihuanense, T. sinoaestivum, and T. pseudoexcavatum are five commercial truffle species mainly distributed in Europe or China. In this study, an untargeted metabolomics technology based on an ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method was applied to analyze the metabolic profiles and variations among these five truffle species. In our results, a total of 2376 metabolites were identified under positive ion mode, of which 1282 had significantly differential amounts and covered 110 pathways or metabolisms. Principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) revealed a clear separation from each of these five truffles, indicating a significantly different metabolic profile among them, with the biggest difference between T. melanosporum and the other four truffles. The differential metabolites covered various chemical categories, and a detailed analysis was performed for nine metabolic categories, including amino acids, saccharides and nucleosides, organic acids, alkaloids, flavonoids, carnitines, phenols and alcohols, esters, and sulfur compounds. For each of the nine categories, most of metabolites predominantly accumulated in T. melanosporum compared with the other four truffles. Meanwhile, there were significant differences of the average ion intensity in each category among the five truffles, e.g., higher amounts of amino acids was detected in T. panzhihuanense and T. pseudoexcavatum; T. indicum contained significantly more carnitines, while there were more alkaloids in T. melanosporum. Additionally, some metabolites with biological activities were discussed for each category, such as acetyl-L-carnitine, adenine, neobavaisoflavone, and anandamide. Generally, this study may provide the valuable information regarding the variation of the metabolic composition of these five commercial truffle species, and the biological significance of these metabolites was uncovered to explore the metabolic mechanisms of truffles, which would be helpful for further research on the compounds and potential biological functions in truffles that have not yet been investigated.

The GacS/GacA two-component system is essential for virulence in many plant pathogenic bacteria, and thus represents a promising anti-virulence target. In the present study, we isolated and screened rhizobacteria that were capable of inhibiting the expression of the gacS gene in the phytopathogenic bacterium Pseudomonas syringae pv. tomato (Pto) DC3000. One candidate inhibitor bacterium, BR3 was obtained and identified as a Bacillus sp. strain based on 16s rRNA gene sequence analysis. Besides the gacS gene, the GacA-dependent small RNA genes rsmZ and rsmY were repressed transcriptionally when DC3000 was treated with an extract from strain BR3. Importantly, the extract also influenced bacterial motility, the expression of type three secretion system effector AvrPto, and the plant hypersensitive response triggered by strain DC3000. The results suggested that the extract from strain BR3 might offer an alternative method to control bacterial diseases in plants by targeting the GacS/GacA system.

Current evidence to support extensive use of probiotics in inflammatory bowel disease is limited and factors that contribute to the inconsistent effectiveness of clinical probiotic therapy are not completely known. Here, we used Bifidobacterium longum JDM 301 as a model probiotic to study potential factors that may influence the effect of probiotics in experimental colitis. We found that the effect of B. longum JDM 301 in tempering experimental colitis varied across individual mice even with the same genetic background. The probiotic efficacy was highly correlated with the host gut microbial community features. Consumption of a diet rich in fat could exacerbate mucosal injury-induced colitis but could not change the host responsiveness to B. longum JDM 301 treatment, suggesting of potential mechanistic differences between regulating colitis pathogenesis, and modulating probiotic efficacies by the gut microbiota. Together, our results suggest that personalized microbiome features may modify the probiotic therapeutic effect and support the idea of personalized probiotic medicine in inflammatory bowel disease.

Truffles are one group of the most famous ectomycorrhizal fungi in the world. There is little information on the ecological mechanisms of truffle ectomycorrhizal synthesis in vitro. In this study, we investigated the ecological effects of Tuber indicum – Quercus aliena ectomycorrhizal synthesis on microbial communities in the host plant roots and the surrounding soil using high-throughput sequencing and on the metabolic profiles of host plant roots using metabolomics approaches. We observed an increase in the diversity and richness of prokaryotic communities and a decrease in richness of fungal communities in the presence of T. indicum. The microbial community structures in the host roots and the surrounding soil were altered by ectomycorrhizal synthesis in the greenhouse. Bacterial genera Pedomicrobium, Variibacter, and Woodsholea and fungal genera Aspergillus, Phaeoacremonium, and Pochonia were significantly more abundant in ectomycorhizae and the ectomycorrhizosphere soil compared with the corresponding T. indicum-free controls (P < 0.05). Truffle-colonization reduced the abundance of some fungal genera surrounding the host tree, such as Acremonium, Aspergillus, and Penicillium. Putative prokaryotic metabolic functions and fungal functional groups (guilds) were also differentiated by ectomycorrhizal synthesis. The ectomycorrhizal synthesis had great impact on the measured soil physicochemical properties. Metabolic profiling analysis uncovered 55 named differentially abundant metabolites between the ectomycorhizae and the control roots, including 44 upregulated and 11 downregulated metabolites. Organic acids and carbohydrates were two major upregulated metabolites in ectomycorhizae, which were found formed dense interactions with other metabolites, suggesting their crucial roles in sustaining the metabolic functions in the truffle ectomycorrhization system. This study revealed the effects of truffle-colonization on the metabolites of ectomycorrhiza and illustrates an interactive network between truffles, the host plant, soil and associated microbial communities, shedding light on understanding the ecological effects of truffles.

Probiotics might offer an attractive alternative to prevent and control Clostridium difficile (C. difficile) infection (CDI). Limited information is available on the ability of commercially used bifidobacterial strains to inhibit C. difficile. This study examined the anti-clostridial effects of Bifidobacterium longum JDM301, a widely used commercial probiotic strain in China, in vitro and in vivo. In vitro evaluation revealed a significant reduction in C. difficile counts when JDM301 was co-cultured with C. difficile, which was correlated with the significant decrease in clostridial toxin titres (TcdA and TcdB). Furthermore, the cell-free culture supernatants (CFS) of JDM301 inhibited C. difficile growth and degraded TcdA and TcdB. Notably, the results showed that acid pH promoted the degradation of TcdA by CFS from JDM301. Furthermore, comparative studies among 10 B. longum strains were performed, which showed that the inhibitory effect of CFS from JDM301 was similar with the other 8 B. longum strains and higher than strain BLY1. However, when it was neutralized, the significant different was lost. When present together, it was suggested that the acid pH induced by probiotics not only played important roles in the growth inhibition against C. difficile resulting in the reduction of toxins titres, but also directly promoted the degradation of clostridial toxin. In vivo studies proved that JDM301 partially relieved damage to tissues caused by C. difficile and also decreased the number of C. difficile and toxin levels. In summary, our results demonstrated that the commercial strain, JDM301 could be considered a probiotic able to exert anti-toxin capability and most of the CFS from Bifidobacterium were able to inhibit the growth of C. difficile, depending on acid pH. These results highlighted a potential that JDM301 could be helpful in preventing CDI and that most of the bifidobacterial strains could (at least partially) exert protective effects by reducing toxin titres through growth inhibition against toxigenic C. difficile.

Stenotrophomonas maltophilia is an emerging nosocomial pathogen with high resistance to most clinically used antimicrobials. Tigecycline is a potential alternative antimicrobial for S. maltophilia infection treatment, but its resistance mechanism in clinical isolates is not fully elucidated. We investigated the antimicrobial susceptibility of 450 S. maltophilia isolated during 2012–2015 from three university hospitals in Beijing, China. These strains exhibited high susceptibility to minocycline (98.44%), sulfamethoxazole/trimethoprim (87.56%), tigecycline (77.78 %), doxycycline (81.33%), levofloxacin (67.56%), and ticarcillin/clavulanate (73.00%). The susceptibility of tigecycline-nonsusceptible strains (TNS) to doxycycline and levofloxacin was much lower than that of tigecycline-susceptible strains (TSS) (25.00% vs. 97.71% for doxycycline, P < 0.001; 17.00% vs. 82.00% for levofloxacin, P < 0.001). We further selected 48 TNS and TSS and compared the detection rate of eight tetracycline-specific genes by PCR and the expression level of six intrinsic multidrug resistance efflux pumps by real-time PCR. Only one tetB and two tetH genes in TNS and three tetH genes in TSS were detected, and the detection rate had no difference. The average expression level of smeD in TNS was higher than that in TSS [20.59 (11.53, 112.54) vs. 2.07 (0.80, 4.96), P < 0.001], while the average expression levels of smeA, smeI, smeO, smeV, and smrA were not significantly different, indicating that smeDEF was the predominant resistance genetic determinant in clinical S. maltophilia. Higher smeD expression was also observed in levofloxacin- and doxycycline-nonsusceptible isolates than in their corresponding susceptible isolates [16.46 (5.83, 102.24) vs. 2.72 (0.80, 6.25) for doxycycline, P < 0.001; 19.69 (8.07, 115.10) vs. 3.01(1.00, 6.03), P < 0.001], indicating that smeDEF was also the resistance genetic determinant to levofloxacin and doxycycline. The consistent resistance profile and common resistance genetic determinant highlight the importance of rational use of tigecycline for preventing the occurrence and spread of multidrug resistance.

Halophilic fungi have evolved unique osmoadaptive strategies, enabling them to thrive in hypersaline habitats. Here, we conduct morphological and transcriptomic response of endophytic fungus (Aspergillus montevidensis ZYD4) in both the presence and absence of salt stress. Under salt stress, the colony morphology of the A. montevidensis ZYD4 changed drastically and exhibited decreased colony pigmentation. Extensive conidiophores development was observed under salt stress; conidiophores rarely developed in the absence of salt stress. Under salt stress, yellow cleistothecium formation was inhibited, while glycerol and compatible sugars continued to accumulate. Among differentially expressed unigenes (DEGs), 733 of them were up-regulated while 1,619 unigenes were down-regulated. We discovered that genes involved in the accumulation of glycerol, the storage of compatible sugars, organic acids, pigment production, and asexual sporulation were differentially regulated under salt stress. These results provide further understanding of the molecular basis of osmoadaptive mechanisms of halophilic endophytic fungi.

Pichia pastoris is widely used as a platform for heterologous protein expression because of its high volumetric productivity. Multicopy integration of the target gene is commonly used to improve the production of the target protein. Cre/lox recombination system is a powerful tool for the marker rescue during multiple integrations with one selection marker. Here we reported a novel expression vector based on the Cre/lox recombination system for multiple integrations of target gene to construct multicopy expression strain of P. pastoris. PAOX1 promoter was fused to cre to construct a methanol inducible Cre recombinase. The leakage expression of Cre recombinase in Escherichia coli was blocked by introducing the operator gene lacO. The expression vector designed pMCO-AOXα was stable in E. coli and could effectively rescue the Zeocin resistance gene for next round of integration in P. pastoris. Phytase AppA from E. coli was chosen as a reporter gene. Transformants with 2–16 copies of appA were constructed by using a single antibiotic. Expression of appA was gene dosage dependent when

Cold shock proteins (Csps) enable organisms to acclimate to and survive in cold environments and the bacterial CspA family exerts the cold protection via its RNA chaperone activity. However, most Archaea do not contain orthologs to the bacterial csp. TRAM, a conserved domain among RNA modification proteins ubiquitously distributed in organisms, occurs as an individual protein in most archaeal phyla and has a structural similarity to Csp proteins, yet its biological functions remain unknown. Through physiological and biochemical studies on four TRAM proteins from a cold adaptive archaeon Methanolobus psychrophilus R15, this work demonstrated that TRAM is an archaeal Csp and exhibits RNA chaperone activity. Three TRAM encoding genes (Mpsy_0643, Mpsy_3043, and Mpsy_3066) exhibited remarkable cold-shock induced transcription and were preferentially translated at lower temperature (18°C), while the fourth (Mpsy_2002) was constitutively expressed. They were all able to complement the cspABGE mutant of Escherichia coli BX04 that does not grow in cold temperatures and showed transcriptional antitermination. TRAM3066 (gene product of Mpsy_3066) and TRAM2002 (gene product of Mpsy_2002) displayed sequence-non-specific RNA but not DNA binding activity, and TRAM3066 assisted RNases in degradation of structured RNA, thus validating the RNA chaperone activity of TRAMs. Given the chaperone activity, TRAM is predicted to function beyond a Csp.

Aflatoxigenic Aspergillus fungi and associated aflatoxins are ubiquitous in the production and storage of food/feed commodities. Controlling these microbes is a challenge. In this study, the Shewanella algae strain YM8 was found to produce volatiles that have strong antifungal activity against Aspergillus pathogens. Gas chromatography-mass spectrometry profiling revealed 15 volatile organic compounds (VOCs) emitted from YM8, of which dimethyl trisulfide was the most abundant. We obtained authentic reference standards for six of the VOCs; these all significantly reduced mycelial growth and conidial germination in Aspergillus; dimethyl trisulfide and 2,4-bis(1,1-dimethylethyl)-phenol showed the strongest inhibitory activity. YM8 completely inhibited Aspergillus growth and aflatoxin biosynthesis in maize and peanut samples stored at different water activity levels, and scanning electron microscopy revealed severely damaged conidia and a complete lack of mycelium development and conidiogenesis. YM8 also completely inhibited the growth of eight other agronomically important species of phytopathogenic fungi: A. parasiticus, A. niger, Alternaria alternate, Botrytis cinerea, Fusarium graminearum, Fusarium oxysporum, Monilinia fructicola, and Sclerotinia sclerotiorum. This study demonstrates the susceptibility of Aspergillus and other fungi to VOCs from marine bacteria and indicates a new strategy for effectively controlling these pathogens and the associated mycotoxin production during storage and possibly in the field. [ABSTRACT FROM AUTHOR]

During an investigation of fungal diversity from freshwater environments in different regions in Jiangxi Province, China, four interesting species were collected. Morphology coupled with combined gene analysis of an ITS, LSU, SSU, and rpb2 DNA sequence data showed that they belong to the family Pleurotheciaceae. Four new species, Pleurotheciella ganzhouensis, Pla. irregularis, Pla. verrucosa, and Pleurothecium jiangxiense are herein described. Pleurotheciella ganzhouensis is characterized by its capsule-shaped conidia and short conidiophores, while Pla. irregularis has amorphous conidiophores and 3-septate conidia. Pleurotheciella verrucosa has cylindrical or verrucolose conidiogenous cells, 1-septate, narrowly fusiform, meniscus or subclavate conidia. Pleurothecium jiangxiense characterized in having conidiogenous cells with dense cylindrical denticles and short conidiophores. Pleurothecium obovoideum was transferred to Neomonodictys based on phylogenetic evidence. All species are compared with other similar species and comprehensive descriptions, micrographs, and phylogenetic data are provided.