rRNA Gene Sequence Analysis Research Articles

Wood-Inhabiting Nematode, Bursaphelenchus ussuriensis sp. n. (Nematoda: Aphelenchoididae) from David Elm, with Molecular Phylogeny of the Genus Based on Partial Mitochondrial Genomes.

A new nematode species, Bursaphelenchus ussuriensis sp. n. is described in the bark beetle-elm tree association (Scolytus jacobsoni and Ulmus davidiana var. japonica f. suberosa) in the Asian Pacific region of Russia. The new species belongs to the Hofmanni group of Bursaphelenchus and is closest to B. ulmophilus. Its characteristics are as follows: lateral field with three incisures, body length 497-771 µm, post-uterine sac 3.6-5.4 times vulval body diam, 56 (39-66)% of vulva-anus distance, and spicule length 10.3 (9.5-12.5 µm). The new species differs from all species of the Hofmanni group in the closely situated P3 and P4 male caudal papillae and the GP5 small 'glandpapillae' pair on the butterfly-like papillae plate, in the set of P1, P2, P3, P4, GP5; vs. in all other species, the P4 papillae pair is absent in the pattern of P1, P2, P3, GP5. The phylogenetic position of B. ussuriensis sp. n. with other species of the Hofmanni group were reconstructed using the D2-D3 expansion segments of 28S and ITS rRNA gene sequence analysis. Sequences of twelve mitochondrial protein-coding genes of B. cocophilus, B. fraudulentus, B. michalskii, B. ussurensis sp. n., and B. willibaldi were obtained in this study. Phylogenetic relationships among eighteen Bursaphelenchus species based on the analysis of the mtDNA sequence dataset are provided and discussed. A modified diagnosis of the Hofmanni group is proposed.

Exploring Halotolerant Phosphate-Solubilizing Bacteria Isolated from Mangrove Soil for Agricultural and Ecological Benefits

Phosphorus is a vital element for all life forms. Phosphate-solubilizing bacteria transform phosphate into a bioavailable form through solubilization and mineralization processes. The aim of this study is evaluating the role of halotolerant, phosphate-solubilizing bacteria (PSB). having different PGPR traits as biofertilizers. Thirteen bacterial strains were isolated from soil samples of Ras Muhammad mangrove forest and screened for production of different PGPR traits. The most potent microbial candidates were identified by rRNA gene sequencing analysis and uploaded in GenBank as Bacillus safensis [OR341132] and Cytobacillus firmus [OR431197] these showed ability to tolerate salt concentration up to 10%, can fix nitrogen by growing on nitrogen free media with excellent growth and characterized qualitatively and quantitative solubilize phosphorous more than 100µg/ml of insoluble phosphate, hydrolyse phytate and produced IAA showing the highest value in the range of 94.54, 220,38 μg/mL respectively. In pot trials performed in a greenhouse the isolated strains Bacillus safensis [OR341132] and Cytobacillus firmus [OR431197] were able to significantly improve levels of assimilated phosphate, compared to non-inoculated plants. Moreover, mixed treatment (Bacillus safensis +Cytobacillus firmus ) increased soil fertility and consequently improve the growth of parley plant . The study has overall concluded that bacteria isolated from mangrove soil, Bacillus safensis [OR341132] and Cytobacillus firmus [OR431197] could be used as the halotolerant plant growth-promoting rhizobacteria [HT-PGPR] and phosphate-solubilizing bacteria [PSB] and have a good influence on the health of barley [genotype Giza123] plants under salinity conditions during thirty days.

Combined transcriptome and microbiome analysis reveals the thyrotoxic effects of PM2.5 in female rats

Pervasive environmental pollutants, specifically particulate matter (PM2.5), possess the potential to disrupt homeostasis of female thyroid hormone (TH). However, the precise mechanism underlying this effect remains unclear. In this study, we established a model of PM2.5-induced thyroid damage in female rats through intratracheal instillation and employed histopathological and molecular biological methods to observe the toxic effects of PM2.5 on the thyroid gland. Transcriptome gene analysis and 16S rRNA sequencing were utilized to investigate the impact of PM2.5 exposure on the female rat thyroid gland. Furthermore, based on the PM2.5-induced toxic model in female rats, we evaluated its effects on intestinal microbiota, TH levels, and indicators of thyroid function. The findings revealed that PM2.5 exposure induced histopathological damage to thyroid tissue by disrupting thyroid hormone levels (total T3 [TT3], (P < 0.05); total T4 [TT4], (P < 0.05); and thyrotropin hormone [TSH], (P < 0.05)) and functional indices (urine iodine [UI], P > 0.05), thus further inducing histopathological injuries. Transcriptome analysis identified differentially expressed genes (DEGs), primarily concentrated in interleukin 17 (IL-17), forkhead box O (FOXO), and other signaling pathways. Furthermore, exposure to PM2.5 altered the composition and abundance of intestinal microbes. Transcriptome and microbiome analyses demonstrated a correlation between the DEGs within these pathways and the flora present in the intestines. Moreover, 16 S rRNA gene sequencing analysis or DEGs combined with thyroid function analysis revealed that exposure to PM2.5 significantly induced thyroid hormone imbalance. We further identified key DEGs involved in thyroid function-relevant pathways, which were validated using molecular biology methods for clinical applications. In conclusion, the homeostasis of the "gut-thyroid" axis may serve as the underlying mechanism for PM2.5-induced thyrotoxicity in female rats.

Isolation and identification of hoylesella marshii causing pleural infection: a case report

BackgroundHoylesella marshii can be isolated from human oral cavities affected by dental pulp and periodontal infections, as well as from the dental plaque of healthy individuals, making it a common bacterium within the oral microbiota. However, its role in causing pleural infections in humans is rare.Case presentationA case of purulent pleural effusion occurred shortly after discharge in an elderly patient who had undergone surgery for gastric cancer. The infection was identified as being caused by an obligate anaerobe through laboratory culture, and was further identified as Hoylesella marshii causing pleural infection through 16 S rRNA gene sequence analysis. Susceptibility testing guided precise treatment with cefoperazone-sulbactam and metronidazole. The patient’s clinical symptoms improved rapidly, laboratory test indicators gradually returned to normal, and the patient ultimately recovered.ConclusionHoylesella marshii can cause pleural infections in humans. Clinical microbiology laboratories should pay special attention to the cultivation of obligate anaerobes when routine aerobic cultures do not show bacterial growth but bacteria are visible on smear staining, and when conventional identification methods fail to identify the bacterium, analysis based on the highly conserved 16 S rRNA gene sequence can accurately and specifically identify the bacterium, guiding clinicians in formulating precise anti-infection strategies.

Inhibitory Effects of Jiuzao Polysaccharides on Alcoholic Fatty Liver Formation in Zebrafish Larvae and Their Regulatory Impact on Intestinal Microbiota.

The liver is critical in alcohol metabolism, and excessive consumption heightens the risk of hepatic damage, potentially escalating to hepatitis and cirrhosis. Jiuzao, a by-product of Baijiu production, contains a rich concentration of naturally active polysaccharides known for their antioxidative properties. This study investigated the influence of Laowuzeng Jiuzao polysaccharide (LJP) on the development of ethanol-induced alcoholic fatty liver. Zebrafish larvae served as the model organisms for examining the LJPs hepatic impact via liver phenotypic and biochemical assays. Additionally, this study evaluated the LJPs effects on gene expression associated with alcoholic fatty liver and the composition of the intestinal microbiota through transcriptomic and 16 S rRNA gene sequencing analyses, respectively. Our findings revealed that LJP markedly mitigated morphological liver damage and reduced oxidative stress and lipid peroxidation in larvae. Transcriptome data indicated that LJP ameliorated hepatic fat accumulation and liver injury by enhancing gene expression involved in alcohol and lipid metabolism. Furthermore, LJP modulated the development of alcoholic fatty liver by altering the prevalence of intestinal Actinobacteriota and Firmicutes, specifically augmenting Acinetobacter while diminishing Chryseobacterium levels. Ultimately, LJP mitigated alcohol-induced hepatic injury by modulating gene expression related to ethanol metabolism, lipid metabolism, and inflammation and by orchestrating alterations in the intestinal microbiota.

Study on genetic characteristics of Cryptosporidium isolates and first report of C. parvum IIdA24G2 subtype in dairy cattle in China.

Cryptosporidium is an important gastrointestinal parasite that can cause mild to severe diarrhea in various vertebrates, including humans and domestic animals. Infection is prevalent in dairy cattle, particularly calves, resulting in diarrhea and increased mortality with significant production losses. However, the prevalence and identity of Cryptosporidium spp. in cattle in Heilongjiang Province is still poorly known. Our study aimed to investigate the prevalence and species and subtype distribution of Cryptosporidium in cattle in the region. In addition, we evaluated the zoonotic potential of Cryptosporidium isolates and assessed possible transmission routes and health effects of this organism. We collected 909 fecal samples from five different farms in Heilongjiang Province between August and September 2022. The samples underwent Cryptosporidium detection by nested PCR and small subunit (SSU) rRNA gene sequence analysis. Four Cryptosporidium species were identified, including C. parvum, C. bovis, C. ryanae, and C. andersoni, with an overall prevalence of 4.4% (40/909). Based on sequence analysis of the 60 kDa glycoprotein gene of C. parvum and C. bovis, three subtypes of C. parvum were identified, namely two previously known subtypes (IIdA19G1 and IIdA20G1), and one novel subtype (IIdA24G2). Two distinct subtype families were identified in C. bovis (XXVId and XXVIe). The high diversity of Cryptosporidium in dairy cattle and the emergence of a novel subtype of C. parvum in Heilongjiang Province suggest that dairy cattle may serve as a significant source of zoonotic cryptosporidiosis infection in this region.

Evaluation of new candidate probiotic lactobacillus strains isolated from a traditional fermented food- multigrain-millet dosa batter

The food industry is constantly developing new products to meet the increasing global demand of fermented foods, for its health benefits. In this study, the potential probiotics in traditional fermented food - “multigrain-millet” based Dosa batter, and their significant probiotic characteristics was investigated. In addition, the ability of probiotic Lactobacillus to prevent foodborne pathogens was explored. A total collection of 70 isolates were examined from the batter. The six isolates with the best in vitro probiotic characteristics were studied. The six isolates MYSDS57, MYSDS68, MYSDV3, MYSDV2, MYSDV5 and MYSDV6 were identified as Lactiplantibacillus plantarum, Lacticaseibacillus paracasei, Lactobacillus pentosus, Lactiplantibacillus plantarum, Lactiplantibacillus plantarum and Limosilactobacillus fermentum respectively based on 16 S rRNA gene sequencing analysis. All six Lactobacillus were able to tolerate acidic pH (45 %–80 % survivability) and 0.3% bile salt (50 %–80.4 % survivability) up to 5 h of incubation. All tested strains showed higher growth at 37 °C, resistance to different concentrations of phenols (53.3 %–83.6 % of viability) and NaCl (38.2%–49.5% of viability). However, the strains exhibited resistance to antibiotic vancomycin, but no hemolytic and DNase activity. Moreover, six strains showed significantly high values of autoaggregation (54.6%-78.8 %) and cell surface hydrophobicity (70 %-81.7%). The α-glucosidase and α-amylase inhibitory activity ranged from 15.08% to 67.22 % and 50.15%–92.13% respectively. Additionally, the intracellular cell-free supernatant of all six Lactobacillus demonstrated antibacterial activity with the inhibition rate of 64.8 %–86 % (Salmonella typhi), 51.8 %–95.2 % (Escherichia coli), 59.9 %–76.6 % (Listeria monocytogenes), 39.6% −74.3 % (Salmonella paratyphi), 57.4 %–81.3 % (Klebsiella pneumonia), 44 %-67.1% (Staphylococcus aureus) and 7.2 %–54.7 % (Pseudomonas aeruginosa). The strains exhibited higher viability (5.8–7.5 log CFU/mL) to simulated gastric juice, high adhesion to chicken crop epithelial cells and buccal cells. These isolates also reduced the cholesterol level in vitro. Overall, the selected Lactobacillus can be considered promising probiotic candidates for future applications.

Luteibacter jiangsuensis blood stream infection: a first case report

BackgroundLuteibacter jiangsuensis is a gram-negative aerobic bacillus that was first isolated from soil samples at a pesticide factory in China and reported in 2011. Here, we describe the first case of L. jiangsuensis infection in human.Case presentationA 59-year-old Japanese woman undergoing treatment for Crohn’s disease was admitted to our hospital with fever. Clinical examination indicated catheter-related bloodstream infection. The catheter was removed and meropenem was initiated. Morphologically identical glucose non-fermentative gram-negative bacilli were detected from two sets of aerobic blood culture and catheter-tip cultures. MALDI-TOF mass spectrometry failed to identify the bacterium, which was later identified as L. jiangsuensis by 16 S rRNA gene sequencing. Antimicrobial susceptibility test revealed that the isolate was resistant to carbapenem, therefore meropenem was switched to intravenous levofloxacin (500 mg/day). After 14 days of treatment with levofloxacin, the patient was discharged.ConclusionsThis is the first case of L. jiangsuensis infection in human. The strain was identified by 16 S rRNA gene sequence analysis.

Bacterial butyrate mediates the anti-atherosclerotic effect of silybin

Silybin (SIL) is a versatile bioactive compound used for improving liver damage and lipid disorders and is also thought to be beneficial for atherosclerosis (AS). The goal of this study was to investigate the efficacy of SIL in the treatment of AS in ApoE−/−mice fed a high-fat diet and explore the mechanism underlying treatment outcomes. We found that SIL significantly alleviated AS-related parameters, including the extent of aortic plaque formation, hyperlipidemia, and adhesion molecule secretion in the vascular endothelium. 16 S rRNA gene sequencing analysis, together with the application of antibiotics, showed that intestinal butyrate-producing bacteria mediated the ameliorative effect of SIL on AS. Further analysis revealed that SIL facilitated butyrate production by increasing the level of butyryl-CoA: acetate CoA-transferase (BUT). The increased expression of monocarboxylic acid transporter-1 (MCT1) induced by butyrate and MCT4 induced by SIL in the apical and basolateral membranes of colonocytes, respectively, resulted in enhanced absorption of intestinal butyrate into the circulation, leading to the alleviation of arterial endothelium dysfunction. Moreover, the SIL-mediated increase in intestinal butyrate levels restored gut integrity by upregulating the expression of tight junction proteins and promoting gut immunity, thus inhibiting the AS-induced inflammatory response. This is the first study to show that SIL can alleviate AS by modulating the production of bacterial butyrate and its subsequent absorption.

Microbial mechanism underlying the effect of biochar supported nano zero-valent iron on the anaerobic digestion of food waste

Anaerobic digestion (AD) is one of the effective methods to treat the food waste (FW). In this study, biochar supported nano zero-valent iron (BC-nZVI) was prepared by carbon thermal reduction process. The effects of concentrations (1, 2 and 3 g/L) of BC-nZVI on methane production, microorganisms and metabolic mechanism during the AD of food waste were investigated. The results showed that 1 g/L of BC-nZVI was the best concentration for methane production. The cumulative methane production was enhanced by 29.54% at BC-nZVI 1 g/L. Microbial community analysis showed that BC-nZVI mainly increased the abundances of hydrolytic bacteria (including Bacteroidetes_vadinHA17, Proteiniphilum, Syntrophobacter) and acetoclast (Methanosaeta). Further exploration of the mechanism using PICRUSt2 version based on 16 S rRNA gene sequence analysis indicated that the addition of BC-nZVI promoted the abundances of enzymes related to methane metabolism such as the phosphate acetyltransferase and the methyl-coenzyme M reductase alpha subunit, which made the AD system stable.

The exploration of dominant spoilage bacteria in blue mussels (Mytilus edulis) stored under different modified atmospheres by MALDI-TOF MS in combination with 16S rRNA sequencing

Few studies have addressed species-level identification of spoilage bacteria in blue mussels packed under modified atmospheres (MAs). We investigated the effect of MAs and seasons on the tentative species-level of dominant spoilage bacteria in blue mussels. Summer (s) and winter (w) blue mussels were stored at 4 °C in the atmospheres (%CO2/O2/N2): A40s (30/40/30), B60s (40/60/0), C60s (0/60/40), A40w (30/40/30), and D75w (25/75/0). In total, 122 culturable isolates were obtained at the final stage of shelf life, when mortality was high (56–100%) and total psychrotrophic bacteria counted >7 log CFU g−1. Biochemical properties were analyzed using gram reactions, catalase and oxidase activities, and salt tolerance tests. Culturable isolates were identified through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16 S rRNA gene sequence analysis. Spoilage potential tests were investigated by evaluating protease, lipase, and fermentation activities as well as gas and H2S production. The culturable isolates showed tolerance to varied salt concentrations. Psychromonas arctica, Pseudoalteromonas elyakovii, and Shewanella frigidimarina were dominating in specific MAs. Winter blue mussels resulted in a higher variation of spoilage bacteria, including S. frigidimarina, S. vesiculosa, S. polaris, Micrococcus luteus, Paeniglutamicibacter terrestris sp. nov., and Alteromonas sp.

Antibacterial activity of exopolysaccharide produced by bee gut-resident Enterococcus sp. BE11 against marine fish pathogens

BackgroundIn recent years, the demand for innovative antimicrobial agents has grown, considering the growing problem of antibiotic resistance in aquaculture. Adult Apis mellifera honeybees’ gut represents an outstanding habitat to isolate novel lactic acid bacteria (LAB) able to produce prominent antimicrobial agents.MethodsIn the current study, twelve LAB were isolated and purified from the gut of adult Apis mellifera. The isolates were screened for exopolysaccharide (EPS) production. The most promising isolate BE11 was identified biochemically and molecularly using 16 S rRNA gene sequence analysis as Enterococcus sp. BE11 was used for the mass production of EPS. The partially purified BE11-EPS features were disclosed by its physicochemical characterization. Moreover, the antimicrobial activity of BE11 cell free supernatant (CFS) and its EPS was investigated against some fish pathogens namely, Pseudomonas fluorescens, Streptococcus agalactiae, Aeromonas hydrophila, Vibrio sp. and Staphylococcus epidermidis using well-cut diffusion method.ResultsThe physicochemical characterization of BE11-EPS revealed that the total carbohydrate content was estimated to be ~ 87%. FTIR and NMR analysis ascertained the presence of galactose and glucose residues in the EPS backbone. Moreover, the GC-MS analysis verified the heterogeneous nature of the produced BE11-EPS made up of different monosaccharide moieties: galactose, rhamnose, glucose, arabinose sugar derivatives, and glucuronic acid. BE11 CFS and its EPS showed promising antimicrobial activity against tested pathogens as the inhibition zone diameters (cm) ranged from 1.3 to 1.7 and 1.2–1.8, respectively.ConclusionThe bee gut-resident Enterococcus sp. BE11, CFS, and EPS were found to be promising antimicrobial agents against fish pathogens and biofilm producers affecting aquaculture. To the best of our knowledge, this is the first study to purify and make a chemical profile of an EPS produced by a member of the bee gut microbiota as a potential inhibitor for fish pathogens.

Endophytic Bacillus sp. AP10 harboured in Arabis paniculata mediates plant growth promotion and manganese detoxification

Phytoremediation of heavy metal-polluted soils assisted by plant-associated endophytes, is a suitable method for plant growth and manganese (Mn) removal in contaminated soils. This investigation was conducted to evaluate the Mn-resistant endophytic resources of the Mn hyperaccumulator Arabis paniculata and their functions in the phytoremediation of Mn2+ toxicity. This study isolated an endophytic bacterium with high Mn resistance and indole-3-acetic acid (IAA) production form A. paniculata and identified it as Bacillus sp. AP10 using 16 S rRNA gene sequencing analysis. The effects of Bacillus sp. AP10 on the alleviation of Mn2+ toxicity in Arabidopsis thaliana seedlings and the molecular mechanisms were further investigated using biochemical tests and RNA-seq analysis. Under Mn2+ stress, Bacillus sp. AP10 increased the biomass, chlorophyll content and the translocation factor (TF) values of Mn in the aerial parts, while decreased the malondialdehyde (MDA) content of A. thaliana seedlings compared with that of control plants. The differentially expressed genes (DEGs) and enrichment analysis showed that Bacillus sp. AP10 could significantly increase the expression of key genes involved in cell-wall loosening, which may improve plant growth under Mn stress. Superoxide dismutase (SOD)-encoding genes were detected as DEGs after AP10 treatment. Moreover, AP10 regulated the expression of genes responsible for phenylpropanoid pathway, which may promote antioxidant flavonoids accumulation for reactive oxygen species (ROS) scavenging to improve Mn tolerance. The activation of ATP-binding cassette (ABC) transporter gene expression especially ABCB1 after AP10 stimulation, explained the elevation of metal ion binding or transport related to enhanced Mn accumulation in plants. Futhermore, AP10 might alleviate Mn toxicity through enhancing abscisic acid (ABA) responsive gene expression and ABA biosynthesis. These findings provide new insights into the functions and regulatory mechanism of Bacillus sp. AP10 in promoting plant growth, and tolerance, improving Mn accumulation and alleviating Mn2+ toxicity in plants. The application of Bacillus sp. AP10 as potential phytoremediators may be a promising strategy in Mn2+ contaminated fields. Availability of data and materialsThe datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.

Differential distribution patterns and assembly processes of soil microbial communities under contrasting vegetation types at distinctive altitudes in the Changbai Mountain.

Diversity patterns and community assembly of soil microorganisms are essential for understanding soil biodiversity and ecosystem processes. Investigating the impacts of environmental factors on microbial community assembly is crucial for comprehending the functions of microbial biodiversity and ecosystem processes. However, these issues remain insufficiently investigated in related studies despite their fundamental significance. The present study aimed to assess the diversity and assembly of soil bacterial and fungal communities to altitude and soil depth variations in mountain ecosystems by using 16S and ITS rRNA gene sequence analyses. In addition, the major roles of environmental factors in determining soil microbial communities and assembly processes were further investigated. The results showed a U-shaped pattern of the soil bacterial diversity at 0-10 cm soil depth along altitudes, reaching a minimum value at 1800 m, while the fungal diversity exhibited a monotonically decreasing trend with increasing altitude. At 10-20 cm soil depth, the soil bacterial diversity showed no apparent changes along altitudinal gradients, while the fungal Chao1 and phylogenetic diversity (PD) indices exhibited hump-shaped patterns with increasing altitude, reaching a maximum value at 1200 m. Soil bacterial and fungal communities were distinctively distributed with altitude at the same depth of soil, and the spatial turnover rates in fungi was greater than in bacteria. Mantel tests suggested soil physiochemical and climate variables significantly correlated with the β diversity of microbial community at two soil depths, suggesting both soil and climate heterogeneity contributed to the variation of bacterial and fungal community. Correspondingly, a novel phylogenetic null model analysis demonstrated that the community assembly of soil bacterial and fungal communities were dominated by deterministic and stochastic processes, respectively. The assembly processes of bacterial community were significantly related to the soil DOC and C:N ratio, while the fungal community assembly processes were significantly related to the soil C:N ratio. Our results provide a new perspective to assess the responses of soil microbial communities to variations with altitude and soil depth.

Lactulose regulates gut microbiota dysbiosis and promotes short-chain fatty acids production in acute pancreatitis patients with intestinal dysfunction

BackgroundIntestinal dysfunction is one of the common complications in the early stage of acute pancreatitis (AP), which often associates with bad outcome. Lactulose, as a prebiotic, has been widely used to improve gut health, yet its effect on AP is unclear. MethodsThis was a prospective, randomized trial of moderate severe AP patients complicated with intestinal dysfunction. A total of 73 participants were randomly assigned to receive either lactulose or Chinese herb rhubarb for 1 week. The primary efficacy endpoint was the recovery of intestinal function. The serum levels of inflammatory cytokines and gut barrier indexes were examined. The fecal samples from patients before and after treatment were collected. 16 S rRNA gene sequencing analysis was performed to explore the composition of gut microbiota and the amount of short-chain fatty acids (SCFAs) were detected by gas chromatography-mass spectrometry (GC-MS). ResultsThe intestinal dysfunction was prominently improved after 7 days of treatment with either lactulose or rhubarb. The serum levels of cytokines and gut permeability index were decreased after treatment, with stronger down-regulated degree in lactulose group than rhubarb. The potential beneficial genus Bifidobacterium was enriched in lactulose group, while pathogenic bacteria including Escherichia-Shigella and Neisseria were abundant in rhubarb group. Of note, the level of SCFAs was remarkably increased after treatment, with higher amount in lactulose group than rhubarb group. ConclusionsLactulose could not only restore intestinal function but also regulate gut microbiota and promote the production of SCFAs.

Diversity of Prokaryotic Microbiota in Iloilo River, Iloilo Province, Philippines Through Partial 16S rrna Gene Sequence Analysis

Diversity of Prokaryotic Microbiota in Iloilo River, Iloilo Province, Philippines Through Partial 16S rrna Gene Sequence Analysis

Identification and Differentiation of Closely Related Members of Bacillus cereus Group by Multiplex PCR

Highly similar genetic and phenotypic traits of at least eight bacterial species forming the ‘Bacillus cereus group’ create their precise identification and differentiation quite difficult. The present study explores the applicability of a previously suggested multiplex-PCR method for the accurate identification of the candidate Bacillus species. Out of the 257 Bacillus isolates collected from soil, 44 were identified as B. thuringiensis and 39 as B. cereus by chromogenic cultural method using Bacillus agar, although few of them shared similar colony characteristics. Identification by the multiplex PCR in a thermo cycler using 5 different sets of primer-pairs, however produced distinct amplification corresponding to the bacterial species. Four of those pairs, named BMSH, BCJH, BTJH and BASH were designed based on gyrB gene that produced amplicons of four different sizes: 604, 475, 299 and 253 bp and were specific for B. mycoides, B. cereus, B. thuringiensis, and B. anthracis respectively. The remaining one of the sets was used as an internal control which was a universal primerpair, BCGSH, designed targeting a housekeeping gene, groEL that could produce an amplicon of 400 bp in polymerase chain reactions for all members of the B. cereus group, When probing the chromosomes extracted from 257 Bacillus isolates by multiplex PCR; 48, 39 and 5 were identified as B. thuringiensis, B. cereus, and B. anthracis respectively, however the rest of the isolates did not any amplification. Interestingly, the phylogenetic tree, constructed based on partial sequences of 16S rRNA genes of selected isolates including the reference strain of B. thuringiensis (HD-73, sotto) could not differentiate the species, instead posited those in a single cluster. The multiplex PCR, therefore, proved to be a sensitive and reliable method for the identification of the bacterial candidates of Bacillus cereus group than that of cultural and rRNA gene sequence analyses.&#x0D; Bangladesh J Microbiol, Volume 39, Number 1, June 2022, pp 21-29

Diversity of duckweed (&lt;i&gt;Lemnaceae&lt;/i&gt;) associated yeasts and their plant growth promoting characteristics

&lt;abstract&gt; &lt;p&gt;The diversity of duckweed (&lt;italic&gt;Lemnaceae&lt;/italic&gt;) associated yeasts was studied using a culture-dependent method. A total of 252 yeast strains were isolated from 53 duckweed samples out of the 72 samples collected from 16 provinces in Thailand. Yeast identification was conducted based on the D1/D2 region of the large subunit (LSU) rRNA gene sequence analysis. It revealed that 55.2% and 44.8% yeast species were Ascomycota and Basidiomycota duckweed associated yeasts, respectively. Among all, &lt;italic&gt;Papiliotrema laurentii&lt;/italic&gt;, a basidiomycetous yeast, was found as the most prevalent species showing a relative of frequency and frequency of occurrence of 21.8% and 25%, respectively. In this study, high diversity index values were shown, indicated by the Shannon-Wiener index (&lt;italic&gt;H′&lt;/italic&gt;), Shannon equitability index (&lt;italic&gt;E&lt;sub&gt;H&lt;/sub&gt;&lt;/italic&gt;) and Simpson diversity index (&lt;italic&gt;1-D&lt;/italic&gt;) values of 3.48, 0.86 and 0.96, respectively. The present results revealed that the yeast community on duckweed had increased species diversity, with evenness among species. Principal coordinate analysis (PCoA) revealed no marked differences in yeast communities among duckweed genera. The species accumulation curve showed that the observed species richness was lower than expected. Investigation of the plant growth promoting traits of the isolated yeast on duckweed revealed that 178 yeast strains produced indole-3-acetic acid (IAA) at levels ranging from 0.08–688.93 mg/L. Moreover, siderophore production and phosphate solubilization were also studied. One hundred and seventy-three yeast strains produced siderophores and exhibited siderophores that showed 0.94–2.55 activity units (AU). One hundred six yeast strains showed phosphate solubilization activity, expressed as solubilization efficiency (SE) units, in the range of 0.32–2.13 SE. This work indicates that duckweed associated yeast is a potential microbial resource that can be used for plant growth promotion.&lt;/p&gt; &lt;/abstract&gt;

Occurrence of Streptomyces tauricus in mangrove soil of Mangalore region in Dakshina Kannada as a source for antimicrobial peptide.

Microbial resistance and deprivation of the effective drugs have become the foremost problem that propels to seek out for advanced approach. This concept initiated a need to search for more effective antimicrobial compounds from reliable sources. The Streptomyces is grouped under phylum Actinobacteria and are considered prolific producers of antibiotics, around 70% of presently available antibiotics are contributed by Streptomyces alone. In this study, Mangroves of the Mangalore Coast offered a unique source for screening Actinomyces group of microorganisms. We investigated on the four soil samples collected from Mangrove swamps of Mangalore, Karnataka, India. Based on their culture traits, the 18 distinct Actinomyces isolates were analyzed through a series of morphological and biochemical tests on starch casein nitrate (SCN) media. Culture biomasses were subjected for intracellular protein extraction through acetone precipitation method; the extracted proteins from each Actinomyces isolate were examined for antimicrobial activity against test organisms. The isolate ANTB-YKMU4 showed potential antimicrobial activity against significant number of test organisms; Bacillus cereus, Proteus vulgaris, Staphylococcus aureus, Salmonella typhimurium, and Pseudomonas aeruginosa. The isolate ANTB-YKMU4 through 16 s rRNA gene sequence analysis was identified as Streptomyces tauricus strain with GenBank accession no. MW785875.1. The S. tauricus further cultivated for efficient biomass growth on SCN media for subsequent protein extraction and purification by a series of Electrophoretic and chromatographic techniques. Thus, by intracellular extractions from S. tauricus resulted in the identification of peptide with a molecular weight of 266 Da that was characterized by LC-MS.

Phylogenetic relationships among Bradyrhizobium species nodulating groundnut (Arachis hypogea L.), jack bean (Canavalia ensiformis L.) and soybean (Glycine max Merr.) in Eswatini

This study assessed the genetic diversity and phylogenetic relationships of rhizobial isolates obtained from root nodules of groundnut, jack bean and soybean planted in different locations within Eswatini. Seventy-six rhizobial isolates were studied using ERIC-PCR (enterobacterial repetitive intergenic consensus) fingerprinting and PCR amplification of 16S rRNA, housekeeping genes (atpD, dnaK, glnll and rpoB) and symbiotic genes (nifH and nodC). The dendrogram generated from the ERIC-PCR banding patterns grouped the test rhizobial isolates into 16 major clusters (Cluster I–XVI), with three isolates, namely TUTAHeS60, TUTGMeS3 and TUTAHeS127, forming outgroups of Clusters IV, VI and IX, respectively. Furthermore, the 76 test isolates were grouped into 56 ERIC-PCR types at 70% similarity level. The phylogenetic analysis of the 16S rRNA gene and multilocus sequence analysis of four housekeeping (atpD, dnaK, glnII and rpoB) and two symbiotic (nifH and nodC) genes showed that all three legumes (groundnut, jack bean and soybean) were nodulated by bacterial symbionts belonging to the genus Bradyrhizobium, with some isolates exhibiting high divergence from the known reference type strains. The results also showed that B. arachidis, B. iriomotense and B. canariense were the closest type strains to the groundnut isolates, while B. pachyrhizi and B. elkanii were the closest relatives to the bacterial symbionts associated with the nodulation of both jack bean and soybean. This study is the first report to describe of the bacterial symbionts nodulating jack bean in African soils.