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https://www.readbyqxmd.com/read/27933233/isolation-and-characterisation-of-crude-oil-sludge-degrading-bacteria
#1
Linda U Obi, Harrison I Atagana, Rasheed A Adeleke
BACKGROUND: The use of microorganisms in remediating environmental contaminants such as crude oil sludge has become a promising technique owing to its economy and the fact it is environmentally friendly. Polycyclic aromatic hydrocarbons (PAHs), as the major components of oil sludge, are hydrophobic and recalcitrant. An important way of enhancing the rate of PAH desorption is to compost crude oil sludge by incorporating commercial surfactants, thereby making them available for microbial degradation...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27933046/phylogenetic-signals-of-salinity-and-season-in-bacterial-community-composition-across-the-salinity-gradient-of-the-baltic-sea
#2
Daniel P R Herlemann, Daniel Lundin, Anders F Andersson, Matthias Labrenz, Klaus Jürgens
Understanding the key processes that control bacterial community composition has enabled predictions of bacterial distribution and function within ecosystems. In this study, we used the Baltic Sea as a model system to quantify the phylogenetic signal of salinity and season with respect to bacterioplankton community composition. The abundances of 16S rRNA gene amplicon sequencing reads were analyzed from samples obtained from similar geographic locations in July and February along a brackish to marine salinity gradient in the Baltic Sea...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27933043/antimicrobial-susceptibility-of-flavobacterium-psychrophilum-from-chilean-salmon-farms-and-their-epidemiological-cut-off-values-using-agar-dilution-and-disk-diffusion-methods
#3
Claudio D Miranda, Peter Smith, Rodrigo Rojas, Sergio Contreras-Lynch, J M Alonso Vega
Flavobacterium psychrophilum is the most important bacterial pathogen for freshwater farmed salmonids in Chile. The aims of this study were to determine the susceptibility to antimicrobials used in fish farming of Chilean isolates and to calculate their epidemiological cut-off (COWT) values. A number of 125 Chilean isolates of F. psychrophilum were isolated from reared salmonids presenting clinical symptoms indicative of flavobacteriosis and their identities were confirmed by 16S rRNA polymerase chain reaction...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27931940/evolution-of-bacterial-diversity-during-two-phase-olive-mill-waste-alperujo-composting-by-16s-rrna-gene-pyrosequencing
#4
Germán Tortosa, Antonio Castellano-Hinojosa, David Correa-Galeote, Eulogio J Bedmar
Microorganisms are the main contributing factor responsible for organic matter degradation during composting. In this research, the 454-pyrosequencing of the 16S rRNA gene was used to elucidate evolution of bacterial diversity during mesophilic, thermophilic and maturation composting stages of the two-phase olive mill waste ("alperujo"), the main by-product of the Spanish olive oil industry. Two similar piles were performance composting AL with sheep manure as bulking agent. Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria were the main phyla found in genomic libraries from each composting phase...
November 29, 2016: Bioresource Technology
https://www.readbyqxmd.com/read/27931939/ex-situ-biogas-upgrading-and-enhancement-in-different-reactor-systems
#5
Panagiotis G Kougias, Laura Treu, Daniela Peñailillo Benavente, Kanokwan Boe, Stefano Campanaro, Irini Angelidaki
Biogas upgrading is envisioned as a key process for clean energy production. The current study evaluates the efficiency of different reactor configurations for ex-situ biogas upgrading and enhancement, in which externally provided hydrogen and carbon dioxide were biologically converted to methane by the action of hydrogenotrophic methanogens. The methane content in the output gas of the most efficient configuration was >98%, allowing its exploitation as substitute to natural gas. Additionally, use of digestate from biogas plants as a cost efficient method to provide all the necessary nutrients for microbial growth was successful...
December 2, 2016: Bioresource Technology
https://www.readbyqxmd.com/read/27931748/lentil-lens-culinaris-medik-nodulates-with-genotypically-and-phenotypically-diverse-rhizobia-in-ethiopian-soils
#6
Wondwosen Tena, Endalkachew Wolde-Meskel, Tulu Degefu, Fran Walley
Forty-eight lentil-nodulating rhizobia were isolated from soil samples collected from diverse agro-ecological locations in Ethiopia, and characterized based on 76 phenotypic traits. Furthermore, 26 representative strains were selected and characterized using multilocus sequence analyses (MLSA) of core (16S rRNA, recA, atpD, glnII and gyrB) and symbiotic (nodA and nifH) genes. Numerical analysis of phenotypic characteristics showed that the 48 test strains fell into three major distinct clusters. The phylogenetic trees based on 16S rRNA genes showed that they belong to the Rhizobium genus...
November 24, 2016: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/27931360/molecular-biological-methods-in-environmental-engineering
#7
Guocai Zhang, Li Wei, Chein-Chi Chang, Yuhua Zhang, Dong Wei
Bacteria, acting as catalysts, perform the function of degrading pollutants. Molecular biological techniques play an important role in research on the community analysis, the composition and the functions of complex microbial communities. The development of secondary high-throughput pyrosequencing techiniques enhances the understanding of the composition of the microbial community. The literatures of 2015 indicated that 16S rDNA gene as genetic tag is still the important method for bacteria identification and classification...
October 2016: Water Environment Research: a Research Publication of the Water Environment Federation
https://www.readbyqxmd.com/read/27930727/airway-microbiota-in-bronchoalveolar-lavage-fluid-from-clinically-well-infants-with-cystic-fibrosis
#8
Theresa A Laguna, Brandie D Wagner, Cynthia B Williams, Mark J Stevens, Charles E Robertson, Cole W Welchlin, Catherine E Moen, Edith T Zemanick, Jonathan K Harris
BACKGROUND: Upper airway cultures guide the identification and treatment of lung pathogens in infants with cystic fibrosis (CF); however, this may not fully reflect the spectrum of bacteria present in the lower airway. Our objectives were to characterize the airway microbiota using bronchoalveolar lavage fluid (BALF) from asymptomatic CF infants during the first year of life and to investigate the relationship between BALF microbiota, standard culture and clinical characteristics. METHODS: BALF, nasopharyngeal (NP) culture and infant pulmonary function testing data were collected at 6 months and one year of age during periods of clinical stability from infants diagnosed with CF by newborn screening...
2016: PloS One
https://www.readbyqxmd.com/read/27930272/dyella-acidisoli-sp-nov-dyella-flagellata-sp-nov-and-dyella-nitratireducens-sp-nov-isolated-from-forest-soil
#9
Mei-Hong Chen, Fan Xia, Ying-Ying Lv, Xiang-Yue Zhou, Li-Hong Qiu
Bacterial strains 4M-Z03T, 4M-K16T and DHG59T were isolated from forest soil samples collected from the Dinghushan Biosphere Reserve, Guangdong Province, PR China (112º 31' E 23º 10' N). The three strains grew well at 28 °C, pH 5.0-6.0 on R2A medium. On the basis of 16S rRNA gene sequence analysis, the three strains, together with D. humi DHG40T, formed a distinct phyletic clade within the genus Dyella, and the sequence similarities between any strains of the clade ranged from 97.8 to 98.5 %. Sequence analysis of concatenated partial gyrB, lepA and recA gene sequences also strongly suggested that the three strains represented three novel species of the genus Dyella...
December 8, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27930270/halofilum-ochraceum-gen-nov-sp-nov-a-new-gammaproteobacterium-isolated-from-a-marine-solar-saltern
#10
Jun Xia, Jin-Xin Zhao, Jin Sang, Guan-Jun Chen, Zong-Jun Du
A Gram-stain-negative, oxidase-negative, catalase-positive, facultative anaerobe, designated XJ16T, was isolated from a marine solar saltern on the coast of Weihai, China. Cells of the strain XJ16T were long and rod-shaped. The colonies were ochre in color and were able to reduce nitrate to nitrite. Optimal growth occurred at 33-37 °C (range, 20-45 °C) and in the presence of 8-10 % (w/v) NaCl (range, 2-20 %, w/v). The pH range for growth was found to be 6.5-9.5, with optimum growth at pH 7.5-8.0. A phylogenetic analysis based on the 16S rRNA gene sequence demonstrated that strain XJ16T was related to the phylum Proteobacteria...
December 8, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27930269/lysobacter-humi-sp-nov-a-novel-species-isolated-from-soil-in-south-korea
#11
Dongwook Lee, Jun Hyeong Jang, Seho Cha, Taegun Seo
A yellow-pigmented and strictly aerobic bacterial strain, designated FJY8T, was isolated from the soil of Goyang, South Korea. The cells of FJY8T are Gram-negative, non-motile rods. Colonies were circular, convex and transparent. Strain FJY8T grew optimally at 30°C, 0 % (w/v) NaCl and pH 8. Phylogenetic analysis of the 16S rRNA gene sequence of FJY8T revealed a clear affiliation of this bacterium to the family Lysobacteraceae and it was related to members of the genus Lysobacter, Lysobacter xinjiangensis KCTC 22558T being its closest relative (98...
December 8, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27926825/mycobacterium-malmesburyense-sp-nov-a-novel-non-tuberculous-mycobacterium-species-revealed-by-multiple-gene-sequence-characterization
#12
Nomakorinte Gcebe, Victor Rutten, Nicolaas Gey van Pittius, Brendon Naicker, Anita Michel
Non-tuberculous mycobacteria (NTM) are ubiquitous in the environment and an increasing number of NTM species have been isolated and characterized from both humans and animals, highlighting the zoonotic potential of these bacteria. Host exposure to NTM may impact on cross-reactive immune responsiveness which may affect diagnosis of bovine tuberculosis and may also play a role in the variability of the efficacy of Mycobacterium bovis BCG vaccination against tuberculosis. In this study we characterized 10 NTM isolates originating from water, soil, nasal swabs of cattle and African buffalo as well as bovine tissue samples...
December 5, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27926823/aliidiomarina-soli-sp-nov-isolated-from-saline-alkaline-soil
#13
Lian Xu, Ji-Quan Sun, Li-Juan Wang, Xiao-Zhen Liu, Yin-Yao Ji, Zhong-Qiu Shao, Xiao-Lei Wu
A Gram-staining-negative, motile, non-spore-forming bacterium designated strain Y4G10-17T was isolated from the saline-alkali farmland top soil, Inner Mongolia, northern China. Strain Y4G10-17T could grow at 4-45°C (with 30°C as the optimal temperature), pH 6.0-12.0 (optimal at pH 9.0), and in the presence of 1.0-12.0 % (w/v) NaCl (optimal at 4.0-6.0 %). Phylogenetic analysis based on the eight different copies of the 16S rRNA gene sequences revealed that strain Y4G10-17T shared the highest sequence similarities with Aliidiomarina maris CF12-14T, 97...
December 7, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27926821/algoriphagus-aestuariicola-sp-nov-isolated-from-estuary-sediment
#14
Xiaomeng Jia, Baolei Jia, Kyung Hyun Kim, Che Ok Jeon
A Gram-staining-negative and strictly aerobic bacterium, designated strain S2-A1T, was isolated from estuary sediment in South Korea. Cells of strain S2-A1T were oxidase- and catalase-positive rods without a gliding motility. Growth was observed at 15-40 °C (optimum, 37 °C), at pH 6.0-10.0 (optimum, pH 7.0-7.5) and in the presence of 0-4.0 % (w/v) NaCl (optimum, 0.5-1.0 %). The sole respiratory quinone was MK-7. Iso-C15:0, summed feature 3 (comprising C16:1 ω7c/C16:1 ω6c) and summed feature 9 (comprising iso-C17:1 ω9c/C16:0 10-methyl) were found as the major fatty acids (>5 % of the total fatty acids)...
December 7, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27926820/altererythrobacter-salegens-sp-nov-a-slightly-halophilic-bacterium-isolated-from-surface-sediment
#15
Xiaoyan Liang, Huina Lin, Kailing Wang, Yunjing Liao, Qiliang Lai, Ying Xu, Changyun Wang
A Gram-negative, rod-shaped and slightly halophilic bacterium, strain XY-R17T, was isolated from the surface sediment of Mai Po Inner Deep Bay Ramsar Site birdwatch in Hong Kong. The 16S rRNA gene sequence of strain XY-R17T exhibited a 96.5% similarity to that of the type strain Altererythrobacter atlanticus. Optimal growth occurred at pH 7.0-7.5, 3%-8% (w/v) NaCl, 28-30˚C. The major respiratory quinone was Ubiquinone-10. The principal fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c), summed feature 3 (C16:1ω7c and/or C16:1ω6c) and 11-methyl C18:1ω7c...
December 5, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27926817/description-of-immundisolibacter-cernigliae-gen-nov-sp-nov-a-high-molecular-weight-polycyclic-aromatic-hydrocarbon-degrading-bacterium-within-the-class-gammaproteobacteria-and-proposal-of-immundisolibacterales-ord-nov-and-immundisolibacteraceae-fam-nov
#16
Elizabeth M Corteselli, Michael D Aitken, David R Singleton
The bacterial strain TR3.2T was isolated from aerobic bioreactor-treated soil from a polycyclic aromatic hydrocarbon (PAH)-contaminated site in Salisbury, North Carolina, USA. Strain TR3.2T was identified as a member of "Pyrene Group 2" or "PG2", a previously uncultivated cluster of organisms associated with the degradation of high-molecular-weight PAHs by stable-isotope probing. Based on its 16S rRNA gene sequence the strain was classified as a member of the class Gammaproteobacteria but possessed only 90...
December 7, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27925791/reemergence-of-lower-airway-microbiota-in-lung-transplant-patients-with-cystic-fibrosis
#17
Saad A Syed, Fiona J Whelan, Barbara Waddell, Harvey R Rabin, Michael D Parkins, Michael G Surette
RATIONALE: Chronic lung infections are a hallmark of cystic fibrosis; they are responsible for progressive airway destruction and ultimately lead to respiratory death or the requirement for life-saving bilateral lung transplant. Furthermore, recurrent isolation of airway pathogens such as Pseudomonas aeruginosa in the allograft after transplant is associated with adverse outcomes, including bronchiolitis obliterans syndrome and acute infections. Little information exists on the impact of bilateral lung transplant on the lower-airway microbiota...
December 2016: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/27925061/molecular-detection-of-anaplasma-species-in-dogs-in-colombia
#18
Giovanni Vargas-Hernandez, Marcos Rogério André, Diana Maria Cendales, Keyla Carstens Marques de Sousa, Luiz Ricardo Gonçalves, Mariana Cristina Hoeppner Rondelli, Rosangela Zacarias Machado, Mirela Tinucci-Costa
Anaplasma platys and A. phagocytophilum are tick-borne pathogens that parasitize platelets and neutrophils, respectively, of humans and animals. The former is the etiological agent of canine cyclic thrombocytopenia, while the latter is that of canine granulocytic anaplasmosis. This work involved the detection and identification of Anaplasma species in blood samples from dogs in Colombia, using molecular techniques. Between December 2008 and April 2009, blood samples were drawn from the cephalic vein of 91 dogs in the central-western region of Colombia (cities of Bogota, Villavicencio and Bucaramanga) and stored in tubes containing EDTA...
December 1, 2016: Revista Brasileira de Parasitologia Veterinária, Brazilian Journal of Veterinary Parasitology
https://www.readbyqxmd.com/read/27924912/next-generation-systematics-an-innovative-approach-to-resolve-the-structure-of-complex-prokaryotic-taxa
#19
Vartul Sangal, Michael Goodfellow, Amanda L Jones, Edward C Schwalbe, Jochen Blom, Paul A Hoskisson, Iain C Sutcliffe
Prokaryotic systematics provides the fundamental framework for microbiological research but remains a discipline that relies on a labour- and time-intensive polyphasic taxonomic approach, including DNA-DNA hybridization, variation in 16S rRNA gene sequence and phenotypic characteristics. These techniques suffer from poor resolution in distinguishing between closely related species and often result in misclassification and misidentification of strains. Moreover, guidelines are unclear for the delineation of bacterial genera...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924593/analysis-of-16s-rrna-gene-amplicon-sequences-using-the-qiime-software-package
#20
Blair Lawley, Gerald W Tannock
The study of microbial ecology has undergone a paradigm shift in recent years, with rapid advances in molecular and bioinformatic tools allowing researchers with wide-ranging interests and backgrounds access to community profiling methods. While these advances have undoubtedly led to exciting new understanding of many systems, the array of protocols available and the idiosyncrasies of particular approaches can lead to confusion or, at worst, erroneous interpretation of results. Here, we describe a workflow from raw 16S rRNA gene amplicon sequence data, generated on an Illumina MiSeq instrument, to microbial community taxonomy profiles and basic diversity measures...
2017: Methods in Molecular Biology
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