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https://www.readbyqxmd.com/read/28106880/discovery-of-anaerobic-lithoheterotrophic-haloarchaea-ubiquitous-in-hypersaline-habitats
#1
Dimitry Y Sorokin, Enzo Messina, Francesco Smedile, Pawel Roman, Jaap S Sinninghe Damsté, Sergio Ciordia, Maria Carmen Mena, Manuel Ferrer, Peter N Golyshin, Ilya V Kublanov, Nazar I Samarov, Stepan V Toshchakov, Violetta La Cono, Michail M Yakimov
Hypersaline anoxic habitats harbour numerous novel uncultured archaea whose metabolic and ecological roles remain to be elucidated. Until recently, it was believed that energy generation via dissimilatory reduction of sulfur compounds is not functional at salt saturation conditions. Recent discovery of the strictly anaerobic acetotrophic Halanaeroarchaeum compels to change both this assumption and the traditional view on haloarchaea as aerobic heterotrophs. Here we report on isolation and characterization of a novel group of strictly anaerobic lithoheterotrophic haloarchaea, which we propose to classify as a new genus Halodesulfurarchaeum...
January 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/28097050/microbial-communities-mediating-algal-detritus-turnover-under-anaerobic-conditions
#2
Jessica M Morrison, Chelsea L Murphy, Kristina Baker, Richard M Zamor, Steve J Nikolai, Shawn Wilder, Mostafa S Elshahed, Noha H Youssef
BACKGROUND: Algae encompass a wide array of photosynthetic organisms that are ubiquitously distributed in aquatic and terrestrial habitats. Algal species often bloom in aquatic ecosystems, providing a significant autochthonous carbon input to the deeper anoxic layers in stratified water bodies. In addition, various algal species have been touted as promising candidates for anaerobic biogas production from biomass. Surprisingly, in spite of its ecological and economic relevance, the microbial community involved in algal detritus turnover under anaerobic conditions remains largely unexplored...
2017: PeerJ
https://www.readbyqxmd.com/read/28087803/epiphytic-planctomycetes-communities-associated-with-three-main-groups-of-macroalgae
#3
Joana Bondoso, Filipa Godoy-Vitorino, Vanessa Balagué, Josep M Gasol, Jens Harder, Olga Maria Lage
Planctomycetes, a unique group of widespread and understudied bacteria, are known to be associated with macroalgae. The temporal dynamics and the host-specific association of planctomycetal communities on Fucus spiralis, Ulva sp. and Chondrus crispus from two locations in the North Coast of Portugal were assessed both by denaturing gradient gel electrophoresis (DGGE) with group-specific primers and 16S rDNA amplicon libraries. The epiphytic planctomycetal communities showed a significant association with the host macroalgal species independently of the geographical location and the season...
January 12, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28087277/identification-of-ubact-a-ubiquitin-like-protein-along-with-other-homologous-components-of-a-conjugation-system-and-the-proteasome-in-different-gram-negative-bacteria
#4
Gilad Lehmann, Ronald G Udasin, Ido Livneh, Aaron Ciechanover
Systems analogous to the eukaryotic ubiquitin-proteasome system have been previously identified in Archaea, and Actinobacteria (gram-positive), but not in gram-negative bacteria. Here, we report the bioinformatic identification of a novel prokaryotic ubiquitin-like protein, which we name UBact. The phyletic distribution of UBact covers at least five gram-negative bacterial phyla, including Nitrospirae, Armatimonadetes, Verrucomicroba, Nitrospinae, and Planctomycetes. Additionally, it was identified in seven candidate (uncultured) phyla and one Archaeon...
January 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28081358/microbial-diversity-during-fermentation-of-sweet-paste-a-chinese-traditional-seasoning-using-pcr-denaturing-gradient-gel-electrophoresis
#5
Ping Mao, Yuanliang Hu, Tingting Liao, Zhaoting Wang, Shumiao Zhao, Yunxiang Liang, Yongmei Hu
The aim of this study was to elucidate the changes in the microbial community and biochemical properties of a traditional sweet paste during fermentation. PCR-denaturing gradient gel electrophoresis (DGGE) analysis showed that Aspergillus oryzae was the predominant species in the koji and the majority of the fungi isolated belonged to 2 Zygosaccharomyces species in the mash. The bacterial DGGE profiles revealed the presence of Bacillus subtilis during fermentation, and Lactobacillus acidipiscis, Lactobacillus pubuzihii, Lactobacillus sp, Staphylococcus kloosi and several uncultured bacteria were also detected in the mash after 14 days of main fermentation...
January 12, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28049922/comparison-of-fecal-microbiota-of-three-captive-carnivore-species-inhabiting-korea
#6
Choa An, Yumiko Okamoto, Siyu Xu, Kyung Yeon Eo, Junpei Kimura, Naomichi Yamamoto
This study aimed at characterizing fecal microbiota of three captive carnivore species of leopard cats Prionailurus bengalensis, Eurasian otters Lutra lutra and raccoon dogs Nyctereutes procyonoides. We used DNA barcoding sequencing to analyze 16S rRNA genes of uncultured bacteria in the feces collected in the Seoul Zoo. The sequencing analyses revealed that: 1) Firmicutes was the most dominant phylum for all three animals; 2) bacterial genus-rank compositions were distinct across species of the animals; and 3) bacterial community memberships were different across species of the studied animals...
December 30, 2016: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28049838/insights-into-the-lifestyle-of-uncultured-bacterial-natural-product-factories-associated-with-marine-sponges
#7
Gerald Lackner, Eike Edzard Peters, Eric J N Helfrich, Jörn Piel
The as-yet uncultured filamentous bacteria "Candidatus Entotheonella factor" and "Candidatus Entotheonella gemina" live associated with the marine sponge Theonella swinhoei Y, the source of numerous unusual bioactive natural products. Belonging to the proposed candidate phylum "Tectomicrobia," Candidatus Entotheonella members are only distantly related to any cultivated organism. The Ca E. factor has been identified as the source of almost all polyketide and modified peptides families reported from the sponge host, and both Ca Entotheonella phylotypes contain numerous additional genes for as-yet unknown metabolites...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28040137/prenatal-diagnosis-of-familial-transmission-of-17q12-microduplication-associated-with-no-apparent-phenotypic-abnormality
#8
Chih-Ping Chen, Chung-Hu Fu, Yi-Hui Lin, Schu-Rern Chern, Peih-Shan Wu, Yen-Ni Chen, Shin-Wen Chen, Wayseen Wang
OBJECTIVE: We present prenatal diagnosis of familial transmission of 17q12 duplication associated with no apparent phenotypic abnormality. CASE REPORT: A 36-year-old woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Cytogenetic analysis revealed a karyotype of 46,XY. Array comparative genomic hybridization of uncultured amniocytes revealed a 1.42-Mb duplication of 17q12 or arr 17q12 (34,822,465-36,243,365) × 3 encompassing 12 Online Mendelian Inheritance in Man (OMIM) genes including LHX1, ACACA, and HNF1B...
December 2016: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28032398/cultivation-and-characterisation-of-the-surface-markers-and-carbohydrate-profile-of-human-corneal-endothelial-cells
#9
Richárd Nagymihály, Zoltán Veréb, Réka Albert, Laura Sidney, Harminder Dua, Andrew Hopkinson, Goran Petrovski
BACKGROUND: To characterise human corneal endothelial cell (HCEnC) cultures generated by the peel-and-digest method based on their surface protein/carbohydrate expression pattern. METHODS: QPCR was used to compare expression of Vimentin, CD90, Cytokeratin-19, ZO-1, Claudin 14 in cultured HCEnC and cell line B4G12 versus stromal cells. Fluorescence-activated cell sorting (FACS) was used to assess surface protein distribution of cultured and uncultured HCEnC. Distribution of surface proteins/ carbohydrates was visualised by immunofluorescent and lectin staining...
December 29, 2016: Clinical & Experimental Ophthalmology
https://www.readbyqxmd.com/read/28028613/microbial-diversity-and-autotrophic-activity-in-kamchatka-hot-springs
#10
Alexander Yu Merkel, Nikolay V Pimenov, Igor I Rusanov, Alexander I Slobodkin, Galina B Slobodkina, Ivan Yu Tarnovetckii, Evgeny N Frolov, Arseny V Dubin, Anna A Perevalova, Elizaveta A Bonch-Osmolovskaya
Microbial communities of Kamchatka Peninsula terrestrial hot springs were studied using molecular, radioisotopic and cultural approaches. Analysis of 16S rRNA gene fragments performed by means of high-throughput sequencing revealed that aerobic autotrophic sulfur-oxidizing bacteria of the genus Sulfurihydrogenibium (phylum Aquificae) dominated in a majority of streamers. Another widely distributed and abundant group was that of anaerobic bacteria of the genus Caldimicrobium (phylum Thermodesulfobacteria). Archaea of the genus Vulcanisaeta were abundant in a high-temperature, slightly acidic hot spring, where they were accompanied by numerous Nanoarchaeota, while the domination of uncultured Thermoplasmataceae A10 was characteristic for moderately thermophilic acidic habitats...
December 27, 2016: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28025221/bacteria-associated-with-piezodorus-guildinii-hemiptera-pentatomidae-with-special-reference-to-those-transmitted-by-feeding
#11
Claudia Husseneder, Jong-Seok Park, Andrea Howells, Chinmay V Tikhe, Jeffrey A Davis
The redbanded stink bug, Piezodorus guildinii (Westwood) (Hemiptera: Heteroptera: Pentatomidae), is a rapidly growing pest damaging southern US agriculture. Pentatomid stink bugs are known to vector bacterial, fungal, and viral plant diseases. However, bacteria associated with redbanded stink bugs and their vector potential have not yet been assessed. In this study, we 1) cultured and identified bacteria transmitted by feeding of redbanded stink bug and 2) described bacteria from guts of redbanded stink bug individuals using next-generation sequencing of 16S rRNA genes...
December 26, 2016: Environmental Entomology
https://www.readbyqxmd.com/read/28018655/inferring-phage-bacteria-infection-networks-from-time-series-data
#12
Luis F Jover, Justin Romberg, Joshua S Weitz
In communities with bacterial viruses (phage) and bacteria, the phage-bacteria infection network establishes which virus types infect which host types. The structure of the infection network is a key element in understanding community dynamics. Yet, this infection network is often difficult to ascertain. Introduced over 60 years ago, the plaque assay remains the gold standard for establishing who infects whom in a community. This culture-based approach does not scale to environmental samples with increased levels of phage and bacterial diversity, much of which is currently unculturable...
November 2016: Royal Society Open Science
https://www.readbyqxmd.com/read/28018324/abundance-of-common-aerobic-anoxygenic-phototrophic-bacteria-in-a-coastal-aquaculture-area
#13
Yuki Sato-Takabe, Hironori Nakao, Takafumi Kataoka, Taichi Yokokawa, Koji Hamasaki, Kohei Ohta, Satoru Suzuki
Aerobic anoxygenic phototrophic bacteria (AAnPB) rely on not only heterotrophic but also phototrophic energy gain. AAnPB are known to have high abundance in oligotrophic waters and are the major portion of the bacterial carbon stock in the environment. In a yearlong study in an aquaculture area in the Uwa Sea, Japan, AAnPB, accounted for 4.7 to 24% of the total bacteria by count. Since the cell volume of AAnPB is 2.23 ± 0.674 times larger than the mean for total bacteria, AAnPB biomass is estimated to account for 10-53% of the total bacterial assemblage...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28004369/mycorrhizal-colonization-status-of-lowland-rice-oryza-sativa-l-in-the-southeastern-region-of-china
#14
Xun-Wen Chen, Fu-Yong Wu, Hui Li, Wai-Fung Chan, Sheng-Chun Wu, Ming-Hung Wong
The accumulation, distribution, and speciation of contaminants, such as arsenic, in rice can be affected by soil microorganisms such as arbuscular mycorrhizal fungi (AMF). As a potential measure to control contaminant acquisition in rice, the status and performance of AMF in the field need to be investigated. Root samples of rice plants were collected in seven different cities in Guangdong, Jiangxi, Hubei, and Jiangsu Provinces in China in order to investigate the colonization rate of AMF. The total DNA of the roots was extracted, followed by PCR and sequencing, and further confirmed the existence of AMF...
December 21, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/27999569/local-and-regional-diversity-reveals-dispersal-limitation-and-drift-as-drivers-for-groundwater-bacterial-communities-from-a-fractured-granite-formation
#15
E D Beaton, Bradley S Stevenson, Karen J King-Sharp, Blake W Stamps, Heather S Nunn, Marilyne Stuart
Microorganisms found in terrestrial subsurface environments make up a large proportion of the Earth's biomass. Biogeochemical cycles catalyzed by subsurface microbes have the potential to influence the speciation and transport of radionuclides managed in geological repositories. To gain insight on factors that constrain microbial processes within a formation with restricted groundwater flow we performed a meta-community analysis on groundwater collected from multiple discrete fractures underlying the Chalk River Laboratories site (located in Ontario, Canada)...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27986719/effects-of-actinomycete-secondary-metabolites-on-sediment-microbial-communities
#16
Nastassia V Patin, Michelle Schorn, Kristen Aguinaldo, Tommie Lincecum, Bradley S Moore, Paul R Jensen
: Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity...
December 16, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27986403/temperature-dependence-of-nitrogen-removal-activity-by-anammox-bacteria-enriched-at-low-temperatures
#17
Giri Park, Masashi Takekawa, Satoshi Soda, Michihiko Ike, Kenji Furukawa
The anaerobic ammonium oxidation (anammox) process, which is applicable at ambient temperature, is necessary to develop more versatile nitrogen removal technologies. In this study, two anammox reactors, Low-R1 and Low-R2 inoculated with activated sludge respectively in Kumamoto and Hokkaido, Japan, achieved nitrogen removal rates (NRRs) of 1.5 kg-N/m(3)/day at 20°C. The specific anammox activity (SAA) of the Low-R1 and Low-R2 sludge samples had peaks, respectively, of 2.8±0.3 mg-N/g-VSS/h at 25°C and 4...
December 14, 2016: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/27984592/inferring-aggregated-functional-traits-from-metagenomic-data-using-constrained-non-negative-matrix-factorization-application-to-fiber-degradation-in-the-human-gut-microbiota
#18
Sébastien Raguideau, Sandra Plancade, Nicolas Pons, Marion Leclerc, Béatrice Laroche
Whole Genome Shotgun (WGS) metagenomics is increasingly used to study the structure and functions of complex microbial ecosystems, both from the taxonomic and functional point of view. Gene inventories of otherwise uncultured microbial communities make the direct functional profiling of microbial communities possible. The concept of community aggregated trait has been adapted from environmental and plant functional ecology to the framework of microbial ecology. Community aggregated traits are quantified from WGS data by computing the abundance of relevant marker genes...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27974879/unusually-high-archaeal-diversity-in-a-crystallizer-pond-pomorie-salterns-bulgaria-revealed-by-phylogenetic-analysis
#19
Margarita Kambourova, Iva Tomova, Ivanka Boyadzhieva, Nadja Radchenkova, Evgenia Vasileva-Tonkova
Recent studies on archaeal diversity in few salterns have revealed heterogeneity between sites and unique structures of separate places that hinder drawing of generalized conclusions. Investigations on the archaeal community composition in P18, the biggest crystallizer pond in Pomorie salterns (PS) (34% salinity), demonstrated unusually high number of presented taxa in hypersaline environment. Archaeal clones were grouped in 26 different operational taxonomic units (OTUs) assigned to 15 different genera from two orders, Halobacteriales and Haloferacales...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27959874/microbial-quality-and-suitability-of-roof-harvested-rainwater-in-rural-villages-for-crop-irrigation-and-domestic-use
#20
Mosimanegape Jongman, Lise Korsten
The study aimed at assessing the microbiological quality and suitability of roof-harvested rainwater (RHRW) for crop irrigation and domestic use. In total, 80 rainwater tanks (246 samples) across three rural villages (Ga-Molepane, Jericho and Luthngele) were visited. Culture-based techniques were used to isolate bacterial microbes and identities were confirmed using matrix-assisted laser desorption/ionization time of flight (MALDI-TOF-MS). Uncultured fungal populations were also identified using pyrosequencing...
December 2016: Journal of Water and Health
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