scholarly journals Methylocella Species Are Facultatively Methanotrophic

2005 ◽  
Vol 187 (13) ◽  
pp. 4665-4670 ◽  
Author(s):  
Svetlana N. Dedysh ◽  
Claudia Knief ◽  
Peter F. Dunfield
Keyword(s):  
Methane Oxidation ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Methanotrophic Bacteria ◽  
Soluble Methane Monooxygenase ◽  
Cell Counts ◽  
Carbon Compounds ◽  
Methane Fluxes ◽  
The One ◽  
Pcr Targeting

ABSTRACT All aerobic methanotrophic bacteria described to date are unable to grow on substrates containing carbon-carbon bonds. Here we demonstrate that members of the recently discovered genus Methylocella are an exception to this. These bacteria are able to use as their sole energy source the one-carbon compounds methane and methanol, as well as the multicarbon compounds acetate, pyruvate, succinate, malate, and ethanol. To conclusively verify facultative growth, acetate and methane were used as model substrates in growth experiments with the type strain Methylocella silvestris BL2. Quantitative real-time PCR targeting the mmoX gene, which encodes a subunit of soluble methane monooxygenase, showed that copies of this gene increased in parallel with cell counts during growth on either acetate or methane as the sole substrate. This verified that cells possessing the genetic basis of methane oxidation grew on acetate as well as methane. Cloning of 16S rRNA genes and fluorescence in situ hybridization with strain-specific and genus-specific oligonucleotide probes detected no contaminants in cultures. The growth rate and carbon conversion efficiency were higher on acetate than on methane, and when both substrates were provided in excess, acetate was preferably used and methane oxidation was shut down. Our data demonstrate that not all methanotrophic bacteria are limited to growing on one-carbon compounds. This could have major implications for understanding the factors controlling methane fluxes in the environment.

scholarly journals Prevalence and molecular detection of fluoroquinolone-resistant genes (qnrA and qnrS) in Escherichia coli isolated from healthy broiler chickens

2018 ◽  
pp. 1720-1724 ◽  
Author(s):  
Shahin Mahmud ◽  
K. H. M. Nazmul Hussain Nazir ◽  
Md. Tanvir Rahman
Keyword(s):  
Escherichia Coli ◽  
Broiler Chickens ◽  
Molecular Detection ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Diffusion Method ◽  
Isolation And Identification ◽  
E Coli ◽  
Pcr Targeting ◽  
Apparently Healthy

Aim: The present study was carried out to determine the prevalence and molecular detection of fluoroquinolone-resistant Escherichia coli carrying qnrA and qnrS genes in healthy broiler chickens in Mymensingh, Bangladesh, and also to identify the genes responsible for such resistance. Materials and Methods: A total of 65 cloacal swabs were collected from apparently healthy chickens of 0-14 days (n=23) and 15-35 days (n=42) old. The samples were cultured onto Eosin Methylene Blue Agar, and the isolation and identification of the E. coli were performed based on morphology, cultural, staining, and biochemical properties followed by polymerase chain reaction (PCR) targeting E. coli 16S rRNA genes. The isolates were subjected to antimicrobial susceptibility test against five commonly used antibiotics under fluoroquinolone (quinolone) group, namely gatifloxacin, levofloxacin, moxifloxacin, ofloxacin, and pefloxacin by disk diffusion method. Detection of qnrA and qnrS genes was performed by PCR. Results: Among the 65 cloacal samples, 54 (83.08%) were found to be positive for E. coli. Antibiotic sensitivity test revealed that, of these 54 isolates, 18 (33.33%) were found to be resistant to at least one fluoroquinolone antibiotic. The highest resistance was observed against pefloxacin (61.11%). By PCR, of 18 E. coli resistant to fluoroquinolone, 13 (72.22%) were found to be positive for the presence of qnrS. None of the isolates were found positive for qnrA. Conclusion: Fluoroquinolone-resistant E. coli harboring qnrS genes is highly prevalent in apparently healthy broiler chickens and possesses a potential threat to human health.

scholarly journals Enhanced Adsorptive Bioremediation of Heavy Metals (Cd2+, Cr6+, Pb2+) by Methane-Oxidizing Epipelon

2020 ◽  
Vol 8 (4) ◽  
pp. 505 ◽  
Author(s):  
Muhammad Faheem ◽  
Sadaf Shabbir ◽  
Jun Zhao ◽  
Philip G Kerr ◽  
Nasrin Sultana ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Methane Oxidation ◽  
Metal Removal ◽  
Heavy Metal Removal ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Aqueous Environment ◽  
Type I ◽  
Methane Concentrations

Cadmium (Cd), chromium (Cr) and lead (Pb) are heavy metals that have been classified as priority pollutants in aqueous environment while methane-oxidizing bacteria as a biofilter arguably consume up to 90% of the produced methane in the same aqueous environment before it escapes into the atmosphere. However, the underlying kinetics and active methane oxidizers are poorly understood for the hotspot of epipelon that provides a unique micro-ecosystem containing diversified guild of microorganisms including methane oxidizers for potential bioremediation of heavy metals. In the present study, the Pb2+, Cd2+and Cr6+ bioremediation potential of epipelon biofilm was assessed under both high (120,000 ppm) and near-atmospheric (6 ppm) methane concentrations. Epipelon biofilm demonstrated a high methane oxidation activity following microcosm incubation amended with a high concentration of methane, accompanied by the complete removal of 50 mg L−1 Pb2+ and 50 mg L−1 Cd2+ (14 days) and partial (20%) removal of 50 mg L−1 Cr6+ after 20 days. High methane dose stimulated a faster (144 h earlier) heavy metal removal rate compared to near-atmospheric methane concentrations. DNA-based stable isotope probing (DNA-SIP) following 13CH4 microcosm incubation revealed the growth and activity of different phylotypes of methanotrophs during the methane oxidation and heavy metal removal process. High throughput sequencing of 13C-labelled particulate methane monooxygenase gene pmoA and 16S rRNA genes revealed that the prevalent active methane oxidizers were type I affiliated methanotrophs, i.e., Methylobacter. Type II methanotrophs including Methylosinus and Methylocystis were also labeled only under high methane concentrations. These results suggest that epipelon biofilm can serve as an important micro-environment to alleviate both methane emission and the heavy metal contamination in aqueous ecosystems with constant high methane fluxes.

scholarly journals Diversity and Seasonal Changes of Uncultured Planctomycetales in River Biofilms

2004 ◽  
Vol 70 (9) ◽  
pp. 5094-5101 ◽  
Author(s):  
I. H. M. Brümmer ◽  
A. D. M. Felske ◽  
I. Wagner-Döbler
Keyword(s):  
16S Rrna ◽  
Seasonal Changes ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Elbe River ◽  
Cell Counts ◽  
Gradient Gel Electrophoresis ◽  
Temperature Gradient Gel Electrophoresis ◽  
River Biofilm ◽  
The Elbe River

ABSTRACT Cell counts of planctomycetes showed that there were high levels of these organisms in the summer and low levels in the winter in biofilms grown in situ in two polluted rivers, the Elbe River and the Spittelwasser River. In this study 16S rRNA-based methods were used to investigate if these changes were correlated with changes in the species composition. Planctomycete-specific clone libraries of the 16S rRNA genes found in both rivers showed that there were seven clusters, which were distantly related to the genera Pirellula, Planctomyces, and Gemmata. The majority of the sequences from the Spittelwasser River were affiliated with a cluster related to Pirellula, while the majority of the clones from the Elbe River fell into three clusters related to Planctomyces and one deeply branching cluster related to Pirellula. Some clusters also contained sequences derived from freshwater environments worldwide, and the similarities to our biofilm clones were as high as 99.8%, indicating the presence of globally distributed freshwater clusters of planctomycetes that have not been cultivated yet. Community fingerprints of planctomycete 16S rRNA genes were generated by temperature gradient gel electrophoresis from Elbe River biofilm samples collected monthly for 1 year. Sixteen bands were identified, and for the most part these bands represented organisms related to the genus Planctomyces. The fingerprints showed that there was strong seasonality of most bands and that there were clear differences in the summer and the winter. Thus, seasonal changes in the abundance of Planctomycetales in river biofilms were coupled to shifts in the community composition.

scholarly journals Distinctive Microbial Community Structure in Highly Stratified Deep-Sea Brine Water Columns

2013 ◽  
Vol 79 (11) ◽  
pp. 3425-3437 ◽  
Author(s):  
S. Bougouffa ◽  
J. K. Yang ◽  
O. O. Lee ◽  
Y. Wang ◽  
Z. Batang ◽  
...  
Keyword(s):  
Deep Sea ◽  
Sea Water ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Populations ◽  
Content Type ◽  
Deep Sea Water ◽  
Cell Counts ◽  
Red Sea Rift ◽  
Group I

ABSTRACTAtlantis II and Discovery are two hydrothermal and hypersaline deep-sea pools in the Red Sea rift that are characterized by strong thermohalo-stratification and temperatures steadily peaking near the bottom. We conducted comprehensive vertical profiling of the microbial populations in both pools and highlighted the influential environmental factors. Pyrosequencing of the 16S rRNA genes revealed shifts in community structures vis-à-vis depth. High diversity and low abundance were features of the deepest convective layers despite the low cell density. Surprisingly, the brine interfaces had significantly higher cell counts than the overlying deep-sea water, yet they were lowest in diversity. Vertical stratification of the bacterial populations was apparent as we moved from theAlphaproteobacteria-dominated deep sea to thePlanctomycetaceae- orDeferribacteres-dominated interfaces to theGammaproteobacteria-dominated brine layers. Archaeal marine group I was dominant in the deep-sea water and interfaces, while several euryarchaeotic groups increased in the brine. Across sites, microbial phylotypes and abundances varied substantially in the brine interface of Discovery compared with Atlantis II, despite the near-identical populations in the overlying deep-sea waters. The lowest convective layers harbored interestingly similar microbial communities, even though temperature and heavy metal concentrations were very different. Multivariate analysis indicated that temperature and salinity were the major influences shaping the communities. The harsh conditions and the low-abundance phylotypes could explain the observed correlation in the brine pools.

scholarly journals THE BIOLOGICAL PROPERTIES OF SOYBEAN NODULE BACTERIA WITH THE DIFFERENT SPEED OF GROWTH

2010 ◽  
Vol 10 ◽  
pp. 50-64
Author(s):  
D.V. Krutуlo
Keyword(s):  
16S Rrna ◽  
Biological Properties ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soybean Nodule ◽  
Bradyrhizobium Sp ◽  
The One ◽  
Symbiotic Properties ◽  
Slow Growing ◽  
Intensive Growth

The phenotypical and genotypic properties of soybean microsymbionts with the different speed of growth were studied. It was established that the strains with the intensive growth were specific to the host-plant, but had differed by their serological, chemotaxonomical and symbiotic properties. The investigated intensive-growing strains were combined into the one serogroup by their antigenic content. The similarity of fatty acids spectrum was observed for the strains with the intensive growth Bradyrhizobium sp. КВ1-1, slow-growing strains B. japonicum 634b and B. japonicum КС2-3. The quantitative and qualitative differences in monosaccharides contents of EPS of the studied strains were revealed. Presence of xylose (2,7 %) and increased contents of rhamnose (18,4 %) were shown to be different in EPS of strain Bradyrhizobium sp. КВ1- 1 and EPS of strains B. japonicum КС2-3 and B. japonicum 634b. Analysis of the sequences of the 16S rRNA genes allowed attributing the strain with the intensive growth to the Bradyrhizobium genus. Genes consistency analysis of 16S rRNA had allowed to refer the intensivegrowing strains to the Bradyrhizobium genus. It was shown that studied intensive-growing strains had formed the nonspecific symbiosis with cow pea.

scholarly journals Evidence for a Growth Zone for Deep-Subsurface Microbial Clades in Near-Surface Anoxic Sediments

2020 ◽  
Vol 86 (19) ◽  
Author(s):  
Karen G. Lloyd ◽  
Jordan T. Bird ◽  
Joy Buongiorno ◽  
Emily Deas ◽  
Richard Kevorkian ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Sediment Cores ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
White Oak ◽  
Deep Subsurface ◽  
Near Surface ◽  
Cell Abundance ◽  
Cell Counts ◽  
Doubling Times

ABSTRACT Global marine sediments harbor a large and highly diverse microbial biosphere, but the mechanism by which this biosphere is established during sediment burial is largely unknown. During burial in marine sediments, concentrations of easily metabolized organic compounds and total microbial cell abundance decrease. However, it is unknown whether some microbial clades increase with depth. We show total population increases in 38 microbial families over 3 cm of sediment depth in the upper 7.5 cm of White Oak River (WOR) estuary sediments. Clades that increased with depth were more often associated with one or more of the following: anaerobes, uncultured, or common in deep marine sediments relative to those that decreased. Maximum doubling times (in situ steady-state growth rates could be faster to balance cell decay) were estimated as 2 to 25 years by combining sedimentation rate with either quantitative PCR (qPCR) or the product of the fraction read abundance of 16S rRNA genes and total cell counts (FRAxC). Doubling times were within an order of magnitude of each other in two adjacent cores, as well as in two laboratory enrichments of Cape Lookout Bight (CLB), NC, sediments (average difference of 28% ± 19%). qPCR and FRAxC in sediment cores and laboratory enrichments produced similar doubling times for key deep subsurface uncultured clades Bathyarchaeota (8.7 ± 1.9 years) and Thermoprofundales/MBG-D (4.1 ± 0.7 years). We conclude that common deep subsurface microbial clades experience a narrow zone of growth in shallow sediments, offering an opportunity for selection of long-term subsistence traits after resuspension events. IMPORTANCE Many studies show that the uncultured microbes that dominate global marine sediments do not actually increase in population size as they are buried in marine sediments; rather, they exist in a sort of prolonged torpor for thousands of years. This is because, although studies have shown biomass turnover in these clades, no evidence has ever been found that deeper sediments have larger populations for specific clades than shallower layers. We discovered that they actually do increase population sizes during burial, but only in the upper few centimeters. This suggests that marine sediments may be a vast repository of mostly nongrowing microbes with a thin and relatively rapid area of cell abundance increase in the upper 10 cm, offering a chance for subsurface organisms to undergo natural selection.

scholarly journals Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil

2014 ◽  
Vol 11 (12) ◽  
pp. 3353-3368 ◽  
Author(s):  
Y. Zheng ◽  
R. Huang ◽  
B. Z. Wang ◽  
P. L. E. Bodelier ◽  
Z. J. Jia
Keyword(s):  
16S Rrna ◽  
Nitrogen Cycling ◽  
Methane Oxidation ◽  
Paddy Soil ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Type I ◽  
Ammonia Oxidizers ◽  
Oxidation Activity ◽  
Type Ia

Abstract. Pure culture studies have demonstrated that methanotrophs and ammonia oxidizers can both carry out the oxidation of methane and ammonia. However, the expected interactions resulting from these similarities are poorly understood, especially in complex, natural environments. Using DNA-based stable isotope probing and pyrosequencing of 16S rRNA and functional genes, we report on biogeochemical and molecular evidence for growth stimulation of methanotrophic communities by ammonium fertilization, and that methane modulates nitrogen cycling by competitive inhibition of nitrifying communities in a rice paddy soil. Pairwise comparison between microcosms amended with CH4, CH4+Urea, and Urea indicated that urea fertilization stimulated methane oxidation activity 6-fold during a 19-day incubation period, while ammonia oxidation activity was significantly suppressed in the presence of CH4. Pyrosequencing of the total 16S rRNA genes revealed that urea amendment resulted in rapid growth of Methylosarcina-like MOB, and nitrifying communities appeared to be partially inhibited by methane. High-throughput sequencing of the 13C-labeled DNA further revealed that methane amendment resulted in clear growth of Methylosarcina-related MOB while methane plus urea led to an equal increase in Methylosarcina and Methylobacter-related type Ia MOB, indicating the differential growth requirements of representatives of these genera. An increase in 13C assimilation by microorganisms related to methanol oxidizers clearly indicated carbon transfer from methane oxidation to other soil microbes, which was enhanced by urea addition. The active growth of type Ia methanotrops was significantly stimulated by urea amendment, and the pronounced growth of methanol-oxidizing bacteria occurred in CH4-treated microcosms only upon urea amendment. Methane addition partially inhibited the growth of Nitrosospira and Nitrosomonas in urea-amended microcosms, as well as growth of nitrite-oxidizing bacteria. These results suggest that type I methanotrophs can outcompete type II methane oxidizers in nitrogen-rich environments, rendering the interactions among methane and ammonia oxidizers more complicated than previously appreciated.

scholarly journals Bacterial Populations Colonizing and Degrading Rice Straw in Anoxic Paddy Soil

2001 ◽  
Vol 67 (3) ◽  
pp. 1318-1327 ◽  
Author(s):  
Sabine Weber ◽  
Stephan Stubner ◽  
Ralf Conrad
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Rice Straw ◽  
Paddy Soil ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Blot Hybridization ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Dot Blot ◽  
Cell Counts

ABSTRACT Rice straw is a major substrate for the production of methane, a greenhouse gas, in flooded rice fields. The bacterial community degrading rice straw under anoxic conditions was investigated with molecular methods. Rice straw was incubated in paddy soil anaerobically for 71 days. Denaturing gradient gel electrophoresis (DGGE) of the amplified bacterial 16S rRNA genes showed that the composition of the bacterial community changed during the first 15 days but then was stable until the end of incubation. Fifteen DGGE bands with different signal intensities were excised, cloned, and sequenced. In addition, DNA was extracted from straw incubated for 1 and 29 days and the bacterial 16S rRNA genes were amplified and cloned. From these clone libraries 16 clones with different electrophoretic mobilities on a DGGE gel were sequenced. From a total of 31 clones, 20 belonged to different phylogenetic clusters of the clostridia, i.e., clostridial clusters I (14 clones), III (1 clone), IV (1 clone), and XIVa (4 clones). One clone fell also within the clostridia but could not be affiliated to one of the clostridial clusters. Ten clones grouped closely with the genera Bacillus (3 clones), Nitrosospira (1 clone), Fluoribacter (1 clones), andAcidobacterium (2 clones) and with clone sequences previously obtained from rice field soil (3 clones). The relative abundances of various phylogenetic groups in the rice straw-colonizing community were determined by fluorescence in situ hybridization (FISH). Bacteria were detached from the incubated rice straw with an efficiency of about 80 to 90%, as determined by dot blot hybridization of 16S rRNA in extract and residue. The number of active (i.e., a sufficient number of ribosomes) Bacteria detected with a general eubacterial probe (Eub338) after 8 days of incubation was 61% of the total cell counts. This percentage decreased to 17% after 29 days of incubation. Most (55%) of the active cells on day 8 belonged to the genus Clostridium, mainly to clostridial clusters I (24%), III (6%), and XIVa (24%). An additional 5% belonged to theCytophaga-Flavobacterium cluster of theCytophaga-Flavobacterium-Bacteroides phylum, 4% belonged to the α, β, and γ Proteobacteria, and 1.3% belonged to the Bacillus subbranch of the gram-positive bacteria with a low G+C content. The results show that the bacterial community colonizing and decomposing rice straw developed during the first 15 days of incubation and was dominated by members of different clostridial clusters, especially clusters I, III, and XIVa.

scholarly journals Prevalence of Arcobacter and Other Pathogenic Bacteria in River Water in Nepal

Water ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 1416 ◽  
Author(s):  
Rajani Ghaju Shrestha ◽  
Sarmila Tandukar ◽  
Dinesh Bhandari ◽  
Samendra P. Sherchan ◽  
Yasuhiro Tanaka ◽  
...  
Keyword(s):  
16S Rrna ◽  
River Water ◽  
Quantitative Pcr ◽  
Water Samples ◽  
Pathogenic Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
One Year ◽  
Bagmati River ◽  
Pcr Targeting

This study aims to determine the diversity of pathogenic bacteria in the Bagmati River, Nepal, during a one-year period. A total of 18 river water samples were collected from three sites (n = 6 per site) along the river. Bacterial DNA, which were extracted from the water samples, were analyzed for bacterial 16S rRNA genes by next-generation sequencing for 13 of 18 samples, and by quantitative PCR targeting Arcobacter for all 18 samples. The 16S rRNA sequencing identified an average of 97,412 ± 35,909 sequences/sample, which were then categorized into 28 phyla, 61 classes, and 709 bacterial genera. Eighteen (16%) genera of 111 potential pathogenic bacteria were detected with abundance ratios of >1%; Arcobacter, Acinetobacter, and Prevotella were the dominant genera. The Arcobacter abundance ratios were 28.6% (n = 1), 31.3 ± 15.8% (n = 6), and 31.8 ± 17.2% (n = 6) at the upstream, midstream, and downstream sites, respectively. Arcobacter was detected in 14 (78%) of 18 samples tested, with concentrations ranging from 6.7 to 10.7 log10 copies/100 mL, based on quantitative PCR. Our results demonstrate the poor bacterial quality of the Bagmati River water, suggesting a need for implementing more measures to reduce fecal contamination in the river water.

scholarly journals Comparative Analysis of Acidobacterial Genomic Fragments from Terrestrial and Aquatic Metagenomic Libraries, with Emphasis on Acidobacteria Subdivision 6

2010 ◽  
Vol 76 (20) ◽  
pp. 6769-6777 ◽  
Author(s):  
Anna M. Kielak ◽  
Johannes A. van Veen ◽  
George A. Kowalchuk
Keyword(s):  
De Novo ◽  
Gene Annotation ◽  
Trna Synthetase ◽  
Gene Organization ◽  
Open Reading Frames ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Homologous Gene ◽  
Range Of Functions ◽  
Pcr Targeting

ABSTRACT The bacterial phylum Acidobacteria has a widespread distribution and is one of the most common and diverse phyla in soil habitats. However, members of this phylum have often been recalcitrant to cultivation methods, hampering the study of this presumably important bacterial group. In this study, we used a cultivation-independent metagenomic approach to recover genomic information from soilborne members of this phylum. A soil metagenomic fosmid library was screened by PCR targeting acidobacterial 16S rRNA genes, facilitating the recovery of 17 positive clones. Recovered inserts appeared to originate from a range of Acidobacteria subdivisions, with dominance of subdivision 6 (10 clones). Upon full-length insert sequencing, gene annotation identified a total of 350 open reading frames (ORFs), representing a broad range of functions. Remarkably, six inserts from subdivision 6 contained a region of gene synteny, containing genes involved in purine de novo biosynthesis and encoding tRNA synthetase and conserved hypothetical proteins. Similar genomic regions had previously been observed in several environmental clones recovered from soil and marine sediments, facilitating comparisons with respect to gene organization and evolution. Comparative analyses revealed a general dichotomy between marine and terrestrial genes in both phylogeny and G+C content. Although the significance of this homologous gene cluster across subdivision 6 members is not known, it appears to be a common feature within a large percentage of all acidobacterial genomic fragments recovered from both of these environments.

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