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https://www.readbyqxmd.com/read/28213734/dehalococcoides-and-general-bacterial-ecology-of-differentially-trichloroethene-dechlorinating-flow-through-columns
#1
Babur S Mirza, Darwin L Sorensen, Daniel J McGlinn, R Ryan Dupont, Joan E McLean
The diversity of Dehalococcoides mccartyi (Dhc) and/or other organohalide respiring or associated microorganisms in parallel, partial, or complete trichloroethene (TCE) dehalogenating systems has not been well described. The composition of Dhc populations and the associated bacterial community that developed over 7.5 years in the top layer (0-10 cm) of eight TCE-fed columns were examined using pyrosequencing. Columns biostimulated with one of three carbon sources, along with non-stimulated controls, developed into complete (ethene production, whey amended), partial (cis-dichloroethene (DCE) and VC, an emulsified oil with nonionic surfactant), limited (<5 % cis-DCE and 95 % TCE, an emulsified oil), and non- (controls) TCE dehalogenating systems...
February 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28213706/plant-microbial-association-in-petroleum-and-gas-exploration-sites-in-the-state-of-assam-north-east-india-significance-for-bioremediation
#2
Hemen Sarma, N F Islam, M N V Prasad
The state of Assam in north-east India gained popularity in Asia because of discovery of oil. Pollution due to petroleum and gas exploration is a serious problem in Assam. Oil and gas exploration by various agencies in Assam resulted in soil pollution due to hydrocarbons (HCs) and heavy metals (HMs). Bioremediation gained considerable significance in addressing petroleum hydrocarbon polluted sites in various parts of the world. In this investigation, we have observed 15 species of plants belonging to grass growing on the contaminated soils...
February 17, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28213337/effect-of-advanced-oxidation-on-n-nitrosodimethylamine-ndma-formation-and-microbial-ecology-during-pilot-scale-biological-activated-carbon-filtration
#3
Dong Li, Ben Stanford, Eric Dickenson, Wendell O Khunjar, Carissa L Homme, Erik J Rosenfeldt, Jonathan O Sharp
Water treatment combining advanced oxidative processes with subsequent exposure to biological activated carbon (BAC) holds promise for the attenuation of recalcitrant pollutants. Here we contrast oxidation and subsequent biofiltration of treated wastewater effluent employing either ozone or UV/H2O2 followed by BAC during pilot-scale implementation. Both treatment trains largely met target water quality goals by facilitating the removal of a suite of trace organics and bulk water parameters. N-nitrosodimethylamine (NDMA) formation was observed in ozone fed BAC columns during biofiltration and to a lesser extent in UV/H2O2 fed columns and was most pronounced at 20 min of empty bed contact time (EBCT) when compared to shorter EBCTs evaluated...
February 2, 2017: Water Research
https://www.readbyqxmd.com/read/28211914/eco-evolutionary-feedbacks-can-rescue-cooperation-in-microbial-populations
#4
Clara Moreno-Fenoll, Matteo Cavaliere, Esteban Martínez-García, Juan F Poyatos
Bacterial populations whose growth depends on the cooperative production of public goods are usually threatened by the rise of cheaters that do not contribute but just consume the common resource. Minimizing cheater invasions appears then as a necessary mechanism to maintain these populations. However, that invasions result instead in the persistence of cooperation is a prospect that has yet remained largely unexplored. Here, we show that the demographic collapse induced by cheaters in the population can actually contribute to the rescue of cooperation, in a clear illustration of how ecology and evolution can influence each other...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28210795/observational-comparisons-of-intestinal-microbiota-characterizations-immune-enzyme-activities-and-muscle-amino-acid-compositions-of-loach-in-paddy-fields-and-ponds-in-sichuan-province
#5
Song Yang, Yuanliang Duan, Jie Zhang, Jian Zhou, Ya Liu, Jun Du, Liulan Zhao, Zongjun Du, Shuaishuai Han
A balanced intestinal microbial ecosystem is crucial for the growth and health of animals because it can influence the digestion and absorption of nutrients in the intestine. Different culture conditions may change the ecology of microbial in intestine and thus affect the overall growth performance of an animal. In this study, we compared intestinal morphologies, microbiota characterizations, immune enzyme activities, and muscle amino acid compositions of loach cultured in paddy fields and ponds. The fish were fed with the same diets from May 5 to November 5 (2015) in three paddy or ponds...
February 16, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28209775/evidence-for-environmental-and-ecological-selection-in-a-microbe-with-no-geographic-limits-to-gene-flow
#6
Kerry A Whittaker, Tatiana A Rynearson
The ability for organisms to disperse throughout their environment is thought to strongly influence population structure and thus evolution of diversity within species. A decades-long debate surrounds processes that generate and support high microbial diversity, particularly in the ocean. The debate concerns whether diversification occurs primarily through geographic partitioning (where distance limits gene flow) or through environmental selection, and remains unresolved due to lack of empirical data. Here we show that gene flow in a diatom, an ecologically important eukaryotic microbe, is not limited by global-scale geographic distance...
February 16, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28202080/mentholation-affects-the-cigarette-microbiota-by-selecting-for-bacteria-resistant-to-harsh-environmental-conditions-and-selecting-against-potential-bacterial-pathogens
#7
Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Emma Claye, Kelsey R Babik, Molly C Reid, Eoghan M Smyth, Lauren E Hittle, Joseph N Paulson, Raul Cruz-Cano, Mihai Pop, Stephanie S Buehler, Pamela I Clark, Amy R Sapkota, Emmanuel F Mongodin
BACKGROUND: There is a paucity of data regarding the microbial constituents of tobacco products and their impacts on public health. Moreover, there has been no comparative characterization performed on the bacterial microbiota associated with the addition of menthol, an additive that has been used by tobacco manufacturers for nearly a century. To address this knowledge gap, we conducted bacterial community profiling on tobacco from user- and custom-mentholated/non-mentholated cigarette pairs, as well as a commercially-mentholated product...
February 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28201744/synthetic-microbial-ecology-and-the-dynamic-interplay-between-microbial-genotypes
#8
Jan Dolinšek, Felix Goldschmidt, David R Johnson
No abstract text is available yet for this article.
November 1, 2016: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28197142/home-made-cost-effective-preservation-buffer-is-a-better-alternative-to-commercial-preservation-methods-for-microbiome-research
#9
Sebastian Menke, Mark A F Gillingham, Kerstin Wilhelm, Simone Sommer
The investigation of wildlife gastrointestinal microbiomes by next-generation sequencing approaches is a growing field in microbial ecology and conservation. Such studies often face difficulties in sample preservation if neither freezing facilities nor liquid nitrogen (LQN) are readily available. Thus, in order to prevent microbial community changes because of bacterial growth after sampling, preservation buffers need to be applied to samples. However, the amount of microbial community variation attributable to the different preservation treatments and potentially affecting biological interpretation is hardly known...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28197130/mineralizing-filamentous-bacteria-from-the-prony-bay-hydrothermal-field-give-new-insights-into-the-functioning-of-serpentinization-based-subseafloor-ecosystems
#10
Céline Pisapia, Emmanuelle Gérard, Martine Gérard, Léna Lecourt, Susan Q Lang, Bernard Pelletier, Claude E Payri, Christophe Monnin, Linda Guentas, Anne Postec, Marianne Quéméneur, Gaël Erauso, Bénédicte Ménez
Despite their potential importance as analogs of primitive microbial metabolisms, the knowledge of the structure and functioning of the deep ecosystems associated with serpentinizing environments is hampered by the lack of accessibility to relevant systems. These hyperalkaline environments are depleted in dissolved inorganic carbon (DIC), making the carbon sources and assimilation pathways in the associated ecosystems highly enigmatic. The Prony Bay Hydrothermal Field (PHF) is an active serpentinization site where, similar to Lost City (Mid-Atlantic Ridge), high-pH fluids rich in H2 and CH4 are discharged from carbonate chimneys at the seafloor, but in a shallower lagoonal environment...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28196961/bacterial-topography-of-the-healthy-human-lower-respiratory-tract
#11
Robert P Dickson, John R Erb-Downward, Christine M Freeman, Lisa McCloskey, Nicole R Falkowski, Gary B Huffnagle, Jeffrey L Curtis
Although culture-independent techniques have refuted lung sterility in health, controversy about contamination during bronchoscope passage through the upper respiratory tract (URT) has impeded research progress. We sought to establish whether bronchoscopic sampling accurately reflects the lung microbiome in health and to distinguish between two proposed routes of authentic microbial immigration, (i) dispersion along contiguous respiratory mucosa and (ii) subclinical microaspiration. During bronchoscopy of eight adult volunteers without lung disease, we performed seven protected specimen brushings (PSB) and bilateral bronchoalveolar lavages (BALs) per subject...
February 14, 2017: MBio
https://www.readbyqxmd.com/read/28194679/soil-properties-and-microbial-ecology-of-a-paddy-field-after-repeated-applications-of-domestic-and-industrial-sewage-sludges
#12
Xiaoyan Liu, Wuxing Liu, Qingling Wang, Longhua Wu, Yongming Luo, Peter Christie
The effects of repeated application of two types of sewage sludge, domestic and industrial (petrochemical, PSS) sludges, into paddy fields over a 5-year period on the soil properties and microbial ecology were studied and compared with conventional NPK fertilizer application. Soil organic matter and total nitrogen contents were significantly higher in the two sludge treatments than that in fertilized plots after 5 years. Soil concentrations of potentially toxic metals were low after 5 years of both sludge treatments, but the polycyclic aromatic hydrocarbons (PAHs) showed differences between the two sludge types...
February 14, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28191504/distinct-biogeographic-patterns-for-archaea-bacteria-and-fungi-along-the-vegetation-gradient-at-the-continental-scale-in-eastern-china
#13
Bin Ma, Zhongmin Dai, Haizhen Wang, Melissa Dsouza, Xingmei Liu, Yan He, Jianjun Wu, Jorge L M Rodrigues, Jack A Gilbert, Philip C Brookes, Jianming Xu
The natural forest ecosystem in Eastern China, from tropical forest to boreal forest, has declined due to cropland development during the last 300 years, yet little is known about the historical biogeographic patterns and driving processes for the major domains of microorganisms along this continental-scale natural vegetation gradient. We predicted the biogeographic patterns of soil archaeal, bacterial, and fungal communities across 110 natural forest sites along a transect across four vegetation zones in Eastern China...
January 2017: MSystems
https://www.readbyqxmd.com/read/28187207/a-multi-objective-constraint-based-approach-for-modeling-genome-scale-microbial-ecosystems
#14
Marko Budinich, Jérémie Bourdon, Abdelhalim Larhlimi, Damien Eveillard
Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs) for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients...
2017: PloS One
https://www.readbyqxmd.com/read/28185400/microdiversity-shapes-the-traits-niche-space-and-biogeography-of-microbial-taxa
#15
REVIEW
Alyse A Larkin, Adam C Martiny
With rapidly improving sequencing technologies, scientists have recently gained the ability to examine diverse microbial communities at high genomic resolution, revealing that both free-living and host-associated microbes partition their environment at fine phylogenetic scales. This "microdiversity," or closely related (>97% similar 16S rRNA gene) but ecologically and physiologically distinct sub-taxonomic groups, appears to be an intrinsic property of microorganisms. However, the functional implications of microdiversity as well as its effects on microbial biogeography are poorly understood...
February 10, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28183913/a-prominent-glycyl-radical-enzyme-in-human-gut-microbiomes-metabolizes-trans-4-hydroxy-l-proline
#16
B J Levin, Y Y Huang, S C Peck, Y Wei, A Martínez-Del Campo, J A Marks, E A Franzosa, C Huttenhower, E P Balskus
The human microbiome encodes vast numbers of uncharacterized enzymes, limiting our functional understanding of this community and its effects on host health and disease. By incorporating information about enzymatic chemistry into quantitative metagenomics, we determined the abundance and distribution of individual members of the glycyl radical enzyme superfamily among the microbiomes of healthy humans. We identified many uncharacterized family members, including a universally distributed enzyme that enables commensal gut microbes and human pathogens to dehydrate trans-4-hydroxy-l-proline, the product of the most abundant human posttranslational modification...
February 10, 2017: Science
https://www.readbyqxmd.com/read/28179422/viruses-comprise-an-extensive-pool-of-mobile-genetic-elements-in-eukaryote-cell-cultures-and-human-clinical-samples
#17
Jakob Thannesberger, Hans-Joerg Hellinger, Ingeborg Klymiuk, Marie-Theres Kastner, Franz J J Rieder, Martina Schneider, Susanne Fister, Thomas Lion, Karin Kosulin, Johannes Laengle, Michael Bergmann, Thomas Rattei, Christoph Steininger
Viruses shape a diversity of ecosystems by modulating their microbial, eukaryotic, or plant host metabolism. The complexity of virus-host interaction networks is progressively fathomed by novel metagenomic approaches. By using a novel metagenomic method, we explored the virome in mammalian cell cultures and clinical samples to identify an extensive pool of mobile genetic elements in all of these ecosystems. Despite aseptic treatment, cell cultures harbored extensive and diverse phage populations with a high abundance of as yet unknown and uncharacterized viruses (viral dark matter)...
February 8, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28179014/mirkat-s-a-community-level-test-of-association-between-the-microbiota-and-survival-times
#18
Anna Plantinga, Xiang Zhan, Ni Zhao, Jun Chen, Robert R Jenq, Michael C Wu
BACKGROUND: Community-level analysis of the human microbiota has culminated in the discovery of relationships between overall shifts in the microbiota and a wide range of diseases and conditions. However, existing work has primarily focused on analysis of relatively simple dichotomous or quantitative outcomes, for example, disease status or biomarker levels. Recently, there is also considerable interest in the relationship between the microbiota and censored survival outcomes, such as in clinical trials...
February 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28177786/response-of-microbial-communities-to-roxarsone-under-different-culture-conditions
#19
Yaci Liu, Zhaoji Zhang, Yasong Li, Yuhong Fei
Roxarsone is a feed additive widely used in broiler and swine industry that has the potential to contaminate environment, mainly via the use of poultry manure as fertilizer, which results in release of inorganic arsenic to the soil and water. This study was conducted to investigate the roxarsone degradation and the response of microbial community under different culture conditions using high-throughput sequencing technology. Poultry litter was incubated for 288 h in the presence of roxarsone under light aerobic, dark aerobic, or dark anaerobic conditions, showing that roxarsone was completely degraded after 48 h of dark anaerobic incubation, while 79...
January 20, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28177399/impacts-of-endemic-earthworms-megascolecidae-in-biosolids-amended-soil
#20
Young-Nam Kim, Brett Robinson, Jacqui Horswell, Stephane Boyer, Nicholas Dickinson
Biosolids can be a valuable fertilizer for agriculture and in ecological restoration, although there are concerns about contaminants. Earthworm activity, including vermicomposting of biosolids, may influence the efficacy of their use. We investigated how two New Zealand endemic anecic species of (cf. ) responded to biosolids amendment and affected the mobility of nutrients and trace elements as well as greenhouse gas emissions in biosolids-amended soil. Earthworms were incubated with mixtures of biosolids-amended soil (0, 6...
January 2017: Journal of Environmental Quality
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