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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 -
PloS One 2021In recent years, Sporosarcina pasteurii (S. pasteurii) has become one of the most popular bacteria in microbially induced calcium carbonate precipitation (MICP). Various...
In recent years, Sporosarcina pasteurii (S. pasteurii) has become one of the most popular bacteria in microbially induced calcium carbonate precipitation (MICP). Various applications have been developed based on the efficient urease that can induce the precipitation of calcium carbonate. However, the metabolic mechanism related to biomineralization of S. pasteurii has not been clearly elucidated. The process of bacterial culture and biomineralization consumes a large amount of urea or ammonium salts, which are usually used as agricultural fertilizers, not to mention probable environmental pollutions caused by the excessive use of these raw materials. Therefore, it is urgent to reveal the mechanism of nitrogen utilization and metabolism of S. pasteurii. In this paper, we compared the growth and gene expression of S. pasteurii under three different culture conditions through transcriptome analyses. GO and KEGG analyses revealed that both ammonium and urea were direct nitrogen sources of S. pasteurii, and the bacteria could not grow normally in the absence of ammonium or urea. To the best of our knowledge, this paper is the first one to reveal the nitrogen utilization mechanism of S. pasteurii through transcriptome methods. Furthermore, the presence of ammonium might promote the synthesis of intracellular ATP and enhance the motility of the bacteria. There should be an ATP synthesis mechanism associated with urea hydrolysis catalyzed by urease in S. pasteurii.
Topics: Adenosine Triphosphate; Ammonium Compounds; Biosynthetic Pathways; Cell Wall; Down-Regulation; Flagella; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Gene Ontology; Genes, Bacterial; Nitrogen; Sporosarcina; Transcriptome; Up-Regulation; Urea; Urease
PubMed: 33561150
DOI: 10.1371/journal.pone.0246818 -
Nucleic Acids Research Apr 2024RNA ligases are important enzymes in molecular biology and are highly useful for the manipulation and analysis of nucleic acids, including adapter ligation in...
RNA ligases are important enzymes in molecular biology and are highly useful for the manipulation and analysis of nucleic acids, including adapter ligation in next-generation sequencing of microRNAs. Thermophilic RNA ligases belonging to the RNA ligase 3 family are gaining attention for their use in molecular biology, for example a thermophilic RNA ligase from Methanobacterium thermoautotrophicum is commercially available for the adenylation of nucleic acids. Here we extensively characterise a newly identified RNA ligase from the thermophilic archaeon Palaeococcus pacificus (PpaRnl). PpaRnl exhibited significant substrate adenylation activity but low ligation activity across a range of oligonucleotide substrates. Mutation of Lys92 in motif I to alanine, resulted in an enzyme that lacked adenylation activity, but demonstrated improved ligation activity with pre-adenylated substrates (ATP-independent ligation). Subsequent structural characterisation revealed that in this mutant enzyme Lys238 was found in two alternate positions for coordination of the phosphate tail of ATP. In contrast mutation of Lys238 in motif V to glycine via structure-guided engineering enhanced ATP-dependent ligation activity via an arginine residue compensating for the absence of Lys238. Ligation activity for both mutations was higher than the wild-type, with activity observed across a range of oligonucleotide substrates with varying sequence and secondary structure.
Topics: RNA Ligase (ATP); Substrate Specificity; Archaeal Proteins; Planococcaceae; Protein Engineering; Mutation; Models, Molecular; Adenosine Triphosphate; Oligonucleotides
PubMed: 38421610
DOI: 10.1093/nar/gkae149 -
Molecules (Basel, Switzerland) Dec 2020AJ003 produces glycosyl-4,4'-diaponeurosporen-4'-ol-4-oic acid as its main carotenoid. Five carotenoid pathway genes were presumed to be present in the genome of...
AJ003 produces glycosyl-4,4'-diaponeurosporen-4'-ol-4-oic acid as its main carotenoid. Five carotenoid pathway genes were presumed to be present in the genome of AJ003; however, 4,4-diaponeurosporene oxidase (CrtP) was non-functional, and a gene encoding aldehyde dehydrogenase (AldH) was not identified. In the present study, a genome mining approach identified two missing enzymes, CrtP2 and AldH2454, in the glycosyl-4,4'-diaponeurosporen-4'-ol-4-oic acid biosynthetic pathway. Moreover, CrtP2 and AldH enzymes were functional in heterologous and generated two carotenoid aldehydes (4,4'-diapolycopene-dial and 4,4'-diaponeurosporene-4-al) and two carotenoid carboxylic acids (4,4'-diaponeurosporenoic acid and 4,4'-diapolycopenoic acid). Furthermore, the genes encoding CrtP2 and AldH2454 were located at a distance the carotenoid gene cluster of .
Topics: Aldehyde Dehydrogenase; Carotenoids; Databases, Protein; Genome, Bacterial; Metabolic Networks and Pathways; Oxidoreductases; Planococcaceae
PubMed: 33322786
DOI: 10.3390/molecules25245892 -
Microbial Ecology May 2024Biocrust inoculation and microbially induced carbonate precipitation (MICP) are tools used in restoring degraded arid lands. It remains unclear whether the ecological...
Biocrust inoculation and microbially induced carbonate precipitation (MICP) are tools used in restoring degraded arid lands. It remains unclear whether the ecological functions of the two tools persist when these methods are combined and subjected to freeze-thaw (FT) cycles. We hypothesized a synergetic interaction between MICP treatment and biocrust under FT cycles, which would allow both components to retain their ecological functions. We grew cyanobacterial (Nostoc commune) biocrusts on bare soil and on MICP (Sporosarcina pasteurii)-treated soil, subjecting them to repeated FT cycles simulating the Mongolian climate. Generalized linear modeling revealed that FT cycling did not affect physical structure or related functions but could increase the productivity and reduce the nutrient condition of the crust. The results confirm the high tolerance of MICP-treated soil and biocrust to FT cycling. MICP treatment + biocrust maintained higher total carbohydrate content under FT stress. Our study indicates that biocrust on biomineralized soil has a robust enough structure to endure FT cycling during spring and autumn and to promote restoration of degraded lands.
Topics: Soil Microbiology; Soil; Freezing; Cyanobacteria; Carbonates; Ecosystem; Sporosarcina
PubMed: 38730059
DOI: 10.1007/s00248-024-02389-w -
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 -
Food Microbiology Sep 2019The Minas artisanal cheese is a traditional product in its way of producing. Produced in the Minas Gerais state, Brazil, this cheese is made using raw cow's milk with...
The Minas artisanal cheese is a traditional product in its way of producing. Produced in the Minas Gerais state, Brazil, this cheese is made using raw cow's milk with the addition of an endogenous starter culture called "pingo", responsible for inoculating specific microorganisms that could enhance flavor and sensorial aspects. There are seven regions able to produce and commercialize this product - Araxá, Campo das Vertentes, Canastra Cerrado, Serra do Salitre, Serro and Triângulo Mineiro. This study aimed to assess the bacterial community of raw milk, endogenous starter culture and to uncover possible shifts in the bacterial community of the rind and core of cheeses at sixty days of ripening located in the Serra do Salitre region by Illumina MiSeq 16S rRNA gene amplicon sequencing. Raw milk and starter culture are responsible for inoculating specific bacteria into the cheese, with Planococcaceae and Streptococcaceae being prevalent throughout ripening time. The Planococcaceae family seems to develop strong interactions with the Leuconostocaceae family on the surface of these cheeses, and is associated with environmental aspects of the region, probably leading to a microbial signature of these products. Additionally, abiotic factors such as geographical location, moisture and acidity are major drivers in the microbial shift.
Topics: Animals; Bacteria; Brazil; Cheese; Environment; Food Microbiology; Microbiota; Milk; RNA, Ribosomal, 16S; Sensation; Taste; Time Factors
PubMed: 31027793
DOI: 10.1016/j.fm.2019.02.016 -
Microbial Cell Factories Jun 2024Microbially induced calcium carbonate precipitation has been extensively researched for geoengineering applications as well as diverse uses within the built environment....
BACKGROUND
Microbially induced calcium carbonate precipitation has been extensively researched for geoengineering applications as well as diverse uses within the built environment. Bacteria play a crucial role in producing calcium carbonate minerals, via enzymes including carbonic anhydrase-an enzyme with the capability to hydrolyse CO, commonly employed in carbon capture systems. This study describes previously uncharacterised carbonic anhydrase enzyme sequences capable of sequestering CO2 and subsequentially generating CaCO biominerals and suggests a route to produce carbon negative cementitious materials for the construction industry.
RESULTS
Here, Bacillus subtilis was engineered to recombinantly express previously uncharacterised carbonic anhydrase enzymes from Bacillus megaterium and used as a whole cell catalyst allowing this novel bacterium to sequester CO and convert it to calcium carbonate. A significant decrease in CO was observed from 3800 PPM to 820 PPM upon induction of carbonic anhydrase and minerals recovered from these experiments were identified as calcite and vaterite using X-ray diffraction. Further experiments mixed the use of this enzyme (as a cell free extract) with Sporosarcina pasteurii to increase mineral production whilst maintaining a comparable level of CO sequestration.
CONCLUSION
Recombinantly produced carbonic anhydrase successfully sequestered CO and converted it into calcium carbonate minerals using an engineered microbial system. Through this approach, a process to manufacture cementitious materials with carbon sequestration ability could be developed.
Topics: Calcium Carbonate; Bacillus subtilis; Carbon Dioxide; Carbonic Anhydrases; Sporosarcina; Bacillus megaterium; Carbon Sequestration; Chemical Precipitation; Bacterial Proteins
PubMed: 38858761
DOI: 10.1186/s12934-024-02437-7 -
Scientific Reports Oct 2021Microbially induced calcium carbonate precipitation (MICP)/Biocementation has emerged as a promising technique for soil engineering applications. There are chiefly two...
Microbially induced calcium carbonate precipitation (MICP)/Biocementation has emerged as a promising technique for soil engineering applications. There are chiefly two methods by which MICP is applied for field applications including biostimulation and bioaugmentation. Although bioaugmentation strategy using efficient ureolytic biocementing culture of Sporosarcina pasteurii is widely practiced, the impact of native ureolytic microbial communities (NUMC) on CaCO mineralisation via S. pasteurii has not been explored. In this paper, we investigated the effect of different concentrations of NUMC on MICP kinetics and biomineral properties in the presence and absence of S. pasteurii. Kinetic analysis showed that the biocementation potential of S. pasteurii is sixfold higher than NUMC and is not significantly impacted even when the concentration of the NUMC is eight times higher. Micrographic results revealed a quick rate of CaCO precipitation by S. pasteurii leading to generation of smaller CaCO crystals (5-40 µm), while slow rate of CaCO precipitation by NUMC led to creation of larger CaCO crystals (35-100 µm). Mineralogical results showed the predominance of calcite phase in both sets. The outcome of current study is crucial for tailor-made applications of MICP.
Topics: Calcium Carbonate; Chemical Precipitation; Crystallization; Kinetics; Microbiota; Sporosarcina
PubMed: 34675302
DOI: 10.1038/s41598-021-00315-5 -
Molecules (Basel, Switzerland) Sep 2020Antarctic regions are characterized by low temperatures and strong UV radiation. This harsh environment is inhabited by psychrophilic and psychrotolerant organisms,...
Antarctic regions are characterized by low temperatures and strong UV radiation. This harsh environment is inhabited by psychrophilic and psychrotolerant organisms, which have developed several adaptive features. In this study, we analyzed two Antarctic bacterial strains, sp. ANT_H30 and sp. ANT_H53B. The physiological analysis of these strains revealed their potential to produce various biotechnologically valuable secondary metabolites, including surfactants, siderophores, and orange pigments. The genomic characterization of ANT_H30 and ANT_H53B allowed the identification of genes responsible for the production of carotenoids and the in silico reconstruction of the pigment biosynthesis pathways. The complex manual annotation of the bacterial genomes revealed the metabolic potential to degrade a wide variety of compounds, including xenobiotics and waste materials. Carotenoids produced by these bacteria were analyzed chromatographically, and we proved their activity as scavengers of free radicals. The quantity of crude carotenoid extracts produced at two temperatures using various media was also determined. This was a step toward the optimization of carotenoid production by Antarctic bacteria on a larger scale.
Topics: Carotenoids; Genome, Bacterial; Genomics; Multigene Family; Phylogeny; Planococcus Bacteria; Rhodococcus
PubMed: 32977394
DOI: 10.3390/molecules25194357