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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 -
Biology Oct 2023The Barents Sea is one of the most rapidly changing Arctic regions, with an unprecedented sea ice decline and increase in water temperature and salinity. We have studied...
The Barents Sea is one of the most rapidly changing Arctic regions, with an unprecedented sea ice decline and increase in water temperature and salinity. We have studied the diversity of prokaryotic communities using 16S metabarcoding in the western and northeastern parts of the Barents Sea along the Kola Section and the section from Novaya Zemlya to Franz Joseph Land. The hypothesis-independent clustering method revealed the existence of two distinct types of communities. The most common prokaryotic taxa were shared between two types of communities, but their relative abundance was different. It was found that the geographic location of the sampling sites explained more than 30% of the difference between communities, while no statistically significant correlation between environmental parameters and community composition was found. The representatives of the , and genera were dominant in samples from both types of communities. The first type of community was also dominated by members of , , and an unclassified representative of the family. The second type of community also had a significant proportion of , SAR92, SAR11 Clade I, NS9, and SUP05 representatives. The origin of these communities can be explained by the influence of environmental factors or by the different origins of water masses. This research highlights the importance of studying biogeographic patterns in the Barents Sea in comparison with those in the North Atlantic and Arctic Ocean prokaryote communities.
PubMed: 37887020
DOI: 10.3390/biology12101310 -
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 -
International Journal of Biological... Jan 2022β-carotene is a natural compound with immense healthcare benefits. To overcome insolubility and lack of stability which restricts its application, in this study,... (Comparative Study)
Comparative Study
Comparative performance evaluation of chitosan based polymeric microspheres and nanoparticles as delivery system for bacterial β-carotene derived from Planococcus sp. TRC1.
β-carotene is a natural compound with immense healthcare benefits. To overcome insolubility and lack of stability which restricts its application, in this study, β-carotene from Planococcus sp. TRC1 was entrapped into formulations of chitosan‑sodium alginate microspheres (MF1, MF2 and MF3) and chitosan nanoparticles (NF1, NF2 and NF3). The maximum entrapment efficiency (%) and loading capacity (%) were 80.6 ± 4.28 and 26 ± 3.05 (MF2) and 92.1 ± 3.44 and 41.86 ± 4.65 (NF2) respectively. Korsmeyer-Peppas model showed best fit with release, revealing non-Fickian diffusion. Thermal and UV treatment exhibited higher activation energy (kJ/mol), 17.76 and 15.57 (MF2) and 37.03 and 19.33 (NF2) compared to free β-carotene (3.7 and 3.9), uncovering enhanced stability. MF2 and NF2 revealed swelling index (%) 721 ± 1.7 and 18.1 ± 1.5 (pH 6.8) and particle size 69.5 ± 3.2 μm and 92 ± 2.5 nm respectively. FESEM, FT-IR, XRD and DSC depicted spherical morphology, intactness of functional groups and masking of crystallinity. The IC (μg ml) values for antioxidant and anticancer (A-549) activities were 33.1 ± 1.7, 45.1 ± 2.8, 39.3 ± 2.9 and 31.3 ± 1.7, 27.9 ± 2.4, 25.3 ± 2.2 for β-carotene, MF2 and NF2 respectively with no significant cytotoxicity on HEK-293 cells and RBCs (p > 0.05). This comparative study of microspheres and nanoparticles may allow the diverse applications of an unconventional bacterial β-carotene with promising stability and efficacies.
Topics: Alginates; Chemistry, Pharmaceutical; Chitosan; Diffusion; Drug Carriers; Drug Compounding; Drug Delivery Systems; HEK293 Cells; Humans; Microspheres; Nanoparticles; Particle Size; Planococcaceae; Spectroscopy, Fourier Transform Infrared; beta Carotene
PubMed: 34863970
DOI: 10.1016/j.ijbiomac.2021.11.167 -
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 -
ACS Synthetic Biology Nov 2018Ureolytic bacteria ( e.g., Sporosarcina pasteurii) can produce calcium carbonate (CaCO). Tailoring the size and shape of biogenic CaCO may increase the range of useful...
Ureolytic bacteria ( e.g., Sporosarcina pasteurii) can produce calcium carbonate (CaCO). Tailoring the size and shape of biogenic CaCO may increase the range of useful applications for these crystals. However, wild type Sporosarcina pasteurii is difficult to genetically engineer, limiting control of the organism and its crystal precipitates. Therefore, we designed, constructed, and compared different urease operons and expression levels for CaCO production in engineered Escherichia coli strains. We quantified urease expression and calcium uptake and characterized CaCO crystal phase and morphology for 13 engineered strains. There was a weak relationship between urease expression and crystal size, suggesting that genes surrounding the urease gene cluster affect crystal size. However, when evaluating strains with a wider range of urease expression levels, there was a negative relationship between urease activity and polycrystal size (e.g., larger crystals with lower activity). The resulting range of crystal morphologies created by the rationally designed strains demonstrates the potential for controlling biogenic CaCO precipitation.
Topics: Calcium; Calcium Carbonate; Crystallization; Escherichia coli; Genetic Engineering; Multigene Family; Operon; Plasmids; Sporosarcina; Urease
PubMed: 30384588
DOI: 10.1021/acssynbio.8b00194 -
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 -
Bioresource Technology Nov 2022Anaerobic digestion of kitchen waste with grass after hyperthermophilic pretreatment was performed in semi-continuously operated reactors. The greatest methane yield of...
Anaerobic digestion of kitchen waste with grass after hyperthermophilic pretreatment was performed in semi-continuously operated reactors. The greatest methane yield of 293 NmlCH/gVS (volatile solids) was reported for the mixture of both substrates at 55 °C with a solids retention time of 30 d and the corresponding organic lading rate of 1.72 kgVS/m/d. In contrast, pretreated grass subjected to thermophilic digestion produced only 131 NmlCH/gVS. However, when mesophilic conditions were applied, the digestion process turned into dark fermentation, especially visible for the mixture. Metagenomic analysis revealed the dominance Ruminococcaceae, Atopobiaceae and Lactobacillaceae at a family level in mesophilic processes, whereas Petrotogaceae, Synergistaceae, Hungateiclostridiaceae, Planococcaceae and two methanogens Methanosarcinaceae and Methanothermobacteriaceae were the most frequent microbes of thermophilic digestion. Kitchen waste can successfully be co-digested with hyperthermophilically pretreated grass at high loading rates, however the digesters must be operated at thermophilic temperatures.
PubMed: 36195216
DOI: 10.1016/j.biortech.2022.128053