ITS rRNA Gene Research Articles

Microencapsulated Microbial Seed Coating Could Improve Soil Environment and Maize Grain Yield in Saline Soil

Soil salinization is one of the major challenges for modern agriculture, posing a great threat to soil health and food security. Field experiments were conducted to evaluate the effect of seed coating on soil environment and maize growth in saline soils. Three treatments were applied to maize seeds: coating with a microencapsulated microbial agent (ME), coating with microbial only (MB), and no coating (CK). High-throughput sequencing of soil bacterial and fungal 16S and ITS rRNA genes was performed using the Illumina HiSeq platform to analyze the effects of these treatments on soil bacterial and fungal diversity and community structure. Additionally, the influence of different treatments on endogenous hormones and yield of maize were investigated. It was found that the coating with a microencapsulated microbial agent led to decreases in pH and electrical conductivity (EC), while increasing the content of soil available phosphorus. This coating improved soil microbial diversity, significantly increasing the relative abundance of the main bacteria genera, Bacillus (34.9%), and the main fungal genera, Mortierella (190.4%). The treatment also significantly enhanced indole-3-acetic acid (IAA) by 51.2%, contributing to improvements in resistance to salt stress. The germination rate increased by 22.9%, the 100-grain weight increased by 12.7%, and grain yield increased by 14.3%. The use of the microencapsulated microbial agent effectively mitigated the adverse effects of salt stress on maize plants. This approach is beneficial for promoting sustainable agriculture in saline soils.

Molecular and morphological characterisation of Ditylenchoides anyae sp. n. (Nematoda: Anguinoidea) from Iran

Summary A new species, Ditylenchoides anyae sp. n., recovered from soil in the headland areas of non-cultivated fields in Alborz Province, Iran, is described and illustrated based on its morphological, morphometric, and molecular characters. The new species was characterised by a slender body and length of 784 (663-925) μm (females) and 667-712 μm (males), lip region continuous, stylet length 6.4 (6.0-7.0) μm, lateral fields with four incisures, and excretory pore situated 110 (82-137) μm from the anterior end, median bulb of pharynx fusiform, non-muscular, and non-valvate, isthmus elongate, slender ending at a pyriform basal pharyngeal bulb not overlapping intestine, vulva with distinct and relatively large lateral flaps, a well-developed post-vulval uterine sac, 31.3 (27-35) μm long, a female tail elongate-conoid with pointed terminus; and male with adanal bursa and spicules 21-22 μm long. The new species was characterised using the D2-D3 expansion segments of 28S rRNA, ITS rRNA, and partial 18S rRNA gene sequences. Phylogenetic analyses of the genus Ditylenchoides are given based on the analysis of these genes.

Paradendryphiella arenariae an endophytic fungus of Centella asiatica inhibits the bacterial pathogens of fish and shellfish.

Aquaculture has been considered a major food-producing sector in the world during the last few decades. The foremost constraint in the development of aquaculture is bacterial disease control and management. Since various fish pathogens are resistant to conservative treatments, it is essential to screen new and effective alternative antibacterial agents. Endophytic fungi are microorganisms that live in the plant's internal tissues without harming its host. Endophytic fungi have proven themselves as reliable sources of novel bioactive compounds that can be used as antibacterial agents. In the present study, fifteen morphologically different endophytic fungi were isolated from the fresh and healthy stem section of Centella asiatica. The active endophytic fungal crude extracts were tested for agar well diffusion assay, Minimum Inhibitory Concentration, Minimum Bactericidal Concentration assays, Time-kill kinetic analysis, Brine shrimp lethality assay. Agar plug diffusion and agar well diffusion assays revealed that endophytic fungus CAS1 exhibits maximum antagonistic activity against bacterial fish pathogens. The ethyl acetate crude extract of CAS1 exhibited the maximum zone of inhibitions against Aeromonas hydrophila (21 ± 0.11 mm), Aeromonas caviae (18 ± 0.1 mm), Edwardsiella tarda (23 ± 0.11 mm), Vibrio anguillarum (19 ± 0.05 mm) and Vibrio harveyi (20 ± 0.27 mm). The MIC and MBC values extract varied reliant on the trial pathogens ranging between 12.5-100 μg/mL and 25-100μg/mL correspondingly. The morphological and molecular characterization of potential isolate CAS1 was confirmed as Paradendryphiella arenariae by 18S rRNA ITS gene sequencing with 99.18% identity. This is the foremost findings to study the antagonistic effect of Paradendryphiella arenariae isolated from the stem of Centella asiatica against bacterial fish pathogens which can be used as natural effective antibacterial agents in aquaculture.

Vishniacozyma floricola sp. nov., a flower-related tremellomycetous yeast species from Europe.

During the course of two independent studies conducted in Hungary and Spain, four conspecific yeast strains were isolated from flowers of different plant species. DNA sequences of two barcoding regions, the D1/D2 domain of the LSU rRNA gene and the internal transcribed spacer (ITS) region (ITS1-5.8S rRNA gene-ITS2), revealed that the four strains represent an undescribed Vishniacozyma (family Bulleribasidiaceae, Basidiomycota) species. In terms of pairwise sequence similarities and according to our phylogenetic analyses of the concatenated DNA sequences of the ITS region and the D1/D2 domain of the LSU rRNA gene, the undescribed species is most closely related to Vishniacozyma melezitolytica, a yeast species of phylloplane origin. The novel species differs from the type strain of V. melezitolytica by 8 substitutions and 3 insertion/deletion (indels) and 11 substitutions and 5 indels along the D1/D2 domain of the LSU rRNA gene and the ITS region, respectively. In addition to the DNA sequence divergences, the two species differ in some physiological characters as well. We propose the species Vishniacozyma floricola sp. nov. to accommodate the above-noted strains (holotype, NCAIM Y.02320; isotype, CBS 18939; MycoBank number, 856028).

Genetic Diversity of the Species of the Genus Deschampsia P.Beauv. (Poaceae) Based on the Analysis of the ITS Region: Polymorphism Proves Distant Hybridization.

The species of the genus Deschampsia are difficult for identification, and the genus is difficult for taxonomic treatment. The regions of 35S rRNA genes were studied for the species of the genus Deschampsia of different geographical origin with a method of sequencing by Sanger (ITS1-5.8S rRNA gene-ITS2, 14 species) and with a method of a locus-specific next-generation sequencing (NGS) on the Illumina platform (ITS1-5.8S rRNA, 7 species). All species of Deschampsia formed one clade; the species, referred by some authors on the basis of morphological characters to the species D. cespitosa s.l., entered one subclade. Subantarctic species formed a separate subclade and their ribotypes formed their own subnetwork. Avenella flexuosa, earlier referred to Deschampsia, entered the other clade, though this species contains some ribotypes common with some Deschampsia species. Deschampsia pamirica and related mountain species have their own specific ribotype groups. On the network of the ribotypes, one can see that D. cespitosa from Great Britain forms a network with some species, but D. cespitosa from the USA forms its own network. Ribotype analysis of each sample revealed traces of introgression with Deyeuxia/Calamagrostis in D. cespitosa and with A. flexuosa and probable introgression of Northern and subantarctic species.

Revealing the Response of Cucumber Soil Microbial Community Composition and Function to Nitrogen Addition in Northern Chinese Greenhouses

At present, the soil of Chinese greenhouses is experiencing severe nitrogen input in the form of fertilizer, which will cause damage to the soil environment and restrict crop growth in the long run. The response of potential functions of microorganisms as drivers of nutrient cycling and material transformation to nitrogen enrichment has rarely been reported in northern vegetable planting systems. Therefore, we set up four cucumber pot experiments with different nitrogen addition rates (0, 258, 516, and 1032 kg N ha−1 yr−1) in the greenhouse. Bacterial and fungal communities were detected by 16S and ITS rRNA gene sequencing, and bacterial and fungal functional groups were predicted using the FAPROTAX and FUNGuild databases. The findings showed that nitrogen addition induced soil acidification (a decrease of 0.25–1.63 units) significantly reduced microbial diversity and changed the community composition of bacteria and fungi. The relative abundance of bacterial functional groups associated with the nitrogen cycle increased significantly when medium and high levels of nitrogen were added. Conversely, the bacterial functional groups involved in the carbon cycle exhibited the opposite pattern. In this study, NO3− and soil pH were the main factors affecting the soil microbial community and its functional groups. Our results highlight that hydrocarbon degradation and saprophytic fungi may play key roles in yield formation during cucumber cultivation in northern solar greenhouses. In general, adopting a fertilization strategy that ensures low-medium nitrogen availability can contribute to the sustainable progress of facility agriculture.

Sychnotylenchus kulinichi sp. n. (Nematoda: Anguinoidea) from the Primorsky Krai of Russia with a tabular key to the genus Sychnotylenchus Rühm, 1956

Summary A new species of the genus Sychnotylenchus Rühm, 1956, S. kulinchi sp. n., inhabiting the bark beetle galleries of Pityogenes chalcographus in Pinus koraiensis was found in the Primorsky Krai of Russia. The new species differs morphologically from the closely related species S. yasinskii and S. mayor in having a shorter body length (626-1030 vs 1250-1280 and 1935-1455 μm, respectively) and from S. sparnugus in having a greater value of the ratio between spicule length and tail length (0.9-11 vs less than 0.7). Phylogenetic analysis of the partial 18S rRNA, D2-D3 expansion segments of the 28S rRNA, the ITS rRNA and COI gene sequences showed that the Russian S. kulinichi sp. n. population grouped with populations from Israel and an unspecified locality that were identified incorrectly as Ditylenchus forepolitor, which are considered conspecific with S. kulinichi sp. n. in this study. Phylogenetic analyses aiming to clarify the controversial taxonomic status of Neoditylenchus and Sychnotylenchus species indicated that, although the genus Sychnotylenchus was paraphyletic in some phylogenetic trees, testing of alternative topologies for the 18S rRNA, D2-D3 of 28S rRNA and ITS rRNA gene trees and datasets using the maximum likelihood method did not exclude the monophyly of this genus and did not justify the validity of the genus Neoditylenchus, which should be considered a junior synonym of Sychnotylenchus as proposed by Fortuner & Maggenti (1987). Molecular phylogeny showed close relationships of Sychnotylenchus with plant-parasitic nematodes from the genera Ficotylus, Orrina and Pterotylenchus, and also with the insect-associated genus Neomisticius. A polytomous key listing 24 morphological diagnostic characters for the identification of 33 species of Sychnotylenchus is provided, along with a table listing associated bark beetle species.

Comparative Analysis of Airborne Bacterial and Fungal Communities in South-Eastern Italy and in Albania Using the Compositional Analysis of 16S and ITS rRNA Gene Sequencing Datasets

This study investigates airborne bacterial and fungal communities in south-eastern Italy and Albania using advanced DNA-based techniques and compositional data analysis (CoDa). We assess the significance of airborne microbial communities, detailing our methodologies for site selection, sample collection, DNA extraction, and data analysis. Our results reveal distinct differences in microbial composition between the two regions, driven by local environmental factors. Specifically, Albanian samples showed higher abundances of bacterial species such as Rubellimicrobium roseum and Sphingomonas cynarae, while Italian samples were characterized by a prevalence of Truepera radiovictrix and Rubrobacter radiotolerans. In terms of fungi, Albanian sites exhibited greater abundance of Mycosphaerella tassiana, Aureobasidium pullulans, and Ascochyta herbicola. Aitchison distance-based dendrograms and principal component analysis (PCA) biplots, utilizing singular value decomposition, clearly delineated a geographical separation of microbial communities, underscoring the impact of regional atmospheric conditions on microbial composition. In the discussion, we interpret these findings in the context of regional environmental factors, highlighting their implications for understanding regional differences in airborne microbial communities. The conclusion emphasizes the effectiveness of advanced DNA techniques and CoDa in environmental microbiology, offering insights into how local environmental conditions shape microbial communities and suggesting directions for future research and public health considerations.

Exploring the impact of plant genotype and fungicide treatment on endophytic communities in tomato stems.

This study examines how plant genotype can influence the microbiome by comparing six tomato genotypes (Solanum lycopersicum) based on their traditional vs. commercial backgrounds. Using Illumina-based sequencing of the V6-V8 regions of 16S and ITS2 rRNA genes, we analyzed and compared the endophytic bacterial and fungal communities in stems to understand how microbiota can differ and be altered in plant genotypes and the relation to human manipulation. Our results reflect that traditional genotypes harbor significantly more exclusive microbial taxa and a broader phylogenetic background than the commercial ones. Traditional genotypes were significantly richer in Eurotiomycetes and Sordariomycetes fungi, while Lasiosphaeriaceae was more prevalent in commercial genotypes. TH-30 exhibited the highest bacterial abundance, significantly more than commercial genotypes, particularly in Actinomycetia, Bacteroidia, and Gammaproteobacteria. Additionally, traditional genotypes had higher bacterial diversity, notably in orders like Cytophagales, Xanthomonadales, and Burkholderiales. Moreover, we performed an evaluation of the impact of a systemic fungicide (tebuconazole-dichlofluanide) to simulate a common agronomic practice and determined that a single fungicide treatment altered the stem endophytic microbiota. Control plants had a higher prevalence of fungal orders Pleosporales, Helotiales, and Glomerellales, while treated plants were dominated by Sordariomycetes and Laboulbeniomycetes. Fungal community diversity significantly decreased, but no significant impact was observed on bacterial diversity. Our study provides evidence that the background of the tomato variety impacts the fungal and bacterial stem endophytes. Furthermore, these findings suggest the potential benefits of using of traditional genotypes as a source of novel beneficial microbiota that may prove highly valuable in unpredicted challenges and the advancement in sustainable agriculture.

Biological Decline of Alfalfa Is Accompanied by Negative Succession of Rhizosphere Soil Microbial Communities.

The growth and biological decline of alfalfa may be linked to the rhizosphere microbiome. However, plant-microbe interactions in the rhizosphere of alfalfa and associated microbial community variations with stand age remain elusive. This study explored the successional pattern of rhizosphere microbial communities across different aged alfalfa stands and its relationship with alfalfa decline. Rhizosphere soils were collected from 2- and 6-year-old alfalfa stands. Control soils were collected from interspaces between alfalfa plants in the same stands. Soil bacterial and fungal communities were characterized by 16S and ITS rRNA gene sequencing, respectively. Specific microbial taxa colonized the rhizosphere soils, but not the control soils. The rhizosphere-specific taxa mainly included potentially beneficial genera (e.g., Dechloromonas, Verrucomicrobium) in the young stand and harmful genera (e.g., Peziza, Campylocarpon) in the old stand. Alfalfa roots regulated soil microbial communities by selective promotion or inhibition of distinct taxa. The majority of time-enriched taxa were reported as harmful fungi, whose relative abundances were negatively correlated with plant traits. Time-depleted taxa were mostly known as beneficial bacteria, which had relative abundances positively correlated with plant traits. The relative abundances of functional bacterial genes associated with vancomycin biosynthesis, zeatin biosynthesis, and amino acid metabolism trended lower in rhizosphere soils from the old stand. An upward trend was observed for fungal pathogens and wood saprotrophs with increasing stand age. The results suggest that root activity drives the negative succession of rhizosphere microbial communities during alfalfa decline in old stands.

Successions of Bacterial and Fungal Communities in Biological Soil Crust under Sand-Fixation Plantation in Horqin Sandy Land, Northeast China

Biological soil crusts (BSCs) serve important functions in conserving biodiversity and ecological service in arid and semi-arid regions. Afforestation on shifting sand dunes can induce the formation of BSC on topsoil, which can accelerate the restoration of a degraded ecosystem. However, the studies on microbial community succession along BSC development under sand-fixation plantations in desertification areas are limited. This paper investigated the soil properties, enzymatic activities, and bacterial and fungal community structures across an age sequence (0-, 10-, 22-, and 37-year-old) of BSCs under Caragana microphylla sand-fixation plantations in Horqin Sandy Land, Northeast China. The dynamics in the diversities and structures of soil bacterial and fungal communities were detected via the high-throughput sequencing of the 16S and ITS rRNA genes, respectively. The soil nutrients and enzymatic activities all linearly increased with the development of BSC; furthermore, soil enzymatic activity was more sensitive to BSC development than soil nutrients. The diversities of the bacterial and fungal communities gradually increased along BSC development. There was a significant difference in the structure of the bacterial/fungal communities of the moving sand dune and BSC sites, and similar microbial compositions among different BSC sites were found. The successions of microbial communities in the BSC were characterized as a sequential process consisting of an initial phase of the faster recoveries of dominant taxa, a subsequent slower development phase, and a final stable phase. The quantitative response to BSC development varied with the dominant taxa. The secondary successions of the microbial communities of the BSC were affected by soil factors, and soil moisture, available nutrients, nitrate reductase, and polyphenol oxidase were the main influencing factors.

Dynamics of Cellulose Degradation by Soil Microorganisms from Two Contrasting Soil Types.

The search for active cellulolytic consortia among soil microorganisms is of significant applied interest, but the dynamics of the formation of such communities remain insufficiently studied. To gain insight into the formation of an active cellulolytic community, the experiment was designed to examine the colonization of a sterile substrate (cellulose) by microorganisms from two soil types: sod-podzolic and chernozem. To achieve this, the substrate was placed in the soil and incubated for six months. To assess microbiome dynamics, the experiment employed sequencing of 16S rRNA gene fragment and ITS2 amplicon libraries at four time points. It was demonstrated that, from the second month of the experiment, the prokaryotic component of the communities reached a state of stability, with a community composition specific to each soil type. The results demonstrated no relationship between changes in community diversity and soil respiration. There also was no significant shift in the community diversity throughout the chronosequence. Furthermore, the taxonomic composition of the community shifted towards a decrease in the proportion of Pseudomonadota and an increase in representatives of the Bacteroidota, Bacillota, and Verrucomicrobiota phyla. The network analysis of the community demonstrated that, in contrast to sod-podzolic soil, chernozem is distinguished by a higher modularity, with the formation of taxon-specific groups of microorganisms at each stage of the chronoseries. These differences are attributed to the alterations in the eukaryotic component of the community, particularly in the prevalence of nematodes and predatory fungi, which in turn influenced the cellulolytic community.

Response of stream habitat and microbiomes to spruce budworm defoliation: New considerations for outbreak management.

Defoliation by eastern spruce budworm is one of the most important natural disturbances in Canadian boreal and hemi-boreal forests with annual area affected surpassing that of fire and harvest combined, and its impacts are projected to increase in frequency, severity, and range under future climate scenarios. Deciding on an active management strategy to control outbreaks and minimize broader economic, ecological, and social impacts is becoming increasingly important. These strategies differ in the degree to which defoliation is suppressed, but little is known about the downstream consequences of defoliation and, thus, the implications of management. Given the disproportionate role of headwater streams and their microbiomes on net riverine productivity across forested landscapes, we investigated the effects of defoliation by spruce budworm on headwater stream habitat and microbiome structure and function to inform management decisions. We experimentally manipulated a gradient of defoliation among 12 watersheds during a spruce budworm outbreak in the Gaspésie Peninsula, Québec, Canada. From May through October of 2019-2021, stream habitat (flow rates, dissolved organic matter [DOM], water chemistry, and nutrients), algal biomass, and water temperatures were assessed. Bacterial and fungal biofilm communities were examined by incubating six leaf packs for five weeks (mid-August to late September) in one stream reach per watershed. Microbiome community structure was determined using metabarcoding of 16S and ITS rRNA genes, and community functions were examined using extracellular enzyme assays, leaf litter decomposition rates, and taxonomic functional assignments. We found that cumulative defoliation was correlated with increased streamflow rates and temperatures, and more aromatic DOM (measured as specific ultraviolet absorbance at 254 nm), but was not correlated to nutrient concentrations. Cumulative defoliation was also associated with altered microbial community composition, an increase in carbohydrate biosynthesis, and a reduction in aromatic compound degradation, suggesting that microbes are shifting to the preferential use of simple carbohydrates rather than more complex aromatic compounds. These results demonstrate that high levels of defoliation can affect headwater stream microbiomes to the point of altering stream ecosystem productivity and carbon cycling potential, highlighting the importance of incorporating broader ecological processes into spruce budworm management decisions.

Microbial life in preferential flow paths in subsurface clayey till revealed by metataxonomy and metagenomics

BackgroundSubsurface microorganisms contribute to important ecosystem services, yet little is known about how the composition of these communities is affected by small scale heterogeneity such as in preferential flow paths including biopores and fractures. This study aimed to provide a more complete characterization of microbial communities from preferential flow paths and matrix sediments of a clayey till to a depth of 400 cm by using 16S rRNA gene and fungal ITS2 amplicon sequencing of environmental DNA. Moreover, shotgun metagenomics was applied to samples from fractures located 150 cm below ground surface (bgs) to investigate the bacterial genomic adaptations resulting from fluctuating exposure to nutrients, oxygen and water.ResultsThe microbial communities changed significantly with depth. In addition, the bacterial/archaeal communities in preferential flow paths were significantly different from those in the adjacent matrix sediments, which was not the case for fungal communities. Preferential flow paths contained higher abundances of 16S rRNA and ITS gene copies than the corresponding matrix sediments and more aerobic bacterial taxa than adjacent matrix sediments at 75 and 150 cm bgs. These findings were linked to higher organic carbon and the connectivity of the flow paths to the topsoil as demonstrated by previous dye tracer experiments. Moreover, bacteria, which were differentially more abundant in the fractures than in the matrix sediment at 150 cm bgs, had higher abundances of carbohydrate active enzymes, and a greater potential for mixotrophic growth.ConclusionsOur results demonstrate that the preferential flow paths in the subsurface are unique niches that are closely connected to water flow and the fluctuating ground water table. Although no difference in fungal communities were observed between these two niches, hydraulically active flow paths contained a significantly higher abundance in fungal, archaeal and bacterial taxa. Metagenomic analysis suggests that bacteria in tectonic fractures have the genetic potential to respond to fluctuating oxygen levels and can degrade organic carbon, which should result in their increased participation in subsurface carbon cycling. This increased microbial abundance and activity needs to be considered in future research and modelling efforts of the soil subsurface.

Integrative analysis of microbiome and metabolome revealed the effect of microbial inoculant on microbial community diversity and function in rhizospheric soil under tobacco monoculture.

Over-application of chemical fertilizers and continuous cropping obstacles seriously restrict the sustainable development of tobacco production. Localized fertilization of beneficial microbes has potential advantages in achieving higher productivity, but the underlying biological mechanisms of interactions between rhizospheric microorganisms and the related metabolic cycle remain poorly characterized. Here, an integrative analysis of microbiomes with non-targeted metabolomics was performed on 30 soil samples of rhizosphere, root surrounding, and bulk soils from flue-cured tobacco under continuous and non-continuous monocropping systems. The analysis was conducted using UPLC-MS/MS platforms and high-throughput amplicon sequencing targeting the bacterial 16S rRNA gene and fungal ITS gene. The microbial inoculant consisted of Bacillus subtilis, B. velezensis, and B. licheniformis at the ratio of 1:1:1 in effective microbial counts, improved the cured leaf yield and disease resistance of tobacco, and enhanced nicotine and nitrogen contents of tobacco leaves. The bacterial taxa Rhizobium, Pseudomonas, Sphingomonadaceae, and Burkholderiaceae of the phylum Proteobacteria accumulated in high relative abundance and were identified as biomarkers following the application of the microbial inoculant. Under continuous monocropping, metabolomics demonstrated that the application of the microbial inoculant significantly affected the soil metabolite spectrum, and the differential metabolites were significantly enriched to the synthesis and degradation of nicotine (nicotinate and nicotinamide metabolism and biosynthesis of alkaloids derived from nicotinic acid). In addition, microbes were closely related to the accumulation of metabolites through correlation analysis. The interactions between plant roots and rhizospheric microorganisms provide valuable information for understanding how these beneficial microbes affect complex biological processes and the adaption capacity of plants to environments.IMPORTANCEThis study elaborated on how the microbial fertilizer significantly changed overall community structures and metabolite spectrum of rhizospheric microbes, which provide insights into the process of rhizosphere microbial remolding in response to continuous monocropping. we verified the hypothesis that the application of the microbial inoculant in continuous cropping would lead to the selection of distinct microbiota communities by establishing models to correlate biomarkers. Through correlation analysis of the microbiome and metabolome, we proved that rhizospheric microbes were closely related to the accumulation of metabolites, including the synthesis and degradation of nicotine. The interactions between plant roots and rhizospheric microorganisms provide valuable information for understanding how these beneficial microbes affect complex biological processes and the adaption capacity of plants to environments.

Microbial Biogeography along the Gastrointestinal Tract of a Wild Chinese Muntjac (Muntiacus reevesi).

The gut microbiota plays an important role in host nutrient absorption, immune function, and behavioral patterns. Much research on the gut microbiota of wildlife has focused on feces samples, so the microbial composition along the gastrointestinal tract of wildlife is not well reported. To address this gap, we performed high-throughput sequencing of 16s rRNA genes and ITs rRNA genes in the gastrointestinal contents of a wild adult male Chinese muntjac (Muntiacus reevesi) to comparatively analyze the microbial diversity of different gastrointestinal regions. The results showed that the dominant bacterial phyla were Firmicutes (66.19%) and Bacteroidetes (22.7%), while the dominant fungal phyla were Ascomycetes (72.81%). The highest bacterial diversity was found in the stomach, and the highest fungal diversity was found in the cecum. The microbial communities of the large intestine and small intestine were of similar structures, which were distinct from that of the stomach. These results would facilitate the continued exploration of the microbial composition and functional diversity of the gastrointestinal tract of wild Chinese muntjacs and provide a scientific basis for microbial resource conservation of more wildlife.

Shifts in fungal community diversity and potential function under natural forest succession and planted forest restoration in the Kunyu Mountains, East China.

Soil fungi participate in various ecosystem processes and are important factors driving the restoration of degraded forests. However, little is known about the changes in fungal diversity and potential functions under the development of different vegetation types during natural (secondary forest succession) and anthropogenic (reforestation) forest restoration. In this study, we selected typical forest succession sequences (including Pinus densiflora Siebold & Zucc., pine-broadleaf mixed forest of P. densiflora and Quercus acutissima Carruth., and Q. acutissima), as well as natural secondary deciduous broadleaved mixed forests and planted forests of Robinia pseudoacacia on Kunyu Mountain for analysis. We used ITS rRNA gene sequencing to characterize fungal communities and used the FUNGuild database to predict fungal functional groups. The results showed that forest succession affected fungal β-diversity, but not the α-diversity. There was a significant increase in Basidiomycota and a decrease in Ascomycota in the later successional stage, accompanied by an increase in the functional groups of ectomycorrhizal fungi (ECM). Conversely, planted forests exhibited decreased fungal α-diversity and altered community compositions, characterized by fewer Basidiomycota and more Ascomycota and Mucoromycota. Planted forests led to a decrease in the relative abundances of ECM and an increase in animal pathogens. The TK content was the major factor explaining the distinction in fungal communities among the three successional stages, whereas pH, AP, and NH4 + were the major factors explaining community variations between natural and planted forests. Changes in vegetation types significantly affected the diversity and functional groups of soil fungal communities during forest succession and reforestation, providing key insights for forest ecosystem management in temperate forests.

Distinct changes in tomato-associated multi-kingdom microbiomes during Meloidogyne incognita parasitism

BackgroundThe interplay between root-knot nematode (RKN) parasitism and the complex web of host-associated microbiota has been recognized as pivotal for effective management of the pest. However, studies assessing this relationship have focussed on the bacterial and fungal communities, neglecting the unicellular eukaryotic members. Here, we employed amplicon sequencing analysis of the bacterial 16S rRNA, fungal ITS and eukaryotic 18S rRNA genes, and comprehensively examined how the microbiome composition, diversity and networking developed with time in the rhizospheres and roots of RKN-inoculated and non-inoculated tomato plants.ResultsAs expected, infection with the RKN Meloidogyne incognita decreased plant growth. At individual timepoints, we found distinct bacterial, fungal and eukaryote community structures in the RKN-inoculated and non-inoculated rhizospheres and roots, and RKN inoculation affected several taxa in the root-associated microbiome differentially. Correlation analysis revealed several bacterial and fungal and few protist taxa that correlated negatively or positively with M. incognita. Moreover, network analysis using bacterial, fungal and eukaryotic data revealed more dynamic networks with higher robustness to disturbances in the RKN-inoculated than in the non-inoculated rhizospheres/roots. Hub taxa displayed a noticeable successional pattern that coincided with different phases of M. incognita parasitism. We found that fungal hubs had strong negative correlations with bacteria and eukaryotes, while positive correlations characterized hub members within individual kingdoms.ConclusionOur results reveal dynamic tomato-associated microbiomes that develop along different trajectories in plants suffering M. incognita infestation and non-infested plants. Overall, the results identify stronger associations between RKN and bacterial and fungal taxa than between eukaryotic taxa and RKN, suggesting that fungal and bacterial communities could play a larger role in the regulation of RKN. The study identifies several putative RKN-antagonistic bacterial and fungal taxa and confirms the antagonistic potential previously identified in other taxa.

Molecular Identification of Encephalitazoon intestinalis and the Prevalence of Renal Microsporidiosis in Renal Transplant Recipients in Türkiye.

In patients with end-stage kidney disease, kidney transplantation is the kidney replacement therapy option that provides the most successful survival. However, immunosuppression agents administered after kidney transplantation can increase the risk of opportunistic infections. Microsporidia are obligate intracellular pathogens that can be fatal in immunosuppressed patients. The present study aimed to determine the prevalence of microsporidia in kidney transplantation recipients and the molecular characterization of the detected species. To evaluate the prevalence of renal microsporidiosis in kidney transplant recipients, the urine samples from a total of 325 patients were analyzed by real-time and nested polymerase chain reaction for Encephalitozoon spp. and Enterocytozoon bieneusi. Only one (0.4%) sample from the adult patient was positive for the Encephalitozoon species, while no positivity was found in pediatric patients. It was determined as Encephalitozoon intestinalis by ITS rRNA gene region sequence analysis. A microsporidia species obtained from humans in Türkiye has been characterized for the first time and registered in GenBank. Our epidemiological results show that the prevalence of renal microsporidiosis in kidney transplant recipients is very low. In addition, as a result of the phylogenetic analysis of the detected isolate, it was observed that it was 100% identical to the isolates reported from dogs in Kayseri, Türkiye. This situation provided essential data regarding the zoonotic transmission dynamics of microsporidia.

Population genomics resolves cryptic species of the ecologically flexible genus Laspinema (Cyanobacteria).

Cyanobacterial taxonomy is entering the genomic era, but only a few taxonomic studies have employed population genomics, which provides a framework and a multitude of tools to understand species boundaries. Phylogenomic and population genomic analyses previously suggested that several cryptic lineages emerged within the genus Laspinema. Here, we apply population genomics to define boundaries between these lineages and propose two new cryptic species, Laspinema olomoucense and L. palackyanum. Moreover, we sampled soil and puddles across Central Europe and sequenced the 16S rRNA gene and 16S-23S ITS region of the isolated Laspinema strains. Together with database mining of 16S rRNA gene sequences, we determined that the genus Laspinema has a cosmopolitan distribution and inhabits a wide variety of habitats, including freshwater, saline water, mangroves, soil crusts, soils, puddles, and the human body.