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Microbial Cell Factories Mar 2022The genus Planococcus is comprised of halophilic bacteria generally reported for the production of carotenoid pigments and biosurfactants. In previous work, we showed...
BACKGROUND
The genus Planococcus is comprised of halophilic bacteria generally reported for the production of carotenoid pigments and biosurfactants. In previous work, we showed that the culturing of the orange-pigmented Planococcus sp. CP5-4 isolate increased the evaporation rate of industrial wastewater brine effluent, which we attributed to the orange pigment. This demonstrated the potential application of this bacterium for industrial brine effluent management in evaporation ponds for inland desalination plants. Here we identified a C-carotenoid biosynthetic gene cluster responsible for pigment biosynthesis in Planococcus sp. CP5-4 through isolation of mutants and genome sequencing. We further compare the core genes of the carotenoid biosynthetic gene clusters identified from different Planococcus species' genomes which grouped into gene cluster families containing BGCs linked to different carotenoid product chemotypes. Lastly, LC-MS analysis of saponified and unsaponified pigment extracts obtained from cultures of Planococcus sp. CP5-4, revealed the structure of the main (predominant) glucosylated C-carotenoid fatty acid ester produced by Planococcus sp. CP5-4.
RESULTS
Genome sequence comparisons of isolated mutant strains of Planococcus sp. CP5-4 showed deletions of 146 Kb and 3 Kb for the non-pigmented and "yellow" mutants respectively. Eight candidate genes, likely responsible for C-carotenoid biosynthesis, were identified on the wild-type genome region corresponding to the deleted segment in the non-pigmented mutant. Six of the eight candidate genes formed a biosynthetic gene cluster. A truncation of crtP was responsible for the "yellow" mutant phenotype. Genome annotation revealed that the genes encoded 4,4'-diapolycopene oxygenase (CrtNb), 4,4'- diapolycopen-4-al dehydrogenase (CrtNc), 4,4'-diapophytoene desaturase (CrtN), 4,4'- diaponeurosporene oxygenase (CrtP), glycerol acyltransferase (Agpat), family 2 glucosyl transferase 2 (Gtf2), phytoene/squalene synthase (CrtM), and cytochrome P450 hydroxylase enzymes. Carotenoid analysis showed that a glucosylated C-carotenoid fatty acid ester, methyl 5-(6-C)-glucosyl-5, 6'-dihydro-apo-4, 4'-lycopenoate was the main carotenoid compound produced by Planococcus sp. CP5-4.
CONCLUSION
We identified and characterized the carotenoid biosynthetic gene cluster and the C-carotenoid compound produced by Planococcus sp. CP5-4. Mass-spectrometry guided analysis of the saponified and unsaponified pigment extracts showed that methyl 5-glucosyl-5, 6-dihydro-apo-4, 4'-lycopenoate esterified to heptadecatrienoic acid (C). Furthermore, through phylogenetic analysis of the core carotenoid BGCs of Planococcus species we show that various C-carotenoid product chemotypes, apart from methyl 5-glucosyl-5, 6-dihydro-apo-4, 4'-lycopenoate and 5-glucosyl-4, 4-diaponeurosporen-4'-ol-4-oic acid, may be produced that could offer opportunities for a variety of applications.
Topics: Carotenoids; Multigene Family; Phylogeny; Planococcus Bacteria; South Africa
PubMed: 35305628
DOI: 10.1186/s12934-022-01752-1 -
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 -
BMC Microbiology Oct 2021Extremophiles have attracted much attention in the last few decades, as they possess different properties by producing certain useful metabolites. However, the secondary...
BACKGROUND
Extremophiles have attracted much attention in the last few decades, as they possess different properties by producing certain useful metabolites. However, the secondary metabolism of the extremophiles of Antarctic krill has received little attention.
RESULTS
In this study, a new bacterial strain MSAK28401 from Antarctic krill was isolated and identified. The results of analysis on phenotypic, chemotaxonomic, and genomic characteristics showed that the strain MSAK28401 belongs to the genus Planococcus. Cells of this strain were coccoid (0.89-1.05 μm) and aerobic. The majority of the fatty acid content was C anteiso (37.67 ± 0.90%) followed by C ω7c alcohol (10.37 ± 1.22%) and C iso (9.36 ± 0.71%). The calculated average nucleotide identity and DNA-DNA hybridization values between the strain MSAK28401 and type strains P. citreus DSM 20549 and P. rifietoensis M8 were lower than 91 and 70%, respectively. The strain MSAK28401 (=KCTC 43283 and MCCC 1k05448) represented a new member of the genus Planococcus and was named P. alpniumensis sp. nov. Moreover, genes involved in the degradation of aromatic compounds (e.g., salicylate, gentisate, and quinate) were found in the genome, implying that strain MSAK28401 has an aromatic compound as its potential metabolite. This work will help us understand the genomic characteristics and potential metabolic pathway of Planococcus from Antarctic krill.
CONCLUSIONS
This study reported the genomic information and phenotypic characteristics of the new strain P. alpniumensis MSAK28401 isolated from Antarctic krill, and provided the genome information of Planococcus strains for further studying the function roles in aromatic compound metabolism.
Topics: Animals; Antarctic Regions; Bacterial Proteins; DNA, Bacterial; Euphausiacea; Extremophiles; Fatty Acids; Genome, Bacterial; Nucleic Acid Hybridization; Phenotype; Phylogeny; Planococcus Bacteria; Secondary Metabolism; Sequence Analysis, DNA
PubMed: 34686131
DOI: 10.1186/s12866-021-02347-3 -
PloS One 2022Auxospore production is a sexual reproductive strategy by diatoms to re-attain normal size after the size-reducing effect of clonal reproduction. Aside from the minimum...
Auxospore production is a sexual reproductive strategy by diatoms to re-attain normal size after the size-reducing effect of clonal reproduction. Aside from the minimum size threshold used as a sex clock by diatoms, the environmental or chemical triggers that can induce sex in diatoms are still not well understood. Here we investigated the influence of six marine bacteria from five families on the production of sexual cells and auxospores of the ubiquitous marine polar centric diatom, Odontella sp. Microbiome association and co-occurrence with the diatom in culture and in nature were investigated using 16S rRNA amplicon sequencing. Indole acetic acid (IAA) secretion, a phytohormone that regulates plants' growth and sexual development, was explored as a potential inducer of sexual reproduction in Odontella and compared between bacterial associates. We found that Odontella co-cultured with Flavobacteriaceae (Polaribacter and Cellulophaga) have significantly more sexual cells and auxospores than bacteria-free Odontella and Odontella co-cultured with other bacteria from Vibrionaceae (Vibrio), Pseudoalteromonadaceae (Pseudoalteromonas), Rhodobacteraceae (Sulfitobacter), or Planococcaceae (Planococcus) family. Differences in IAA secretion were observed between bacterial isolates, but this did not correspond consistently with the diatom's clonal growth or production of sexual cells and auxospores. Microbiome composition survey of Odontella cultures showed that the diatom harbors homologous sequences of the four bacterial isolates at varying proportions, with Sulfitobacter and Polaribacter at high abundances. Microbiome surveys at Santa Cruz Wharf, Monterey Bay, from 2014-2015 showed that Odontella abundance is positively correlated with Flavobacteriaceae and Rhodobacteraceae abundances. Our study demonstrates that specific members of the diatom microbiome can enhance the host's sexual reproduction, with the interkingdom interaction driven by partner compatibility and long-term association. Sex-enhancing bacteria may even be needed by the diatom host to carry out the optimal inducement of sex under normal conditions, allowing for size restitution and maintaining genetic diversity in culture and in nature.
Topics: Humans; Animals; Diatoms; RNA, Ribosomal, 16S; Plant Growth Regulators; Microbiota; Arthropods; Reproduction; Rhodobacteraceae
PubMed: 36260629
DOI: 10.1371/journal.pone.0276305 -
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 -
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 -
Astrobiology Oct 2022The search for life elsewhere in the Universe goes together with the search for liquid water. Life as we know it requires water; however, it is possible for microbial...
The search for life elsewhere in the Universe goes together with the search for liquid water. Life as we know it requires water; however, it is possible for microbial life to exist under hyperarid conditions with a minimal amount of water. We report on the ability of two typical terrestrial bacteria ( and sp) and two extremophiles (-20201027-1 sp and ) to grow and survive in three martian soil (regolith) simulants (Mohave Mars Simulant-1 [MMS-1] F, Mars Global Simulant-1 [MGS-1], and JSC Mars-1A [JSC]). Survival and growth were assessed over a 21-day period under terrestrial conditions and with water:soil (vol:wt) ratios that varied from 0.25:1 to 5:1. We found that and sp grew best in the simulants MMS and JSC, respectively, while growth rates were better in the JSC simulant. As expected, did not show significant growth. Our results indicate that these martian simulants and thus martian regolith, with minimal or no added nutrients or water, can support the growth of extremophiles such as and . Similar extremophiles on early Mars may have survived to the present in near-surface ecological niches analogous to those where these organisms exist on Earth.
Topics: Cyanobacteria; Escherichia coli; Extraterrestrial Environment; Extremophiles; Mars; Soil; Water
PubMed: 36000998
DOI: 10.1089/ast.2022.0022 -
3 Biotech Oct 2023is a genus of Gram-positive bacteria known for potential industrial and agricultural applications. Here, we report the first draft genome sequence and phylogenomic...
UNLABELLED
is a genus of Gram-positive bacteria known for potential industrial and agricultural applications. Here, we report the first draft genome sequence and phylogenomic analysis of a CRISPR-carrying, multidrug-resistant, novel candidate sp. NCCP-2050 isolated from agricultural soil in Pakistan. The strain NCCP-2050 exhibited significant resistance to various classes of antibiotics, including fluoroquinolones (i.e., ciprofloxacin, levofloxacin, ofloxacin, moxifloxacin, and bacitracin), cephalosporins (cefotaxime, ceftazidime, cefoperazone), rifamycins (rifampicin), macrolides (erythromycin), and glycopeptides (vancomycin). sp. NCCP-2050 consists of genome size of 3,463,905 bp, comprised of 3639 annotated genes, including 82 carbohydrate-active enzyme genes and 39 secondary metabolite genes. The genome also contained 80 antibiotic resistance, 162 virulence, and 305 pathogen-host interaction genes along with two CRISPR arrays. Based on phylogenomic analysis, digital DNA-DNA hybridization, and average nucleotide identity values (i.e., 35.4 and 88.5%, respectively) it was suggested that strain NCCP-2050 might represent a potential new species within the genus .
SUPPLEMENTARY INFORMATION
The online version contains supplementary material available at 10.1007/s13205-023-03748-z.
PubMed: 37663752
DOI: 10.1007/s13205-023-03748-z -
Frontiers in Microbiology 2021Protease-producing bacteria play vital roles in degrading organic matter of aquaculture system, while the knowledge of diversity and bacterial community structure of...
Protease-producing bacteria play vital roles in degrading organic matter of aquaculture system, while the knowledge of diversity and bacterial community structure of protease-producing bacteria is limited in this system, especially in the tropical region. Herein, 1,179 cultivable protease-producing bacterial strains that belonged to Actinobacteria, Firmicutes, and Proteobacteria were isolated from tropical aquaculture systems, of which the most abundant genus was , followed by . The diversity and relative abundance of protease-producing bacteria in sediment were generally higher than those in water. Twenty-one genera from sediment and 16 genera from water were identified, of which dominated by in both and dominated by in water were the dominant genera. The unique genera in sediment or water accounted for tiny percentage may play important roles in the stability of community structure. Eighty isolates were clustered into four clusters (ET-1-ET-4) at 58% of similarity by ERIC-PCR (enterobacterial repetitive intergenic consensus-polymerase chain reaction), which was identified as a novel branch of . Additionally, strains belonged to ET-3 and ET-4 were detected in most aquaculture ponds without outbreak of epidemics, indicating that these protease-producing bacteria may be used as potential beneficial bacteria for wastewater purification. Environmental variables played important roles in shaping protease-producing bacterial diversity and community structure in aquaculture systems. In sediment, dissolved oxygen (DO), chemical oxygen demand (COD), and salinity as the main factors positively affected the distributions of dominant genus () and unique genera ( and ), whereas temperature negatively affected that of (except ). In water, as unique genus and were negatively affected by NO -N and NO -N, respectively, whereas pH as the main factor positively affected the distribution of . These findings will lay a foundation for the development of protease-producing bacterial agents for wastewater purification and the construction of an environment-friendly tropical aquaculture model.
PubMed: 33613508
DOI: 10.3389/fmicb.2021.638129 -
Biology Mar 2022The Taklimakan Desert located in China is the second-largest shifting sand desert in the world and is known for its harsh conditions. Types of γ-rays or UV...
The Taklimakan Desert located in China is the second-largest shifting sand desert in the world and is known for its harsh conditions. Types of γ-rays or UV radiation-resistant bacterial strains have been isolated from this desert. However, there is no information regarding the proportions of the radiation-resistant strains in the total culturable microbes. We isolated 352 bacterial strains from nine sites across the Taklimakan Desert from north to south. They belong to Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. The phylum Actinobacteria was the most predominant in abundance and Firmicutes had the highest species richness. Bacteroidetes had the lowest abundance and was found in four sites only, while the other three phyla were found in every site but with different distribution profiles. After irradiating with 1000 J/m and 6000 J/m UV-C, the strains with survival rates higher than 10% occupied 72.3% and 36.9% of all culturable bacteria, respectively. The members from Proteobacteria had the highest proportions, with survival rates higher than 10%. After radiation with 10 kGy γ-rays, sp. TKL1057 and sp. TKL1152 showed higher radiation-resistant capabilities than R1. Besides obtaining several radiation-resistant extremophiles, this study measured the proportions of the radiation-resistant strains in the total culturable microbes for the first time. This study may help to better understand the origin of radioresistance, especially by quantitatively comparing proportions of radiation-resistant extremophiles from different environments in the future.
PubMed: 35453702
DOI: 10.3390/biology11040501