Detecting and characterizing new endofungal bacteria in new hosts: Pandoraea sputorum and Mycetohabitans endofungorum in Rhizopus arrhizus.

The fungus Rhizopus arrhizus (=R. oryzae) is commonly saprotrophic, exhibiting a nature of decomposing organic matter. Additionally, it serves as a crucial starter in food fermentation and can act as a pathogen causing mucormycosis in humans and animals. In this study, two distinct endofungal bacteria (EFBs), associated with individual strains of R. arrhizus, were identified using live/dead staining, fluorescence in situ hybridization, transmission electron microscopy, and 16S rDNA sequencing. The roles of these bacteria were elucidated through antibiotic treatment, pure cultivation, and comparative genomics. The bacterial endosymbionts, Pandoraea sputorum EFB03792 and Mycetohabitans endofungorum EFB03829, were purified from the host fungal strains R. arrhizus XY03792 and XY03829, respectively. Notably, this study marks the first report of Pandoraea as an EFB genus. Compared to its free-living counterparts, P. sputorum EFB03792 exhibited 28 specific virulence factor-related genes, six specific CE10 family genes, and 74 genes associated with type III secretion system (T3SS), emphasizing its pivotal role in invasion and colonization. Furthermore, this study introduces R. arrhizus as a new host for EFB M. endofungorum, with EFB contributing to host sporulation. Despite a visibly reduced genome, M. endofungorum EFB03829 displayed a substantial number of virulence factor-related genes, CE10 family genes, T3SS genes, mobile elements, and significant gene rearrangement. While EFBs have been previously identified in R. arrhizus, their toxin-producing potential in food fermentation has not been explored until this study. The discovery of these two new EFBs highlights their potential for toxin production within R. arrhizus, laying the groundwork for identifying suitable R. arrhizus strains for fermentation processes.

Fucoxanthin Alleviates Dextran Sulfate Sodium-Induced Colitis and Gut Microbiota Dysbiosis in Mice.

The purpose of this study was to evaluate the preventive role and underlying mechanisms of fucoxanthin (Fx) on dextran sulfate sodium (DSS)-induced colitis in mice. The present data demonstrated that oral administration of Fx (50 and 200 mg/kg body weight/day) for 36 days significantly alleviated the severity of colitis in DSS-treated mice, as evidenced by attenuating body weight loss, bloody stool, diarrhea, shortened colon length, colonic epithelium distortion, a thin mucus layer, goblet cell depletion, damaged crypts, and extensive infiltration of inflammatory cells in the colonic mucosa. Additionally, Fx notably relieved DSS-induced intestinal epithelial barrier dysfunction via maintaining the tight junction function and preventing excessive apoptosis of colonic epithelial cells. Moreover, Fx effectively diminished colonic inflammation and oxidative stress in DSS-treated mice, and its mechanisms might be due to blunting the activation of NF-κB and NLRP3 inflammasome signaling pathways. Furthermore, Fx also modulates DSS-induced gut microbiota dysbiosis via recovering the richness and diversity of gut microbiota and reshaping the structure of gut microbiota, such as increasing the Firmicutes and Bacteroidota (F/B) ratio and elevating the relative abundance of some potential beneficial bacteria, including Lactobacillaceae and Lachnospiraceae. Overall, Fx might be developed as a promising functional ingredient to prevent colitis and maintain intestinal homeostasis.

Three New Species of Gongronella (Cunninghamellaceae, Mucorales) from Soil in Hainan, China Based on Morphology and Molecular Phylogeny.

The genus Gongronella is important in agriculture and industry by secreting various natural bioactive metabolites such as chitosanases and organic acids. During the most recent 8 years, a total of 14 new species have been described, remarkably enriching the diversity of this genus. In this study, we added three more new species to this valuable genus, based on a combination of morphological traits and phylogenetic information. Six strains of the genus Gongronella were isolated from soil collected in Hainan Province, China. Phylogenetic analyses of ITS and LSU rDNA sequences grouped these strains into three independent clades. According to their unique morphological characteristics, they were classified as G. multiramosa sp. nov., G. qichaensis sp. nov. and G. oleae sp. nov. The G. multiramosa was characterized by multiple branched sporangiophores and was closely related to G. pedratalhadensis. The G. qichaensis was characterized by obscure collars and closely related to G. butleri, G. hydei and G. banzhaoae. The G. oleae was characterized by the presence of oil droplets in the sporangiospores and was closely related to G. chlamydospora and G. multispora. Their descriptions and illustrations were provided, and their differences from morphological allies and phylogenetic-related species are discussed.

An integrated high-flux cold atomic beam source for strontium.

We present the design, construction, and characterization of an integrated cold atomic beam source for strontium (Sr), which is based on a compact Zeeman slower for slowing the thermal atomic beam and an atomic deflector for selecting the cold flux. By adopting arrays of permanent magnets to produce the magnetic fields of the slower and the deflector, we effectively reduce the system size and power compared to traditional systems with magnetic coils. After the slower cooling, one can employ additional transverse cooling in the radial direction and improve the atom collimation. The atomic deflectors employ two stages of two-dimensional magnetic-optical trapping (MOT) to deflect the cold flux, whose atomic speed is lower than 50 m/s, by 20° from the thermal atomic beam. We characterize the cold atomic beam flux of the source by measuring the loading rate of a three-dimensional MOT. The loading rates reach up to 109 atoms/s. The setup is compact, highly tunable, lightweight, and requires low electrical power, which addresses the challenge of reducing the complexity of building optical atomic clocks and quantum simulation devices based on Sr.

Spatiotemporal variations of ecosystem security pattern in Horqin sandy dune meadow alternating area, China.

The natural and geographical environment of ecologically fragile areas in northern China is complex. Due to heavy human disturbance and impacts of climate change, the sustainable development of ecosystems is facing serious challenges. Constructing ecological security pattern can provide decision-making basis for ecological environment protection in desertification areas. Based on land use change data of Horqin dune-meadow interphase area from 1985 to 2021, we identified ecological sources with the importance of ecosystem services and ecological sensitivity, and constructed the ecological security pattern using the minimum cumulative resistance model. We further analyzed the ecological security pattern and its development trend in 1985, 1995, 2005, 2015 and 2021, and explored the ecological spatial layout adjustment strategy. The results showed that the proportion of source area in the ecological security pattern of the study area was always small and scattered from 1985 to 2021, the network of ecological corridors was low, and the connectivity between ecological patches was lacking. The ecological security pattern had experienced a trend of deterioration first and then gradually improving. Ecological policies such as returning farmland to forest and grassland and afforestation had significantly improved the environmental security. We optimized the study area by combining the cultivated land suitability evaluation method. The ecological security pattern showed a spatial trend of 'dual-core, scattered and semi-surrounded'. The results could provide references for the construction of county-scale ecological security pattern in ecologically fragile areas and the ecological management of Horqin sands.

Insights into the Ecological Diversification of the Hymenochaetales based on Comparative Genomics and Phylogenomics With an Emphasis on Coltricia.

To elucidate the genomic traits of ecological diversification in the Hymenochaetales, we sequenced 15 new genomes, with attention to ectomycorrhizal (EcM) Coltricia species. Together with published data, 32 genomes, including 31 Hymenochaetales and one outgroup, were comparatively analyzed in total. Compared with those of parasitic and saprophytic members, EcM species have significantly reduced number of plant cell wall degrading enzyme genes, and expanded transposable elements, genome sizes, small secreted proteins, and secreted proteases. EcM species still retain some of secreted carbohydrate-active enzymes (CAZymes) and have lost the key secreted CAZymes to degrade lignin and cellulose, while possess a strong capacity to degrade a microbial cell wall containing chitin and peptidoglycan. There were no significant differences in secreted CAZymes between fungi growing on gymnosperms and angiosperms, suggesting that the secreted CAZymes in the Hymenochaetales evolved before differentiation of host trees into gymnosperms and angiosperms. Nevertheless, parasitic and saprophytic species of the Hymenochaetales are very similar in many genome features, which reflect their close phylogenetic relationships both being white rot fungi. Phylogenomic and molecular clock analyses showed that the EcM genus Coltricia formed a clade located at the base of the Hymenochaetaceae and divergence time later than saprophytic species. And Coltricia remains one to two genes of AA2 family. These indicate that the ancestors of Coltricia appear to have originated from saprophytic ancestor with the ability to cause a white rot. This study provides new genomic data for EcM species and insights into the ecological diversification within the Hymenochaetales based on comparative genomics and phylogenomics analyses.

The genome and transcriptome of Sarocladium terricola provide insight into ergosterol biosynthesis.

Sarocladium terricola is a species of ascomycete fungus that has been recognized as a biocontrol agent for managing animal and plant pathogens, and exhibits significant potential as a feed additive. In this study, we utilized a combination of short-read Illumina sequencing and long-read PacBio sequencing to sequence, assemble, and analyze the genome of S. terricola. The resulting genome consisted of 11 scaffolds encompassing 30.27 Mb, with a GC content of 54.07%, and 10,326 predicted protein coding gene models. We utilized 268 single-copy ortholog genes to reconstruct the phylogenomic relationships among 26 ascomycetes, and found that S. terricola was closely related to two Acremonium species. We also determined that the ergosterol content of S. terricola was synthesized to nearly double levels when cultured in potato dextrose media compared to bean media (4509 mg/kg vs. 2382 mg/kg). Furthermore, transcriptome analyses of differentially expressed genes suggested that the ergosterol synthesis genes ERG3, ERG5, and ERG25 were significantly up-regulated in potato dextrose media. These results will help us to recognize metabolic pathway of ergosterol biosynthesis of S. terricloa comprehensivelly.

Ferrostatin-1 attenuates pathological angiogenesis in oxygen-induced retinopathy via inhibition of ferroptosis.

Retinopathy of prematurity (ROP) is a vision-threatening ocular disease that occurs in premature infants, but the underlying mechanism is still unclear. Since oxidative stress has been well documented in the ROP development, we aimed to investigate whether ferroptosis, a new type of cell death characterized by lipid peroxidation and iron overload, is also involved in ROP. We detected the lipid peroxidation, oxidative stress and the expression of ferroptosis markers in the retina of mouse model of oxygen-induced retinopathy. After ferroptosis inhibitor, ferrostatin-1, was administered by intravitreal injection, ferroptosis marker, lipid peroxidation, retinal vasculature and glial cell activation were examined. We found decreased expression of SLC7A11 and GPX4, increased expression of FTH1 and TFRC, as well as increase of lipid peroxidation in the retina of OIR mice. Ferrostatin-1 administration significantly reduced lipid peroxidation, and also reversed the change of ferroptosis marker. Neovascular area and avascular area were suppressed and the pathological vasculature changes including acellular vessels and ghost pericytes were decreased. Microglial cell and Müller cell activation was not evidently influenced by ferrostatin-1 treatment. Our findings suggest that ferroptosis is involved in the pathological angiogenesis and might be a promising target for ROP therapy.

Nanopore sequencing of full rRNA operon improves resolution in mycobiome analysis and reveals high diversity in both human gut and environments.

High-throughput sequencing has substantially improved our understanding of fungal diversity. However, the short read (<500 bp) length of current second-generation sequencing approaches provides limited taxonomic and phylogenetic resolution for species discrimination. Longer sequences containing more information are highly desired to provide greater taxonomic resolution. Here, we amplified full-length rRNA operons (~5.5 kb) and established a corresponding fungal rRNA operon database for ONT sequences (FRODO), which contains ONT sequences representing eight phyla, 41 classes, 109 orders, 256 families, 524 genera and 1116 species. We also benchmarked the optimal method for sequence classification and determined that the RDP classifier based on our FRODO database was capable of improving the classification of ONT reads, with an average of 98%-99% reads correctly classified at the genus or species level. We investigated the applicability of our approach in three representative mycobiomes, namely, the soil, marine and human gut mycobiomes, and found that the gut contains the largest number of unknown species (over 90%), followed by the marine (42%) and soil (33.8%) mycobiomes. We also observed a distinct difference in the composition of the marine and soil mycobiomes, with the highest richness and diversity detected in soils. Overall, our study provides a systematic approach for mycobiome studies and revealed that the previous methods might have underestimated the diversity of mycobiome species. Future application of this method will lead to a better understanding of the taxonomic and functional diversity of fungi in environmental and health-related mycobiomes.

Comparative Genomics of Mortierellaceae Provides Insights into Lipid Metabolism: Two Novel Types of Fatty Acid Synthase.

Fungal species in the family Mortierellaceae are important for their remarkable capability to synthesize large amounts of polyunsaturated fatty acids, especially arachidonic acid (ARA). Although many genomes have been published, the quality of these data is not satisfactory, resulting in an incomplete understanding of the lipid pathway in Mortierellaceae. We provide herein two novel and high-quality genomes with 55.32% of syntenic gene pairs for Mortierella alpina CGMCC 20262 and M. schmuckeri CGMCC 20261, spanning 28 scaffolds of 40.22 Mb and 25 scaffolds of 49.24 Mb, respectively. The relative smaller genome for the former is due to fewer protein-coding gene models (11,761 vs. 13,051). The former yields 45.57% of ARA in total fatty acids, while the latter 6.95%. The accumulation of ARA is speculated to be associated with delta-5 desaturase (Delta5) and elongation of very long chain fatty acids protein 3 (ELOVL3). A further genomic comparison of 19 strains in 10 species in three genera in the Mortierellaceae reveals three types of fatty acid synthase (FAS), two of which are new to science. The most common type I exists in 16 strains of eight species of three genera, and was discovered previously and consists of a single unit with eight active sites. The newly revealed type II exists only in M. antarctica KOD 1030 where the unit is separated into two subunits α and ß comprised of three and five active sites, respectively. Another newly revealed type III exists in M. alpina AD071 and Dissophora globulifera REB-010B, similar to type II but different in having one more acyl carrier protein domain in the α subunit. This study provides novel insights into the enzymes related to the lipid metabolism, especially the ARA-related Delta5, ELOVL3, and FAS, laying a foundation for genetic engineering of Mortierellaceae to modulate yield in polyunsaturated fatty acids.

The Umbelopsis ramanniana Sensu Lato Consists of Five Cryptic Species.

Umbelopsis ramanniana is one of the most commonly reported species within the genus and an important oleaginous fungus. The morphology of the species varies remarkably in sporangiospores, columellae and chlamydospores. However, phylogenetic analyses based on ITS and nLSU rDNA had previously shown insufficiency in achieving species level identification in the genus Umbelopsis. In this study, by applying a polyphasic approach involving multi-gene (nSSU, ITS, nLSU, act1, MCM7 and cox1) phylogeny, morphology and maximum growth temperature, U. ramanniana sensu lato was revealed as a polyphyletic group and resolved with five novel taxa, namely U. curvata, U. dura, U. macrospora, U. microsporangia and U. oblongielliptica. Additionally, a key for all currently accepted species in Umbelopsis was also updated.

The Early Terrestrial Fungal Lineage of Conidiobolus-Transition from Saprotroph to Parasitic Lifestyle.

Fungi of the Conidiobolus group belong to the family Ancylistaceae (Entomophthorales, Entomophthoromycotina, Zoopagomycota) and include over 70 predominantly saprotrophic species in four similar and closely related genera, that were separated phylogenetically recently. Entomopathogenic fungi of the genus Batkoa are very close morphologically to the Conidiobolus species. Their thalli share similar morphology, and they produce ballistic conidia like closely related entomopathogenic Entomophthoraceae. Ballistic conidia are traditionally considered as an efficient tool in the pathogenic process and an important adaptation to the parasitic lifestyle. Our study aims to reconstruct the phylogeny of this fungal group using molecular and genomic data, ancestral lifestyle and morphological features of the conidiobolus-like group and the direction of their evolution. Based on phylogenetic analysis, some species previously in the family Conidiobolaceae are placed in the new families Capillidiaceae and Neoconidiobolaceae, which each include one genus, and the Conidiobolaceae now includes three genera. Intermediate between the conidiobolus-like groups and Entomophthoraceae, species in the distinct Batkoa clade now belong in the family Batkoaceae. Parasitism evolved several times in the Conidiobolus group and Ancestral State Reconstruction suggests that the evolution of ballistic conidia preceded the evolution of the parasitic lifestyle.

Phylogeny, Divergence Time Estimation and Biogeography of the Genus Onnia (Basidiomycota, Hymenochaetaceae).

Species of Onnia are important tree pathogens and play a crucial role in forest ecosystems. The species diversity and distribution of Onnia have been studied, however, its evolutionary history is poorly understood. In this study, we reconstructed the phylogeny of Onnia using internal transcribed spacers (ITS) and large subunit (LSU) rDNA sequence data. Molecular clock analyses developed the divergence times of Onnia based on a dataset (ITS + LSU rDNA + rpb1 + rpb2 + tef1α). Reconstruct Ancestral State in Phylogenies (RASP) was used to reconstruct the historical biogeography for the genus Onnia with a Dispersal Extinction Cladogenesis (DEC) model. Here, we provide a robust phylogeny of Onnia, with a description of a new species, Onnia himalayana from Yunnan Province, China. Molecular clock analyses suggested that the common ancestor of Onnia and Porodaedalea emerged in the Paleogene period with full support and a mean stem age of 56.9 Mya (95% highest posterior density of 35.9-81.6 Mya), and most species occurred in the Neogene period. Biogeographic studies suggest that Asia, especially in the Hengduan-Himalayan region, is probably the ancestral area. Five dispersals and two vicariances indicate that species of Onnia were rapidly diversified. Speciation occurred in the Old World and New World due to geographic separation. This study is the first inference of the divergence times, biogeography, and speciation of the genus Onnia.

The complete mitochondrial genome of Porodaedalea mongolica (Hymenochaetaceae, Basidiomycota).

Most Porodaedalea species are important phytopathogenic and medicinal fungi. Recently, several Porodaedalea species including P. mongolica were newly described. In the present study, the complete sequence of mitochondrial genome of P. mongolica was determined, with a size of 114,176 bp and a GC content of 28.98%, containing two ribosomal RNA subunit, 26 transfer RNA, and 54 protein-coding genes (PCGs). The comparative analyses indicated that the amino acids of 14 core PCGs were highly conserved in Porodaedalea. Phylogenetic analysis of Porodaedalea was performed based on mitogenomic data and provided a new insight to the phylogeny of the Porodaedalea. The complete mitogenome sequence provides important data for further study of Porodaedalea.

Species Diversity and Ecological Habitat of Absidia (Cunninghamellaceae, Mucorales) with Emphasis on Five New Species from Forest and Grassland Soil in China.

Although species of Absidia are known to be ubiquitous in soil, animal dung, and insect and plant debris, the species diversity of the genus and their ecological habitats have not been sufficiently investigated. In this study, we describe five new species of Absidia from forest and grassland soils in southwestern China, with support provided by phylogenetic, morphological, and physiological evidence. The species diversity and ecological habitat of Absidia are summarized. Currently, 22 species are recorded in China, which mainly occur in soil, especially in tropical and subtropical forests and mountains. An updated key to the species of Absidia in China is also provided herein. This is the first overview of the Absidia ecological habitat.

The complete mitochondrial genome of Linnemannia amoeboidea (W. Gams) Vandepol & Bonito (Mortierellales: Mortierellaceae).

The complete mitochondrial genome of Linnemannia amoeboidea (W. Gams) Vandepol & Bonito 2020 (Strain no.: CBS 889.72) was sequenced under the next-generation sequencing platform. It was the second one in the family Mortierellaceae Luerss. 1877. The circular genome was 49,702 bp in size, with a GC content of 20.86%. Gene prediction revealed 15 PCGs, two rRNA genes, 26 tRNA genes, one rnpB gene and seven ORFs. Phylogenetic analyses showed that L. amoeboidea was closely related to Podila verticillate (Linnem.) Vandepol & Bonito 2020.

[Spatial Distribution Characteristics of VOCs and Its Impact on Ozone Formation Potential in Rizhao City in Summer].

GC-SAW was used to carry out online sampling analysis of the main business sources, residential sources, and roads in Rizhao City from August 22 to 29 in 2020. The spatial distribution characteristics of various volatile organic compounds (VOCs) in the atmosphere were obtained, and the chemical reactivity of the main components was studied. The results showed that the VOCs with carbon atoms greater than 5 (VOCC>5) were mainly toluene propylbenzene and n-octane, and the spatial distribution was significant; the average ρ(TVOCC>5) in the port area, downtown area, and industrial area were 80.5, 115.3, and 118.1 µg·m-3, respectively. Combined with road traffic impact and industrial production emissions, the maximum ρ(TVOCC>5) on the main roads in Rizhao City appeared near the Yingbin Road; the concentration value was 164.37 µg·m-3; the ρ(BTEX) in adhesive processing, painting, and glass factories reached 432.34, 1010.84, and 1989.85 µg·m-3, respectively. The chemical reactivity analysis of the main components of VOCC>5 showed that BTEX and n-octane were the important active components of ozone formation in Rizhao City.

Taxonomy and Phylogeny of Four New Species in Absidia (Cunninghamellaceae, Mucorales) From China.

Four new species within the genus Absidia, A. globospora, A. medulla, A. turgida, and A. zonata, are proposed based on a combination of morphological traits, physiological features, and molecular evidences. A. globospora is characterized by globose sporangiospores, a 1.0- to 3.5-µm-long papillary projection on columellae, and sympodial sporangiophores. A. medulla is characterized by cylindrical to oval sporangiospores, a 1.0- to 4.5-µm-long bacilliform projection on columellae, and spine-like rhizoids. A. turgida is characterized by variable sporangiospores, up to 9.5-µm-long clavate projections on columellae, and swollen top of the projection and inflated hyphae. A. zonata is characterized by cylindrical to oval sporangiospores, a 2.0- to 3.5-µm-long spinous projection on columellae, and as many as eight whorled sporangiophores. Phylogenetic analyses based on sequences of internal transcribed spacer rDNA and D1-D2 domains of LSU rDNA support the novelty of these four species within the Absidia. All new species are illustrated, and an identification key to all the known species of Absidia in China is included.

Transcriptome Reveals Roles of Lignin-Modifying Enzymes and Abscisic Acid in the Symbiosis of Mycena and Gastrodia elata.

Gastrodia elata is a well-known medicinal and heterotrophic orchid. Its germination, limited by the impermeability of seed coat lignin and inhibition by abscisic acid (ABA), is triggered by symbiosis with fungi such as Mycena spp. However, the molecular mechanisms of lignin degradation by Mycena and ABA biosynthesis and signaling in G. elata remain unclear. In order to gain insights into these two processes, this study analyzed the transcriptomes of these organisms during their dynamic symbiosis. Among the 25 lignin-modifying enzyme genes in Mycena, two ligninolytic class II peroxidases and two laccases were significantly upregulated, most likely enabling Mycena hyphae to break through the lignin seed coats of G. elata. Genes related to reduced virulence and loss of pathogenicity in Mycena accounted for more than half of annotated genes, presumably contributing to symbiosis. After coculture, upregulated genes outnumbered downregulated genes in G. elata seeds, suggesting slightly increased biological activity, while Mycena hyphae had fewer upregulated than downregulated genes, indicating decreased biological activity. ABA biosynthesis in G. elata was reduced by the downregulated expression of 9-cis-epoxycarotenoid dioxygenase (NCED-2), and ABA signaling was blocked by the downregulated expression of a receptor protein (PYL12-like). This is the first report to describe the role of NCED-2 and PYL12-like in breaking G. elata seed dormancy by reducing the synthesis and blocking the signaling of the germination inhibitor ABA. This study provides a theoretical basis for screening germination fungi to identify effective symbionts and for reducing ABA inhibition of G. elata seed germination.

Complete mitochondrial genome of Neoconidiobolus thromboides (Entomophthorales: Ancylistaceae).

Neoconidiobolus thromboides is a pandemic species in the genus Neoconidiobolus. In this article, we report the first complete sequence of mitochondrial genome from a common entomophthoroid fungus Neoconidiobolus thromboides under Illumina next-generation sequencing system. The total length of the mitogenome is 34,984 bp with a GC content of 26.99%. The gene annotation revealed 56 genes, including 30 protein-coding genes (PCGs), two ribosomal RNA genes (rDNAs), 24 transfer RNA (tRNA) genes. Phylogenetic analyses of 14 concatenated conserved PCGs indicated that N. thromboides was grouped with Capillidium heterosporum and Conidiobolus sp.