Ribosomal DNA Sequences Research Articles

Resveratrol Attenuates Diquat-Induced Oxidative Stress by Regulating Gut Microbiota and Metabolome Characteristics in Piglets.

Previous studies have shown that dietary resveratrol (RES) reduces diarrhea and attenuates oxidative stress in piglets challenged with diquat. However, the effect of dietary resveratrol on the gut microbiota of these piglets, as well as the potential relationships between intestinal microflora and metabolites, remain unclear. Here, 16S ribosomal DNA sequencing and metabolome analyses were performed to investigate the effect of RES on the gut microbiota and metabolome of diquat-challenged piglets. A total of 18 weaned piglets (aged 28 ± 2 days) were divided into the control group (basal diet), diquat group (basal diet + diquat challenge), and RES group (basal diet containing 90 mg/kg RES + diquat challenge). Compared with the control group, piglets in the diquat group showed enriched relative abundance of the phyla Firmicutes and Actinobacteria, the genus Ruminococcaceae UCG-005, and members of the Eubacterium coprostanoligenes group. Noteworthy, RES supplementation significantly reduced the levels of these microorganisms. In contrast, the relative abundance of some beneficial bacterial species in the RES group, such as the genera Clostridium sensu stricto 1 and Lachnospiraceae unclassified were significantly higher than in the diquat and control groups. Metabolomic analysis indicated that some metabolites, including indole-3-carbinol, 5-hydroxyindole-3-acetic acid, and uridine, were significantly upregulated upon RES supplementation. In particular, the relative abundance of uridine, indole, and alpha- and beta-dihydroresveratrol was significantly higher in the RES group than in the control group. Moreover, most gut bacterial genera were found to be highly correlated with altered gut microbiota-related metabolites. These findings suggest that dietary supplementation with resveratrol may alter the composition and metabolites of colonic microbiota in diquat-challenged piglets, which provides important insights into the use of resveratrol as a feed additive for gut microbial regulation in piglets with inflammatory and oxidative stress-associated disorders.

Révision du genre Ammodaucus (Apiaceae) en Afrique du Nord

Chatelain, C., M. Chambouleyron, M. Charrier, J.-F. Léger & M. Perret (2021). Revision of the genus Ammodaucus (Apiaceae) in North Africa. Candollea 76: 191–200. In French, English and French abstracts. Recent collections from southern Anti-Atlas and northern oceanic Sahara identified as Ammodaucus leucotrichus Coss. & Durieu and Cuminum maroccanum Davis & Hedge (Apiaceae) led us to present a taxonomic revision of the genus Ammodaucus Coss. & Durieu in northern Africa, which is based on morphological and molecular data. Phylogenetic inferences based on original and previously published ITS ribosomal DNA sequences clearly demonstrated that Cuminum maroccanum is not related to the genus Cuminum L. but instead nested within Ammodaucus, which forms a distinct lineage in the subtribe Daucinae. Two clades within Ammodaucus are recognised. The first one includes the accessions corresponding to Cuminum maroccanum, characterized by having long bracteoles and fusiform mericarps and the second one includes the accessions corresponding to Ammodaucus leucotrichus, which displays short bracteoles and oboval mericarps. On this basis, the species Cuminum maroccanum is transferred to the genus Ammodaucus and the name Ammodaucus leucotrichus subsp. nanocarpus Beltrán-Tej. is included in the synonymy. Received: January 11, 2021; Accepted: June 3, 2021; First published online: July 7, 2021

Chemical and Microbiological Evaluation of Vermicompost Made from School Food Waste in Japan

Vermicomposting technology is an environmentally friendly, sustainable, and low-cost tool used to convert agronomical and food waste into manure, facilitated by the decomposition and digestion by earthworms. In this study, we evaluated the chemical properties and microbial diversity of vermicompost (VC) derived from school lunch waste, which has long been a serious problem in many countries including Japan. The results revealed that 18-week-old VC promoted the root elongation of plants, and also showed a higher germination index (GI) and higher cation exchange capacity (CEC), indicating that vermicompost made from school food waste is an acceptable manure. As a result of the microbiome analysis by the sequencing of 16S ribosomal DNA (rDNA) using next generation sequencing (NGS), higher ratios of Bacillus, Pseudomonas, and Paenibacillus species, which may include beneficial bacteria for plant growth, were detected in VC than in the control compost (CC). These results demonstrate the significance of vermicompost in utilizing waste from school lunch, suggesting the possibility of implementing a waste recycling system that leads to reducing and recycling food waste in schools.

Description of Myxidium pseudocuneiforme n. sp. (Myxosporea: Myxidiidae) from Cyprinus carpio in China, with the resolution on a taxonomic dilemma of Myxidium cuneiforme.

Investigations on myxozoan parasites of fish from Chongqing in China, revealed two Myxidium cuneiforme-like myxosporeans infecting the gallbladder of Cyprinus carpio carpio and Carassius auratus. We researched their myxospore morphology, and analyzed their genetic similarity and phylogenic relationships to other myxozoans based on small subunit ribosomal DNA (18S rDNA) sequences. Although both parasites recovered were morphologically similar, the myxosporean isolated from C.auratus was consistent in morphology to Myxidium cuneiforme, which was described from this host species. The parasite isolated from C. c.carpio had overlapping myxospore dimensions to M.cuneiforme, but on average, the polar capsules were not as long. More importantly, this parasite was genetically distinct from M.cuneiforme with 96.3% and 96.5% similarity in two sequences of 18S rDNA, and we propose the name Myxidium pseudocuneiforme n. sp. for this myxozoan from common carp. Its mature myxospores are ellipsoidal and asymmetric with pointed ends in valvular view, arc-shaped or fusiform in sutural view. The pyriform polar capsules are equal in size, and polar filament with 5-6 coils. This study highlights that molecular characteristics and host specificity are indispensable for myxozoan species identification when presented with the taxonomic dilemma of whether we are observing one species that exhibits slight morphological differences or multiple, but similar, species in different hosts.

Discovery of Novel Backusella (Backusellaceae, Mucorales) Isolated from Invertebrates and Toads in Cheongyang, Korea.

Three novel fungal species, Backusella chlamydospora sp. nov., B. koreana sp. nov., and B. thermophila sp. nov., as well as two new records, B. oblongielliptica and B. oblongispora, were found in Cheongyang, Korea, during an investigation of fungal species from invertebrates and toads. All species are described here using morphological characters and sequence data from internal transcribed spacer sequences of ribosomal DNA and large subunit of the ribosomal DNA. Backusella chlamydospora is different from other Backusella species by producing chlamydospores. Backusella koreana can be distinguished from other Backusella species by producing abundant yeast-like cells. Backusella thermophila is characterized by a variable (subglobose to oblong, applanate to oval, conical and ellipsoidal to pyriform) columellae and grows well at 37 °C. Multigene phylogenetic analyses of the combined ITS and LSU rDNA sequences data generated from maximum likelihood and MrBayes analyses indicate that B. chlamydospora, B. koreana, and B. thermophila form distinct lineages in the family Backusellaceae. Detailed descriptions, illustrations, phylogenetic tree, and taxonomic key to the Backusella species present in Korea are provided.

Molecular authentication of Euphorbia schimperiana Scheele using internal transcribed spacer sequences of nuclear ribosomal DNA

The Internal Transcribed Spacers (ITS) sequences of nuclear ribosomal DNA (nrDNA) are commonly used in plant molecular phylogenetics for the molecular based taxonomic identification and DNA barcoding because of shorter length and easy to amplify by using the universal primers, and further has discrimination ability to distinguish the taxon at lower taxonomic level. The present molecular phylogenetic analysis of ITS nrDNA sequences focuses to determine the taxonomic status of an unresolved medicinally important species Euphorbia schimperiana Scheele of the family Euphorbiaceae reported from Saudi Arabia. The combined length of the entire ITS region in E. schimperiana is 644 nucleotides. The study reveals that E. schimperiana shows a close proximity with the members of the subgenus Esula.
 Bangladesh J. Plant Taxon. 28(1): 125-130, 2021 (June)

Intragenomic sequence variations in the second internal transcribed spacer (ITS2) ribosomal DNA of the malaria vector Anopheles stephensi.

Second Internal Transcribed Spacer (ITS2) ribosomal DNA (rDNA) sequence is a widely used molecular marker for species-identification or -delimitation due to observed concerted evolution which is believed to homogenize rDNA copies in an interbreeding population. However, intra-specific differences in ITS2 of Anopheles stephensi have been reported. This study reports the presence of intragenomic sequence variation in the ITS2-rDNA of An. stephensi and hypothesizes that observed intra-specific differences in this species may have resulted due to ambiguous DNA sequence-chromatogram resulting from intragenomic heterogeneity. Anopheles stephensi collected from different parts of India were sequenced for complete ITS2 and the variable region of 28S-rDNA (d1-d3 domains). Intragenomic variations were found in ITS2 region of all An. stephensi sequenced, but no such variation was observed in d1 to d3 domains of 28S-rDNA. Cloning and sequencing of ITS2 through the d3 domain of the 28S region of rDNA from representative samples from northern, central, and southern India confirmed the presence of intragenomic variation in ITS2 due to transitions at three loci and two bp indel in a di-nucleotide microsatellite locus. Multiple haplotypes were observed in ITS2 raised from such variations. Due to the absence of detectable intragenomic sequence variation in the d1 to d3 domain of 28S rDNA of An. stephensi, this region can serve as an ideal reference sequence for taxonomic and phylogenetic studies. The presence of intragenomic variation in rDNA should be carefully examined before using this as a molecular marker for species delimitation or phylogenetic analyses.

Genome-wide DNA methylation profiling and gut flora analysis in intestinal polyps patients.

The intestinal polyp is the precancerous lesion of colorectal cancer. DNA methylation and intestinal microbiota may play an important role in the development of intestinal polyp. In this study, we included 10 patients with intestinal polyps who received the colonoscopy examination. We applied the Illumina Human Methylation 850K array to investigate the epigenome-wide DNA methylation patterns. Then, we filtered out the hub genes in the protein-protein interaction networks using functional epigenetic modules analysis. We also analyzed the colonizing bacteria on the surface of polyps compared with those in normal colonic mucosal epithelium with 16S ribosomal DNA sequencing. We identified 323 hypermethylated sites and 7992 hypomethylated sites between intestinal polyps and normal samples. Five hub genes, including CREB1, LPA, SVIL and KRT18, were identified in five modules. Hypomethylation of CREB1 is a candidate marker of colorectal adenoma. Gut microbiota analysis showed that Butyricicoccus was significantly decreased in the intestinal polyp groups. In conclusion, we identified DNA methylation disparities in intestinal polyps compared with normal tissue, of which methylation of CREB1 may hold clinical significance in colorectal cancer progress. Colonizing bacteria in the colonic epithelium might be related to the formation of intestinal polyps.

Phylogeny and taxonomy of Catenularia and similar fungi with catenate conidia.

The genus Catenularia (Chaetosphaeriaceae) was reviewed, and its relationships with morphologically similar fungi were evaluated using molecular and morphological data. Eleven species are accepted, four of which have been verified with molecular DNA data. The correct epithet ‘cupulifera’ is proposed for the type species C. cupuliferacomb. nov. Four other combinations are proposed, namely C. catenulatacomb. nov., C. elsikiicomb. nov., C. minorcomb. nov. and C. novae-zelandiaecomb. nov.Catenularia is an uncommon fungus inhabiting mainly decaying bark, wood and bamboo culms of various hosts and shows a widespread geographical distribution. It is circumscribed for fungi with mononematous, macronematous, simple conidiophores with terminal monophialides, usually accompanied with capitate hyphae. The conidia are aseptate, brown, cuneiform to rounded-obconic with an angular outline, adhering in chains. The diagnostic values of taxonomic characteristics of capitate hyphae and conidia (i.e. colour, shape in transverse section, setulae and formation) at the generic level were evaluated. An account of morphology, taxonomy and phylogeny of species accepted in Catenularia is provided. Based on ribosomal DNA sequences, Chalarodes obpyramidatasp. nov., characterised by catenate, angular, hyaline conidia with apical setulae, is revealed as closely related to Catenularia. The new genus Fuscocatenulagen. nov. is proposed for catenularia-like fungi having pigmented conidia with protracted maturation and round outline, with two species accepted, F. submersacomb. nov. and F. variegatacomb. nov. A new species Nawawia antennatasp. nov. is introduced and Nawawia is compared with morphologically similar taxa.

Evaluation of the bioformulation of potent native strains of Trichoderma spp. against the foot rot/gummosis of Kinnow mandarin

BackgroundFoot rot/gummosis of citrus, caused by Phytophthora spp., is the most important disease of citrus, responsible for the yield losses of 10 to 30% in fruit production in major citrus growing countries. Considering the burden of disease, the present study was undertaken to evaluate different native potent strains of Trichoderma spp. against the foot rot/gummosis of citrus.ResultsBased on molecular characteristics, i.e., ITS ribosomal DNA sequence analysis, 3 isolates of Phytophthora nicotianae var. parasitica and 7 isolates of Trichoderma (6 isolates of T. asperellum and one of T. harzianum) were identified. Trichoderma isolates and Metalaxyl-M + Mancozeb were used to assess antagonistic activity against the foot rot/gummosis under field conditions. T. asperellum T20 mutant reduced gummosis lesion size (95.67%), improved feeder root density (0.0236 cm3), increased number (990.16), and yield of fruits (168.83 kg).ConclusionsThe talc-based bioformulation of T20 mutant (T. asperellum) strain, used as a soil treatment, was able to manage effectively the gummosis/foot rot of citrus and also exhibited the highest yield.

Isolation and Identification of Natural Colorant Producing Soil-Borne Aspergillus niger from Bangladesh and Extraction of the Pigment.

Natural colorants have been used in several ways throughout human history, such as in food, dyes, pharmaceuticals, cosmetics, and many other products. The study aimed to isolate the natural colorant-producing filamentous fungi Aspergillus niger from soil and extract pigments for its potential use specially for food production. Fourteen soil samples were collected from Madhupur National Park at Madhupur Upazila in the Mymensingh district, Bangladesh. The Aspergillus niger was isolated and identified from the soil samples by following conventional mycological methods (cultural and morphological characteristics), followed by confirmatory identification by a polymerase chain reaction (PCR) of conserved sequences of ITS1 ribosomal DNA using specific oligonucleotide primers. This was followed by genus- and species-specific primers targeting Aspergillus niger with an amplicon size of 521 and 310 bp, respectively. For pigment production, a mass culture of Aspergillus niger was conducted in Sabouraud dextrose broth in shaking conditions for seven days. The biomass was subjected to extraction of the pigments following an ethanol-based extraction method and concentrated using a rotary evaporator. Aspergillus niger could be isolated from three samples. The yield of extracted brown pigment from Aspergillus niger was 0.75% (w/v). Spectroscopic analysis of the pigments was carried out using a UV–VIS spectrophotometer. An in vivo experiment was conducted with mice to assess the toxicity of the pigments. From the colorimetric and sensory evaluations, pigment-supplemented products (cookies and lemon juice) were found to be more acceptable than the control products. This could be the first attempt to use Aspergillus niger extracted pigment from soil samples in food products in Bangladesh, but for successful food production, the food colorants must be approved by a responsible authority, e.g., the FDA or the BSTI. Moreover, fungal pigments could be used in the emerging fields of the food and textile industries in Bangladesh.

P157 Microbiome Analysis Reveals That Ralstonia is Responsible for Decreased Renal Function in Patients with Ulcerative Colitis

Abstract Background Inflammatory bowel diseases (IBDs), such as ulcerative colitis (UC), are characterized by a disturbance of the normal gut microbiota and contribute to the development of chronic kidney disease (CKD). The incidence of CKD is higher in individuals with UC, but the causal link is unknown. Therefore, we investigated the role of gut microbiota in decreasing renal function in patients with UC Methods We performed 16S ribosomal DNA sequencing using ileocecal mucosal samples from nine individuals with UC and CKD (UC+CKD), 29 individuals with UC only, and 12 healthy controls. We also analyzed the operational taxonomic units, microbial diversity, and correlation with renal function. Co-culture assay using kidney organoids and Caco-2 cells was performed. Figure 1. The taxonomic composition of the gut microbiota of the study population and comparison of the 10 most abundant genera and species in the UC + CKD, UC, and control groups. Results Bacterial species diversity was significantly decreased in the UC+CKD group compared to that in the other groups based on Shannon and inverse Simpson indexes. At the genus level, Ralstonia had significantly greater abundance in the UC+CKD and UC groups compared to the control group. At the species level, unclassified Ralstonia species and Citrobacter portucalensis showed higher abundance in the UC+CKD group compared to the other groups. The relative abundance of Ralstonia showed a negative correlation with the estimated glomerular filtration rate (eGFR), but a positive correlation with the serum uric acid level. Ralstonia pickettii represented a negative correlation with eGFR, and induced damaging changes to kidney organoids in co-culture assay. Figure 2. The correlation between the relative abundance of Ralstonia with renal function (indicated by eGFR) and serum uric acid level. Effects of Ralstonia pickettii on Caco-2 cells and kidney organoids. (A) mRNA expression of pro-inflammatory cytokine genes in Caco-2 cells treated with and without Ralstonia pickettii, reflecting the inflammation seen in ulcerative colitis. Conclusion Gut microbial community profiles of the UC+CKD group are different from those of the UC group. Furthermore, Ralstonia pickettii contributes in decreasing renal function in patients with UC.

Muscular microsporidian infection in Arctic char Salvelinus alpinus from two lakes in Nunavik, Quebec, Canada.

Arctic char Salvelinus alpinus is an important cultural and subsistence resource for Inuit communities. Muscular infections by microsporidia were diagnosed for the first time in Arctic char originating from 2 different lakes in Nunavik (Quebec, Canada). The consumption of these infected fish was associated with digestive tract disorders in people. To better characterize microsporidiosis in these char populations, a cross-sectional study was conducted on 91 fish. The microsporidium was classified as a member of the Microsporidium collective genus by morphological evaluation and phylogenetic analysis using small subunit ribosomal DNA sequence data. The presence and severity of infection were determined histologically. Microsporidian infection occurred in 61% of the fish (56/91) and was significantly associated with an increase in their age, length and weight. The severity of infection (percentage of muscle area affected by microsporidia) was mild in most cases (<1% of the total muscle area). Based on multiple linear regression modeling, the severity of infection was significantly greater in females and negatively correlated with the body condition. Despite a high prevalence, the low pathogenicity of the infection suggests that microsporidiosis has little impact on these char populations. Moreover, since digestive-tract disorders following ingestion of fish infected by microsporidia have never been reported in humans, it seems unlikely that it was responsible for the reported clinical signs. Anisakid larvae are occasionally observed in these char populations. Digestive-tract infection associated with ingestion of these larvae should thus be considered as a potential differential diagnosis in these Inuit communities.

Genetic structure and evidence for coexistence of three taxa of Bithynia (Gastropoda: Bithyniidae), the intermediate host of Opisthorchis viverrini sensu lato (Digenea: Opisthorchiidae) in Thailand examined by mitochondrial DNA sequences analyses

The freshwater snails, Bithynia are the first intermediate hosts of the liver fluke, Opisthorchis viverrini, the causative agent of cholangiocarcinoma (CCA) in Southeast Asia. In Thailand, there are three traditionally recognized taxa of Bithynia: Bithynia funiculata; B. siamensis siamensis; B. s. goniomphalos. This study examines the geographical distribution and genetic structure of Bithynia species from five previously reported water catchments and six new catchments in Thailand. Of these, three new catchments Kok, Wang, and Nan are from the north and the remaining three new catchments are Phetchaburi, Prachuap Khiri Khan Coast, Mae Klong from the west of Thailand. We sampled 291 Bithynia snails from 52 localities in 11 catchment systems in the northern, western and central regions of Thailand. Mitochondrial cytochrome c oxidase subunit 1 (COI) and 16S ribosomal DNA (16S rDNA) sequences were used to examine genetic diversity of Bithynia snails which revealed 200 and 27 haplotypes of COI and 16S rDNA, respectively. However, as 16S rDNA is a conserved gene, it is not suitable to distinguish Bithynia at the species and sub-species levels in our study. The phylogenetic tree and haplotype network analyses included sequences of COI from GenBank. B. funiculata was found only in the north of Thailand and the genetic structure did not differ among populations. Genetic differentiation (ΦST) analyses showed that B. s. goniomphalos contained three distinct lineages. Lineage I contained B. s. goniomphalos from the vast majority of catchment systems in Thailand and Lao PDR. Lineage II contained all B. s. goniomphalos from the Prachin Buri and Bang Pakong catchment systems in eastern and central Thailand, including samples from all catchment systems in Cambodia. While lineage III contained B. s. goniomphalos from the Songkram and Nam Kam catchment systems in Thailand and the Nam Ngum and Huai Som Pak catchment systems in Lao PDR. Furthermore, results showed that all samples of B. s. siamensis were classified into one lineage and placed phylogenetically between B. s. goniomphalos lineages I and II. Thus, the taxonomic status of B. s. goniomphalos and B. s. siamensis requires reassessment, and they should be reclassified as belonging to the species complex “Bithynia siamensis sensu lato”.

Exploration of Crucial Mediators for Carotid Atherosclerosis Pathogenesis Through Integration of Microbiome, Metabolome, and Transcriptome.

BackgroundCarotid atherosclerosis (CAS) is an important cause of stroke. Although interactions between the gut microbiome and metabolome have been widely investigated with respect to the pathogenesis of cardiovascular diseases, information regarding CAS remains limited.Materials and MethodsWe utilized 16S ribosomal DNA sequencing and untargeted metabolomics to investigate the alterations in the gut microbiota and plasma metabolites of 32 CAS patients and 32 healthy controls. The compositions of the gut microbiota differed significantly between the two groups, and a total of 11 differentially enriched genera were identified. In the metabolomic analysis, 11 and 12 significantly changed metabolites were screened in positive (POS) and negative (NEG) modes, respectively. α-N-Phenylacetyl-L-glutamine was an upregulated metabolite in CAS patients detected in both POS and NEG modes and had the highest | log2(fold change)| in POS mode. In addition, transcriptomic analysis was performed using the GSE43292 dataset.ResultsA total of 132 differentially expressed genes (DEGs) were screened. Among the upregulated DEGs in CAS patients, FABP4 exhibited the highest | log2(fold change)|. Furthermore, FABP4 was positively associated with Acidaminococcus and had the highest Spearman’s correlation coefficient and the most significant p-value among the microbiota–DEG pairs.ConclusionIn this study, we investigated the potential “microbiota–metabolite–gene” regulatory axis that may act on CAS, and our results may help to establish a theoretical basis for further specialized study of this disease.

Analysis of the Gut Microbiota: An Emerging Source of Biomarkers for Immune Checkpoint Blockade Therapy in Non-Small Cell Lung Cancer.

Simple SummaryThe immune checkpoint blockade (ICB), and concretely the blockade of the PD1/PDL1 axis, has opened up a new standard of treatment for non-small cell lung cancer (NSCLC). However, despite substantial advances in clinical care, many patients still remain refractory to these therapies. Biomarkers such as PD-L1 expression and tumor mutational burden have been associated with ICB efficacy, but the mechanisms underlying variable responses are not yet fully understood. Recently, the differential composition of the gut microbiota was studied as one of the variables accounting for interpatient heterogeneity in ICB responses. To better understand the potential role of the gut microbiota as a biomarker for immunotherapy, we prospectively collected microbiota samples from advanced NSCLC patients starting treatment with ICB. The identification of certain bacteria genera associated with clinical outcomes to ICB in NSCLC may provide novel potential predictive and prognostic biomarkers useful for patient selection and therapy optimization.Background: The human gut harbors around 1013–1014 microorganisms, collectively referred to as gut microbiota. Recent studies have found that the gut microbiota may have an impact on the interaction between immune regulation and anti-cancer immunotherapies. Methods: In order to characterize the diversity and composition of commensal microbiota and its relationship with response to immune checkpoint blockade (ICB), 16S ribosomal DNA (rDNA) sequencing was performed on 69 stool samples from advanced non-small cell lung cancer (NSCLC) patients prior to treatment with ICB. Results: The use of antibiotics and ICB-related skin toxicity were significantly associated with reduced gut microbiota diversity. However, antibiotics (ATB) usage was not related to low ICB efficacy. Phascolarctobacterium was enriched in patients with clinical benefit and correlated with prolonged progression-free survival, whereas Dialister was more represented in patients with progressive disease, and its higher relative abundance was associated with reduced progression-free survival and overall survival, with independent prognostic value in multivariate analysis. Conclusions: Our results corroborate the relation between the baseline gut microbiota composition and ICB clinical outcomes in advanced NSCLC patients, and provide novel potential predictive and prognostic biomarkers for immunotherapy in NSCLC.

Fulvifomes nonggangensis and F. tubogeneratus (Hymenochaetales, Basidiomycota): Two New Species from Southern China Based on Morphological and Molecular Evidences

Two new species of Fulvifomes are described from specimens collected in rainforests of Nonggang Nature Reserve of southern China, based on morphological characteristics and molecular phylogenetic analysis of the internal transcribed spacer (ITS) and nuclear large subunit ribosomal DNA (nLSU) sequences. Fulvifomes nonggangensis sp. nov. is characterized by perennial, sessile and solitary basidiocarps, applanate pileus, small cystidioles of 9.9–15.4 × 2.9–3.5 μm, large pores of 5–6 per mm, a dimitic hyphal system, and broadly ellipsoid basidiospores of 4.3–5.3 × 3.3–4.2 μm. F. tubogeneratus sp. nov. is characterized by perennial, sessile, and imbricate basidiocarps, a duplex context, small pores of 7–8 per mm, a dimitic hyphal system, and ovoid to subglobose basidiospores of 5.72 × 5.00 μm.

Fungal endophytes from leaves of Mandevilla catimbauensis (Apocynaceae): diversity and potential for L-asparaginase production.

In this study, we examined endophytic fungi in leaves of Mandevilla catimbauensis, an endemic plant species found in the Brazilian dry forest (Caatinga), and endophytic fungi's potential to produce L-asparaginase (L-ASNase). In total, 66 endophytes were isolated, and the leaf-fragment colonisation rate was 11.78%. Based on morphology, internal transcribed spacer (ITS), and partial large subunit (LSU) of ribosomal DNA sequencing, the endophytic fungi isolated belonged to six Ascomycota orders (Botryosphaeriales, Capnodiales, Diaporthales, Eurotiales, Marthamycetales, and Pleosporales). Phyllosticta species were the most frequent endophytes isolated (23 isolates [45.1%] from two species). The Shannon-Wiener and Fisher alpha index average values were 0.56 and 3.26, respectively. Twenty endophytes were randomly selected for the L-ASNase production test, of which fourteen isolates showed potential to produce the enzyme (0.48-2.22 U g-1), especially Phyllosticta catimbauensis URM 7672 (2.22 U g-1) and Cladosporium sp. G45 (2.11 U g-1). Phyllosticta catimbauensis URM 7672 was selected for the partial optimisation of L-ASNase production because of its ability to generate considerable amounts of enzyme. We obtained the highest L-ASNase activity (3.47 U g-1), representing an increase of 36.02% in enzymatic production, under the following experimental conditions: a pH of 4.2, 1.0% inoculum concentration, and 2.5% L-asparagine concentration. Our study showed that M. catimbauensis harbours an important diversity of endophytic fungi with biotechnological potential for L-ASNase production.

Immune and intestinal microbiota responses to aerial exposure stress in Chinese mitten crab (Eriocheir sinensis)

Desiccation is an important environmental stressor during crabs culture and transportation. In this study, we investigated oxidative damage, antioxidant capacity, immune-related enzyme activity and intestinal microbiota responses of Eriocheir sinensis subjected to aerial exposure stress for 96 h. The results revealed a significant increase in lipid peroxide (LPO) and malondialdehyde (MDA) levels in the hepatopancreas after aerial exposure (p < 0.05). Antioxidant activities including superoxide dismutase (SOD) and total antioxidant capacity (T-AOC) showed significant variations (p < 0.05). Alkaline phosphatase (AKP) and acid phosphatase (ACP) activity both increased to the maximum levels at 12 h, and were significantly lower than those of controls at 72 h and 96 h respectively (p < 0.05). High-throughput 16S ribosomal DNA (rDNA) sequencing revealed that aerial exposure stress altered bacterial diversity, and changed the composition of intestinal microbes. Specifically, abundance of beneficial bacteria Citrobacter decreased, while abundance of pathogenic bacteria Acinetobacter increased. The results revealed that prolonged period of air exposure stress adversely affects the antioxidant status, immune function, and intestinal flora in E. sinensis. This work could help to uncover the mechanisms of aerial exposure stress responses in this species.

Tissue and/or developmental stage specific methylation of nrDNA in Capsicum annuum.

The nuclear ribosomal DNA (nrDNA) sequences are often used for phylogenetic analysis among organisms. Because DNA cytosine methylation and nucleolar dominancy are two common epigenetic mechanisms of nrDNA, we hypothesized that internal transcribed spacer 1 (ITS1), 5.8S rRNA and ITS2 of nrDNA sequences could be used as epigenetic biomarkers. Thus, this research was undertaken to study level and pattern of site-specific cytosine methylation of ITS1, 5.8S and ITS2 in nine tissues and/or developmental stage of pepper Capsicum annuum L. cultivar Demre Sivrisi. Tissues studied consisted of young and old roots at 30 and 90days after sowing (das), mature dry seeds and seeds at 26days of post anthesis (dpa), flowering buds at 1day before flowering, pericarps at 3, 15 and 65 dpa. Levels and patterns of DNA cytosine methylation were identified at single base resolution using bisulfite conversion sequencing. Results of this study revealed that DNA cytosine level and pattern of ITS1, 5.8S and ITS2 were different in most tissues and/or developmental stages studied. In addition, methylation levels of CG, CHG and CHH contexts were also significantly different among the regions. Based on the findings of this study, it was concluded that high level of methylation of nrDNA sequences was relatively higher as observed in transposable element and promoter. On the other hand, its tissue-specific gene expression was effective as that of gene body and promoter methylation. Overall findings revealed that methylation levels of nrDNA could be used as biomarkers for tissue identification or age estimation in plants.