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Wei Xie, Haiwei Luo, Senthil K Murugapiran, Jeremy A Dodsworth, Songze Chen, Ying Sun, Brian P Hedlund, Peng Wang, Huaying Fang, Minghua Deng, Chuanlun Zhang
Marine group II archaea are widely distributed in global oceans and dominate the total archaeal community within the upper euphotic zone of temperate waters. However, factors controlling the distribution of MGII are poorly delineated and the physiology and ecological functions of these still-uncultured organisms remain elusive. In this study, we investigated the planktonic MGII associated with particles and in free-living forms in the Pearl River Estuary (PRE) over a 10-month period. We detected high abundance of particle-associated MGII in PRE (up to ∼108 16S rRNA gene copies/L), which was around 10-fold higher than the free-living MGII in the same region, and an order of magnitude higher than previously reported in other marine environments...
December 13, 2017: Environmental Microbiology
Eric D Becraft, Tanja Woyke, Jessica Jarett, Natalia Ivanova, Filipa Godoy-Vitorino, Nicole Poulton, Julia M Brown, Joseph Brown, M C Y Lau, Tullis Onstott, Jonathan A Eisen, Duane Moser, Ramunas Stepanauskas
Recent advances in single-cell genomic and metagenomic techniques have facilitated the discovery of numerous previously unknown, deep branches of the tree of life that lack cultured representatives. Many of these candidate phyla are composed of microorganisms with minimalistic, streamlined genomes lacking some core metabolic pathways, which may contribute to their resistance to growth in pure culture. Here we analyzed single-cell genomes and metagenome bins to show that the "Candidate phylum Rokubacteria," formerly known as SPAM, represents an interesting exception, by having large genomes (6-8 Mbps), high GC content (66-71%), and the potential for a versatile, mixotrophic metabolism...
2017: Frontiers in Microbiology
Ramunas Stepanauskas, Elizabeth A Fergusson, Joseph Brown, Nicole J Poulton, Ben Tupper, Jessica M Labonté, Eric D Becraft, Julia M Brown, Maria G Pachiadaki, Tadas Povilaitis, Brian P Thompson, Corianna J Mascena, Wendy K Bellows, Arvydas Lubys
The original version of this Article contained errors in the units of concentration of three reagents listed in the Methods. These errors have all been corrected in both the PDF and HTML versions of the Article.
December 12, 2017: Nature Communications
Anwesha Ghosh, Punyasloke Bhadury
In mangrove environments, bacterioplankton communities constitute an important component of aquatic biota and play a major role in ecosystem processes. Variability of bacterioplankton communities from Sundarbans mangrove, located in the Indian subcontinent in South Asia and sits on the apex of Bay of Bengal, was investigated over monsoon and post-monsoon seasons. The study was undertaken in two stations in Sundarbans using 16S rRNA clone library and Illumina MiSeq approaches with focus on the functionally important members that participate in coastal biogeochemical cycling...
December 11, 2017: Environmental Science and Pollution Research International
Jing Leng, Xuchuan Liu, Chunyong Zhang, Renjun Zhu, Huaming Mao
A total of 6,219 positive clones were obtained by constructing a BAC library of uncultured ruminal fungi of gayal, and two clones (xynF1 and eglF2) with lignocellulolytic enzyme activity were selected. The sequencing results showed that xynF1 and eglF2 had 903-bp, and 1,995-bp, open reading frames likely to encode β-xylanase (XynF1) and β-glucosidase (EglF2), respectively. The amino acid sequence of XynF1 had 99% coverage and 95% homology to the endo-β-1,4-xylanase encoded by the cellulase gene of Orpinomyces sp...
December 8, 2017: Journal of General and Applied Microbiology
Pedro J Torres, Scott T Kelley
The emergence of high-throughput sequencing technologies has deepened our understanding of complex microbial communities and greatly facilitated the study of as-yet uncultured microbes and viruses. Studies of complex microbial communities require high-quality data to generate valid results. Here, we detail current methods of microbial and viral community sample acquisition, DNA extraction, sample preparation, and sequencing on Illumina high-throughput platforms. While using appropriate analytical tools is important, it must not overshadow the need for establishing a proper experimental design and obtaining sufficient numbers of samples for statistical purposes...
2018: Methods in Molecular Biology
Toshifumi Osaka, Eri Moriyama, Shunichi Arai, Yasuhiro Date, Junji Yagi, Jun Kikuchi, Satoshi Tsuneda
The imbalance of gut microbiota is known to be associated with inflammatory bowel disease, but it remains unknown whether dysbiosis is a cause or consequence of chronic gut inflammation. In order to investigate the effects of gut inflammation on microbiota and metabolome, the sequential changes in gut microbiota and metabolites from the onset of colitis to the recovery in dextran sulfate sodium-induced colitic mice were characterized by using meta 16S rRNA sequencing and proton nuclear magnetic resonance (¹H-NMR) analysis...
December 6, 2017: Nutrients
Arindam Chakraborty, Ekramul Islam
Despite the fact that the nitrogen (N) fixers act as the key regulator of ecosystem process, a detailed study of their abundance, diversity, and dynamics in arsenic (As)-contaminated rice fields is missing so far. DNA extracted from soil followed by 16S rRNA and nifH gene-based real-time qPCR, clone library analysis, and DNA sequencing were used to examine the status of the total and diazotrophic communities in two agricultural fields with and without arsenic contamination history during one rice cultivation season...
December 5, 2017: Environmental Science and Pollution Research International
Max Crüsemann, Raphael Reher, Isabella Schamari, Alexander O Brachmann, Tsubasa Ohbayashi, Markus Kuschak, Davide Malfacini, Alexander Seidinger, Marta Pinto-Carbó, René Richarz, Tatjana Reuter, Stefan Kehraus, Asis Hallab, Misty Attwood, Helgi B Schiöth, Peter Mergaert, Yoshitomo Kikuchi, Till F Schäberle, Evi Kostenis, Daniela Wenzel, Christa E Müller, Jörn Piel, Aurélien Carlier, Leo Eberl, Gabriele Maria Koenig
The cyclic depsipeptide FR900359 (FR), isolated from the tropical plant Ardisia crenata, displays a strong and selective inhibition of Gq proteins, making it an indispensable pharmacological tool to study Gq-related processes, as well as a promising drug candidate. Gq inhibition is a novel mode of action for defense chemicals and crucial for the ecological function of FR, as shown by in vivo experiments on mice, affinity to insect Gq proteins and insect toxicity studies. The uncultured endosymbiont of A. crenata, 'Candidatus Burkholderia crenata' was sequenced, revealing the FR nonribosomal peptide synthetase (frs) gene cluster...
December 1, 2017: Angewandte Chemie
Yizhi Song, Li Cui, José Ángel Siles López, Jiabao Xu, Yong-Guan Zhu, Ian P Thompson, Wei E Huang
The emergence and widespread distribution of antimicrobial resistant (AMR) bacteria has led to an increasing concern with respect to potential environmental and public health risks. Culture-independent and rapid identification of AMR bacteria in-situ in complex environments is important in understanding the role of viable but non-culturable and antibiotic persistent bacteria and in revealing potential pathogens without waiting for colony formation. In this study, a culture-independent and non-destructive phenotyping approach, so called Raman Deuterium Stable Isotope Probing (Raman-DIP), was developed to identify AMR bacteria in the River Thames...
November 30, 2017: Scientific Reports
Daniele Cristina Voltarelli, Brígida Kussumoto de Alcântara, Michele Lunardi, Alice Fernandes Alfieri, Raquel de Arruda Leme, Amauri Alcindo Alfieri
Bacteria classified in Mycoplasma (M. bovis and M. bovigenitalium) and Ureaplasma (U. diversum) genera are associated with granular vulvovaginitis that affect heifers and cows at reproductive age. The traditional means for detection and speciation of mollicutes from clinical samples have been culture and serology. However, challenges experienced with these laboratory methods have hampered assessment of their impact in pathogenesis and epidemiology in cattle worldwide. The aim of this study was to develop a PCR strategy to detect and primarily discriminate between the main species of mollicutes associated with reproductive disorders of cattle in uncultured clinical samples...
November 24, 2017: Animal Reproduction Science
Stefan W Grötzinger, Ram Karan, Eva Strillinger, Stefan Bader, Annika Frank, Israa S Al Rowaihi, Anastassja Akal, Wiebke Wackerow, John A Archer, Magnus Rueping, Dirk Weuster-Botz, Michael Groll, Jörg Eppinger, Stefan T Arold
Because only 0.01% of prokaryotic genospecies can be cultured and in situ observations are often impracticable, culture-independent methods are required to understand microbial life and harness potential applications of microbes. Here, we report a methodology for the production of proteins with desired functions based on single amplified genomes (SAGs) from unculturable species. We use this method to resurrect an alcohol dehydrogenase (ADH/D1) from an uncharacterized halo-thermophilic archaeon collected from a brine pool at the bottom of the Red Sea...
November 30, 2017: ACS Chemical Biology
Tan Suet May Amelia, Al-Ashraf Abdullah Amirul, Kesaven Bhubalan
We report data associated with the identification of three polyhydroxyalkanoate synthase genes (phaC) isolated from the marine bacteria metagenome of Aaptos aaptos marine sponge in the waters of Bidong Island, Terengganu, Malaysia. Our data describe the extraction of bacterial metagenome from sponge tissue, measurement of purity and concentration of extracted metagenome, polymerase chain reaction (PCR)-mediated amplification using degenerate primers targeting Class I and II phaC genes, sequencing at First BASE Laboratories Sdn Bhd, and phylogenetic analysis of identified and known phaC genes...
February 2018: Data in Brief
Juan Lopera, Ian J Miller, Kerry L McPhail, Jason C Kwan
A symbiotic lifestyle frequently results in genome reduction in bacteria; the isolation of small populations promotes genetic drift and the fixation of deletions and deleterious mutations over time. Transitions in lifestyle, including host restriction or adaptation to an intracellular habitat, are thought to precipitate a wave of sequence degradation events and consequent proliferation of pseudogenes. We describe here a verrucomicrobial symbiont of the tunicate Lissoclinum sp. that appears to be undergoing such a transition, with low coding density and many identifiable pseudogenes...
November 2017: MSystems
Sviatlana Marozava, Housna Mouttaki, Hubert Müller, Nidal Abu Laban, Alexander J Probst, Rainer U Meckenstock
An anaerobic culture (1MN) was enriched with 1-methylnaphthalene as sole source of carbon and electrons and Fe(OH)3 as electron acceptor. 1-Naphthoic acid was produced as a metabolite during growth with 1-methylnaphthalene while 2-naphthoic acid was detected with naphthalene and 2-methylnaphthalene. This indicates that the degradation pathway of 1-methylnaphthalene might differ from naphthalene and 2-methylnaphthalene degradation in sulfate reducers. Terminal restriction fragment length polymorphism and pyrosequencing revealed that the culture is mainly composed of two bacteria related to uncultured Gram-positive Thermoanaerobacteraceae and uncultured gram-negative Desulfobulbaceae...
November 24, 2017: Biodegradation
David Renault, Franck Déniel, Jessica Vallance, Emilie Bruez, Jean-Jacques Godon, Patrice Rey
In soilless culture, slow filtration is used to eliminate plant pathogenic microorganisms from nutrient solutions. The present study focused on the characterization and the potential functions of microbial communities colonizing the nutrient solutions recycled on slow filters during a whole cultivation season of 7 months in a tomato growing system. Bacterial microflora colonizing the solutions before and after they flew through the columns were studied. Two filters were amended with Pseudomonas putida (P-filter) or Bacillus cereus strains (B-filter), and a third filter was a control (C-filter)...
November 25, 2017: Microbial Ecology
Vitaly V Kadnikov, Yulia A Frank, Andrey V Mardanov, Alexey V Beletsky, Olga V Karnachuk, Nikolai V Ravin
We report on the metagenome of a deep subsurface aquifer in the Tomsk region of Russia, sampled via an oil exploration borehole drilled to a depth of 2.8 km. Methanogenic archaea were present in the water along with members of various bacterial phyla, including Firmicutes, Chloroflexi, Bacteroidetes, Ignavibacteriae, and uncultured candidate divisions.
November 22, 2017: Genome Announcements
Lihui Du, Xiaoran Fan, Fang Liu, Qi Zhou, Jian Yuan, Xingrong Ju
The microbiological and chemical changes in Taihu white prawn (Exopalaemon modestus) during ice storage were evaluated. For the microbiological changes, total viable counts were obtained. PCR coupled with denatured gradient gel electrophoresis was then performed to investigate the changes in microflora. For the chemical changes, total volatile basic nitrogen was determined and biogenic amines were detected. The initial total viable count was 6.2 log CFU/g, which increased to 7.1 log CFU/g after storage at 0°C for 10 days...
November 22, 2017: Journal of Food Protection
Lingzhan Miao, Peifang Wang, Chao Wang, Jun Hou, Yu Yao, Jun Liu, Bowen Lv, Yangyang Yang, Guoxiang You, Yi Xu, Zhilin Liu, Songqi Liu
Environmental concerns regarding the potential ecological risks of metallic oxide nanoparticles (MNPs) in aquatic ecosystems are increasing; sediment is considered a sink for these MNPs. Although several studies have studied the potential impact of MNPs on microbial communities in freshwater and estuarine sediments, limited information is available regarding the influence of MNPs on the metabolic activity of surficial sediment microbial communities and related biogeochemical conditions. To address these issues, a microcosm approach was established to study the metabolic response of surficial sediment microbial communities to a single addition of TiO2 or CeO2 NPs (5 mg/L) using oxygen microelectrodes, enzyme activity measurements, and high-throughput sequencing...
November 7, 2017: Water Research
S François, D Filloux, M Frayssinet, P Roumagnac, D P Martin, M Ogliastro, R Froissart
Metagenomics studies have revolutionized the field of biology by revealing the presence of many previously unisolated and uncultured micro-organisms. However, one of the main problems encountered in metagenomic studies is the high percentage of sequences that cannot be assigned taxonomically using commonly used similarity-based approaches (e.g. BLAST or HMM). These unassigned sequences are allegorically called « dark matter » in the metagenomic literature and are often referred to as being derived from new or unknown organisms...
November 14, 2017: Virus Research
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