16S RNA Gene Research Articles

Genetic profiling of virulence genes among Pseudomonas Aeruginosa isolates recovered from diseased chickens

Pseudomonas aeruginosa (P. aeruginosa) is regarded as an opportunistic organism for bird species. Also is one can be mentioned as an example of an environment-associated infection that results in severe disease in poultry farms, Indeed, we detected the incidence of P. aeruginosa in chickens and also discovered the implicated virulence genes and antibiotic-resistant mechanism. Two hundred cases were collected from broiler and layer chicken organs (heart blood, heart, and lungs) that suffered from some respiratory manifestation and septicemia in addition to yolk sacs from one-day-old chicks, which were examined bacteriologically and Serologically. The studied isolates were tested against eight antimicrobial discs. Bacterial DNA was analyzed using polymerase chain reaction (PCR) against six virulence genes (lasL, lasB toxA, exoU, exoT, and oprl genes). Eighteen isolates out of 200 (9%) of P. aeruginosa were defined. Serologically the isolates were related to more serogroup (O1,O4,O6, O11 and O12) P. aeruginosa. PCR defined the existence of P. aeruginosa by detection of the 16SRNA gene. All isolates showed 100% multidrug resistance (MDR) to more than one antimicrobial disc (sulfamethoxazole, erythromycin, tetracycline, and ampicillin). Conversely, those isolates exhibited 100% sensitivity to ciprofloxacin, and four of them showed sensitivity to norfloxacin with a percentage of (22.2%). In addition to 15 isolates showed resistance of 83.3% percent to streptomycin and nalidixic acid. By PCR test, all examined P. aeruginosa strains carried four virulence genes (lasI, toxA, exoU, and oprl). However, only three strains carried lasB, and four carried the exoT gene. In conclusion, we confirmed the presence of different factors of virulence for P. aeruginosa and MDR to more than one antimicrobial drug. So, restricting Pseudomonas infection in poultry requires strict biosecurity measures to control and eradicate the infection by P. aeruginosa

Z-ligustilide alleviates atherosclerosis by reconstructing gut microbiota and sustaining gut barrier integrity through activation of cannabinoid receptor 2

BackgroundZ-Ligustilide (ZL) is an essential phthalide found in Ligusticum chuanxiong Hort, a commonly used traditional Chinese medicine for treating atherosclerosis (AS) clinically. ZL has been shown to be effective in treating AS. However, the underlying mechanism of ZL against AS and its potential targets remain elusive. PurposeThe purpose of this research was to assess the influence of ZL on AS and explore the role of the gut microbiome in mediating this effect. MethodsA well-established AS mouse model, apolipoprotein E deficient (ApoE-/-) mice was used to examine the effects of ZL on AS, inflammation, and the intestinal barrier. To analyze the changes in gut microbial community, we employed the 16S rRNA gene sequencing. Antibiotic cocktail and fecal microbiota transplantation (FMT) were employed to clarify the contribution of the gut microbiota to the anti-AS effects of ZL. The mechanism through which ZL provided protective effects on AS and the intestinal barrier was explored by untargeted metabolomics, as well as by validating the involvement of cannabinoid receptor 2 (CB2R) in mice and Caco-2 cells. ResultsOral administration of ZL inhibited the development of atherosclerotic lesions, improved plaque stability, inhibited the increase in serum and atherosclerotic inflammation, and improved intestinal barrier function. Fecal bacteria from ZL-treated mice induced similar beneficial effects on AS and the intestinal barrier. We used 16S RNA gene sequencing to reveal a significant increase in Rikenella abundance in both ZL-treated mice and ZL-FMT mice, which was associated with the beneficial effects of ZL. Further function prediction analysis of the gut microbiota and CB2R antagonist intervention experiment in mice and Caco-2 cells showed that the activation of CB2R resulted in the enhancement of the intestinal barrier by ZL. Furthermore, the analysis of metabolomic profiling revealed the enrichment of capsaicin upon ZL treatment, which induced the activation of CB2R in human colon epithelial cells. ConclusionOur study is the first to demonstrate that oral treatment with ZL has the potential to alleviate AS by reducing inflammation levels and enhancing the intestinal barrier function. This mechanism relies on the gut microbiota in a CB2R-dependent manner, suggesting promising strategies and ideas for managing AS. This study provides insights into a novel mechanism for treating AS with ZL.

Preparation and evaluation activity of silica nanoparticles against bacterial oral infections: in vitro study

Background: Oral infections are commonly encountered among populations and frequently result in chronic inflammatory conditions that impact the dental structures (e.g., caries), the gingival tissues surrounding the dental elements (e.g., gingivitis and endodontic lesions), as well as the supporting structures of the teeth (e.g., periodontitis). Objectives: The objective of this study is to ascertain the minimum inhibitory concentrations of silica nanoparticles in order to evaluate the antibacterial efficacy of these nanoparticles against oral pathogens. Materials and Methods: A total of 100 clinical samples were collected from individuals suffering from diverse oral infections. They were diagnosed based on the culture and microscopic characteristics, as well as the diagnosis with Vitek2 device for the purpose of diagnosis for the level of species. Molecular identification of Viridians Streptococci was performed using PCR to detect the 16sRNA gene. The study also involved the synthesis of silica nanoparticles (SiNPs) using the sol-gel technique. Characterization of the SiNPs was conducted through X-ray diffraction (XRD), transmission electron microscopy (TEM), and field emission scanning electron microscopy with energy-dispersive X-ray spectroscopy (FESEM-EDX). The minimum inhibitory concentration (MIC) of the SiNPs against viridans Streptococci was evaluated using a microdilution assay with the blue-resazurin staining method. The agar well diffusion technique was utilized to assess the antibacterial efficacy of biosynthesized silica nanoparticles against Viridans Streptococci in comparison to a standard antibiotic, utilizing the minimum inhibitory concentration (MIC) as a metric. Results: Fifty pathogenic bacterial strains were obtained from clinical specimens, with the genus Streptococcus comprising 27 of these isolates, which corresponds to 54% of the overall total, thereby constituting the highest proportion observed among all species. Molecular identification of Viridans Streptococci in this study, showed that 10/10(100%) isolates were PCR positive for 16sRNA gene has been applied to pathogenic viridians streptococcal only, which include S. mitis, S. oralis and S. sanguinis. Multidrug-resistant isolates showed significant resistance to various antibiotics, including Erythromycin, Cefotaxime, Cefepime, Ceftriaxone, and Penicillin. Clindamycin also showed resistance. Augmentin showed the highest antimicrobial activity, while Trimethoprim-sulfamethoxazole, Ampicillin, and Vancomycin showed commendable activity. The MIC for the synthesized silica nanoparticles against Viridans Streptococci was determined to be 3.13 mg/mL across all bacterial isolates. The study showed that the bio-synthesized silica nanoparticles had a higher inhibition than the standard antibiotic disc Vancomycin (VA) at a concentration of 3.13 mg/ml, as the average diameter of inhibition reached 26.2 mm, respectively. Conclusion: Silica nanoparticles demonstrated significant efficacy in combating Viridans Streptococci, which are implicated in the etiology of oral infections.

Si-Ni-San ameliorates cholestatic liver injury by favoring P. goldsteinii colonization

Ethnopharmacological relevanceCurrent treatment options for cholestatic liver diseases are limited, and addressing impaired intestinal barrier has emerged as a promising therapeutic approach. Si-Ni-San (SNS) is a Traditional Chinese Medicine (TCM) formula commonly utilized in the management of chronic liver diseases. Our previous studies have indicated that SNS effectively enhanced intestinal barrier function through the modulation of gut microbiota. Aim of the studyThis study aims to verify the therapeutic effects of SNS on cholestatic liver injury, focusing on elucidating the underlying mechanism involving the gut-liver axis. Materials and methodsThe 16s RNA gene sequencing, non-targeted metabolomics were used to investigate the effects of SNS on the gut microbiota dysbiosis. Fecal microbiota transplantation (FMT) was conducted to identify potential beneficial probiotics underlying the therapeutic effects of SNS. ResultsOur results demonstrated that SNS significantly ameliorated cholestatic liver injury induced by partial bile duct ligation (pBDL). Additionally, SNS effectively suppressed cholestasis-induced inflammation and barrier dysfunction in both the small intestine and colon. While SNS did not impact the intestinal FXR-FGF15-hepatic CYP7A1 axis, it notably improved gut microbiota dysbiosis and modulated the profile of microbial metabolites, including beneficial secondary bile acids and tryptophan derivatives. Furthermore, gut microbiota depletion experiments and FMT confirmed that the therapeutic benefits of SNS in cholestatic liver disease are dependent on gut microbiota modulation, particularly through the promotion of the growth of potential probiotic P. goldsteinii. Moreover, a synergistic improvement in cholestatic liver injury was observed with the co-administration of P. goldsteinii and SNS. ConclusionOur study underscores that SNS effectively alleviates cholestatic liver injury by addressing gut microbiota dysbiosis and enhancing intestinal barrier function, supporting its rational clinical utilization. Furthermore, we highlight P. goldsteinii as a promising probiotic candidate for the management of cholestatic liver diseases.

Phytoplasma Associated with White-backed Planthopper on Rice Plants in Sidrap Regency, South Sulawesi

South Sulawesi is one of the largest rice production centers in Indonesia. Several important diseases of rice plants, such as those caused by viruses and phytoplasmas, can be transmitted by insect vectors, especially leafhoppers and stem plant. Symptoms of diseases caused by viruses and phytoplasmas are quite diverse but visually similar and difficult to distinguish. This study aims to analyze the presence of phytoplasma associated with white-backed planthopper which are commonly found in rice plantations. The research method used is by conducting surveys and explorations of insect samples in six villages in Sidrap District. White-back planthoppers found on rice plantations showing symptoms of yellowing and stunted leaves were sampled for further analysis, including total DNA isolation of insects, standard PCR amplification for insect and Nested-PCR for phytoplasma identification, gene sequencing for both amplicons, and nucleotide analysis using BLAST method and Mega X program. The PCR with CO1 primer successfully amplified a 700 bp amplicon from insects, whereas nested-PCR using fP1/rP7 primers followed by m23SR/R16F2n amplified phytoplasma supposedly around 1800 bp and 1250 bp of 16S RNA gene, respectively. The DNA sequencing analysis results indicate that the insect samples were identified as 83% Sogatella vibix species based on homology percentage analysis using BLAST and Mega X Program. As for the phytoplasma, it leans more towards the 16SrI group or Candidatus phytoplasma asteris (Aster yellows phytoplasma) with a homology percentage of 99%.

The effect of different sweeteners on the oral microbiome: a randomized clinical exploratory pilot study

ABSTRACT Introduction The aim of the study was to evaluate the modulating effects of five commonly used sweetener (glucose, inulin, isomaltulose, tagatose, trehalose) containing mouth rinses on the oral microbiome. Methods A single-centre, double-blind, parallel randomized clinical trial was performed with healthy, 18–55-year-old volunteers (N = 65), who rinsed thrice-daily for two weeks with a 10% solution of one of the allocated sweeteners. Microbiota composition of supragingival dental plaque and the tongue dorsum coating was analysed by 16S RNA gene amplicon sequencing of the V4 hypervariable region (Illumina MiSeq). As secondary outcomes, dental plaque red fluorescence and salivary pH were measured. Results Dental plaque microbiota changed significantly for two groups: inulin (F = 2.0239, p = 0.0006 PERMANOVA, Aitchison distance) and isomaltulose (F = 0.67, p = 0.0305). For the tongue microbiota, significant changes were observed for isomaltulose (F = 0.8382, p = 0.0452) and trehalose (F = 1.0119, p = 0.0098). In plaque, 13 species changed significantly for the inulin group, while for tongue coating, three species changed for the trehalose group (ALDEx2, p < 0.1). No significant changes were observed for the secondary outcomes. Conclusion The effects on the oral microbiota were sweetener dependant with the most pronounced effect on plaque microbiota. Inulin exhibited the strongest microbial modulating potential of the sweeteners tested. Further full-scale clinical studies are required.

Comprehensive Analysis of Gut Microbiota Composition and Functional Metabolism in Children with Autism Spectrum Disorder and Neurotypical Children: Implications for Sex-Based Differences and Metabolic Dysregulation.

This study aimed to investigate the gut microbiota composition in children with autism spectrum disorder (ASD) compared to neurotypical (NT) children, with a focus on identifying potential differences in gut bacteria between these groups. The microbiota was analyzed through the massive sequencing of region V3-V4 of the 16S RNA gene, utilizing DNA extracted from stool samples of participants. Our findings revealed no significant differences in the dominant bacterial phyla (Firmicutes, Bacteroidota, Actinobacteria, Proteobacteria, Verrucomicrobiota) between the ASD and NT groups. However, at the genus level, notable disparities were observed in the abundance of Blautia, Prevotella, Clostridium XI, and Clostridium XVIII, all of which have been previously associated with ASD. Furthermore, a sex-based analysis unveiled additional discrepancies in gut microbiota composition. Specifically, three genera (Megamonas, Oscilibacter, Acidaminococcus) exhibited variations between male and female groups in both ASD and NT cohorts. Particularly noteworthy was the exclusive presence of Megamonas in females with ASD. Analysis of predicted metabolic pathways suggested an enrichment of pathways related to amine and polyamine degradation, as well as amino acid degradation in the ASD group. Conversely, pathways implicated in carbohydrate biosynthesis, degradation, and fermentation were found to be underrepresented. Despite the limitations of our study, including a relatively small sample size (30 ASD and 31 NT children) and the utilization of predicted metabolic pathways derived from 16S RNA gene analysis rather than metagenome sequencing, our findings contribute to the growing body of evidence suggesting a potential association between gut microbiota composition and ASD. Future research endeavors should focus on validating these findings with larger sample sizes and exploring the functional significance of these microbial differences in ASD. Additionally, there is a critical need for further investigations to elucidate sex differences in gut microbiota composition and their potential implications for ASD pathology and treatment.

Gut microbiota response to consumption of milks fermented with specific strains of Lactococcus lactis with hypocholesterolemic effect

The alteration of structure and function of gut microbiota (dysbiosis) appears to be a major factor associated with metabolic disorders such as dyslipidemia and subsequent development of cardiovascular diseases. However, the consumption of fermented milks is a promising strategy to enhance health and restore the function of gut microbiota; specifically, in individuals with intestinal dysbiosis and hypercholesterolemia. Therefore, the aim of the present study was to evaluate the potential association between gut microbiota and the hypocholesterolemic effect of fermented milks with Lactococcus lactis NRRL B-571 (FM-571), NRRL B-572 (FM-572) and NRRL B-600 (FM-600) in Sprague–Dawley rats. Fermented milks were administered to hypercholesterolemic Sprague–Dawley rats during seven weeks. At the end of the experimental period, fecal and colonic microbiota were characterized using 16S RNA gene sequencing. Also, the short chain fatty acids (SCFAs) content was quantified in feces. Results showed that a high-cholesterol diet (HCD) altered the bacterial community in both fecal and mucosal samples. The consumption of fermented milks, specifically FM-572 promoted changes in the structure (beta diversity) in fecal, but not in mucosal microbiota. The levels of SCFAs in feces were improved after fermented milks consumption. From all SCFAs, butyrate was negatively correlated with total cholesterol, LDL-C (p < 0.05) and positively correlated with HDL-C (p < 0.05). Furthermore, Ruminococcaceae, Lactobacillaceae, Lachnospiraceae and Oscillospiraceae families, were negatively associated with total cholesterol, LDL-C (p < 0.05) and positively associated with HDL-C (p < 0.05). The abundance of these families was increased in groups treated with fermented milks, particularly with FM-572 (p < 0.05). Thus, the in vivo hypocholesterolemic effect after the consumption of milks fermented with Lactococcus lactis strains may be related with the modulation of fecal microbiota associated with the increase of butyrate-producing bacteria. Furthermore, these associations may suggest that butyrate may influence the cholesterol metabolism, resulting in the decreasing cholesterol levels.Graphical

Isolation and Molecular Detection of Bacteria Causing Omphalitis in Poultry with Look on Antibiotic and Disinfectant Resistance

Antimicrobial resistance is an international concern and creates critical health issues for both humans and animals. This research aimed to ascertain the prevalence of isolates, antibiotic, and disinfectant resistance patterns from omphalitis suspected chicks in Dinajpur, Bangladesh. A total of 24 yolk swab samples were collected from different hatcheries for microbiological analysis and antibiotic sensitivity tests. The PCR employing 16s and 23s RNA genes was conducted to detect Escherichia coli and invA genes were used to detect Salmonella spp. and 23S rRNA genes were applied for Staphylococcus spp. A total of 35 isolates were identified where 14 (40%) E.coli, 10 (28.58%) Salmonella spp., and 11 (31.42%) Staphylococcus spp. from day 1-8, respectively. The largest amount of bacteria on day 5, including day 7 (20%), followed by days 3, 4, and 6, including 6 (17.14%) observed, respectively. The PCR band of E. coli was detected at 232 bp, Salmonella spp. 284 bp and Staphylococcus spp. 1267 bp respectively. E. coli was highly resistant to Amoxicillin (100%), followed by Tetracycline (83.33%), whereas highly sensitive to cefotaxime (100%), Gentamicin and Co-trimoxazole (83.33%). Salmonella spp. indicates high susceptibility to Cefotaxime, Co-trimoxazole, and Ceftazidime (83.33%), followed by Gentamicin (66.67%) respectively, whereas Staphylococcus spp. was found to be highly resistant to Methicillin (100%) and Ampicillin (100%) followed by Gentamicin and Tetracycline (83.33%) respectively. The MAR index calculation of isolated E. coli, Salmonella spp., and Staphylococcus spp. from different sources of poultry hatcheries was measured at 0.77, 0.79, and 0.77, which affect the newly hatched chicks in poultry industries. Therefore, an urgent surveillance program is needed to fight antimicrobial resistance in poultry production sectors in Bangladesh.

Impact of temperature stress on Pyropia yezoensis and its inhabitant microbiota to promote aquaculture

The diverse inhabitant microbiota of Pyropia yezoensis can establish both beneficial and harmful interactions that effect community structure. It is complex to understand the seaweed microbial diversity and their ecological and functional regulations which are affected by numerous environmental factors. In this study, temperature stress was focused to understand the metagenomics of P. yezoensis microbiota, its functional annotation and the metabolites regulation of P. yezoensis. The samples of P. yezoensis from yellow sea of China were divided into two groups i.e low temperature 5°C (LT) and High temperature 25°C (HT). The genes and functional level analysis were followed by using metagenomic sequencing analysis and sequencing of 16sRNA gene. The Pyropia yezoensis samples were also analyzed through LCMS for metabolites regulation due to effects of microbiota and temperature stress. According to taxonomic classification analysis, Proteobacteria, Bacteroidetes, and Firmicutes were predominant in both samples with over-representation of these species in high temperature stress samples. A diverse relationship between the bacterial communities residing in the LT and HT samples was explored through discriminant analysis. The functional prediction of bacterial communities from KEGG analysis revealed a notable increase in HT predicted genes associated to amino acid metabolism, carbohydrate metabolism, energy metabolism, co-factors and vitamins metabolism, membrane transport, and nucleotide metabolism. The provoked chemical signaling and transportation response from the bacterial community, leading to activation of metabolic genes to utilize the available substrates of seaweed. The LCMS illustrated that the primary metabolites of Pyropia yezoensis were down regulated due to effect of high temperature which indicates a negative effect on the growth and health of Pyropia, while the secondary metabolites were up-regulated showing the defensive mechanism against unbearable stress. These up and down regulated metabolites also activated their respective pathways, suggesting the adoptive mechanism of P. yezoensis in response of high temperature.

Broiler Chicken Cecal Microbiome and Poultry Farming Productivity: A Meta-Analysis.

The cecal microbial community plays an important role in chicken growth and development via effective feed conversion and essential metabolite production. The aim of this study was to define the microbial community's variants in chickens' ceca and to explore the most significant association between the microbiome compositions and poultry farming productivity. The meta-analysis included original data from 8 control broiler chicken groups fed with a standard basic diet and 32 experimental groups supplemented with various feed additives. Standard Illumina 16S-RNA gene sequencing technology was used to characterize the chicken cecal microbiome. Zootechnical data sets integrated with the European Production Effectiveness Factor (EPEF) were collected. Analysis of the bacterial taxa abundance and co-occurrence in chicken cecal microbiomes revealed two alternative patterns: Bacteroidota-dominated with decreased alpha biodiversity; and Bacillota-enriched, which included the Actinomycetota, Cyanobacteriota and Thermodesulfobacteriota phyla members, with increased biodiversity indices. Bacillota-enriched microbiome groups showed elevated total feed intake (especially due to the starter feed intake) and final body weight, and high EPEF values, while Bacteroidota-dominated microbiomes were negatively associated with poultry farming productivity. The meta-analysis results lay the basis for the development of chicken growth-promoting feed supplementations, aimed at the stimulation of beneficial and inhibition of harmful bacterial patterns, where relevant metagenomic data can be a tool for their control and selection.

Approach towards sustainable leather: Characterization and effective industrial application of proteases from Bacillus sps. for ecofriendly dehairing of leather hide

Tanneries are one of the most polluted industries known for production of massive amount of solid and liquid wastes without proper management and disposal. In this project we demonstrated the ecofriendly single step dehairing of leather hides with minimum pollution load. In this study, Bacillus species (Bacillus paralicheniformis strain BL.HK, Bacillus cereus strain BS.P) capable of producing proteases was successfully isolated by employing the new optimized selective media named M9-PEA as confirmed by 16sRNA genes sequencing. Sequence of 1493 bp long 16S rRNA genes of Bacillus paralicheniformis strain BL.HK and Bacillus cereus strain BS. P was submitted to GenBank under the accession number OP612692.1, OP612721.1 respectively The Bacillus paralicheniformis strain BL.HK, Bacillus cereus strain BS.P produced extracellur proteases of 28 and 37 KDa as resolved by SDS-PAGE respectively. The enzymes showed temperature optima at 50 °C and 55 °C and pH optima at 8.5, 9.5 respectively. The Proteases of Bacillus paralicheniformis strain BL.HK, Bacillus cereus strain BS.P were employed for dehairing of animal hides. The process resulted in significant removal of interfibriller substances without damage to collagen layer after one hour treatment, which was confirmed by histology, scanning electron microscopy. The quantification of various skin constituents (collagen, uronic acid, hexosamines, and GAGs) and pollution load parameters revealed that enzymatic treatment are more reliable. The results of skin application trials at industrial level with complete elimination of chemicals remark the biotechnological potential of these proteases for ecofriendly dehairing of animal hides without affecting the quality of the leathers produced.

Detection of Bacteroides fragilis LuxR gene, involved in quorum sensing, among colitis patients in Mosul, Iraq

Bacteroides fragilis is the most anaerobic bacteria that infect humans, particularly in the abdominal cavity. Its pathogenesis is linked to numerous virulence factors. Understanding these factors and exploring alternative options for the use of antibiotics in the treatment of this bacterium, molecular techniques offer several advantages over traditional culture techniques because they are easier and more specific. The present study aimed to use specific primers for the 16sRNA and LuxR genes to identify B. fragilis. Genetic identification of the B. fragilis isolates was performed using the 16SrRNA gene, and the obtained sequences were submitted to National Centre for Biotechnology Information (NCBI) with accession numbers (OQ448827, OQ448828). Each strain was assigned a unique strain name, AS. AWB94 and AS. AWB79. From the total of all samples, it was found that the growth of various types of bacteria constituted ( 76%), and the samples that did not have growth formed (24%). It was noted that Bacteroidetes constituted only two isolates (2.7%), and these two isolates possessed the gene for quorum sensing (luxR gene), while the results confirmed that they do not possess the sialidase (nanH) enzyme gene. Both isolates possessed the quorum sensing gene (LuxR) out of one hundred samples. This suggests that the isolates have a quorum-sensing mechanism responsible for cell-to-cell communication, multidrug resistance, and biofilm formation.

Degradation of SDS by psychrotolerant Staphylococcus saprophyticus and Bacillus pumilus isolated from Southern Ocean water samples.

Bioremediation of surfactants in water bodies holds significant ecological importance as they are contaminants of emerging concern posing substantial threats to the aquatic environment. Microbes exhibiting special ability in terms of bioremediation of contaminants have always been reported to thrive in extraordinary environmental conditions that can be extreme in terms of temperature, lack of nutrients, and salinity. Therefore, in the present investigation, a total of 46 bacterial isolates were isolated from the Indian sector of the Southern Ocean and screened for degradation of sodium dodecyl sulphate (SDS). Further, two Gram-positive psychrotolerant bacterial strains, ASOI-01 and ASOI-02 were identified with significant SDS degradation potential. These isolates were further studied for growth optimization under different environmental conditions. The strains were characterized as Staphylococcus saprophyticus and Bacillus pumilus based on morphological, biochemical, and molecular (16S RNA gene) characteristics. The study reports 88.9% and 93.4% degradation of SDS at a concentration of 100 mgL-1, at 20°C, and pH 7 by S. saprophyticus ASOI-01 and B. pumilus ASOI-02, respectively. The experiments were also conducted in wastewater samples where a slight reduction in degradation efficiency was observed with strains ASOI-01 and ASOI-02 exhibiting 76.83 and 64.93% degradation of SDS respectively. This study infers that these bacteria can be used for the bioremediation of anionic surfactants from water bodies and establishes the potential of extremophilic microbes for the utilization of sustainable wastewater management.

Molecular detection of ‘Candidatus phytoplasma aurantifolia’ associated with virescence and phyllody of Zinnia peruviana: A new record for India

AbstractZinnia peruviana (Asteraceae) is an annual flowering plant cultivated in various gardens of Mysore, the south of Karnataka state, India. During 2021, phytoplasma‐like symptoms such as virescence and phyllody were observed on Zinnia in Mysore local gardens. A total of 10 symptomatic and five asymptomatic samples were collected, and the DNA was amplified by PCR using primers specific to 16S RNA and secA genes. The nucleotide sequence analysis showed that the 16S RNA and SecA gene sequences were most similar to those of ‘Ca. P. aurantifolia’, with identities greater than 99%. The phytoplasma sequence from this study shared a common clade with ‘Ca. P. aurantifolia’ when phylogenetic analysis was done. Similarly, the reference sequences for the 16S rRNA and SecA region confirmed the identity of the phytoplasma associated with the leaves of Zinnia. This is the new host record for ‘Ca. P. aurantifolia’ (16SrII‐D) phytoplasma associated with Z. peruviana from India.

Asynchronous application of modified biochar and exogenous fungus Scedosporium sp. ZYY for enhanced degradation of oil-contaminated intertidal mudflat sediment.

Intertidal mudflats are susceptible to oil pollution due to their proximity to discharges from industries, accidental spills from marine shipping activities, oil drilling, pipeline seepages, and river outflows. The experimental study was divided into two periods. In the first period, microcosm trials were carried out to examine the effect of chemically modified biochar on biological hydrocarbon removal from sediments. The modified biochar's surface area increased from 2.544 to 25.378 m2/g, followed by a corresponding increase in the hydrogen-carbon and oxygen-carbon ratio, indicating improved stability and polarity. In the second period, the effect of exogenous fungus - Scedoporium sp. ZYY on the bacterial community structure was examined in relation to total petroleum hydrocarbon (TPH) removal. The maximum TPH removal efficiency of 82.4% was achieved in treatments with the modified biochar, followed by a corresponding increase in Fluorescein diacetate hydrolysis activity. Furthermore, high-throughput 16S RNA gene sequencing employed to identify changes in the bacterial community of the original sediment and treatments before and after fungal inoculation revealed Proteobacteria as the dominant phylum. In addition, it was observed that Scedoporium sp. ZYY promoted the proliferation of specific TPH-degraders, particularly, Hyphomonas adhaerens which accounted for 77% of the total degrading populations in treatments where TPH removal was highest. Findings in this study provide valuable insights into the effect of modified biochar and the fundamental role of exogenous fungus towards the effective degradation of oil-contaminated intertidal mudflat sediments.

Geographic distribution of bacterial communities of inland waters in China

Microorganisms are integral to freshwater ecological functions and, reciprocally, their activity and diversity are shaped by the ecosystem state. Yet, the diversity of bacterial community and its driving factors at a large scale remain elusive. To bridge this knowledge gap, we delved into an analysis of 16S RNA gene sequences extracted from 929 water samples across China. Our analyses revealed that inland water bacterial communities showed a weak latitudinal diversity gradient. We found 530 bacterial genera with high relative abundance of hgcI clade. Among them, 29 core bacterial genera were identified, that is strongly linked to mean annual temperature and nutrient loadings. We also detected a non-linear response of bacterial network complexity to the increasing of human pressure. Mantel analysis suggested that MAT, HPI and P loading were the major factors driving bacterial communities in inland waters. The map of taxa abundance showed that the abundant CL500-29 marine group in eastern and southern China indicated high eutrophication risk. Our findings enhance our understanding of the diversity and large-scale biogeographic pattern of bacterial communities of inland waters and have important implications for microbial ecology.

Identification of environmental Actinobacteria in buildings by means of chemotaxonomy, 16S rRNA sequencing, and MALDI-TOF MS.

The manuscript addresses the challenges in identifying environmental bacteria using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) Biotyper-based protein profiling. The matter of the studies-actinobacterial strains-has been isolated mostly from building materials that originated from a confirmed moisture-damaged situation. Polyphasic taxonomy, 16S RNA gene sequencing, and MALDI-TOF mass spectrometry were applied for identification purposes. In this experimental paper, a few important facts are highlighted. First, Actinobacteria are abundant in the natural as well as built environment, and their identification on the species and genus levels is difficult and time-consuming. Second, MALDI-TOF MS is an effective tool for identifying bacterial environmental strains, and in parallel, continuous enrichment of the proteomics mass spectral databases is necessary for proper identification. Third, the chemical approach aids in the taxonomical inquiry of Actinobacteria environmental strains.

First Report of Foliar Nematode (Aphelenchoides pseudobesseyi) on Soybean in Colombia

Soybean (Glycine max L.) is produced in over 70,000 ha in the Altillanura Region, eastern Colombia (Agronet 2023). From 2018 to 2020, foliar symptoms like green stem and foliar retention of soybean, which in Brazil can cause up to 100% soybean yield losses (Meyer et al. 2017), were observed in soybean fields in Colombia. During 2020, samples from symptomatic plants in reproductive stages (R1-R8) were collected from different commercial soybean fields in the Altillanura Region. Over 200 samples were processed, using an incubation method described in Coyne et al. (2014). Nematodes were recovered from photosynthetic leaf tissues and enlarged nodes/buds with population densities ranging from 13 to 132 and 36 to 936 nematodes/10g, respectively. Adult females were morphologically and molecularly characterized as Aphelenchoides pseudobesseyi (Oliveira et al. 2019; Subbotin et al. 2020). Female body length (n = 20) ranged from 653.3 to 806.3 μm (mean = 723 μm ± 52.7), stylet length from 11.0 to 12.3 μm (11.8 μm ± 0.3), body diameter from 14.8 to 17.9 μm (16.3 μm ± 1.1), post-uterine sac length from 38.7 to 51.9 μm (44.6 μm ± 5.1), vulva to anus from 145.5 to 223.2 μm (172.2 μm ± 22.4), and 26% of the vulva-anus distance. Genomic DNA was extracted (QIAGEN DNeasy® Blood &amp; Tissue kit) from a pool of nematodes. The D2A/D3B (Tenente et al. 2004) primers were used to amplify and sequence the D2/D3 expansion region of the 28S rRNA gene. PCR product (~759 bp) was purified, sequenced, deposited in GenBank (OQ930285), and compared to previously deposited sequences (e.g., KX356756, KY510840, KY510839, KY510841, KT692694, KY510842, MH187565) by means of the BLAST algorithm. Similarly, 988F and 18SR-Burs (De Jesus et al. 2016) primers were used to amplify and sequence the near full-length 18S RNA gene (SSU). PCR product was purified, sequenced, deposited in GenBank (OQ954344), and compared to previously deposited sequences (e.g., KT454962, KT943534, KT943535, KY510835, KY510836, KY510837, KY510838, MH187565). Phylogenetic Bayesian analysis (Ronquist et al. 2012) of the of the D2/D3 and 18S regions placed this nematode from Colombia in the A. pseudobesseyi clade (PP = 100). To fulfill a modified Koch’s postulates, the A. pseudobesseyi population described above was used in a greenhouse assay. In total, 120 soybean plants (cv. Flor Blanca) were infected with 200 A. pseudobesseyi (females + males)/plant. Briefly, at cotyledon stage (VC), 50 µl aliquot containing 50 A. pseudobesseyi was delivered onto each cotyledon and unifoliolate leaves (200 nematodes/plant). Sterile water was delivered to 80 plants which served as control. Plants were kept in the greenhouse at approximately 25°C and covered with clear plastic bag for 72 h to maintain over 90% relative humidity. After 15, 30, 45, and 60 days, soybean plants (n = 20) were processed, A. pseudobesseyi quantified, and the average reproduction factor (final population/initial population) was 0.1, 2.9, 14.0, and 1.8, respectively. Infected plants showed symptoms of blistering leaves with malformation (midrib vein twist), and A. pseudobesseyi was not observed in control plants. To our knowledge, this is the first report of A. pseudobesseyi parasitizing soybean buds and leaves in Colombia. Soybean is an important commodity for the Altillanura Region, and it is important to monitor the risk posed by this nematode. Furthermore, a better understanding of the nematode-host interaction and epidemiology in Colombia soybean producing regions is needed.

Characteristics of Groundwater Microbial Community Composition and Environmental Response in the Yimuquan Aquifer, North China Plain

To explore the intricate interrelationship between groundwater microbial communities and hydrochemical characteristics in the Mancheng District, Baoding City, samples from karst groundwater and porous groundwater were collected. Hydrochemical analysis and the 16s RNA gene V4-V5 region sequencing method were used to detail the water environmental characteristics and microbial community distribution pattern in the study area. The hydrochemical results reveal notable differences in major ion contents and other hydrochemical indices between karst water and porous water. Microbial community analysis demonstrates that Proteobacteria, Actinobacteria, and Firmicutes are the dominant taxa in both types of water bodies, albeit with significant variations in their proportions across distinct water bodies. The observed disparities in microbial communities between karst water and porous water underscore the influence of environmental factors such as ion concentration and pH on microbial distribution. Redundancy Analysis (RDA) indicates notable associations between microbial community composition and environmental factors in both types of groundwater environments. Studying the distribution pattern of microbial communities and the connection with environmental factors in two types of groundwater lays a crucial foundation for interpreting the functional roles of microbes in groundwater ecosystems.