scholarly journals Identification of Unknown Carboxydovore Bacteria Dominant in Deciduous Forest Soil via Succession of Bacterial Communities,coxLGenotypes, and Carbon Monoxide Oxidation Activity in Soil Microcosms

2015 ◽  
Vol 82 (4) ◽  
pp. 1324-1333 ◽  
Author(s):  
Isabelle Lalonde ◽  
Philippe Constant
Keyword(s):  
Co Oxidation ◽  
Reference Sequence ◽  
Energy Yield ◽  
Rrna Gene ◽  
Type I ◽  
Oxidation Activity ◽  
Soil Microcosms ◽  
Content Type ◽  
Oxidation Rates ◽  
Uptake Activity

ABSTRACTSurveys of thecoxLgene, encoding the large subunit of the CO dehydrogenase, are used as a standard approach in ecological studies of carboxydovore bacteria scavenging atmospheric CO. Recent soil surveys unveiled that the distribution ofcoxLsequences encompassing the atypical genotypecoxLtype I group x was correlated to the CO oxidation activity. Based on phylogenetic analysis including the availablecoxLreference genome sequences, this unusual genotype was assigned to an unknown member of theDeltaproteobacteria, with thecoxLsequence fromHaliangium ochraceumbeing the sole and closest reference sequence. Here we seek to challenge the proposed taxonomic assignation of thecoxLgroup x genotype through the monitoring of CO consumption activity and microbial community successions during the colonization of sterile soil microcosms inoculated with indigenous microorganisms. In our study, we established that the estimated population density ofDeltaproteobacteriawas too small to account for the abundance of thecoxLgroup x genotype detected in soil. Furthermore, we computed a correlation network to relate 16S rRNA gene profiles with the succession ofcoxLgenotypes and CO uptake activity in soil. We found that most of thecoxLgenotypes for which the colonization profile displayed covariance with CO uptake activity were related to potential carboxydovore bacteria belonging toActinobacteriaandAlphaproteobacteria. Our analysis did not provide any evidence thatcoxLgroup x genotypes belonged toDeltaproteobacteria. Considering the colonization profile of CO-oxidizing bacteria and the theoretical energy yield of measured CO oxidation rates in soil microcosms, we propose that unknown carboxydovore bacteria harboring the atypicalcoxLgroup x genotype are mixotrophicK-strategists.

Thioalkalivibrio sulfidiphilus sp. nov., a haloalkaliphilic, sulfur-oxidizing gammaproteobacterium from alkaline habitats

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1884-1889 ◽  
Author(s):  
Dimitry Y. Sorokin ◽  
Maria S. Muntyan ◽  
Anzhela N. Panteleeva ◽  
Gerard Muyzer
Keyword(s):  
Soda Lake ◽  
16S Rrna Gene Sequencing ◽  
Salinity Range ◽  
Rrna Gene ◽  
Type I ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bisphosphate Carboxylase ◽  
Content Type ◽  
Link Type ◽  
Sulfur Oxidizing

A moderately salt-tolerant and obligately alkaliphilic, chemolithoautotrophic sulfur-oxidizing bacterium, strain HL-EbGr7T, was isolated from a full-scale bioreactor removing H2S from biogas under oxygen-limited conditions. Another strain, ALJ17, closely related to HL-EbGr7T, was isolated from a Kenyan soda lake. Cells of the isolates were relatively long, slender rods, motile by a polar flagellum. Although both strains were obligately aerobic, micro-oxic conditions were preferred, especially at the beginning of growth. Chemolithoautotrophic growth was observed with sulfide and thiosulfate in a pH range of 8.0–10.5 (optimum at pH 10.0) and a salinity range of 0.2–1.5 M total Na+ (optimum at 0.4 M). The genome sequence of strain HL-EbGr7T demonstrated the presence of genes encoding the reverse Dsr pathway and a truncated Sox pathway for sulfur oxidation and enzymes of the Calvin–Benson cycle of autotrophic CO2 assimilation with ribulose-bisphosphate carboxylase/oxygenase (RuBisCO) type I. The dominant cellular fatty acids were C18 : 1ω7, C16 : 0 and C19 : 0 cyclo. Based on 16S rRNA gene sequencing, the two strains belonged to a single phylotype within the genus Thioalkalivibrio in the Gammaproteobacteria . Despite being related most closely to Thioalkalivibrio denitrificans , the isolates were unable to grow by denitrification. On the basis of phenotypic and phylogenetic analysis, the novel isolates are proposed to represent a novel species, Thioalkalivibrio sulfidiphilus sp. nov., with the type strain HL-EbGr7T ( = NCCB 100376T  = UNIQEM U246T).

scholarly journals Biological H2 and CO oxidation activities are sensitive to compositional change of soil microbial communities

2020 ◽  
Vol 66 (4) ◽  
pp. 263-273
Author(s):  
Julien Saavedra-Lavoie ◽  
Anne de la Porte ◽  
Sarah Piché-Choquette ◽  
Claude Guertin ◽  
Philippe Constant
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Co Oxidation ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Oxidative Capacity ◽  
Rrna Gene ◽  
Soil Microbial Diversity ◽  
Soil Microcosms ◽  
Soil Microbial

Trace gas uptake by microorganisms controls the oxidative capacity of the troposphere, but little is known about how this important function is affected by changes in soil microbial diversity. This article bridges that knowledge gap by examining the response of the microbial community-level physiological profiles (CLPPs), carbon dioxide (CO2) production, and molecular hydrogen (H2) and carbon monoxide (CO) oxidation activities to manipulation of microbial diversity in soil microcosms. Microbial diversity was manipulated by mixing nonsterile and sterile soil with and without the addition of antibiotics. Nonsterile soil without antibiotics was used as a reference. Species composition changed significantly in soil microcosms as a result of dilution and antibiotic treatments, but there was no difference in species richness, according to PCR amplicon sequencing of the bacterial 16S rRNA gene. The CLPP was 15% higher in all dilution and antibiotic treatments than in reference microcosms, but the dilution treatment had no effect on CO2 production. Soil microcosms with dilution treatments had 58%–98% less H2 oxidation and 54%–99% lower CO oxidation, relative to reference microcosms, but did not differ among the antibiotic treatments. These results indicate that H2 and CO oxidation activities respond to compositional changes of microbial community in soil.

scholarly journals Abundance and Activity of Methanotrophic Bacteria in Littoral and Profundal Sediments of Lake Constance (Germany)

2008 ◽  
Vol 75 (1) ◽  
pp. 119-126 ◽  
Author(s):  
M. Rahalkar ◽  
J. Deutzmann ◽  
B. Schink ◽  
I. Bussmann
Keyword(s):  
Methane Oxidation ◽  
Lake Constance ◽  
Type I ◽  
Sediment Depth ◽  
Oxidation Activity ◽  
Oxidation Rates ◽  
Methane Oxidizing Bacteria ◽  
Littoral Sediment ◽  
Sediment Layers

ABSTRACT The abundances and activities of aerobic methane-oxidizing bacteria (MOB) were compared in depth profiles of littoral and profundal sediments of Lake Constance, Germany. Abundances were determined by quantitative PCR (qPCR) targeting the pmoA gene and by fluorescence in situ hybridization (FISH), and data were compared to methane oxidation rates calculated from high-resolution concentration profiles. qPCR using type I MOB-specific pmoA primers indicated that type I MOB represented a major proportion in both sediments at all depths. FISH indicated that in both sediments, type I MOB outnumbered type II MOB at least fourfold. Results obtained with both techniques indicated that in the littoral sediment, the highest numbers of methanotrophs were found at a depth of 2 to 3 cm, corresponding to the zone of highest methane oxidation activity, although no oxygen could be detected in this zone. In the profundal sediment, highest methane oxidation activities were found at a depth of 1 to 2 cm, while MOB abundance decreased gradually with sediment depth. In both sediments, MOB were also present at high numbers in deeper sediment layers where no methane oxidation activity could be observed.

scholarly journals Organic Cultivation of Triticum turgidum subsp. durum Is Reflected in the Flour-Sourdough Fermentation-Bread Axis

2015 ◽  
Vol 81 (9) ◽  
pp. 3192-3204 ◽  
Author(s):  
Carlo Giuseppe Rizzello ◽  
Ivana Cavoski ◽  
Jelena Turk ◽  
Danilo Ercolini ◽  
Luana Nionelli ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Triticum Turgidum ◽  
Antioxidant Activities ◽  
Farming System ◽  
Rrna Gene ◽  
Type I ◽  
Unifrac Distance ◽  
Content Type ◽  
Organic Cultivation ◽  
Technological Characteristics

ABSTRACTTriticum turgidumsubsp.durumwas grown according to four farming systems: conventional (CONV), organic with cow manure (OMAN) or green manure (OLEG), and without inputs (NOINPUT). Some chemical and technological characteristics differed between CONVand organic flours. As shown by two-dimensional electrophoresis (2-DE) analysis, OMANand OLEGflours showed the highest number of gliadins, and OMANflour also had the highest number of high-molecular-mass glutenins. Type I sourdoughs were prepared at the laboratory level through a back-slopping procedure, and the bacterial ecology during sourdough preparation was described by 16S rRNA gene pyrosequencing. Before fermentation, the dough made with CONVflour showed the highest bacterial diversity. Flours were variously contaminated by genera belonging to theProteobacteria,Firmicutes, andActinobacteria. Mature sourdoughs were completely and stably dominated by lactic acid bacteria. The diversity ofFirmicuteswas the highest for mature sourdoughs made with organic and, especially, NOINPUTflours. Beta diversity analysis based on the weighted UniFrac distance showed differences between doughs and sourdoughs. Those made with CONVflour were separated from the other with organic flours. Lactic acid bacterium microbiota structure was qualitatively confirmed through the culturing method. As shown by PCR-denaturing gradient gel electrophoresis (DGGE) analysis, yeasts belonging to the generaSaccharomyces,Candida,Kazachstania, andRhodotorulaoccurred in all sourdoughs. Levels of bound phenolic acids and phytase and antioxidant activities differed depending on the farming system. Mature sourdoughs were used for bread making. Technological characteristics were superior in the breads made with organic sourdoughs. The farming system is another determinant affecting the sourdough microbiota. The organic cultivation of durum wheat was reflected along the flour-sourdough fermentation-bread axis.

scholarly journals Processing Environment and Ingredients Are Both Sources of Leuconostoc gelidum, Which Emerges as a Major Spoiler in Ready-To-Eat Meals

2015 ◽  
Vol 81 (10) ◽  
pp. 3529-3541 ◽  
Author(s):  
Vasileios Pothakos ◽  
Giuseppina Stellato ◽  
Danilo Ercolini ◽  
Frank Devlieghere
Keyword(s):  
Shelf Life ◽  
Growth Dynamics ◽  
High Growth ◽  
Energy Yield ◽  
Rrna Gene ◽  
Sampling Point ◽  
Putative Gene ◽  
Food Ingredients ◽  
Content Type ◽  
A Minor

ABSTRACTMesophilic and psychrotrophic organism viable counts, as well as high-throughput 16S rRNA gene-based pyrosequencing, were performed with the aim of elucidating the origin of psychrotrophic lactic acid bacteria (LAB) in a ready-to-eat (RTE) meal manufacturing plant. The microbial counts of the products at the end of the shelf life were greatly underestimated when mesophilic incubation was implemented due to overlooked, psychrotrophic members of the LAB.Pseudomonasspp.,Enterobacteriaceae,Streptococcaceae, andLactobacillusspp. constituted the most widespread operational taxonomic units (OTUs), whereasLeuconostocgelidumwas detected as a minor member of the indigenous microbiota of the food ingredients and microbial community of the processing environment, albeit it colonized samples at almost every sampling point on the premises. However,L. gelidumbecame the most predominant microbe at the end of the shelf life. The ability ofL. gelidumto outgrow notorious, spoilage-related taxa likePseudomonas,Brochothrix, andLactobacillusunderpins its high growth dynamics and severe spoilage character under refrigeration temperatures. The use of predicted metagenomes was useful for observation of putative gene repertoires in the samples analyzed in this study. The end products grouped in clusters characterized by gene profiles related to carbohydrate depletion presumably associated with a fast energy yield, a finding which is consistent with the fastidious nature of highly competitive LAB that dominated at the end of the shelf life. The present study showcases the detrimental impact of contamination with psychrotrophic LAB on the shelf life of packaged and cold-stored foodstuffs and the long-term quality implications for production batches once resident microbiota are established in the processing environment.

scholarly journals Methylococcus geothermalis sp. nov., a methanotroph isolated from a geothermal field in the Republic of Korea

2020 ◽  
Vol 70 (10) ◽  
pp. 5520-5530 ◽  
Author(s):  
Samuel Imisi Awala ◽  
Lorraine Araza Bellosillo ◽  
Joo-Han Gwak ◽  
Ngoc-Loi Nguyen ◽  
So-Jeong Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Rrna Gene ◽  
Type I ◽  
Methylococcus Capsulatus ◽  
Intracytoplasmic Membrane ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, aerobic, non-motile and coccoid methanotroph, strain IM1T, was isolated from hot spring soil. Cells of strain IM1T were catalase-negative, oxidase-positive and displayed a characteristic intracytoplasmic membrane arrangement of type I methanotrophs. The strain possessed genes encoding both membrane-bound and soluble methane monooxygenases and grew only on methane or methanol. The strain was capable of growth at temperatures between 15 and 48 °C (optimum, 30–45 °C) and pH values between pH 4.8 and 8.2 (optimum, pH 6.2–7.0). Based on phylogenetic analysis of 16S rRNA gene and PmoA sequences, strain IM1T was demonstrated to be affiliated to the genus Methylococcus . The 16S rRNA gene sequence of this strain was most closely related to the sequences of an uncultured bacterium clone FD09 (100 %) and a partially described cultured Methylococcus sp. GDS2.4 (99.78 %). The most closely related taxonomically described strains were Methylococcus capsulatus TexasT (97.92 %), Methylococcus capsulatus Bath (97.86 %) and Methyloterricola oryzae 73aT (94.21 %). Strain IM1T shared average nucleotide identity values of 85.93 and 85.62 % with Methylococcus capsulatus strains TexasT and Bath, respectively. The digital DNA–DNA hybridization value with the closest type strain was 29.90 %. The DNA G+C content of strain IM1T was 63.3 mol% and the major cellular fatty acids were C16 : 0 (39.0 %), C16 : 1  ω7c (24.0 %), C16 : 1  ω6c (13.6 %) and C16 : 1  ω5c (12.0 %). The major ubiquinone was methylene-ubiquinone-8. On the basis of phenotypic, genetic and phylogenetic data, strain IM1T represents a novel species of the genus Methylococcus for which the name Methylococcus geothermalis sp. nov. is proposed, with strain IM1T (=JCM 33941T=KCTC 72677T) as the type strain.

scholarly journals Macrolide-Resistant Mycoplasma pneumoniae in Adults in Zhejiang, China

2014 ◽  
Vol 59 (2) ◽  
pp. 1048-1051 ◽  
Author(s):  
Zibo Zhou ◽  
Xiangzhi Li ◽  
Xiaojian Chen ◽  
Fangjun Luo ◽  
Changwang Pan ◽  
...  
Keyword(s):  
Mycoplasma Pneumoniae ◽  
Rflp Analysis ◽  
Zhejiang Province ◽  
23S Rrna ◽  
Rrna Gene ◽  
Type I ◽  
Content Type ◽  
23S Rrna Gene ◽  
Resistant Strains ◽  
Domain V

ABSTRACTMycoplasma pneumoniaeis a major pathogen causing community-acquired pneumoniae (CAP), which is generally treated with macrolides. In recent years, however, although macrolide-resistantM. pneumoniaehas been reported frequently, particularly in China, very little is known about the prevalence of macrolide-resistantM. pneumoniaeinfection in adults. In this study, we survey the macrolide-resistantM. pneumoniaein adults in Zhejiang province and characterize the mechanisms of resistance to macrolide. Six hundred fifty throat swab samples were collected from adult patients with CAP from January 2012 to August 2014. These samples were assayed by nested PCR and then cultivated forM. pneumoniae. All isolates were sequenced to determine the mutation in domain V of the 23S rRNA gene. The activities of 10 antibiotics against macrolide-resistantM. pneumoniaeisolates were also investigatedin vitro. Moreover, restriction fragment length polymorphism (RFLP) analysis of the amplified P1 gene was used to type 50 resistant strains. One hundred percent (71/71) ofM. pneumoniaestrains isolated from adults with CAP were resistant to erythromycin (MIC = 128 to >256 μg/ml), clarithromycin (MIC = 128 to >256 μg/ml), and azithromycin (MIC = 32 to >64 μg/ml). Furthermore, all macrolide-resistantM. pneumoniaestrains identified had an A2063G mutation in domain V of the 23S rRNA gene. Forty-six resistant strains (92.0%) were classified into type I strain on the basis of P1 gene PCR-RFLP analysis. According to these findings, it is suggested that macrolide-resistantM. pneumoniaeinfection is very prevalence among adults in Zhejiang province. Thus, there is necessary to perform the epidemiological monitoring of macrolide-resistantM. pneumoniaein the future.

scholarly journals Analysis of Methane Monooxygenase Genes in Mono Lake Suggests That Increased Methane Oxidation Activity May Correlate with a Change in Methanotroph Community Structure

2005 ◽  
Vol 71 (10) ◽  
pp. 6458-6462 ◽  
Author(s):  
Ju-Ling Lin ◽  
Samantha B. Joye ◽  
Johannes C. M. Scholten ◽  
Hendrik Schäfer ◽  
Ian R. McDonald ◽  
...  
Keyword(s):  
Methane Oxidation ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Mono Lake ◽  
Hypersaline Lake ◽  
Type I ◽  
Type Ii ◽  
Oxidation Activity ◽  
Oxidation Rates ◽  
Gradient Gel Electrophoresis

ABSTRACT Mono Lake is an alkaline hypersaline lake that supports high methane oxidation rates. Retrieved pmoA sequences showed a broad diversity of aerobic methane oxidizers including the type I methanotrophs Methylobacter (the dominant genus), Methylomicrobium, and Methylothermus, and the type II methanotroph Methylocystis. Stratification of Mono Lake resulted in variation of aerobic methane oxidation rates with depth. Methanotroph diversity as determined by analysis of pmoA using new denaturing gradient gel electrophoresis primers suggested that variations in methane oxidation activity may correlate with changes in methanotroph community composition.

scholarly journals Antibiotic Sensitivity of 40 Mycoplasma pneumoniae Isolates and Molecular Analysis of Macrolide-Resistant Isolates from Beijing, China

2011 ◽  
Vol 56 (2) ◽  
pp. 1108-1109 ◽  
Author(s):  
Fei Zhao ◽  
Min Lv ◽  
Xiaoxia Tao ◽  
Hui Huang ◽  
Binghua Zhang ◽  
...  
Keyword(s):  
Point Mutation ◽  
Mycoplasma Pneumoniae ◽  
Antibiotic Sensitivity ◽  
Resistant Isolate ◽  
23S Rrna ◽  
Rrna Gene ◽  
Type I ◽  
Content Type ◽  
23S Rrna Gene ◽  
Beijing China

ABSTRACTMICs of eight antibiotics were detected with 40 ChineseMycoplasma pneumoniaeisolates. Thirty-eight isolates (95%) were macrolide resistant. Each macrolide-resistant isolate harbored an A2063G or A2064G point mutation in the 23S rRNA gene. All 40 isolates (100%) were type I strains, but they might have originated from different clones.

Methylomonas koyamae sp. nov., a type I methane-oxidizing bacterium from floodwater of a rice paddy field

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1832-1837 ◽  
Author(s):  
Takuya Ogiso ◽  
Chihoko Ueno ◽  
Dayéri Dianou ◽  
Tran Van Huy ◽  
Arata Katayama ◽  
...  
Keyword(s):  
Paddy Field ◽  
Rice Paddy ◽  
Rrna Gene ◽  
Type I ◽  
Intracytoplasmic Membrane ◽  
Content Type ◽  
Rice Paddy Field ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Bacterium Strain

A novel methane-oxidizing bacterium, strain Fw12E-YT, was isolated from floodwater of a rice paddy field in Japan. Cells of strain Fw12E-YT were Gram-negative, motile rods with a single polar flagellum and type I intracytoplasmic membrane arrangement. The strain grew only on methane or methanol as sole carbon and energy source. It was able to grow at 10–40 °C (optimum 30 °C), at pH 5.5–7.0 (optimum 6.5) and with 0–0.1 % (w/w) NaCl (no growth above 0.5 % NaCl). 16S rRNA gene sequence analysis showed that strain Fw12E-YT is related most closely to members of the genus Methylomonas , but at low levels of similarity (95.0–95.4 %). Phylogenetic analysis of pmoA and mxaF genes indicated that the strain belongs to the genus Methylomonas (97 and 92 % deduced amino acid sequence identities to Methylomonas methanica S1T, respectively). The DNA G+C content of strain Fw12E-YT was 57.1 mol%. Chemotaxonomic data regarding the major quinone (MQ-8) and major fatty acids (C16 : 1 and C14 : 0) also supported its affiliation to the genus Methylomonas . Based on phenotypic, genomic and phylogenetic data, strain Fw12E-YT is considered to represent a novel species of the genus Methylomonas , for which the name Methylomonas koyamae sp. nov. is proposed. The type strain is Fw12E-YT ( = JCM 16701T = NBRC 105905T = NCIMB 14606T).

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