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International Journal of Systematic and... Apr 2020
Erratum: When treated as heterotypic synonyms the names Peshkoff 1939 (Approved Lists 1980) and Peshkoff 1939 (Approved Lists 1980) have priority over the names Krasil'nikov 1949 (Approved Lists 1980) and Prévot 1953 (Approved Lists 1980) and Prévot 1953 (Approved Lists 1980), respectively.
PubMed: 32559832
DOI: 10.1099/ijsem.0.004079 -
Archives of Microbiology Dec 2021A Gram-positive, aerobic and short rod-shaped bacterium designated REN13, was isolated from pit mud of Baijiu, in Sichuan province, China. Strain REN13 could grow at...
A Gram-positive, aerobic and short rod-shaped bacterium designated REN13, was isolated from pit mud of Baijiu, in Sichuan province, China. Strain REN13 could grow at 10-50 ℃, pH 6.0-9.0 and 0-2% (w/v) NaCl, with the optimal growth occurred at 28 ℃, pH 7.0, and 2% (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain REN13 was closely related to Sporosarcina globispora DSM 4 (98.6%). The DNA G + C content of strain REN13 was 41.1 mol %. DDH and ANI value between strain REN13 and S. globispora DSM 4 was 24.4% and 67.6%, respectively. The major fatty acids were iso-C and antesio-C. The respiratory quinone was MK-7, and the polar lipids were phosphatidylethanolamine, phospholipids, phosphatidylglycerol and diphosphatidylglycerol. Based on the above polyphasic taxonomic analysis, strain REN13 represents a novel species of the genus Sporosarcina, for which the name Sporosarcina beigongshangi sp. nov. is proposed. The type strain is strain REN13 (= JCM 34409 = GDMCC 1.2151).
Topics: Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sporosarcina
PubMed: 34877615
DOI: 10.1007/s00203-021-02601-2 -
Microbial Cell Factories Oct 2021Members of the genus Planococcus have been revealed to utilize and degrade solvents such as aromatic hydrocarbons and alkanes, and likely to acquire tolerance to...
BACKGROUND
Members of the genus Planococcus have been revealed to utilize and degrade solvents such as aromatic hydrocarbons and alkanes, and likely to acquire tolerance to solvents. A yellow marine bacterium Planococcus maritimus strain iso-3 was isolated from an intertidal sediment that looked industrially polluted, from the Clyde estuary in the UK. This bacterium was found to produce a yellow acyclic carotenoid with a basic carbon 30 (C) structure, which was determined to be methyl 5-glucosyl-5,6-dihydro-4,4'-diapolycopenoate. In the present study, we tried to isolate and identify genes involved in carotenoid biosynthesis from this marine bacterium, and to produce novel or rare C-carotenoids with anti-oxidative activity in Escherichia coli by combinations of the isolated genes.
RESULTS
A carotenoid biosynthesis gene cluster was found out through sequence analysis of the P. maritimus genomic DNA. This cluster consisted of seven carotenoid biosynthesis candidate genes (orf1-7). Then, we isolated the individual genes and analyzed the functions of these genes by expressing them in E. coli. The results indicated that orf2 and orf1 encoded 4,4'-diapophytoene synthase (CrtM) and 4,4'-diapophytoene desaturase (CrtNa), respectively. Furthermore, orf4 and orf5 were revealed to code for hydroxydiaponeurosporene desaturase (CrtNb) and glucosyltransferase (GT), respectively. By utilizing these carotenoid biosynthesis genes, we produced five intermediate C-carotenoids. Their structural determination showed that two of them were novel compounds, 5-hydroxy-5,6-dihydro-4,4'-diaponeurosporene and 5-glucosyl-5,6-dihydro-4,4'-diapolycopene, and that one rare carotenoid 5-hydroxy-5,6-dihydro-4,4'-diapolycopene is included there. Moderate singlet oxygen-quenching activities were observed in the five C-carotenoids including the two novel and one rare compounds.
CONCLUSIONS
The carotenoid biosynthesis genes from P. maritimus strain iso-3, were isolated and functionally identified. Furthermore, we were able to produce two novel and one rare C-carotenoids in E. coli, followed by positive evaluations of their singlet oxygen-quenching activities.
Topics: Antioxidants; Carotenoids; Escherichia coli; Genes, Bacterial; Planococcaceae
PubMed: 34627253
DOI: 10.1186/s12934-021-01683-3 -
Water Research Feb 2021Reusing produced water (PW) as the subsequent hydraulic fracturing fluid is currently the most economical and dominant practice in the shale oil and gas industry....
Reusing produced water (PW) as the subsequent hydraulic fracturing fluid is currently the most economical and dominant practice in the shale oil and gas industry. However, high Ca present in PW needs to be removed prior to reuse to minimize the potential for well clogging and formation damage. In this study, the microbially induced calcite precipitation (MICP), as an emerging biomineralization technique mediated by ureolytic bacteria, was employed to remove Ca and toxic contaminants from hypersaline PW for the first time. Batch and continuous studies demonstrated the feasibility of MICP for Ca removal from hypersaline PW under low urea and nutrient conditions. Throughout the continuous biofiltration operation with biochar as the media, high removal efficiencies of Ca (~96%), organic contaminants (~100%), and heavy metals (~100% for As, Cd, Mn and Ni, 92.2% for Ba, 94.2% for Sr) were achieved when PW co-treated with synthetic domestic wastewater (SDW) under the condition of PW:SDW = 1:1 & urea 4 g/L. Metagenomic sequencing analysis showed that a stable ureolytic bacterial consortium (containing Sporosarcina and Arthrobacter at the genus level) was constructed in the continuous biofiltration system under hypersaline conditions, which may play a crucial role during the biomineralization process. Moreover, the combination of the MICP and ammonium recovery could significantly reduce the acute toxicity of PW towards Vibrio fischeri by 72%. This research provides a novel insight into the biomineralization of Ca and heavy metals from hypersaline PW through the MICP technique. Considering the low cost and excellent treatment performance, the proposed process has the potential to be used for both hydraulic fracturing reuse and desalination pretreatment on a large scale.
Topics: Biomineralization; Calcium Carbonate; Chemical Precipitation; Sporosarcina; Urea; Water
PubMed: 33360619
DOI: 10.1016/j.watres.2020.116753 -
Journal of Hazardous Materials Jul 2021This study reported a novel facultative anaerobic Cr(VI)-reducing bacteria (Sporosarcina saromensis W5) and investigated its Cr(VI) removal performances and removal...
This study reported a novel facultative anaerobic Cr(VI)-reducing bacteria (Sporosarcina saromensis W5) and investigated its Cr(VI) removal performances and removal mechanisms. The strain W5 was able to grow and reduce Cr(VI) under aerobic and anaerobic environment, and exhibited considerable Cr(VI) reduction capabilities under a wide range of pH (8.0-13.0), temperature (20-40 °C) and initial Cr(VI) concentration (50-800 mg/L). The addition of Cd severely inhibited its growth and Cr(VI) removal, while Cu and Fe significantly enhanced the removal efficiencies. The strain W5 could utilize various electron donors and mediators to accelerate Cr(VI) reduction. Aerobic Cr(VI) reduction mainly occurred in cytoplasm and the final products were soluble organo-Cr(III) complexes. Anaerobic Cr(VI) reduction was located in both cytoplasm and membrane, and the reduction products were soluble organo-Cr(III) complexes and Cr(III) precipitates. The functional groups of hydroxyl, carboxyl and phosphoryl on cell surface participated in the combination with Cr(III). Due to its facultative anaerobic property, S. saromensis W5 offers itself as a promising engineering strain for the bioremediation of Cr(VI)-contaminated areas, especially in hypoxia environments.
Topics: Bacteria; Bacteria, Anaerobic; Biodegradation, Environmental; Chromium; Oxidation-Reduction; Sporosarcina
PubMed: 33609863
DOI: 10.1016/j.jhazmat.2021.125411 -
Nucleic Acids Research Feb 2021Argonaute (Ago) proteins are conserved nucleic acid-guided proteins present in all domains of life. Eukaryotic Argonaute proteins (eAgos) are key players in RNA...
Argonaute (Ago) proteins are conserved nucleic acid-guided proteins present in all domains of life. Eukaryotic Argonaute proteins (eAgos) are key players in RNA interference pathways and function as RNA-guided RNA endonucleases at physiological temperatures. Although eAgos are considered to evolve from prokaryotic Argonaute proteins (pAgos), previously studied pAgos were unable to catalyze RNA-guided RNA cleavage at physiological temperatures. Here, we describe a distinctive pAgo from mesophilic bacteria Kurthia massiliensis (KmAgo). KmAgo utilizes DNA guides to cleave single-stranded DNA (ssDNA) and RNA targets with high activity. KmAgo also utilizes RNA guides to cleave ssDNA and RNA targets at moderate temperatures. We show that KmAgo can use 5' phosphorylated DNA guides as small as 9-mers to cut ssDNA and RNA, like Clostridium butyricum Ago. Small DNA binding confers remarkable thermostability on KmAgo, and we can suppress the guide-independent plasmid processing activity of empty KmAgo by elevating the DNA guide loaded temperature. Moreover, KmAgo performs programmable cleavage of double-stranded DNA and highly structured RNA at 37°C. Therefore, KmAgo can be regarded as a DNA-guided programmable omnipotent nuclease for cleaving most types of nucleic acids efficiently. This study broadens our understanding of Ago proteins and could expand the pAgo-based DNA and RNA manipulation toolbox.
Topics: Argonaute Proteins; Bacterial Proteins; Cations, Divalent; DNA Breaks, Double-Stranded; DNA, Single-Stranded; Planococcaceae; RNA; Temperature
PubMed: 33444443
DOI: 10.1093/nar/gkaa1278 -
Biomolecules Feb 2022Prokaryotic Argonautes (pAgos) from mesophilic bacteria are attracting increasing attention for their genome editing potential. So far, it has been reported that KmAgo...
Prokaryotic Argonautes (pAgos) from mesophilic bacteria are attracting increasing attention for their genome editing potential. So far, it has been reported that KmAgo from can utilize DNA and RNA guide of any sequence to effectively cleave DNA and RNA targets. Here we find that three active pAgos, which have about 50% sequence identity with KmAgo, possess typical DNA-guided DNA target cleavage ability. Among them, RsuAgo from is mainly explored for which can cleave both DNA and RNA targets. Interestingly, RsuAgo-mediated RNA target cleavage occurs only with short guide DNAs in a narrow length range (16-20 nt), and mismatches between the guide and target sequence greatly affect the efficiency of RNA target cleavage. RsuAgo-mediated target cleavage shows a preference for a guide strand with a 5'-terminal A residue. Furthermore, we have found that RsuAgo can cleave double-stranded DNA in a low-salt buffer at 37 °C. These properties of RsuAgo provide a new tool for DNA and RNA manipulation at moderate temperatures.
Topics: Argonaute Proteins; Bacteria; Bacterial Proteins; DNA; Endonucleases; Planococcaceae; RNA
PubMed: 35327547
DOI: 10.3390/biom12030355 -
Current Microbiology May 2022Gut microbiota is a complex ecosystem composed by trillions of microorganisms that are crucial for human health or disease status. Currently, there are two...
Gut microbiota is a complex ecosystem composed by trillions of microorganisms that are crucial for human health or disease status. Currently, there are two methodological options to explore its complexity: metagenomics and culturomics. Culturomics is an approach that uses multiple culture conditions (days of incubation, enrichment factors and growth temperature) and MALDI-TOF mass spectrometry for the identification of bacterial species and sequencing when this method fails. In this paper, we describe how Colturomic's protocol has allowed the first isolation in human sample of Rummeliibacillus suwonensis, a Gram positive, facultative anaerobe bacterium. The bacterium was isolated from feces of a 69 years old male with amyotrophic lateral sclerosis (ALS) recruited for a clinical trial assessing safety and efficacy of fecal microbiota transplantation in ALS. The first isolation of the microorganism dates back to 2013 from the soil of a South Korean mountain area. In this report, morphological description, biochemical characterization and antibiotic susceptibility tests were performed to outline the bacterial properties.
Topics: Aged; Amyotrophic Lateral Sclerosis; Feces; Humans; Male; Planococcaceae; RNA, Ribosomal, 16S
PubMed: 35595837
DOI: 10.1007/s00284-022-02806-8 -
Animals : An Open Access Journal From... Mar 2021Sample storage conditions are an important factor in fecal microbiota analyses in general. The objective of this study was to investigate the effect of sample storage at...
Sample storage conditions are an important factor in fecal microbiota analyses in general. The objective of this study was to investigate the effect of sample storage at room temperature on the equine fecal microbiota composition. Fecal samples were collected from 11 healthy horses. Each sample was divided into 7 sealed aliquots. One aliquot was immediately frozen at -80 °C; the remaining aliquots were stored at room temperature (21 to 22 °C) with one transferred to the freezer at each of the following time points: 6, 12, 24, 48, 72 and 96 h. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. Fibrobacteraceae () and Ruminococcaceae () were enriched in samples from 0 h and 6 h, whereas taxa from the families Bacillaceae, Planococcaceae, Enterobacteriaceae and Moraxellaceae were enriched in samples stored at room temperature for 24 h or greater. Samples frozen within the first 12 h after collection shared similar community membership. The community structure was similar for samples collected at 0 h and 6 h, but it was significantly different between samples frozen at 0 h and 12 h or greater. In conclusion, storage of equine fecal samples at ambient temperature for up to 6 h before freezing following sample collection had minimal effect on the microbial composition. Longer-term storage at ambient temperature resulted in alterations in alpha-diversity, community membership and structure and the enrichment of different taxa when compared to fecal samples immediately frozen at -80 °C.
PubMed: 33803934
DOI: 10.3390/ani11030819 -
Microbial Ecology Oct 2019Class B biosolids are used in dryland wheat (Triticum aestivum L.) production in eastern Washington as a source of nutrients and to increase soil organic matter, but...
Class B biosolids are used in dryland wheat (Triticum aestivum L.) production in eastern Washington as a source of nutrients and to increase soil organic matter, but little is known about their effects on bacterial communities and potential for harboring human pathogens. Moreover, conservation tillage is promoted to reduce erosion and soil degradation. We explored the impacts of biosolids or synthetic fertilizer in combination with traditional (conventional) or conservation tillage on soil bacterial communities. Bacterial communities were characterized from fresh biosolids, biosolid aggregates embedded in soil, and soil after a second application of biosolids using high-throughput amplicon sequencing. Biosolid application significantly affected bacterial communities, even 4 years after their application. Bacteria in the families Clostridiaceae, Norcardiaceae, Anaerolinaceae, Dietziaceae, and Planococcaceae were more abundant in fresh biosolids, biosolid aggregates, and soils treated with biosolids than in synthetically fertilized soils. Taxa identified as Turcibacter, Dietzia, Clostridiaceae, and Anaerolineaceae were highly abundant in biosolid aggregates in the soil and likely originated from the biosolids. In contrast, Oxalobacteriaceae, Streptomyceteaceae, Janthinobacterium, Pseudomonas, Kribbella, and Bacillus were rare in the fresh biosolids, but relatively abundant in biosolid aggregates in the soil, and probably originated from the soil to colonize the substrate. However, tillage had relatively minor effects on bacterial communities, with only a small number of taxa differing in relative abundance between traditional and conventional tillage. Although biosolid-associated bacteria persisted in soil, potentially pathogenic taxa were extremely rare and no toxin genes for key groups (Salmonella, Clostridium) were detectable, suggesting that although fecal contamination was apparent via indicator taxa, pathogen populations had declined to low levels. Thus, biosolid amendments had profound effects on soil bacterial communities both by introducing gut- or digester-derived bacteria and by enriching potentially beneficial indigenous soil populations.
Topics: Bacteria; Fertilizers; Phylogeny; Soil; Soil Microbiology; Triticum; Washington
PubMed: 30796467
DOI: 10.1007/s00248-019-01339-1