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Microbiology Resource Announcements Dec 2022Phage ScienceWizSam was isolated from soil using sp. strain ATCC 21022. The phage genome is 58,217 bp with 96 open reading frames (ORFs). All of the ORFs are...
Phage ScienceWizSam was isolated from soil using sp. strain ATCC 21022. The phage genome is 58,217 bp with 96 open reading frames (ORFs). All of the ORFs are transcribed rightwards. Based on gene content similarity, ScienceWizSam is assigned to phage subcluster AU1.
PubMed: 36342275
DOI: 10.1128/mra.00927-22 -
ISME Communications Mar 2022Niche environmental conditions influence both the structure and function of microbial communities and the cellular function of individual strains. The terrestrial...
Niche environmental conditions influence both the structure and function of microbial communities and the cellular function of individual strains. The terrestrial subsurface is a dynamic and diverse environment that exhibits specific biogeochemical conditions associated with depth, resulting in distinct environmental niches. Here, we present the characterization of seven distinct strains belonging to the genus Arthrobacter isolated from varying depths of a single sediment core and associated groundwater from an adjacent well. We characterized genotype and phenotype of each isolate to connect specific cellular functions and metabolisms to ecotype. Arthrobacter isolates from each ecotype demonstrated functional and genomic capacities specific to their biogeochemical conditions of origin, including laboratory-demonstrated characterization of salinity tolerance and optimal pH, and genes for utilization of carbohydrates and other carbon substrates. Analysis of the Arthrobacter pangenome revealed that it is notably open with a volatile accessory genome compared to previous pangenome studies on other genera, suggesting a high potential for adaptability to environmental niches.
PubMed: 37938300
DOI: 10.1038/s43705-022-00113-8 -
Applied and Environmental Microbiology Nov 2022Proteins immobilized on biosilica which have superior reactivity and specificity and are innocuous to natural environments could be useful biological materials in...
Proteins immobilized on biosilica which have superior reactivity and specificity and are innocuous to natural environments could be useful biological materials in industrial processes. One recently developed technique, living diatom silica immobilization (LiDSI), has made it possible to immobilize proteins, including multimeric and redox enzymes, via a cellular excretion system onto the silica frustule of the marine diatom . However, the number of application examples so far is limited, and the type of proteins appropriate for the technique is still enigmatic. Here, we applied LiDSI to six industrially relevant polypeptides, including protamine, metallothionein, phosphotriesterase, choline oxidase, laccase, and polyamine synthase. Protamine and metallothionein were successfully immobilized on the frustule as protein fusions with green fluorescent protein (GFP) at the N terminus, indicating that LiDSI can be used for polypeptides which are rich in arginine and cysteine. In contrast, we obtained mutants for the latter four enzymes in forms without green fluorescent protein. Immobilized phosphotriesterase, choline oxidase, and laccase showed enzyme activities even after the purification of frustule in the presence of 1% (wt/vol) octylphenoxy poly(ethyleneoxy)ethanol. An immobilized branched-chain polyamine synthase changed the intracellular polyamine composition and silica nanomorphology. These results illustrate the possibility of LiDSI for industrial applications. Proteins immobilized on biosilica which have superior reactivity and specificity and are innocuous to natural environments could be useful biological materials in industrial processes. Living diatom silica immobilization (LiDSI) is a recently developed technique for protein immobilization on the diatom frustule. We aimed to explore the possibility of using LiDSI for industrial applications by successfully immobilizing six polypeptides: (i) protamine (Oncorhynchus keta), a stable antibacterial agent; (ii) metallothionein (Saccharomyces cerevisiae), a metal adsorption molecule useful for bioremediation; (iii) phosphotriesterase (Sulfolobus solfataricus), a scavenger for toxic organic phosphates; (iv) choline oxidase (Arthrobacter globiformis), an enhancer for photosynthetic activity and yield of plants; (v) laccase (Bacillus subtilis), a phenol oxidase utilized for delignification of lignocellulosic materials; and (vi) branched-chain polyamine synthase (Thermococcus kodakarensis), which produces branched-chain polyamines important for DNA and RNA stabilization at high temperatures. This study provides new insights into the field of applied biological materials.
Topics: Diatoms; Green Fluorescent Proteins; Laccase; Silicon Dioxide; Peptides; Polyamines; Phosphoric Triester Hydrolases; Metallothionein; Protamines
PubMed: 36226967
DOI: 10.1128/aem.01153-22 -
Microorganisms Feb 2020The rhizosphere microbiome is key in survival, development, and stress tolerance in plants. Salinity, drought, and extreme temperatures are frequent events in the...
The rhizosphere microbiome is key in survival, development, and stress tolerance in plants. Salinity, drought, and extreme temperatures are frequent events in the Atacama Desert, considered the driest in the world. However, little information of the rhizosphere microbiome and its possible contribution to the adaptation and tolerance of plants that inhabit the desert is available. We used a high-throughput Illumina MiSeq sequencing approach to explore the composition, diversity, and functions of fungal and bacterial communities of the rhizosphere of and native plants from the Atacama Desert. Our results showed that the fungal phyla Ascomycota and Basidiomycota and the bacterial phyla Actinobacteria and Proteobacteria were the dominant taxa in the rhizosphere of both plants. The linear discriminant analysis (LDA) effect size (LefSe) of the rhizosphere communities associated with showed the genera and were the preferential taxa, whereas the genera and was the preferential taxa in Both plant showed similar diversity, richness, and abundance according to Shannon index, observed OTUs, and evenness. Our results indicate that there are no significant differences ( = 0.1) between the fungal and bacterial communities of both plants, however through LefSe, we find taxa associated with each plant species and the PCoA shows a separation between the samples of each species. This study provides knowledge to relate the assembly of the microbiome to the adaptability to drought stress in desert plants.
PubMed: 32033093
DOI: 10.3390/microorganisms8020209 -
Frontiers in Microbiology 2023According to average nucleotide identity (ANI) analysis of the complete genomes, strain 24S4-2 isolated from Antarctica is considered as a potential novel species. sp....
According to average nucleotide identity (ANI) analysis of the complete genomes, strain 24S4-2 isolated from Antarctica is considered as a potential novel species. sp. 24S4-2 could grow and produce ammonium in nitrate or nitrite or even nitrogen free medium. Strain 24S4-2 was discovered to accumulate nitrate/nitrite and subsequently convert nitrate to nitrite intracellularly when incubated in a nitrate/nitrite medium. In nitrogen-free medium, strain 24S4-2 not only reduced the accumulated nitrite for growth, but also secreted ammonia to the extracellular under aerobic condition, which was thought to be linked to nitrite reductase genes and by the transcriptome and RT-qPCR analysis. A membrane-like vesicle structure was detected in the cell of strain 24S4-2 by transmission electron microscopy, which was thought to be the site of intracellular nitrogen supply accumulation and conversion. This spatial and temporal conversion process of nitrogen source helps the strain maintain development in the absence of nitrogen supply or a harsh environment, which is part of its adaption strategy to the Antarctic environment. This process may also play an important ecological role, that other bacteria in the environment would benefit from its extracellular nitrogen source secretion and nitrite consumption characteristics.
PubMed: 36876078
DOI: 10.3389/fmicb.2023.1040201 -
AMB Express May 2022As a kind of refractory organic pollutant, 4-fluorophenol (4-FP) can be degraded by only a few microorganisms with low efficiency because of the great...
As a kind of refractory organic pollutant, 4-fluorophenol (4-FP) can be degraded by only a few microorganisms with low efficiency because of the great electron-withdrawing ability of fluorine atoms. So it is necessary to artificially construct engineered strain to improve the degradation efficiency and meet the requirements of pollutant degradation. In this study, four genes (fpdA2, fpdB, fpdC, and fpdD) for 4-FP degradation from Arthrobacter sp. strain IF1 were optimized and synthesized and then reconstructed into Escherichia coli by a multi-monocistronic vector to obtain recombinant BL-fpd that could degrade 4-FP efficiently. Under optimized induction conditions (inducing the strain by 2 g/L L-arabinose and 1 mM IPTG at 37 ℃), BL-fpd could completely degrade 2 mM 4-FP, 4-chlorophenol, 4-bromophenol, and 4-nitrophenol into β-ketoadipate, which could be further metabolized by the bacteria. FpdA2 showed the highest activity towards 4-bromophenol. The strain could completely degrade 1 mM 4-FP in industrial wastewater within 3 h. This study provided a promising strain for the degradation of 4-FP and some other 4-substituted phenols. The construction technologies of multi-monocistronic expression vector may also be used to construct other organic pollutants degrading bacteria.
PubMed: 35567640
DOI: 10.1186/s13568-022-01396-9 -
Frontiers in Microbiology 2020Ongoing climate change involves increasing snow scarcity, which results in more frequent freeze-thaw cycles (FTCs) in polar and alpine soils. Although repeated FTCs have...
Ongoing climate change involves increasing snow scarcity, which results in more frequent freeze-thaw cycles (FTCs) in polar and alpine soils. Although repeated FTCs have been shown to alter the structure and functions of soil microbial communities, a thorough understanding on the influence of FTCs frequency on polar and especially alpine soil microbiomes is still elusive. Here, we investigated the impact of repeated weekly vs. daily FTC frequencies on the structure and functions of prokaryotic and fungal communities from north- and south-exposed soils from two mountain ridges, one in the Arctic and one in the High-Alps. FTCs affected prokaryotic communities more strongly than fungal communities, where mainly cold-tolerant and opportunistic fungi (e.g., , ) were responsive. Prokaryotic communities were more affected by weekly FTCs than by daily FTCs. Daily FTCs favored fast-growing bacteria (e.g., ), while oligotrophic and largely uncultured taxa (e.g., Verrucomicrobia) benefited from weekly FTCs. FTCs negatively affected microbial respiration but had minor impacts on C-, N- and P-acquiring enzymatic activities. Plausible pre-adaptation of the microbial communities to naturally occurring frequent FTCs at their site of origin did not show a clear influence on the microbial responses to the tested FTCs. Altogether, our study provides an integrative overview on potential structural and functional changes of soil microbial communities in polar and alpine regions in response to the projected increase in FTCs; therefore advancing our understanding on the impact of climate change in these rapidly changing ecosystems.
PubMed: 32523565
DOI: 10.3389/fmicb.2020.00982 -
Microbiology Resource Announcements May 2022Bacteriophages Phives, Kaylissa, and Eraser are siphoviruses infecting Arthrobacter globiformis B-2880 that were isolated in fall 2019 in Long Island, New York, from...
Bacteriophages Phives, Kaylissa, and Eraser are siphoviruses infecting Arthrobacter globiformis B-2880 that were isolated in fall 2019 in Long Island, New York, from soil samples collected in Old Westbury, New York. All three bacteriophages are assigned to phage cluster AZ based on gene content similarity. While many aspects of the genomes are similar across the three phages, the endolysin genes for the phages are different and are located in different locations within the genomes.
PubMed: 35389259
DOI: 10.1128/mra.00178-22 -
Case Reports in Ophthalmology 2024Infectious keratitis, an inflammatory condition of the cornea, poses a significant public health concern globally. Bacterial keratitis, the most common type, primarily...
INTRODUCTION
Infectious keratitis, an inflammatory condition of the cornea, poses a significant public health concern globally. Bacterial keratitis, the most common type, primarily involves and . Timely diagnosis and treatment are crucial to prevent vision loss.
CASE PRESENTATION
This case report presents a 78-year-old male patient with a burning sensation persisting for 1 week. The patient was diagnosed with keratitis caused by Arthrobacter, a Gram-positive coccobacillus commonly found in the environment. While the literature reports a few cases of Arthrobacter species keratitis, limited data exist regarding its clinical course and outcomes. Treatment with ciprofloxacin eye drops resulted in complete resolution of symptoms and a clear cornea upon final follow-up.
CONCLUSION
Arthrobacter, a rare causative agent of keratitis, requires early suspicion for accurate diagnosis and treatment. Despite the limited literature on Arthrobacter keratitis, this case highlights the importance of considering uncommon pathogens in corneal infections. Further research is necessary to understand the prevalence and clinical course of Arthrobacter keratitis.
PubMed: 38623408
DOI: 10.1159/000538474 -
Engineering in Life Sciences Aug 2023The glycoside hydrolase family contains enzymes that break the glycosidic bonds of carbohydrates by hydrolysis. Inulinase is one of the most important industrial enzymes...
The glycoside hydrolase family contains enzymes that break the glycosidic bonds of carbohydrates by hydrolysis. Inulinase is one of the most important industrial enzymes in the family of Glycoside Hydrolases 32 (GH32). In this study, to identify and classify bacterial inulinases initially, 16,002 protein sequences belonging to the GH32 family were obtained using various databases. The inulin-effective enzymes (endoinulinase and exoinulinase) were identified. Eight endoinulinases (EC 3.2.1.7) and 4318 exoinulinases (EC 3.2.1.80) were found. Then, the localization of endoinulinase and exoinulinase enzymes in the cell was predicted. Among them, two extracellular endoinulinases and 1232 extracellular exoinulinases were found. The biochemical properties of 363 enzymes of the genus , , and (most abundant) showed that exoinulinases have an acid isoelectric point up to the neutral range due to their amino acid length. That is, the smaller the protein (336 aa), the more acidic the pI (4.39), and the larger the protein (1207 aa), the pI is in the neutral range (8.84). Also, a negative gravitational index indicates the hydrophilicity of exoinulinases. Finally, considering the biochemical properties affecting protein stability and post-translational changes studies, one enzyme for endoinulinase and 40 enzymes with desirable characteristics were selected to identify their enzyme production sources. To screen and isolate enzyme-containing strains, now with the expansion of databases and the development of bioinformatics tools, it is possible to classify, review and analyze a lot of data related to different enzyme-producing strains. Although, in laboratory studies, a maximum of 20 to 30 strains can be examined. Therefore, when more strains are examined, finally, strains with more stable and efficient enzymes were selected and introduced for laboratory activities. The findings of this study can help researchers to select the appropriate gene source from introduced strains for cloning and expression heterologous inulinase, or to extract native inulinase from introduced strains.
PubMed: 37533727
DOI: 10.1002/elsc.202300003