Micrococcus Antarcticus Research Articles

Community-acquired pneumonia caused by Micrococcus antarcticus: a rare case report

Background Micrococcus antarcticus (M. antarcticus) is an aerobic Gram-positive spherical actinobacterium that was initially isolated from Chinese Great-Wall station in Antarctica in 2000. M. antarcticus was considered to be of low pathogenicity, no previous cases of human infection by this organism have been reported. Here we describe the first report with community-acquired pneumonia (CAP) caused by M. antarcticus.Case presentationAn 87-year-old female was presented to the Central Hospital of Wuhan in November 2023 with a chief complaint of cough, sputum production, and chest tightness for 2 weeks. Microbial culture of the patient’s bronchoalveolar lavage fluid (BALF) and identification of the isolates using Matrix-assisted laser desorption ionization/time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing revealed M. antarcticus infection. Combined with clinical symptoms, laboratory and imaging examination, the patient was diagnosed with CAP. Then cefoperazone/sulbactam and levofloxacin was administrated, the patient’s condition was improved and she was discharged after a week after admission, no abnormalities were detected during a 5-month follow-up.ConclusionsThis case highlights that M. antarcticus, first identified from a patient with CAP, is an extremely rare pathogenic microorganism. Clinicians should be aware of its potential as a pathogen in the diagnosis and treatment of CAP.

The Marine-Origin Exopolysaccharide-Producing Bacteria Micrococcus Antarcticus HZ Inhibits Pb Uptake in Pakchoi (Brassica chinensis L.) and Affects Rhizosphere Microbial Communities.

Exopolysaccharides (EPSs) produced by microorganisms play an important role in biotolerance and reducing heavy metal (HM) contamination by limiting the migration of HMs into plants. However, research on the application of EPS-producing marine bacteria for soil heavy metal remediation remains limited, particularly regarding their mechanisms of HM immobilization in soil and impact on plant growth. In this study, the EPS-producing marine bacterium Micrococcus antarcticus HZ was investigated for its ability to immobilize Pb and produce EPSs in soil filtrate. The effects on the growth quality and biomass of pakchoi (Brassica chinensis L.), as well as bacterial communities in inter-root soil contaminated with Pb, were also investigated. The results indicated that HZ could reduce the Pb concentration in the soil filtrate, achieving a removal rate of 43.25-63.5%. The EPS content and pH levels increased in the presence of Pb. Pot experiments showed that adding HZ significantly increased the biomass of pakchoi (9.45-14.69%), vitamin C (Vc) (9.69-12.92%), and soluble protein content (22.58-49.7%). HZ reduced the Pb content in the roots (17.52-47.48%) and leaves (edible tissues) (43.82-52.83%) of pakchoi. HZ increased soil enzyme activities (alkaline phosphatase, dehydrogenase, and urease), and the contents of ammonium nitrogen and nitrate nitrogen. Additionally, HZ also increased the relative abundance of beneficial bacteria (e.g., Proteobacteria, Cyanobacteria, and Chlorobacteria) in the inter-root soil, which have prophylactic and heavy-metal fixation functions. In summary, HZ reduces effective Pb content in edible tissues, roots, and inter-root soil by regulating inter-root soil microbial community structure, increasing soil pH, nitrogen content, and soil enzyme activity, and altering dominant phylum abundance.

Micrococcus porci sp. nov., Isolated from Feces of Black Pig (Sus scrofa).

An aerobic bacterium, designated as strain KD337-16T, was isolated from the fecal samples of a black pig. It exhibited spherical, non-motile and non−spore-forming, Gram-positive cells. KD337-16T was identified as a member of the genus Micrococcus through 16S rRNA gene sequencing, and its closest relatives were found to be Micrococcus endophyticus YIM 56238T (99.5% similarity), Micrococcus luteus NCTC 2665T (99.1%), Micrococcus yunnanensis YIM 65004T (99.1%), Micrococcus aloeverae AE-6T (99.1%), Micrococcus antarcticus T2T (98.9%), and Micrococcus flavus LW4T (98.7%). Phylogenomic trees were constructed, and strain KD337-16T was found to form its own cluster as an independent lineage of M. flavus LW4T. Between KD337-16T and its close relatives, the average nucleotide identity, average amino acid identity, and digital DNA−DNA hybridization were below the respective species delineation thresholds at 82.1−86.6%, 78.1−86.1%, and 24.4−34.9%. The major cellular fatty acids and polar lipids were anteiso-C15:0 and iso-C15:0, and DPG and PG, respectively. The predominant menaquinone was MK-8(H2). Taken together, the results indicate that strain KD337-16T is a novel species of the genus Micrococcus, for which the name Micrococcus porci sp. nov. is proposed. The type strain is KD337-16T (=BCRC 81318T = NBRC 115578T).

МИКРОБИОЛОГИЧЕСКИЕ И ГИДРОХИМИЧЕСКИЕ ИССЛЕДОВАНИЯ ПРИ ЭКСПЕРИМЕНТАЛЬНОМ КУЛЬТИВИРОВАНИИ РЫБЫ, МОЛЛЮСКОВ И РАСТЕНИЙ

The results of microbiological and hydrochemical studies in the experimental cultivation of fish, mollusks and plants are presented. Microorganisms were identified from the water of the fish-breeding tank: Escherichia coli, Proteus mirabilis, Citrobacter freundii, Enterococcus faecalis, Micrococcus chenggongense, Micrococcus flavus, Micrococcus antarcticus, Micrococcus cohnii, Renibacterium salmoninarum, Alcaligenes faecalis, Sarcina flava, Bacillus pumilus. The hydrochemical parameters of water generally corresponded to the normative indicators and remained at the same level after 66 days of the experiment. At the final stage of the experiments, concentration ammonium ions slightly exceeded the maximum allowable values. Сoncentration of nitrates when connecting growbox decreased to 15,0 mg/l. When taking into account the ichthyogenic sediment obtained from ≈ 90,0 g of feed given to fish (an expensive component of the production fish products), the rationality of its use decreased, as well as production efficiency due to contamination of the cultivation environment. In general, in addition to the ichthyogenic sediment, accumulation of soluble biogens took place in the fish-breeding tank. In the cultivation medium, soluble metabolic products accumulate, which are used as a potential food base for organisms of the next trophic level, until they are completely utilized within the system.

The effects of the recombinant YeaZ of Vibrio harveyi on the resuscitation and growth of soil bacteria in extreme soil environment.

Numerous bacteria entered the viable but non-culturable state due to the stresses of dry and salt in soils. YeaZ of Gram-negative bacteria is a resuscitation promoting factor (Rpf) homologous protein could resuscitate bacteria of natural environment in VBNC state. To investigate the promoting effect of YeaZ on the isolation of viable but non-culturable (VBNC) bacteria from soil samples in extreme environments, the recombinant YeaZ of Vibrio harveyi was prepared and added to the soil samples from volcanic soil and saline soil in Northwest China. The study has shown that YeaZ can promote the recovery and growth of soil microorganisms, and the number of cultivable bacteria in volcanic and saline soil has increased from 0.17 × 103 and 2.03 × 103 cfu⋅ml−1 to 1.00 × 103 and 5.55 × 103 cfu⋅ml−1, respectively. The 16S rDNA gene sequencing and phylogenetic analysis showed that YeaZ played an essential role in the increase of composition and diversity of bacteria. A total of 13 bacterial strains were isolated from the volcanic soil samples, which belong to phyla Actinobacteria, Firmicutes and Gamma-proteobacteria. Four species, including Ornithinimicrobium kibberense, Agrococcus citreus, Stenotrophomonas rhizophila and Pseudomonas zhaodongensis were found in the control group, while Micrococcus antarcticus, Kocuria rose, Salinibacterium xinjiangense, Planococcus antarcticus, Ornithinimicrobium kibberense and Pseudomonas zhaodongensis were isolated from the treatment groups (addition of YeaZ). Twenty-one strains were isolated from the saline soil samples, including eight species from the control group and thirteen species from the treatment groups, among which nine species were only found, including Bacillus oceanisediminis, Brevibacillus brevis, Paenibacillus xylanilyticus, Microbacterium maritypicum, B. subtilis, B. alcalophilus, B. niabensis, Oceanimonas doudoroffii and Zobellella taiwanensis. The results suggest that addition of YeaZ to soil samples can promote the recovery of VBNC. This method has the implications for the discovery of VBNC bacteria that have potential environmental functions.

HEAVY METAL TOLERANT BACTERIA ISOLATED AND DETECTED FROM THE EFFLUENT OF HAZARIBAGH TANNERY INDUSTRY IN DHAKA CITY

The tanning industry is held to be an activity with the high budding for environmental pollution all over the world. Many Bacterial strains isolated from natural resources have been found to possess unique properties which make them useful for environmental cleans ups. So it is very important to find out an alternative ecofriendly way for the treatment of contaminated effluent. The objective of this study was to isolate, explore and pick out natural occurring bacteria capable of reducing heavy metals from tannery effluent collected from the Hazaribagh tannery industry of Dhaka. The pH value of all the effluents samples were ranged from 7.12 to 7.91. Five bacterial strains were confirmed as Bacillus bataviensis, Bacillus aryabhattai, Micrococcus antarcticus, Bacillus proteolyticus and Bacillus paranthracis on the basis of their morphological, cultural, biochemical, and 16S rRNA gene sequencing. Among these five strains, Bacillus bataviensisD1 exhibited higher resistance to cadmium (Cd), chromium (Cr), copper (Cu), lead (Pb) and arsenic (As) up to the amount of 550 µg/mL, 500 µg/mL, 500 µg/mL, 1050 µg/mL and 1100µg/mL respectively. Bacillus aryabhattai D2 and Micrococcus antarcticus D3 showed similar result to chromium (Cr) and Lead (Pb), but Bacillus proteolyticus B1 showed higher resistance to nickel (Ni) that is up to 250 µg/mL. From these results, it can be suggested that the identified heavy metal-adapted bacteria could be useful for the biosorption of heavy metal contaminated effluent.

Production and upgrading of lactic acid: An overview and future prospects

The synthesis of glycosidic structures by catalysis via glycosynthases has gained much interest due to the potential high product yields and specificity of the enzymes. Nevertheless, the characterisation and implementation of new glycosynthases is greatly hampered by the lack of high-throughput methods for reaction analysis and screening of potential glycosynthase variants. Fluoride detection, via silyl ether chemosensors, has recently shown high potential for the identification of glycosynthase mutants in a high-throughput manner, though limited by the low maximal detection concentration. In the present paper, we describe a new version of a glycosynthase activity assay using a silyl ether of p-nitrophenol, allowing fast reliable detection of fluoride even at concentrations of 4 mM and higher. This improvement of detection allows not only screening and identification but also kinetic characterisation of glycosynthases and synthetic reactions in a fast microtiter plate format. The applicability of the assay was successfully demonstrated by the biochemical characterisation of the mesophilic β-glucosynthase of Abg-E358S (Rhizobium radiobacter) and psychrotolerant β-glucosynthase BglU-E377A (Micrococcus antarcticus). The limitation of hyperthermophilic glycosidases as potential glycosynthases, when using glycosyl fluoride donors, was also illustrated by the example of the putative β-galactosidase GalPf from Pyrococcus furiosus.

Lysosomal enzymes in Parkinson's disease

The synthesis of glycosidic structures by catalysis via glycosynthases has gained much interest due to the potential high product yields and specificity of the enzymes. Nevertheless, the characterisation and implementation of new glycosynthases is greatly hampered by the lack of high-throughput methods for reaction analysis and screening of potential glycosynthase variants. Fluoride detection, via silyl ether chemosensors, has recently shown high potential for the identification of glycosynthase mutants in a high-throughput manner, though limited by the low maximal detection concentration. In the present paper, we describe a new version of a glycosynthase activity assay using a silyl ether of p-nitrophenol, allowing fast reliable detection of fluoride even at concentrations of 4 mM and higher. This improvement of detection allows not only screening and identification but also kinetic characterisation of glycosynthases and synthetic reactions in a fast microtiter plate format. The applicability of the assay was successfully demonstrated by the biochemical characterisation of the mesophilic β-glucosynthase of Abg-E358S (Rhizobium radiobacter) and psychrotolerant β-glucosynthase BglU-E377A (Micrococcus antarcticus). The limitation of hyperthermophilic glycosidases as potential glycosynthases, when using glycosyl fluoride donors, was also illustrated by the example of the putative β-galactosidase GalPf from Pyrococcus furiosus.

Development of a colourimetric assay for glycosynthases

The synthesis of glycosidic structures by catalysis via glycosynthases has gained much interest due to the potential high product yields and specificity of the enzymes. Nevertheless, the characterisation and implementation of new glycosynthases is greatly hampered by the lack of high-throughput methods for reaction analysis and screening of potential glycosynthase variants. Fluoride detection, via silyl ether chemosensors, has recently shown high potential for the identification of glycosynthase mutants in a high-throughput manner, though limited by the low maximal detection concentration. In the present paper, we describe a new version of a glycosynthase activity assay using a silyl ether of p-nitrophenol, allowing fast reliable detection of fluoride even at concentrations of 4mM and higher. This improvement of detection allows not only screening and identification but also kinetic characterisation of glycosynthases and synthetic reactions in a fast microtiter plate format. The applicability of the assay was successfully demonstrated by the biochemical characterisation of the mesophilic β-glucosynthase of Abg-E358S (Rhizobium radiobacter) and psychrotolerant β-glucosynthase BglU-E377A (Micrococcus antarcticus). The limitation of hyperthermophilic glycosidases as potential glycosynthases, when using glycosyl fluoride donors, was also illustrated by the example of the putative β-galactosidase GalPf from Pyrococcus furiosus.

Specific amino acids responsible for the cold adaptedness of Micrococcus antarcticus β-glucosidase BglU.

Psychrophilic enzymes display efficient activity at moderate or low temperatures (4-25°C) and are therefore of great interest in biotechnological industries. We previously examined the crystal structure of BglU, a psychrophilic β-glucosidase from the bacterium Micrococcus antarcticus, at 2.2Å resolution. In structural comparison and sequence alignment with mesophilic (BglB) and thermophilic (GlyTn) counterpart enzymes, BglU showed much lower contents of Pro residue and of charged amino acids (particularly positively charged) on the accessible surface area. In the present study, we investigated the roles of specific amino acid residues in the cold adaptedness of BglU. Mutagenesis assays showed that the mutations G261R and Q448P increased optimal temperature (from 25 to 40-45°C) at the expense of low-temperature activity, but had no notable effects on maximal activity or heat lability. Mutations A368P, T383P, and A389E significantly increased optimal temperature (from 25 to 35-40°C) and maximal activity (~1.5-fold relative to BglU). Thermostability of A368P and A389E increased slightly at 30°C. Mutations K163P, N228P, and H301A greatly reduced enzymatic activity-almost completely in the case of H301A. Low contents of Pro, Arg, and Glu are important factors contributing to BglU's psychrophilic properties. Our findings will be useful in structure-based engineering of psychrophilic enzymes and in production of mutants suitable for a variety of industrial processes (e.g., food production, sewage treatment) at cold or moderate temperatures.

Comparative Analysis of the Bonding Modes between Two Antidiabetic Drugs with beta-Glucosidases from Different Species

β-glucosidase is one of the critical enzymes to the type 2 diabetes, which belongs to a large family of glycoside hydrolases. In this article, we attempted to explore the binding modes between two drugs and β-glucosidases by comparing their bonding modes with β-glucosidases from different species. Results showed that the binding orientations and geometrical conformation of synthetic drug (miglitol) and natural product (quercetin) were all different in all active sites, which may be related to the flexibility of the molecules. Compared with the conformations obtained by density functional theory calculations at the B3LYP/6-31G* level, the docking conformations indicated that the -CH2CH2OH group of miglitol and the B ring of quercetin were the most critical groups to the stabilities in the active sites. Finally, protein sequence alignment was performed under default parameters. Although the sequence similarity is not very high between these β-glucosidases, the residues related to the active sites were conservative; especially the one involved in H-bond interactions between three species, namely soil metagenome, Micrococcus antarcticus and termite Neotermes koshunensis.

16S rDNA Phylogenetic and RAPD–PCR Analyses of Petroleum Polycyclic Aromatic Hydrocarbons-Degrading Bacteria Enriched from Oil-Polluted Soils

Petroleum polycyclic aromatic hydrocarbons (PAHs) are health risks to human, as they can be toxic, mutagenic and carcinogenic. As the Kingdom of Saudi Arabia is one of the major petroleum-producing countries, they inevitably suffer from worsening this environmental problem. Therefore, removal of these compounds from the environment is a necessity for ensuring human health. In this study, 54 bacterial isolates were obtained by enrichment techniques from oil-contaminated soil samples. Out of them, seven gram-negative bacterial strains, KKU-J1, KKU-J2, KKU-J4, KKU-J7, KKU-J9, KKU-J14 and KKU-J17, exhibiting ability for petroleum PAHs degradation were selected. The isolates showing the highest growth during screening as demonstrated by the increase in their optical densities (OD600) and a concentration-dependent growth in all examined PAH compounds that grew in it, with strains KKU-J2, KKU-J7 and KKU-J17 were the best. The highest optimum growth rate of \({0.333 \pm 0.0, 0.364 \pm 0.016}\) and \({0.357 \pm 0.004 ({\rm OD}_{600})}\) was recorded for the strains KKU-J2, KKU-J7 and KKU-J17, respectively, when the level of phenanthrene was 100 mg/l. On the other hand, strain KKU-J2 was found to be the best one (\({0.413 \pm 0.0}\)) when the level of naphthalene was 100 mg/l. Molecular identification of the selected isolates was detected based on 16S rRNA gene amplification and partial sequence determination. Alignment results and the comparison of 16S rRNA gene sequences of the isolates to the 16S rRNA gene sequences available in GenBank database, as well as the phylogenetic analysis, confirmed the accurate position of the isolates as Sphingomonas paucimobilis KKU-J1, Pseudomonas alcaligenes KKU-J2, Micrococcus antarcticus KKU-J4, Arthrobacter oxydans KKU-J7, Stenotrophomonas rhizophila KKU-J9, Kocuria rhizophila KKU-J14 and Shinella zoogloeoides KKU-J17. RAPD–PCR fingerprinting was carried out for the seven isolates, and the DNA patterns revealed that there is no correlation between the RAPD profile and geographic origin sites where these isolates were collected from. This study indicates that the contaminated soil samples contain a diverse population of PAH-degrading bacteria, and the use of soil-associated microorganisms could be recommended for PAHs bioremediation in the environment.

Culturable and culture-independent bacterial diversity and the prevalence of cold-adapted enzymes from the Himalayan mountain ranges of India and Nepal.

Bacterial diversity of soil samples collected from different geographical regions of Himalayan mountains was studied through culturable (13 samples) and culture-independent approaches (5 samples based on abundance of diversity indices in each ecological niche). Shannon-Wiener diversity index and total bacterial count ranged from 1.50 ± 0.1 to 2.57 ± 0.15 and 7.8 ± 1.6 × 10(5) to 30.9 ± 1.7 × 10(5) cfu ml(-1) of soil, respectively. Based on morphology and pigmentation, 406 isolates were selected by culturing in different cultivable media at various strengths and concentrations. All the strains were subjected to amplified ribosomal DNA restriction analysis and the representative isolates from each cluster were chosen for 16S rRNA gene sequence-based identification. Soil habitat in Himalayan foot hills was dominated by the genera Arthrobacter, Exiguobacterium, Bacillus, Cedecea, Erwinia, and Pseudomonas. Five 16S rRNA gene libraries from the selected five samples yielded 268 clones and were grouped into 53 phylotypes covering 25 genera including the genus of Ferribacterium, Rothia, and Wautersiella, which were reported for the first time in Himalayan tracks. Principal coordinates analysis indicates that all the clone libraries were clearly separated and found to be significantly different from each other. Further, extracellular investigation of cold-active enzymes showed activity of cellulase (23.71%), pectinase (20.24%), amylase (17.32%), phytase (13.87%), protease (12.72%), and lipase (23.71%) among the isolates. Four isolates namely Exiguobacterium mexicanum (BSa14), Exiguobacterium sibiricum (BZa11), Micrococcus antarcticus (BSb10), and Bacillus simplex (BZb3) showed multiple enzyme activity for five different types of enzymes. In addition, various genera like Exiguobacterium, Erwinia, Mycetecola, Cedecea, Pantoea, and Trichococcus have also shown novel hydrolytic enzyme activity in the Himalayan foothills.

Gene cloning and characterization of a cold-adapted β-glucosidase belonging to glycosyl hydrolase family 1 from a psychrotolerant bacterium Micrococcus antarcticus

The gene bglU encoding a cold-adapted β-glucosidase (BglU) was cloned from Micrococcus antarcticus. Sequence analysis revealed that the bglU contained an open reading frame of 1419 bp and encoded a protein of 472 amino acid residues. Based on its putative catalytic domains, BglU was classified as a member of the glycosyl hydrolase family 1 (GH1). BglU possessed lower arginine content and Arg/(Arg + Lys) ratio than mesophilic GH1 β-glucosidases. Recombinant BglU was purified with Ni2+ affinity chromatography and subjected to enzymatic characterization. SDS-PAGE and native staining showed that it was a monomeric protein with an apparent molecular mass of 48 kDa. BglU was particularly thermolabile since its half-life time was only 30 min at 30 °C and it exhibited maximal activity at 25 °C and pH 6.5. Recombinant BglU could hydrolyze a wide range of aryl-β-glucosides and β-linked oligosaccharides with highest activity towards cellobiose and then p-nitrophenyl-β- d-glucopyranoside (pNPG). Under the optimal conditions with pNPG as substrate, the K m and k cat were 7 mmol/L and 7.85 × 103/s, respectively. This is the first report of cloning and characterization of a cold-adapted β-glucosidase belonging to GH1 from a psychrotolerant bacterium.

Micrococcus flavus sp. nov., isolated from activated sludge in a bioreactor

Bacterial strain LW4(T) was isolated from activated sludge of a wastewater-treatment bioreactor. Cells of strain LW4(T) were Gram-positive cocci, with a diameter of 0.7-1.0 microm. Colonies produced on LB agar plates were yellow, smooth, circular and 0.5-1.5 mm in diameter. Strain LW4(T) was aerobic and grew over the temperature range 26-34 degrees C and pH range 5-9, with optimal growth at 30.5-31.5 degrees C and pH 6.0-6.2. The cell-wall peptidoglycan of strain LW4(T) contained amino acid residues of lysine, glutamic acid, alanine, glycine and aspartic acid. The most abundant cellular fatty acids of strain LW4(T) were anteiso-C(15 : 0) (32.15 %) and iso-C(15 : 0) (31.65 %). Major respiratory quinones were MK-8(H(2)) (57.3 %) and MK-7(H(2)) (32.9 %). The DNA G+C content was 71.4 mol% (T(m)). 16S rRNA gene sequence analysis indicated that strain LW4(T) was phylogenetically related to members of the genus Micrococcus, with similarities ranging from 96.5 to 97.3 %. Levels of DNA-DNA relatedness of strain LW4(T) to Micrococcus luteus DSM 20030(T), Micrococcus lylae DSM 20315(T) and Micrococcus antarcticus AS 1.2372(T) were 55, 48 and 36 %, respectively. Based on these results, it is concluded that strain LW4(T) represents a novel species of the genus Micrococcus, for which the name Micrococcus flavus sp. nov. is proposed. The type strain is strain LW4(T) (=CGMCC 1.5361(T)=JCM 14000(T)).

Characterization of Micrococcus antarcticus sp. nov., a psychrophilic bacterium from Antarctica.

A Gram-positive, cold-adapted, aerobic, spherical actinobacterium (strain T2T) with a quite low cardinal growth temperature was isolated from Chinese Great-Wall station in Antarctica. Sequence comparisons of the 16S rDNA indicated the isolate to be a phylogenetic member of the genus Micrococcus, family Micrococcaceae, in which it represents a novel lineage. The phylogenetic distinctness of the isolate with respect to the type strains Micrococcus luteus and Micrococcus lylae was supported by DNA-DNA similarity values of less than 40%. Chemotaxonomic properties supported the placement of the isolate in the genus Micrococcus. The diagnostic diamino acid of the cell-wall peptidoglycan is lysine. The predominant menaquinones are MK-8 and MK-8(H2). The G + C content of the DNA of the isolate is 66.4 mol%. Genotypic, morphological and physiological characteristics were used to describe a new species of Micrococcus, for which the name Micrococcus antarcticus is proposed. The type strain is T2T (= AS 1.2372T).