Links between soil bacteriobiomes and fungistasis toward fungi infecting the Colorado potato beetle

Entomopathogenic fungi can be inhibited by different soil microorganisms, but the effect of a soil microbiota on fungal growth, survival, and infectivity toward insects is insufficiently understood. We investigated the level of fungistasis toward Metarhizium robertsii and Beauveria bassiana in soils of conventional potato fields and kitchen potato gardens. Agar diffusion methods, 16S rDNA metabarcoding, bacterial DNA quantification, and assays of Leptinotarsa decemlineata survival in soils inoculated with fungal conidia were used. Soils of kitchen gardens showed stronger fungistasis toward M. robertsii and B. bassiana and at the same time the highest density of the fungi compared to soils of conventional fields. The fungistasis level depended on the quantity of bacterial DNA and relative abundance of Bacillus, Streptomyces, and some Proteobacteria, whose abundance levels were the highest in kitchen garden soils. Cultivable isolates of bacilli exhibited antagonism to both fungi in vitro. Assays involving inoculation of nonsterile soils with B. bassiana conidia showed trends toward elevated mortality of L. decemlineata in highly fungistatic soils compared to low-fungistasis ones. Introduction of antagonistic bacilli into sterile soil did not significantly change infectivity of B. bassiana toward the insect. The results support the idea that entomopathogenic fungi can infect insects within a hypogean habitat despite high abundance and diversity of soil antagonistic bacteria

Fungus Metarhizium robertsii and neurotoxic insecticide affect gut immunity and microbiota in Colorado potato beetles

Fungal infections and toxicoses caused by insecticides may alter microbial communities and immune responses in the insect gut. We investigated the effects of Metarhizium robertsii fungus and avermectins on the midgut physiology of Colorado potato beetle larvae. We analyzed changes in the bacterial community, immunity- and stress-related gene expression, reactive oxygen species (ROS) production, and detoxification enzyme activity in response to topical infection with the M. robertsii fungus, oral administration of avermectins, and a combination of the two treatments. Avermectin treatment led to a reduction in microbiota diversity and an enhancement in the abundance of enterobacteria, and these changes were followed by the downregulation of Stat and Hsp90, upregulation of transcription factors for the Toll and IMD pathways and activation of detoxification enzymes. Fungal infection also led to a decrease in microbiota diversity, although the changes in community structure were not significant, except for the enhancement of Serratia. Fungal infection decreased the production of ROS but did not affect the gene expression of the immune pathways. In the combined treatment, fungal infection inhibited the activation of detoxification enzymes and prevented the downregulation of the JAK-STAT pathway caused by avermectins. The results of this study suggest that fungal infection modulates physiological responses to avermectins and that fungal infection may increase avermectin toxicosis by blocking detoxification enzymes in the gut

THE EFFECT OF DEXTRANAL ON THE GUT BACTERIOBIOME OF CALVES

Background. The search for more efficient pro- and prebiotics to improve calves’ health, including decreasing the incidence of intestinal infections and increasing biomass production, has been very actual. The effect of prebiotics, however, is poorly, especially as related to gut microbiome biodiversity.  The aim of this work was to study the influence of dextranal on the growth of calves and their gut(rectum) bacteriobiome. Materials and Methods. Bacteriobiome composition and structure was assessed in the control group (K, conventional diet) and dextranal-receiving group (D) in 18-20 days aged calves  by 16S metabarcoding (V3-V4, Illumina MiSeq). Results. Overall, we found 377 operational taxonomic units (OTU) from 168 genera, 91 families, 55 orders, 30 classes and 11 phyla, with more than the half of the total number of identifies OTUs belonging to the Firmicutes phylum, followed by Bacteroidetes and Actinobacteria. The relative abundance of the phylum-specific nucleotide sequences followed the same order of dominance. Dextranal addition resulted in the increased (11.9 kg/calf, or 15%) of the living body mass of the two-months old calves in group D as compared with group K: consequently, the dextranal-related difference in the calves’ gut bacteriobiome composition and structure can be viewed as beneficial. It primarily concerns the decreased abundance of the opportunistic pathogen Escherichia/Shigella (Gammaproteobacteria) in group D. Overall 73 OTUs, including six dominant ones, were found to be differentially abundant in the groups. However, changes in the relative abundance of some OTUs were difficult to interpret, most likely due to the low strain/species resolution by 16S rRNA gene fragments’ sequences. As for the α- biodiversity, there were no differences between the groups, but the overall trend directed to the increasing α- biodiversity of the calves’ gut bacteriobiome after dextranal treatment. Conclusion. This study reports the first attempt to inventory the gut bacteriobiome of the cattle in the region, and the obtained results provide the basis for a more detailed and taxonomically targeted further research

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

Diacheopsis cinerea A. Vlasenko & V. Vlasenko 2022, sp. nov.

Diacheopsis cinerea A. Vlasenko & V. Vlasenko, sp. nov. (Figs 1A–E, 2A–J) Index Fungorum number: IF557664; Facesoffungi number: FoF 08147 Sporocarps sessile, cylindrical, about 0.7–0.9 mm in diam. and 0.9–1.1 mm in total height, gregarious, scattered or in small groups of 2–8, drab grey, beige, densely clustered. Peridium single, membranous, translucent below, more dense at the top, fugacious above, persisting as a deep cup at the base; transparent, very light, with a slight greyish colour (in transmitted light) in the lower and lateral parts of the sporocarps; in the apex of sporotheca it is light-ocher, transparent (in transmitted light); it is often common in adjacent sporocarps, but with preservation of the side walls between adjacent sporocarps. Dehiscence is apical irregular. After the complete destruction of sporocarps, basal rings remain attached to the substrate. Columella absent. Capillitium dark violet-brown, with expanded nodes of dark brown colour, branched and anastomosed, arising from the base and forming a network connected to the peridium and the base of sporotheca by paler tips. Hypothallus continuous under the group (confluent), thin, light-coloured. Spore-mass dark brown to dark. Spores globose, 10.5–13.0 µm diam. including ornamentation, densely and uniformly covered by warts up to 0.4 µm in total height. In SEM, the ornamentation appears as dense, abundant and regularly distributed, well-developed, coralloid projections on the apex of each wart. Plasmodium not seen. Etymology:— Referring to the colour of sporocarps. Type:— RUSSIA. Altai Territory: near Losikha railway station, dry pine forest, on a fallen tree of Pinus sylvestris, 8 July 2009, leg. A. Vlasenko and V. Vlasenko, NSK 1030140 (holotype), GenBank SSU: MT 386336. Additional specimen examined:— RUSSIA. Altai Territory: near Losikha railway station, pine forest, on dead wood of Pinus sylvestris, 26 August 2019, leg. A. Vlasenko and V. Vlasenko, NSK 1030138 (paratype). Ecology:— Xylobiont. Distribution:— Known only from type locality. Comments:— Phylogenetically, Diacheopsis cinerea grouped with Lamproderma echinosporum and L. gulielmae. We have received data that other species of Diacheopsis are phylogenetically similar to those of the genus Lamproderma (Fig. 3). Diacheopsis metallica is closest to L. cristatum, while D. pauxilla is closest to L. sauteri and L. ovoideoechinulatum. Similar to Lamproderma, the morphological genus Diacheopsis consists of several separate phylogenetic lines. At the same time, the species that represent different phylogenetic lines demonstrate morphological similarities. Classification of the family Stemonitidaceae is not developed and is based on morphological features. Based on a complex of morphological features, we assigned the new species to the genus Diacheopsis. Diacheopsis cinerea has a warty ornamentation of spores, which brings it close to the group of species that have spores with warts: D. laxifila, D. minuta, D. mitchellii, D. pieninica, D. rigidifila, D. vermicularis, D. griseobrunnea and D. serpula. Spores of D. mithellii are very large, 20–21 µm in diam., covered with long spines or warted, about 1 mm in length and with tips that appear frayed under SEM. In comparison, the spores of D. cinerea are significantly smaller, 10.5–13.0 µm in diam., densely and uniformly covered with warts that are up to 0.4 µm in total height. By SEM, their ornamentation consists of dense, abundant, regularly distributed and well-developed coralloid projections on the apex of each wart. Spores of D. pieninica, D. rigidifila, and D. griseobrunnea are less than 9 µm in diam. (spores of D. cinerea are larger than 10 µm in diam.). Spores of D. laxifila are united into clusters while spores of D. cinerea are free. Sporocarps of D. minuta are very small, 0.2–0.4 mm in total height, of bronze colour while sporocarps of D. cinerea are 2–3 mm in total height, and grey-beige in colour. In D. serpula, elongated plasmodiocarps are predominant in the colony but in D. cinerea, sessile sporangia are predominant. Capillitium of D. serpula is without extensions while that of D. cinerea is with numerous filmy brown extensions. Capillitial nodes of D. vermicularis are rounded but in D. cinerea they are triangular and quadrilateral. The capillitial threads of D. vermicularis are colorless or grey and in D. cinerea they are dark violet-brown, and only the ends of threads by which they are attached to the base of sporocarp and peridium are light. The spores of D. vermicularis are light brown, with dark areas consisting of groups of warts (in transmitted light); those of D. cinerea are brown, and evenly ornamented with warts. In shape and size of sporocarps, the new species resembles D. insessa and D. nannengae, but it differs significantly by the structure of capillitium, size of the spores and their ornamentation. Spores of D. insessa are 16–22 µm in diam. and ornamented with long spines while the spores of D. cinerea are less than 14 µm in diam., and ornamented by warts. Spores of D. nannengae are ornamented with short spines while spores of D. cinerea have long warts up to 0.4 µm in total height. The capillitium of D. nannengae arises only from the base of sporotheca but in D. cinerea it arises from the base and forms a network connected by paler tips to the peridium and the base of sporotheca. Samples of D. cinerea were first found by us in 2009 in dry pine forests in the northern part of the “Verkhneobsky pine forest”, located on the right bank of Priobsky Plateau. Diacheopsis cinerea was collected there again 10 years later, which indicates the existence of a stable community of the species. The fructification of the species was observed after prolonged rains.Published as part of Vlasenko, Anastasia V., Vlasenko, Vyacheslav A. & Kabilov, Marsel R., 2022, A new species of Diacheopsis from Russia, pp. 193-200 in Phytotaxa 541 (2) on pages 195-199, DOI: 10.11646/phytotaxa.541.2.9, http://zenodo.org/record/638879

Undisturbed Soil Pedon under Birch Forest: Characterization of Microbiome in Genetic Horizons

Vast areas of land in the forest-steppe of West Siberia are occupied by birch forests, the most common ecosystems there. However, currently, little is known about the microbiome composition in the underlying soil, especially along a sequence of soil genetic horizons. The study aimed at inventorying microbiome in genetic horizons of a typical Phaeozem under undisturbed birch forest in West Siberia. Bacteria and fungi were studied using 16S rRNA genes’ and ITS2 amplicon sequencing with Illumina MiSeq. Proteobacteria and Acidobacteria together accounted for two-thirds of the operational taxonomic units (OTUs) numbers and half of the sequences in each genetic horizon. Acidobacteria predominated in eluvial environments, whereas Proteobacteria, preferred topsoil. The fungal sequences were dominated by Ascomycota and Basidiomycota phyla. Basidiomycota was the most abundant in the topsoil, whereas Ascomycota increased down the soil profile. Thelephoraceae family was the most abundant in the A horizon, whereas the Pyronemataceae family dominants in the AEl horizon, ultimately prevailing in the subsoil. We conclude that soil genetic horizons shape distinct microbiomes, therefore soil horizontation should be accounted for while studying undisturbed soils. This study, representing the first description of bacterio- and mycobiomes in genetic horizons of the Phaeozem profile, provides a reference for future research

Rhizosphere Bacteriobiome of the Husk Tomato Grown in the Open Field in West Siberia

The composition and structure of rhizosphere bacteriobiome of the husk tomato (Physalis philadelphica Lam.) plants grown on Phaeozem in the open field in West Siberia, Russia (55°15’ NL, 83°31’ EL) were studied using Illumina MiSeq sequencing of the V3-V4 hypervariable region of 16S rRNA genes. In total 5898 OTUs (Operational Taxonomic Units) were found in the study, representing 20 phyla and 53 identified and 15 non-identified (below the phylum level) classes. The most OTU-rich phyla were Proteobacteria, Acidobacteria and Actinobacteria, their relative abundance in the total number of sequence reads being 26, 22 and 19%, respectively. Bacteroidetes, Gemmatimonadetes and Verrucomicrobia phyla each accounted for 2 ‒ 4%. The rest 14 of the identified phyla were quite negligible, contributing less than 0.5% each. At the OTUs level, the structure was very even and equitable, as only 7 OTUs had relative abundance ranging from 0.5 to 1.1%. The main dominant OTU represented Bradyrhizobiaceae family, implying the importance of nitrogen-fixing bacteria for plant growth and development without any mineral fertilisation. The dominance biodiversity index was very low (0.001), while Shannon index was rather high (7.5). We believe the presented husk tomato rhizosphere bacteriobiome, as the first study using new generation sequencing platform for this species, will help get a better picture of Solanaceae microbiomes in different environments, thus contributing to a more comprehensive understanding of shaping microbial communities by plant roots

Knockdown of the Ribosomal Protein eL38 in HEK293 Cells Changes the Translational Efficiency of Specific Genes

The protein eL38 is one of the smallest proteins of the mammalian ribosome, which is a component of its large (60S) subunit. The haploinsufficiency of eL38 in mice leads to the Tail-short mutant phenotype characterized by defects in the development of the axial skeleton caused by the poor translation of mRNA subsets of Hox genes. Using the ribosome profiling assay applied to HEK293 cells knocked down of eL38, we examined the effects of the lack of eL38 in 60S subunits on gene expression at the level of translation. A four-fold decrease in the cell content of eL38 was shown to result in significant changes in the translational efficiencies of 150 genes. Among the genes, whose expression at the level of translation was enhanced, there were mainly those associated with basic metabolic processes; namely, translation, protein folding, chromosome organization, splicing, and others. The set of genes with reduced translation efficiencies contained those that are mostly involved in the processes related to the regulation of transcription, including the activation of Hox genes. Thus, we demonstrated that eL38 insufficiency significantly affects the expression of certain genes at the translational level. Our findings facilitate understanding the possible causes of some anomalies in eL38-deficient animals

No-Antibiotic-Pectin-Based Treatment Differently Modified Cloaca Bacteriobiome of Male and Female Broiler Chickens

As the information about the effect of pectin prebiotics on chicken gut microbiota is scarce, by using high throughput metagenomic sequencing with Illumina Miseq we examined the cloaca bacteriobiome of male and female chickens receiving antibiotic- or pectin-containing drinking water. The bacteriobiome was dominated by two phyla (Firmicutes and Proteobacteria) and three classes (Clostridia, Bacilli and Gammaproteobacteria), with the difference displayed by the relative abundance of 42 OTUs. At the level of the major dominant OTUs, prebiotic supplementation drastically increased Enterococcus abundance (from 0 to 11% and 23% in males and females, respectively). The better feed use efficiency and growth performance of the pectin-receiving chickens implied their better health and corroborated putative beneficial role of the altered bacteriobiome, although its ecophysiological and/or pathogenic importance could not be readily inferred. Notably, the gut microbiota response to antibiotics showed more sex-related differential OTUs as compared to the pectin prebiotic (19 vs. 4), suggesting different mechanisms of the studied supplementations in shaping the gut bacteriobiome in different sexes. Therefore, we recommend targeting sex as a separate factor in interventional studies to account for sex-specific peculiarities in the microbiome response and taking into account the male/female ratio of industrial flocks prior to choosing a production technology. The studied prebiotic (pectin) can be used in developing new pre/symbiotic preparations and supplementation regimes as alternatives to antibiotics for stimulating broiler chicken production

Changes in the Transcriptome Caused by Mutations in the Ribosomal Protein uS10 Associated with a Predisposition to Colorectal Cancer

A number of mutations in the RPS20 gene encoding the ribosomal protein uS10 have been found to be associated with a predisposition to hereditary non-polyposis colorectal carcinoma (CRC). We transfected HEK293T cells with constructs carrying the uS10 minigene with mutations identical to those mentioned above and examined the effects of the produced proteins on the cellular transcriptome. We showed that uS10 with mutations p.V50SfsX23 or p.L61EfsX11 cannot be incorporated into 40S ribosomal subunits, while the protein with the missense mutation p.V54L functionally replaces the respective endogenous protein in the 40S subunit assembly and the translation process. The comparison of RNA-seq data obtained from cells producing aberrant forms of uS10 with data for those producing the wild-type protein revealed overlapping sets of upregulated and downregulated differently expressed genes (DEGs) related to several pathways. Among the limited number of upregulated DEGs, there were genes directly associated with the progression of CRC, e.g., PPM1D and PIGN. Our findings indicate that the accumulation of the mutant forms of uS10 triggers a cascade of cellular events, similar to that which is triggered when the cell responds to a large number of erroneous proteins, suggesting that this may increase the risk of cancer