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International Journal of Systematic and... Oct 2023A Gram-stain-positive, catalase-positive, non-motile bacteria, with a rod-coccus cycle (designated as EH-1B-1) was isolated from a soil sample from Union Glacier in...
A Gram-stain-positive, catalase-positive, non-motile bacteria, with a rod-coccus cycle (designated as EH-1B-1) was isolated from a soil sample from Union Glacier in Ellsworth Mountains, Antarctica. Strain EH-1B-1 had an optimal growth temperature of 28 °C and grew at pH 7-10. The major cellular fatty acids were anteiso-C, iso-C, C and anteiso-C. The G+C content based on the whole genome sequence was 63.1 mol%. Strain EH-1B-1 was most closely related to members of the genus , namely and . The strain grew on tryptic soy agar, Reasoner's 2A agar, lysogeny broth agar and nutrient agar. The average nucleotide identity and digital DNA-DNA hybridization values between strain EH-1B-1 and its closest reference type strains ranged from 78 to 88 % and from 20.9 to 36.3 %, respectively. Based on phenotypic, chemotypic and genotypic evidence, it is proposed that strain EH-1B-1 represents a novel species of , for which the name sp. nov. is proposed, with strain EH-1B-1 (RGM 3386=LMG 32961) as the type strain.
Topics: Fatty Acids; Arthrobacter; Phospholipids; Ice Cover; Antarctic Regions; Agar; Base Composition; Phylogeny; DNA, Bacterial; RNA, Ribosomal, 16S; Bacterial Typing Techniques; Sequence Analysis, DNA; Soil Microbiology; Vitamin K 2; Peptidoglycan; Soil
PubMed: 37861393
DOI: 10.1099/ijsem.0.006095 -
Chemosphere Nov 2023BTEX (benzene, toluene, ethylbenzene, xylene) are common pollutants often found in former gasworks sites together with some other contaminants like indene, indane and...
BTEX (benzene, toluene, ethylbenzene, xylene) are common pollutants often found in former gasworks sites together with some other contaminants like indene, indane and naphthalene (Ie, Ia, N). This study aimed to evaluate the inhibitory or stimulative substrate interactions between BTEX, and Ie, Ia, N during aerobic biodegradation. For this, batch bottles, containing originally anaerobic subsurface sediments, groundwater and indigenous microorganisms from a contaminated former gasworks site, were spiked with various substrate combinations (BTEX, BTEXIe, BTEXIa, BTEXN, BTEXIeIa, BTEXIeN, BTEXIaN, BTEXIeIaN). Subsequently concentrations were monitored over time. For the BTEXIeIaN mixture, initial concentrations were between 1 and 5 mg L, and all compounds were completely degraded by the microbial consortia within 39 days of incubation. The experimental data were fitted to a first order kinetic degradation model for interpretation of inhibition/stimulation between the compounds. Results showed that indene, indane, and naphthalene inhibited the degradation of benzene, toluene, ethylbenzene, o-xylene, with benzene being the most affected. M/p-xylene is the only compound whose biodegradation is stimulated by the presence of indene and indane (individually or mixed) but inhibited by the presence of naphthalene. 16S rRNA amplicon sequencing revealed differentiation in the microbial communities within the batches with different substrate mixtures, especially within the two microbial groups Micrococcaceae and Commamonaceae. Indene had more effect on the BTEX microbial community than indane or naphthalene and the presence of indene increased the relative abundance of Micrococcaceae family. In conclusion, co-presence of various pollutants leads to differentiation in degradation processes as well as in microbial community development. This sheds some light on the underlying reasons for that organic compounds present in mixtures in the subsurface of former gasworks sites are either recalcitrant or subjective towards biodegradation, and this understanding helps to further improve the bioremediation of such sites.
Topics: Benzene; Biodegradation, Environmental; Kinetics; RNA, Ribosomal, 16S; Benzene Derivatives; Xylenes; Toluene; Indenes; Environmental Pollutants; Naphthalenes; Microbiota
PubMed: 37558001
DOI: 10.1016/j.chemosphere.2023.139761 -
Archives of Microbiology Dec 2023Due to their non-toxic and non-carcinogenic nature, biopigments have a phenomenal benefit over synthetic pigments, making them a desirable source for human utilization...
Due to their non-toxic and non-carcinogenic nature, biopigments have a phenomenal benefit over synthetic pigments, making them a desirable source for human utilization and a potential alternative to traditional synthetic pigments that are hazardous to the environment and public health. Endosymbiotic interactions between mangrove plants and bacteria could provide an alternate source for the synthesis of unique compounds with potent biomedical applications. Pigmented endophytic bacteria were screened from the explants of Avicennia marina, a mangrove plant, and identified as Micrococcus luteus by molecular characterization. The intracellular pigment was successfully extracted using the sonication-assisted solvent extraction method, and screening factors impacting the pigmentation bioprocess were determined using a one-factor-at-a-time approach. The endophyte produced yellow pigment in the liquid medium, with the maximum growth and pigment production recorded in nutrient broth at 37 ℃ and pH 7 after 96 h of incubation, while the maximum accumulation of pigment was observed in the media supplemented with glucose and tryptone as carbon and nitrogen sources, respectively. The extracted crude pigment was further characterized by ultraviolet, followed by Fourier transform infrared spectroscopy and gas chromatography-mass spectrometry. The obtained crude pigment has been evaluated for its antioxidant and anticancer activity by various assays, such as DPPH radical scavenging activity, FRAP assay, superoxide anion and nitric oxide radical scavenging, metal chelating activity, phosphomolybdenum assay, and MTT assay, respectively, at varying concentrations. The results of our study revealed that the yellow pigment produced by the endophyte showed significant dose-dependent antioxidant and anticancer activity.
Topics: Humans; Antioxidants; Avicennia; Micrococcus luteus; Nutrients; Carbon; Endophytes
PubMed: 38108901
DOI: 10.1007/s00203-023-03751-1 -
Current Microbiology Jul 2023A study was undertaken to determine the effects of a strain of Arthrobacter sp., a Plant Growth-Promoting Bacteria (PGPB), on plant phenology and qualitative composition...
A study was undertaken to determine the effects of a strain of Arthrobacter sp., a Plant Growth-Promoting Bacteria (PGPB), on plant phenology and qualitative composition of Opuntia ficus-indica (L.) Mill. fruits and cladodes. The strain was inoculated in soil, and its effects on cactus pear plants were detected and compared to nontreated plants. Compared to the latter, the treatment with bacteria promoted an earlier plant sprouting (2 months before the control) and fruitification, ameliorating fruit quality (i.e., improved fresh and dry weight: + 24% and + 26%, respectively, increased total solid content by 30% and polyphenols concentrations by 22%). The quality and quantity of monosaccharides of cladodes were also increased by Arthrobacter sp. with a positive effect on their nutraceutical value. In summer, the mean values of xylose, arabinose, and mannose were significantly higher in treated compared to not treated plants (+ 3.54; + 7.04; + 4.76 mg/kg d.w. respectively). A similar trend was observed in autumn, when the cladodes of inoculated plants had higher contents, i.e., 33% xylose, 65% arabinose, and 40% mannose, respect to the controls. In conclusion, Arthrobacter sp. plays a role in the improvement of nutritional and nutraceutical properties of cactus pear plants due to its capabilities to promote plant growth. Therefore, these results open new perspectives in PGPB application in the agro-farming system as alternative strategy to improve cactus pear growth, yield, and cladodes quality, being the latter the main by-product to be utilized for additional industrial uses.
Topics: Fruit; Opuntia; Arthrobacter; Mannose; Arabinose; Xylose; Dietary Supplements
PubMed: 37400738
DOI: 10.1007/s00284-023-03368-z -
Renal Failure Dec 2023
Topics: Humans; Peritoneal Dialysis; Micrococcaceae; Peritonitis
PubMed: 37170866
DOI: 10.1080/0886022X.2023.2210683 -
Bioresource Technology Aug 2023The presence of 2,4-dichlorophenoxyacetic acid (2,4-D), an organochlorine herbicide, in the environment has raised public concern as it poses hazard to both humans and...
The presence of 2,4-dichlorophenoxyacetic acid (2,4-D), an organochlorine herbicide, in the environment has raised public concern as it poses hazard to both humans and the ecosystem. Three potential strains having the capability to degrade 2,4-D were isolated from on site agricultural soil and identified as Arthrobacter sp. SVMIICT25, Sphingomonas sp. SVMIICT11 and Stenotrophomonas sp. SVMIICT13. Over 12 days of incubation, 81-90% of 100 mg/L of 2,4-D degradation was observed at 2% inoculum. A shorter lag phase with 80% of degradation efficiency was observed within 5 days when the inoculum size was increased to 10%. Six microbial consortia were prepared by combining the isolates along with in-house strains, Bacillus sp. and Pseudomonas sp. Consortia R3 (Arthrobacter sp. + Sphingomonas sp.), operated with 10% of inoculum, showed 85-90% degradation within 4 days and 98-100% in 9 days. Further, targeted exo-metabolite analysis confirmed the presence and catabolism of intermediate 2,4-dichlorophenol and 4-chlorophenol compounds.
Topics: Humans; Ecosystem; Biodegradation, Environmental; Herbicides; Pesticides; Microbial Consortia; Soil Pollutants; Arthrobacter; 2,4-Dichlorophenoxyacetic Acid; Soil Microbiology
PubMed: 37037331
DOI: 10.1016/j.biortech.2023.129031 -
International Journal of Molecular... Jan 20244-hydroxybenzoic acid (4-HBA) is an aromatic compound with high chemical stability, being extensively used in food, pharmaceutical and cosmetic industries and therefore...
4-hydroxybenzoic acid (4-HBA) is an aromatic compound with high chemical stability, being extensively used in food, pharmaceutical and cosmetic industries and therefore widely distributed in various environments. Bioremediation constitutes the most sustainable approach for the removal of 4-hydroxybenzoate and its derivatives (parabens) from polluted environments. Sphe3, a strain capable of degrading several aromatic compounds, is able to grow on 4-HBA as the sole carbon and energy source. Here, an attempt is made to clarify the catabolic pathways that are involved in the biodegradation of 4-hydroxybenzoate by Sphe3, applying a metabolomic and transcriptomic analysis of cells grown on 4-HBA. It seems that in Sphe3, 4-hydroxybenzoate is hydroxylated to form protocatechuate, which subsequently is either cleaved in - and/or -positions or decarboxylated to form catechol. Protocatechuate and catechol are funneled into the TCA cycle following either the -ketoadipate or protocatechuate -cleavage branches. Our results also suggest the involvement of the oxidative decarboxylation of the protocatechuate peripheral pathway to form hydroxyquinol. As a conclusion, Sphe3 seems to be a rather versatile strain considering the 4-hydroxybenzoate biodegradation, as it has the advantage to carry it out effectively following different catabolic pathways concurrently.
Topics: Parabens; Catechols; Butyrates; Micrococcaceae
PubMed: 38255919
DOI: 10.3390/ijms25020843 -
Archives of Microbiology Oct 2023Lateritic soil is the reddish to brown-colored soil composed mainly of iron or aluminium oxides, hydroxides, or oxyhydroxides. Information on bacteria that inhabit this...
Characterization of a biofilm-forming, amylase-producing, and heavy-metal-bioremediating strain Micrococcus sp. BirBP01 isolated from oligotrophic subsurface lateritic soil.
Lateritic soil is the reddish to brown-colored soil composed mainly of iron or aluminium oxides, hydroxides, or oxyhydroxides. Information on bacteria that inhabit this soil type, their ecological role, and metabolic potential are scarce. We have isolated and partially characterized a bacterial strain BirBP01 from a lead, calcium, and magnesium-rich, oligotrophic subsurface lateritic soil-sample collected from 12-feet deep horizon of a laterite mining pit in Birbhum district, India. The isolate is a biofilm-forming, Gram-positive bacterium having a sarcinae arrangement, mesophilic, slightly alkaliphilic, able to produce amylase, and resistant against multiple heavy-metals. BirBP01 has the ability to bioremediate 51% of Pb, 30% of Zn, and 22% of Cu through biosorption, possibly into the biofilm matrix. The bioremediating ability of the bacterium alleviated the inhibitory effect of heavy-metals on the germination of chickpea (Cicer arietinum L.) seeds. 16S rRNA gene-based phylogenetic analysis revealed that BirBP01 is a member of the genus Micrococcus. It showed more than 99% identity of the 16S rRNA gene sequence, and clustered within the same branch of the phylogenetic tree, with strains of M. yunnanensis, M. endophyticus, and M. luteus. The ability to produce amylase, and bioremediate heavy-metals signify that Micrococcus sp. BirBP01 could be potentially a good candidate for industrial applications, and to clean up heavy-metal contaminated sites.
Topics: Micrococcus; Soil; RNA, Ribosomal, 16S; Phylogeny; Metals, Heavy; Bacteria; Biofilms; Soil Pollutants; Biodegradation, Environmental
PubMed: 37805972
DOI: 10.1007/s00203-023-03690-x -
Applied and Environmental Microbiology Feb 2024Engineering the plant microbiome with beneficial endophytic bacteria can improve the growth, health, and productivity of the holobiont. Here, we administered two...
Engineering the plant microbiome with beneficial endophytic bacteria can improve the growth, health, and productivity of the holobiont. Here, we administered two beneficial bacterial strains, VR04 sp. and GR12 sp., to micropropagated grapevine cuttings obtained via somatic embryogenesis. While both strains colonized the plant endosphere, only GR12 sp. increased root biomass under nutritional-deficit conditions, as supported by the plant growth promotion traits detected in its genome. Phylogenetic and co-occurrence analyses revealed that the plant native bacterial community, originally dominated by Streptococcaceae and Micrococcaceae, dramatically changed depending on the inoculation treatments, as invading strains differently affected the relative abundance and the interactions of pre-existing taxa. After 30 days of plantlets' growth, became a predominant taxon, and considering untreated plantlets as references, sp. GR12 showed a minor impact on the endophytic bacterial community. On the other hand, sp. VR04 caused a major change in community composition, suggesting an opportunistic colonization pattern. Overall, the results corroborate the importance of preserving the native endophytic community structure and functions during plant microbiome engineering.IMPORTANCEA better comprehension of bacterial colonization processes and outcomes could benefit the use of plant probiotics in the field. In this study, we applied two different beneficial bacteria to grapevine micropropagated plantlets and described how the inoculation of these strains impacts endophytic microbiota assembly. We showed that under nutritional deficit conditions, the response of the receiving endophytic bacterial communities to the invasion of the beneficial strains related to the manifestation of plant growth promotion effects by the inoculated invading strains. sp. GR12 was able to preserve the native microbiome structure despite its effective colonization, highlighting the importance of the plant-endophyte associations for the holobiont performance. Moreover, our approach showed that the use of micropropagated plantlets could be a valuable strategy to study the interplay among the plant, its native microbiota, and the invader on a wider portfolio of species besides model plants, facilitating the application of new knowledge in agriculture.
Topics: Agricultural Inoculants; Phylogeny; Plant Roots; Bacteria; Enterobacteriaceae; Endophytes
PubMed: 38289136
DOI: 10.1128/aem.02078-23 -
Microbiology Spectrum Jun 2024Cystic fibrosis (CF), an inherited genetic disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator gene, results in sticky and thick...
Cystic fibrosis (CF), an inherited genetic disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator gene, results in sticky and thick mucosal fluids. This environment facilitates the colonization of various microorganisms, some of which can cause acute and chronic lung infections, while others may positively impact the disease. , an oral commensal, is relatively abundant in the lungs of CF patients. Recent studies have unveiled its anti-inflammatory properties using three-dimensional lung epithelial cell cultures and mouse models relevant to chronic lung diseases. Apart from this, has been associated with severe infections. However, its metabolic capabilities and genotype-phenotype relationships remain largely unknown. To gain insights into its cellular metabolism and genetic content, we developed the first manually curated genome-scale metabolic model, RM23NL. Through growth kinetics and high-throughput phenotypic microarray testings, we defined its complete catabolic phenome. Subsequently, we assessed the model's effectiveness in accurately predicting growth behaviors and utilizing multiple substrates. We used constraint-based modeling techniques to formulate novel hypotheses that could expedite the development of antimicrobial strategies. More specifically, we detected putative essential genes and assessed their effect on metabolism under varying nutritional conditions. These predictions could offer novel potential antimicrobial targets without laborious large-scale screening of knockouts and mutant transposon libraries. Overall, RM23NL demonstrates a solid capability to predict cellular phenotypes and holds immense potential as a valuable resource for accurate predictions in advancing antimicrobial therapies. Moreover, it can guide metabolic engineering to tailor 's metabolism for desired performance.IMPORTANCECystic fibrosis (CF) is a genetic disorder characterized by thick mucosal secretions, leading to chronic lung infections. is a common bacterium found in various parts of the human body, acting as a normal part of the flora. In people with weakened immune systems, it can become an opportunistic pathogen, while it is prevalent and active in CF airways. Recent studies have highlighted its anti-inflammatory properties in the lower pulmonary system, indicating the intricate relationship between microbes and human health. Herein, we have developed the first manually curated metabolic model of . Our study examined the previously unknown relationships between the bacterium's genotype and phenotype and identified essential genes that impact the metabolism under various conditions. With this, we opt for paving the way for developing new strategies in antimicrobial therapy and metabolic engineering, leading to enhanced therapeutic outcomes in cystic fibrosis and related conditions.
Topics: Cystic Fibrosis; Humans; Micrococcaceae; Genome, Bacterial; Genes, Essential; Animals; Mice; Phenotype
PubMed: 38652457
DOI: 10.1128/spectrum.04006-23