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Foods (Basel, Switzerland) May 2024The composition and continuous succession of natural microbial communities during grape growth play important roles in grape health and flavor quality as well as in...
The composition and continuous succession of natural microbial communities during grape growth play important roles in grape health and flavor quality as well as in characterizing the regional wine terroir. This study explored the diversity and dynamics of fruit epidermal microbes at each growth and developmental stage of Ecolly grapes under an extremely simplified eco-cultivation model, analyzed microbial interactions and associations of weather parameters to specific communities, and emphasized metabolic functional characteristics of microecology. The results indicated that the natural microbial community changed significantly during the grape growth phase. The dominant fungal genera mainly included , , , , , , and , and the dominant bacterial genera mainly contained , , , , , , and . In summary, filamentous fungi gradually shifted to basidiomycetous yeasts along with fruit ripening, with a decline in the number of Gram-negative bacteria and a relative increase in Gram-positive bacteria. The community assembly process reflects the fact that microbial ecology may be influenced by a variety of factors, but the fungal community was more stable, and the bacterial community fluctuated more from year to year, which may reflect their response to weather conditions over the years. Overall, our study helps to comprehensively profile the ecological characteristics of the grape microbial system, highlights the natural ecological viticulture concept, and promotes the sustainable development of the grape and wine industry.
PubMed: 38790880
DOI: 10.3390/foods13101580 -
PeerJ 2024Plastic waste is a global environmental issue that impacts the well-being of humans, animals, plants, and microorganisms. Microplastic contamination has been previously...
BACKGROUND
Plastic waste is a global environmental issue that impacts the well-being of humans, animals, plants, and microorganisms. Microplastic contamination has been previously reported at Kung Wiman Beach, located in Chanthaburi province along with the Eastern Gulf of Thailand. Our research aimed to study the microbial population of the sand and plastisphere and isolate microorganisms with potential plastic degradation activity.
METHODS
Plastic and sand samples were collected from Kung Wiman Beach for microbial isolation on agar plates. The plastic samples were identified by Fourier-transform infrared spectroscopy. Plastic degradation properties were evaluated by observing the halo zone on mineral salts medium (MSM) supplemented with emulsified plastics, including polystyrene (PS), polylactic acid (PLA), polyvinyl chloride (PVC), and bis (2-hydroxyethyl) terephthalate (BHET). Bacteria and fungi were identified by analyzing nucleotide sequence analysis of the 16S rRNA and internal transcribed spacer (ITS) regions, respectively. 16S and ITS microbiomes analysis was conducted on the total DNA extracted from each sample to assess the microbial communities.
RESULTS
Of 16 plastic samples, five were identified as polypropylene (PP), four as polystyrene (PS), four as polyethylene terephthalate (PET), two as high-density polyethylene (HDPE), and one sample remained unidentified. Only 27 bacterial and 38 fungal isolates were found to have the ability to degrade PLA or BHET on MSM agar. However, none showed degradation capabilities for PS or PVC on MSM agar. Notably, sp. PP5 showed the highest hydrolysis capacity of 1.64 ± 0.12. The 16S rRNA analysis revealed 13 bacterial genera, with seven showing plastic degradation abilities: , , , , , , and . This study reports, for the first time of the BHET-degrading properties of the genera and . Additionally, The ITS analysis identified nine fungal genera, five of which demonstrated plastic degradation abilities: , , , , and . Microbial community composition analysis and linear discriminant analysis effect size revealed certain dominant microbial groups in the plastic and sand samples that were absent under culture-dependent conditions. Furthermore, 16S and ITS amplicon microbiome analysis revealed microbial groups were significantly different in the plastic and sand samples collected.
CONCLUSIONS
We reported on the microbial communities found on the plastisphere at Kung Wiman Beach and isolated and identified microbes with the capacity to degrade PLA and BHET.
Topics: Actinomycetales; Agar; Bacteria; Microbiota; Plastics; Polyesters; Polystyrenes; RNA, Ribosomal, 16S; Sand
PubMed: 38590706
DOI: 10.7717/peerj.17165 -
Microorganisms Feb 2024Soil salinization is negatively affecting soils globally, and the spread of this problem is of great concern due to the loss of functions and benefits offered by the...
Soil salinization is negatively affecting soils globally, and the spread of this problem is of great concern due to the loss of functions and benefits offered by the soil resource. In the present study, we explored the diversity of halophilic and halotolerant microorganisms in the arable fraction of a sodic-saline soil without agricultural practices and two soils with agricultural practices (one sodic and one saline) near the geothermal area "Los Negritos" in Villamar, Michoacán state. This was achieved through their isolation and molecular identification, as well as the characterization of their potential for the production of metabolites and enzymes of biotechnological interest under saline conditions. Using culture-dependent techniques, 62 halotolerant and moderately halophilic strains belonging to the genera , , , , , , , , , , , , , , , , and were isolated. The different strains synthesized hydrolytic enzymes under 15% (/) of salts, as well as metabolites with plant-growth-promoting (PGP) characteristics, such as indole acetic acid (IAA), under saline conditions. Furthermore, the production of biopolymers was detected among the strains; members of , , , and showed extracellular polymeric substance (EPS) production, and the strain sp. LNSP3E3-1.2 produced polyhydroxybutyrate (PHB) under 10% (/) of total salts.
PubMed: 38543532
DOI: 10.3390/microorganisms12030482 -
International Journal of Systematic and... Mar 2024A novel bacterial strain, APC 4016, was previously isolated from the skin of a snub-nosed spiny eel, , from a depth of 1000 m in the northern Atlantic Ocean. Cells...
A novel bacterial strain, APC 4016, was previously isolated from the skin of a snub-nosed spiny eel, , from a depth of 1000 m in the northern Atlantic Ocean. Cells were aerobic, cocci, motile, Gram-positive to Gram-variable staining, and gave rise to orange-pigmented colonies. Growth occurred at 4-40 °C (optimum, 25-28 °C), pH 5.5-12 (optimum, pH 7-7.5), and 0-12 % (w/v) NaCl (optimum, 1 %). 16S rRNA gene phylogenetic analysis confirmed that strain APC 4016 belonged to the genus and was most closely related to IFO 12536 (98.98 % 16S similarity). However, digital DNA-DNA hybridization and average nucleotide identity values between these two strains were low, at 20.1 and 83.8 %, respectively. Major (>10 %) cellular fatty acids of strain APC 4016 were iso-C, anteiso-C and C-ω-Alc. The predominant respiratory quinones were menaquinones 5, 6, 7 and 8. The major cellular polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine, and three unknown lipids were also present. The draft genome sequence is 3.6 Mb with a G+C content of 45.25 mol%. This strain was previously shown to have antimicrobial activity and to encode bacteriocin and secondary metabolite biosynthetic gene clusters. Based on the phylogenetic analysis and its distinct phenotypic characteristics, strain APC 4016 is deemed to represent a novel species of the genus , and for which the name sp. nov. is proposed. The type strain of this species is APC 4016 (=DSM 115753=NCIMB 15463).
Topics: Animals; Fatty Acids; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Base Composition; Bacterial Typing Techniques; DNA, Bacterial; Planococcus Bacteria; Eels
PubMed: 38512752
DOI: 10.1099/ijsem.0.006298 -
Microbiome Feb 2024Microbial functioning on marine plastic surfaces has been poorly documented, especially within cold climates where temperature likely impacts microbial activity and the...
Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics.
BACKGROUND
Microbial functioning on marine plastic surfaces has been poorly documented, especially within cold climates where temperature likely impacts microbial activity and the presence of hydrocarbonoclastic microorganisms. To date, only two studies have used metaproteomics to unravel microbial genotype-phenotype linkages in the marine 'plastisphere', and these have revealed the dominance of photosynthetic microorganisms within warm climates. Advancing the functional representation of the marine plastisphere is vital for the development of specific databases cataloging the functional diversity of the associated microorganisms and their peptide and protein sequences, to fuel biotechnological discoveries. Here, we provide a comprehensive assessment for plastisphere metaproteomics, using multi-omics and data mining on thin plastic biofilms to provide unique insights into plastisphere metabolism. Our robust experimental design assessed DNA/protein co-extraction and cell lysis strategies, proteomics workflows, and diverse protein search databases, to resolve the active plastisphere taxa and their expressed functions from an understudied cold environment.
RESULTS
For the first time, we demonstrate the predominance and activity of hydrocarbonoclastic genera (Psychrobacter, Flavobacterium, Pseudomonas) within a primarily heterotrophic plastisphere. Correspondingly, oxidative phosphorylation, the citrate cycle, and carbohydrate metabolism were the dominant pathways expressed. Quorum sensing and toxin-associated proteins of Streptomyces were indicative of inter-community interactions. Stress response proteins expressed by Psychrobacter, Planococcus, and Pseudoalteromonas and proteins mediating xenobiotics degradation in Psychrobacter and Pseudoalteromonas suggested phenotypic adaptations to the toxic chemical microenvironment of the plastisphere. Interestingly, a targeted search strategy identified plastic biodegradation enzymes, including polyamidase, hydrolase, and depolymerase, expressed by rare taxa. The expression of virulence factors and mechanisms of antimicrobial resistance suggested pathogenic genera were active, despite representing a minor component of the plastisphere community.
CONCLUSION
Our study addresses a critical gap in understanding the functioning of the marine plastisphere, contributing new insights into the function and ecology of an emerging and important microbial niche. Our comprehensive multi-omics and comparative metaproteomics experimental design enhances biological interpretations to provide new perspectives on microorganisms of potential biotechnological significance beyond biodegradation and to improve the assessment of the risks associated with microorganisms colonizing marine plastic pollution. Video Abstract.
Topics: Plastics; Bacteria; Multiomics; Biofilms; Biodegradation, Environmental; Microbiota
PubMed: 38389111
DOI: 10.1186/s40168-024-01751-x -
The Journal of General and Applied... May 2024Proteolytic enzymes stand out as the most widely employed category utilized in manufacturing industry. A new protease was separated from Planococcus sp.11815 strain and...
Proteolytic enzymes stand out as the most widely employed category utilized in manufacturing industry. A new protease was separated from Planococcus sp.11815 strain and named as nprS-15615 in this research. The gene of this protease has not been reported, and its enzymatic properties have been studied for the first time. To enhance enzyme production, the Planococcus sp. protease gene was expressed in Bacillus licheniformis 2709. The expression level of nprS-15615 was observed under the control of regulatory elements P. nprS-15615 protease activity reached 1186.24±32.87 U/mL after 48 hours of cultivation in shake flasks which was nearly four times the output of the original bacteria (291.38±25.73U/mL). The optimum temperature and pH of the recombinant protease were 30 ℃ and 8.0, respectively.The enzyme exhibited the highest capacity for hydrolyzing casein and demonstrated resilience towards a NaCl concentration of 10.0% (wt/v). Furthermore, in the presence of 0.5% surfactants, the recombinant protease activity can maintain above 75%, and with the existence of 0.5% liquid detergents, there was basically no loss of enzyme activity which indicated that nprS-15615 had good compatibility with surfactants and liquid detergents. In addition, npS-15615 performed well in the washing experiment, and the washing effect at 20 ℃ can be significantly improved by adding crude enzyme solution in the washing process.
Topics: Detergents; Hydrogen-Ion Concentration; Temperature; Metalloproteases; Recombinant Proteins; Bacterial Proteins; Bacillus licheniformis; Enzyme Stability; Planococcus Bacteria; Caseins; Gene Expression; Cloning, Molecular; Surface-Active Agents; Hydrolysis
PubMed: 37880082
DOI: 10.2323/jgam.2023.09.002 -
PloS One 2023The exponential increase in the prevalence of multidrug resistant bacteria has resulted in limiting surgical treatment options globally, potentially causing...
The exponential increase in the prevalence of multidrug resistant bacteria has resulted in limiting surgical treatment options globally, potentially causing biofilm-related complications, implant failure, and severe consequences. This study aims to isolate and characterize bacteria from post-surgical orthopaedic implant infections and screening for multiple antibiotic resistance. A cross-sectional study was conducted, involving isolation of forty-four dominant pathogenic bacterial isolates from 16 infected implant samples from across Islamabad and Rawalpindi. Out of forty-four, 38% cocci and 61% bacilli were obtained. Approximately 90% of isolates showed multiple antibiotic resistance (MAR) index of more than 0.2. Eleven strains were identified via 16S rRNA gene sequencing as Pseudomonas aeruginosa, Bacillus spp., Planococcus chinensis, Staphylococcus, Escherichia coli and Enterobacter cloacae. The bacterial strain E. coli MB641 showed sensitivity to Polymyxin only, and was resistant to all other antibiotics used. Maximum biofilm forming ability 0.532 ± 0.06, 0.55 ± 0.01 and 0.557 ± 0.07 was observed in Pseudomonas aeruginosa MB663, Pseudomonas aeruginosa MB664 and Bacillus spp. MB647 respectively after 24 hours of incubation. EPS production of bacterial strains was assessed, the polysaccharides and protein content of EPS were found to be in the range of 11-32 μg/ml and 2-10 μg/ml, respectively. Fourier transform infrared spectroscopic analysis of EPS showed the presence of carbohydrates, proteins, alkyl halides, and nucleic acids. X-ray diffraction analysis revealed crystalline structure of EPS extracted from biofilm forming bacteria. These findings suggest a high prevalence of antibiotic-resistant bacteria in orthopaedic implant-associated surgeries, highlighting the urgent need for ongoing monitoring and microorganism testing in infected implants.
Topics: Humans; Escherichia coli; Orthopedics; Pakistan; RNA, Ribosomal, 16S; Cross-Sectional Studies; Virulence; Microbial Sensitivity Tests; Bacteria; Pseudomonas aeruginosa; Drug Resistance, Multiple, Bacterial; Anti-Bacterial Agents; Postoperative Complications
PubMed: 37847701
DOI: 10.1371/journal.pone.0292956 -
International Journal of Microbiology 2023Zambia has seen rapid development in aquaculture, and in recent years, the industry has experienced disease outbreaks where fish have increasingly become a potential...
Zambia has seen rapid development in aquaculture, and in recent years, the industry has experienced disease outbreaks where fish have increasingly become a potential contributor to emerging bacterial zoonotic diseases. The aim of this study was to identify bacterial pathogens with zoonotic potential in apparently healthy fish and water from their habitat. A total of sixty-three fish were sampled, and fifty-nine water samples were collected from the habitats of these fish. Bacteria were cultured from the internal organs of fish and water, and these were identified through standard bacteriological methods comprising morphological characterization, Gram-staining, and a panel of biochemical tests. The following bacterial pathogens with zoonotic potential were identified at a farm prevalence of (13.2%), (2.1%), (2.1%), (0.7%), (6.9%), (2.1%), (0.7%), (18.1%), and (0.7). Other bacteria with varying significance as fish pathogens identified included (2.1%), (1.4%), (1.4%), (2.1%), (10.4%), (3.5%), (1.4%), (1.4%), (2.1%), (4.2%), (6.9%), (1.4%), (1.4%), (6.3%), (1.4%), (1.4%), (0.7%), and (0.7%). The current study provides baseline information for future reference and the implementation of public health guidelines with regard to potential zoonotic diseases in fish.
PubMed: 37333886
DOI: 10.1155/2023/6650378 -
Frontiers in Microbiology 2023Two novel Gram-positive bacteria, designated strains REN8 and REN14, were isolated from pit mud in Sichuan Province, China. REN8 achieved the best growth at 37°C, a pH...
Two novel Gram-positive bacteria, designated strains REN8 and REN14, were isolated from pit mud in Sichuan Province, China. REN8 achieved the best growth at 37°C, a pH of 8.0, and a NaCl concentration of 2%, while REN14 displayed optimal growth at 37°C, a pH of 6.0, and a NaCl concentration of 1%. 16S rRNA and genomic phylogenetic analysis showed that REN8 and REN14 were clustered with the genus . The genomic DNA G + C contents of REN8 and REN14 were 46.7 and 45.1 mol%, respectively. The dDDH and ANI values were 24.5 and 80.43% between REN8 and (the most closely related type strain) and 25.1 and 82.42% between REN14 and (the most closely related type strain). Genomic analysis showed that several carbohydrate-active enzymes and secondary metabolite gene clusters existed in REN8 and REN14. Chemotaxonomic characteristics of REN8 and REN14 included major fatty acids, predominant menaquinones, and polar lipids, all of which were consistent with the genus . Based on the polyphasic taxonomic method, these two strains represent two novel species of the genus ; the name sp. nov. is proposed for the type strain REN8 (=JCM 33964 = GDMCC 1.2213), and the name sp. nov. is proposed for the type strain REN14 (=JCM 34410 = GDMCC 1.2209). The addition of REN8 and REN14 might improve the quality of by considerably increasing the amino acid nitrogen content and acidity and decreasing the bioamine content, with no significant change in alcohol content.
PubMed: 37250023
DOI: 10.3389/fmicb.2023.1139810 -
Molecules (Basel, Switzerland) May 2023Bacterial secondary metabolites are a valuable source of various molecules that have antibacterial and anticancer activity. In this study, ten endosymbiotic bacteria of...
Bacterial secondary metabolites are a valuable source of various molecules that have antibacterial and anticancer activity. In this study, ten endosymbiotic bacteria of aphids, aphid predators and ants were isolated. Bacterial strains were identified according to the 16S rRNA gene. Ethyl acetate fractions of methanol extract (EA-ME) were prepared from each isolated bacterium and tested for their antibacterial activities using the disk diffusion method. The EA-ME of three bacterial species, sp., , , from the pomegranate aphids , , and , respectively, exhibited elevated antibacterial activity against one or several of the five pathogenic bacteria tested. The inhibition zones ranged from 10.00 ± 0.13 to 20.00 ± 1.11 mm, with minimum inhibitory concentration (MIC) values ranging from 0.156 mg/mL to 1.25 mg/mL. The most notable antibacterial activity was found in the EA-ME of against and , with an MIC value of 0.156 mg/mL. The cytotoxic activity of EA-ME was dependent on the cell line tested. The most significant cytotoxicity effect was observed for extracts of and , at 12.5 µg/mL, against the epithelial cells of lung carcinoma (A549), with a cell reduction of 79.4% and 67.2%, respectively. For the EA-ME of and at 12.5 µg/mL, 69.4% and 67.8% cell reduction were observed against human colon cancer (Hct116), respectively. Gas chromatography-mass spectrometry (GC-MS) analysis of three EA-ME revealed the presence of several bioactive secondary metabolites that have been reported previously to possess antibacterial and anticancer properties. To the best of our knowledge, this is the first study to examine the biological activities of endosymbiotic bacteria in aphids, aphid predators and ants. The promising data presented in this study may pave the way for alternative drugs to overcome the continued emergence of multidrug-resistant bacteria, and find alternative drugs to conventional cancer therapies.
Topics: Animals; Humans; Aphids; Pomegranate; Plant Extracts; RNA, Ribosomal, 16S; Anti-Bacterial Agents; Bacteria; Microbial Sensitivity Tests
PubMed: 37241995
DOI: 10.3390/molecules28104255