scholarly journals Novel Biphenyl-Oxidizing Bacteria and Dioxygenase Genes from a Korean Tidal Mudflat

2011 ◽  
Vol 77 (11) ◽  
pp. 3888-3891 ◽  
Author(s):  
Tae Kwon Lee ◽  
Jaejin Lee ◽  
Woo Jun Sul ◽  
Shoko Iwai ◽  
Benli Chai ◽  
...  
Keyword(s):  
Amino Acid ◽  
Stable Isotope ◽  
16S Rrna ◽  
Amino Acid Identity ◽  
Stable Isotope Probing ◽  
Content Type ◽  
Acid Identity ◽  
Rrna Sequences ◽  
Mudflat Sediments ◽  
16S Rrna Sequences

ABSTRACTGene-targeted FLX titanium pyrosequencing integrated with stable isotope probing (SIP) using [13C]biphenyl substrate revealed that tidal mudflat sediments harbor novel aromatic ring hydroxylating dioxygenases (ARHD). More than 80% of the detected ARHD genes comprise four clades (0.5 distance) with 49 to 70% amino acid identity to sequences in public databases. The 16S rRNA sequences enriched in the13C fraction were from theBetaproteobacteria, bacilli (primarilyPaenibacillus-like), and unclassified phyla.

scholarly journals Coproduction of 16S rRNA Methyltransferase RmtD or RmtG with KPC-2 and CTX-M Group Extended-Spectrum β-Lactamases in Klebsiella pneumoniae

2013 ◽  
Vol 57 (5) ◽  
pp. 2397-2400 ◽  
Author(s):  
Maria Fernanda C. Bueno ◽  
Gabriela R. Francisco ◽  
Jessica A. O'Hara ◽  
Doroti de Oliveira Garcia ◽  
Yohei Doi
Keyword(s):  
Amino Acid ◽  
16S Rrna ◽  
Klebsiella Pneumoniae ◽  
Amino Acid Identity ◽  
Aminoglycoside Resistance ◽  
Content Type ◽  
Acid Identity ◽  
Paulo State ◽  
Extended Spectrum ◽  
High Level

ABSTRACTEightKlebsiella pneumoniaeclinical strains with high-level aminoglycoside resistance were collected from eight hospitals in São Paulo State, Brazil, in 2010 and 2011. Three of them produced an RmtD group 16S rRNA methyltransferase, RmtD1 or RmtD2. Five strains were found to produce a novel 16S rRNA methyltransferase, designated RmtG, which shared 57 to 58% amino acid identity with RmtD1 and RmtD2. Seven strains coproduced KPC-2 with or without various CTX-M group extended-spectrum β-lactamases, while the remaining strain coproduced CTX-M-2.

scholarly journals PFM-Like Enzymes Are a Novel Family of Subclass B2 Metallo-β-Lactamases from Pseudomonas synxantha Belonging to the Pseudomonas fluorescens Complex

2019 ◽  
Vol 64 (2) ◽  
Author(s):  
Laurent Poirel ◽  
Mattia Palmieri ◽  
Michael Brilhante ◽  
Amandine Masseron ◽  
Vincent Perreten ◽  
...  
Keyword(s):  
Amino Acid ◽  
Pseudomonas Fluorescens ◽  
Bacterial Species ◽  
Amino Acid Identity ◽  
Chicken Meat ◽  
The Novel ◽  
Content Type ◽  
Acid Identity ◽  
Carbapenem Resistant ◽  
Encoding Genes

ABSTRACT A carbapenem-resistant Pseudomonas synxantha isolate recovered from chicken meat produced the novel carbapenemase PFM-1. That subclass B2 metallo-β-lactamase shared 71% amino acid identity with β-lactamase Sfh-1 from Serratia fonticola. The blaPFM-1 gene was chromosomally located and likely acquired. Variants of PFM-1 sharing 90% to 92% amino acid identity were identified in bacterial species belonging to the Pseudomonas fluorescens complex, including Pseudomonas libanensis (PFM-2) and Pseudomonas fluorescens (PFM-3), highlighting that these species constitute reservoirs of PFM-like encoding genes.

scholarly journals Draft Genome Sequence of Psychrobacter okhotskensis Strain 5179-1A, Isolated from a Raw Cured Ham Storage Crate

2020 ◽  
Vol 9 (29) ◽  
Author(s):  
Joseph Wambui ◽  
Marina Morach ◽  
Nicole Cernela ◽  
Marc J. A. Stevens ◽  
Giovanni Ghielmetti ◽  
...  
Keyword(s):  
16S Rrna ◽  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT We present the draft genome sequence of Psychrobacter okhotskensis strain 5179-1A, which was isolated from a raw cured ham storage crate. Its size and GC content are 3.4 Mb and 43.4%, respectively. The 16S rRNA sequences of strain 5179-1A and P. okhotskensis MD17T are 100% identical.

scholarly journals Differential Engagement of Fermentative Taxa in Gut Contents of the EarthwormLumbricus terrestris

2017 ◽  
Vol 84 (5) ◽  
Author(s):  
Anja B. Meier ◽  
Sindy Hunger ◽  
Harold L. Drake
Keyword(s):  
16S Rrna ◽  
Alimentary Canal ◽  
Alimentary Tract ◽  
Anaerobic Growth ◽  
Gut Contents ◽  
Content Type ◽  
Earthworm Gut ◽  
The Impact ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACTThe earthworm gut is an anoxic, saccharide-rich microzone in aerated soils. The apparent degradation of diverse saccharides in the alimentary canal of the model earthwormLumbricusterrestrisis concomitant with the production of diverse organic acids, indicating that fermentation is an ongoing process in the earthworm gut. However, little is known about how different gut-associated saccharides are fermented. The hypothesis of this investigation was that different gut-associated saccharides differentially stimulate fermentative microorganisms in gut contents ofL. terrestris. This hypothesis was addressed by (i) assessing the fermentation profiles of anoxic gut content microcosms that were supplemented with gut-associated saccharides and (ii) the concomitant phylogenic analysis of 16S rRNA sequences. Galactose, glucose, maltose, mannose, arabinose, fucose, rhamnose, and xylose stimulated the production of fermentation products, including H2, CO2, acetate, lactate, propionate, formate, succinate, and ethanol. Fermentation profiles were dependent on the supplemental saccharide (e.g., glucose yielded large amounts of H2and ethanol, whereas fucose did not, and maltose yielded large amounts of lactate, whereas mannose did not). Approximately 1,750,000 16S rRNA sequences were affiliated with 37 families, and phylogenic analyses indicated that a respective saccharide stimulated a subset of the diverse phylotypes. AnAeromonas-related phylotype displayed a high relative abundance in all treatments, whereas keyEnterobacteriaceae-affiliated phylotypes were stimulated by some but not all saccharides. Collectively, these results reinforce the likelihood that (i) different saccharides stimulate different fermentations in gut contents of the earthworm and (ii) facultative aerobes related toAeromonadaceaeandEnterobacteriaceaecan be important drivers of these fermentations.IMPORTANCEThe feeding habits of earthworms influence the turnover of elements in the terrestrial biosphere. The alimentary tract of the earthworm constitutes an anoxic saccharide-rich microzone in aerated soils that offers ingested microbes a unique opportunity for anaerobic growth. The fermentative activity of microbes in the alimentary tract are responsible for thein situproduction of (i) organic compounds that can be assimilated by the earthworm and (ii) H2that is subject toin vivoemission by the earthworm and can be trophically linked to secondary microbial events in soils. To gain insight on how fermentative members of the gut microbiome might respond to the saccharide-rich alimentary canal, this study examines the impact of diverse gut-associated saccharides on the differential activation of fermentative microbes in gut contents of the model earthwormL. terrestris.

scholarly journals Stable-Isotope Probing Identifies Uncultured Planctomycetes as Primary Degraders of a Complex Heteropolysaccharide in Soil

2015 ◽  
Vol 81 (14) ◽  
pp. 4607-4615 ◽  
Author(s):  
Xiaoqing Wang ◽  
Christine E. Sharp ◽  
Gareth M. Jones ◽  
Stephen E. Grasby ◽  
Allyson L. Brady ◽  
...  
Keyword(s):  
Stable Isotope ◽  
16S Rrna ◽  
Soil Bacteria ◽  
Stable Isotope Probing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Degrading Bacteria ◽  
Aerobic Soil

ABSTRACTThe exopolysaccharides (EPSs) produced by some bacteria are potential growth substrates for other bacteria in soil. We used stable-isotope probing (SIP) to identify aerobic soil bacteria that assimilated the cellulose produced byGluconacetobacter xylinusor the EPS produced byBeijerinckia indica. The latter is a heteropolysaccharide comprised primarily ofl-guluronic acid,d-glucose, andd-glycero-d-mannoheptose.13C-labeled EPS and13C-labeled cellulose were purified from bacterial cultures grown on [13C]glucose. Two soils were incubated with these substrates, and bacteria actively assimilating them were identified via pyrosequencing of 16S rRNA genes recovered from13C-labeled DNA. Cellulose C was assimilated primarily by soil bacteria closely related (93 to 100% 16S rRNA gene sequence identities) to known cellulose-degrading bacteria. However,B. indicaEPS was assimilated primarily by bacteria with low identities (80 to 95%) to known species, particularly by different members of the phylumPlanctomycetes. In one incubation, members of thePlanctomycetesmade up >60% of all reads in the labeled DNA and were only distantly related (<85% identity) to any described species. Although it is impossible with SIP to completely distinguish primary polysaccharide hydrolyzers from bacteria growing on produced oligo- or monosaccharides, the predominance ofPlanctomycetessuggested that they were primary degraders of EPS. Other bacteria assimilatingB. indicaEPS included members of theVerrucomicrobia, candidate division OD1, and theArmatimonadetes. The results indicate that some uncultured bacteria in soils may be adapted to using complex heteropolysaccharides for growth and suggest that the use of these substrates may provide a means for culturing new species.

scholarly journals Characterization ofpara-Nitrophenol-Degrading Bacterial Communities in River Water by Using Functional Markers and Stable Isotope Probing

2015 ◽  
Vol 81 (19) ◽  
pp. 6890-6900 ◽  
Author(s):  
Agnieszka Kowalczyk ◽  
Özge Eyice ◽  
Hendrik Schäfer ◽  
Oliver R. Price ◽  
Christopher J. Finnegan ◽  
...  
Keyword(s):  
Stable Isotope ◽  
16S Rrna ◽  
River Water ◽  
Stable Isotope Probing ◽  
Functional Markers ◽  
Polymorphism Analysis ◽  
Specific Marker ◽  
Environmental Distribution ◽  
Gram Negative ◽  
Content Type

ABSTRACTMicrobial degradation is a major determinant of the fate of pollutants in the environment.para-Nitrophenol (PNP) is an EPA-listed priority pollutant with a wide environmental distribution, but little is known about the microorganisms that degrade it in the environment. We studied the diversity of active PNP-degrading bacterial populations in river water using a novel functional marker approach coupled with [13C6]PNP stable isotope probing (SIP). Culturing together with culture-independent terminal restriction fragment length polymorphism analysis of 16S rRNA gene amplicons identifiedPseudomonas syringaeto be the major driver of PNP degradation in river water microcosms. This was confirmed by SIP-pyrosequencing of amplified 16S rRNA. Similarly, functional gene analysis showed that degradation followed the Gram-negative bacterial pathway and involvedpnpAfromPseudomonasspp. However, analysis of maleylacetate reductase (encoded bymar), an enzyme common to late stages of both Gram-negative and Gram-positive bacterial PNP degradation pathways, identified a diverse assemblage of bacteria associated with PNP degradation, suggesting thatmarhas limited use as a specific marker of PNP biodegradation. Both thepnpAandmargenes were detected in a PNP-degrading isolate,P. syringaeAKHD2, which was isolated from river water. Our results suggest that PNP-degrading cultures ofPseudomonasspp. are representative of environmental PNP-degrading populations.

scholarly journals First Report of the Carbapenemase Gene blaOXA-499 in Acinetobacter pittii

2017 ◽  
Vol 61 (5) ◽  
Author(s):  
Roshan D'Souza ◽  
Naina Adren Pinto ◽  
Paul G. Higgins ◽  
Insik Hwang ◽  
Dongeun Yong ◽  
...  
Keyword(s):  
Amino Acid ◽  
Clinical Isolate ◽  
Amino Acid Identity ◽  
Content Type ◽  
Acid Identity ◽  
First Report ◽  
Carbapenemase Gene ◽  
Acinetobacter Pittii ◽  
Encoding Gene ◽  
First Time

ABSTRACT We identified the carbapenemase gene bla OXA-499, a variant of bla OXA-143, from a clinical isolate of Acinetobacter pittii for the first time. OXA-499 shared 93.1% amino acid identity with OXA-143, and the gene was located on the chromosome. By cloning the OXA-499-encoding gene into the pWH1266 vector and transforming it into susceptible Acinetobacter spp., we were able to show that OXA-499 confers resistance to carbapenems.

scholarly journals Exploration of Two Pectate Lyases from Caldicellulosiruptor bescii Reveals that the CBM66 Module Has a Crucial Role in Pectic Biomass Degradation

2020 ◽  
Vol 86 (16) ◽  
Author(s):  
Hamed I. Hamouda ◽  
Nasir Ali ◽  
Hang Su ◽  
Jie Feng ◽  
Ming Lu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Plant Biomass ◽  
Degradation Products ◽  
Amino Acid Identity ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Module ◽  
Content Type ◽  
Acid Identity ◽  
Pectate Lyases ◽  
Caldicellulosiruptor Bescii

ABSTRACT Pectin deconstruction is the initial step in breaking the recalcitrance of plant biomass by using selected microorganisms that encode pectinolytic enzymes. Pectate lyases that cleave the α-1,4-galacturonosidic linkage of pectin are widely used in industries such as papermaking and fruit softening. However, there are few reports on pectate lyases with good thermostability. Here, two pectate lyases (CbPL3 and CbPL9) from a hyperthermophilic bacterium, Caldicellulosiruptor bescii, belonging to family 3 and family 9 polysaccharide lyases, respectively, were investigated. The biochemical properties of the two CbPLs were shown to be similar under optimized conditions of 80°C to 85°C and pH 8 to 9. However, the degradation products from pectin and polygalacturonic acids (pGAs) were different. A family 66 carbohydrate-binding module (CbCBM66) located in the N terminus of the two CbPLs shares 100% amino acid identity. A CbCBM66-truncated mutant of CbPL9 showed lower activities than the wild type, whereas CbPL3 with a CbCBM66 knockout portion was reported to have enhanced activities, thereby revealing the different effect of CbCBM66. Prediction by the I-TASSER server revealed that CbCBM66 is structurally close to BsCBM66 from Bacillus subtilis; however, the COFACTOR and COACH programs indicated that the substrate-binding sites between CbCBM66 and BsCBM66 are different. Furthermore, a substrate-binding assay indicated that the catalytic domains in the two CbPLs had strong affinities for pectate-related substrates, but CbCBM66 showed a weak interaction with a number of lignocellulosic carbohydrates. Finally, scanning electron microscopy (SEM) analysis and a total reducing sugar assay showed that the two enzymes could improve the saccharification of switchgrass. The two CbPLs are impressive sources for the degradation of plant biomass. IMPORTANCE Thermophilic proteins could be implemented in diverse industrial applications. We sought to characterize two pectate lyases, CbPL3 and CbPL9, from a thermophilic bacterium, Caldicellulosiruptor bescii. The two enzymes share a high optimum temperature, a low optimum pH, and good thermostability at the evaluated temperature. A family 66 carbohydrate-binding module (CbCBM66) was identified in the two CbPLs, sharing 100% amino acid identity. The deletion of CbCBM66 dramatically decreased the activity of CbPL9 but increased the activity and thermostability of CbPL3, suggesting different roles of CbCBM66 in the two enzymes. Moreover, the degradation products of the two CbPLs were different. These results revealed that these enzymes could represent potential pectate lyases for applications in the paper and textile industries.

scholarly journals Extent and Variation of Phage-Borne Bacterial 16S rRNA Gene Sequences in Wastewater Environments

2011 ◽  
Vol 77 (15) ◽  
pp. 5529-5532 ◽  
Author(s):  
Antonio Del Casale ◽  
Paul V. Flanagan ◽  
Michael J. Larkin ◽  
Christopher C. R. Allen ◽  
Leonid A. Kulakov
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Total Bacterial Community ◽  
Rrna Sequences ◽  
16S Rrna Sequences ◽  
Bacterial 16S Rrna Gene

ABSTRACTPhage metagenomes isolated from wastewater over a 12-month period were analyzed. The results suggested that various strains ofProteobacteria,Bacteroidetes, and other phyla are likely to participate in transduction. The patterns of 16S rRNA sequences found in phage metagenomes did not follow changes in the total bacterial community.

scholarly journals Worldwide Prevalence of Class 2 Integrases outside the Clinical Setting Is Associated with Human Impact

2009 ◽  
Vol 75 (15) ◽  
pp. 5100-5110 ◽  
Author(s):  
Carlos M. Rodríguez-Minguela ◽  
Juha H. A. Apajalahti ◽  
Benli Chai ◽  
James R. Cole ◽  
James M. Tiedje
Keyword(s):  
Amino Acid ◽  
16S Rrna ◽  
Swine Manure ◽  
Distribution Patterns ◽  
Amino Acid Identity ◽  
Human Influence ◽  
Acid Identity ◽  
Additional Domain ◽  
Total Dna ◽  
Fecal Waste

ABSTRACT An intI-targeted PCR assay was optimized to evaluate the frequency of partial class 2-like integrases relative to putative, environmental IntI elements in clone libraries generated from 17 samples that included various terrestrial, marine, and deep-sea habitats with different exposures to human influence. We identified 169 unique IntI phylotypes (≤98% amino acid identity) relative to themselves and with respect to those previously described. Among these, six variants showed an undescribed, extended, IntI-specific additional domain. A connection between human influence and the dominance of IntI-2-like variants was also observed. IntI phylotypes 80 to 99% identical to class 2 integrases comprised ∼70 to 100% (n = 65 to 87) of the IntI elements detected in samples with a high input of fecal waste, whereas IntI2-like sequences were undetected in undisturbed settings and poorly represented (1 to 10%; n = 40 to 79) in environments with moderate or no recent fecal or anthropogenic impact. Eleven partial IntI2-like sequences lacking the signature ochre 179 codon were found among samples of biosolids and agricultural soil supplemented with swine manure, indicating a wider distribution of potentially functional IntI2 variants than previously reported. To evaluate IntI2 distribution patterns beyond the usual hosts, namely, the Enterobacteriaceae, we coupled PCR assays targeted at intI and 16S rRNA loci to G+C fractionation of total DNA extracted from manured cropland. IntI2-like sequences and 16S rRNA phylotypes related to Firmicutes (Clostridium and Bacillus) and Bacteroidetes (Chitinophaga and Sphingobacterium) dominated a low-G+C fraction (∼40 to 45%), suggesting that these groups could be important IntI2 hosts in manured soil. Moreover, G+G fractionation uncovered an additional set of 36 novel IntI phylotypes (≤98% amino acid identity) undetected in bulk DNA and revealed the prevalence of potentially functional IntI2 variants in the low-G+C fraction.

Sign in / Sign up

Export Citation Format

Share Document