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Microbial diversity

Marine Landa, Stéphane Blain, Jérôme Harmand, Sébastien Monchy, Alain Rapaport, Ingrid Obernosterer
In the Southern Ocean, natural iron fertilization in the wake of islands leads to annually occurring spring phytoplankton blooms associated with enhanced heterotrophic activity through the release of labile dissolved organic matter (DOM). The aim of this study was to investigate experimentally how diatom-derived DOM affects the composition of Southern Ocean winter water bacterial communities and to identify the most responsive taxa. A bacterial community collected in the naturally iron-fertilized region off Kerguelen Island (KEOPS2 October-November 2011) was grown onboard in continuous cultures, on winter water alone or amended with diatom-derived DOM supplied at identical DOC concentrations...
March 14, 2018: FEMS Microbiology Ecology
Waleed K Mohammed, Natalio Krasnogor, Nicholas S Jakubovics
The ability of microorganisms to regulate gene expression is thought to be critical for survival and growth during the development of polymicrobial biofilms such as dental plaque. The commensal dental plaque colonizer, Streptococcus gordonii, responds to cell-cell contact (coaggregation) with Actinomyces oris by regulating > 20 genes, including those involved in arginine biosynthesis. We hypothesized that an S. gordonii extracellular protease is critical for sensing by providing amino acids that modulate gene expression...
March 14, 2018: FEMS Microbiology Ecology
Xuan Shi, Huu Hao Ngo, Langtao Sang, Pengkang Jin, Xiaochang C Wang, Guanghua Wang
In this study, a pilot combined sewer system was constructed to characterize the pollutant transformation in sewer sediment. The results showed that particulate contaminants deposited from sewage could be transformed into dissolved matter by distinct pollutant transformation pathways. Although the oxidation-reduction potential (ORP) was varied from -80 mV to -340 mV in different region of the sediment, the fermentation was the dominant process in all regions of the sediment, which induced hydrolysis and decomposition of particulate contaminants...
March 13, 2018: Environmental Pollution
Xiaohui Zhao, Fuqiang Fan, Huaidong Zhou, Panwei Zhang, Gaofeng Zhao
In-depth understanding of indigenous microbial assemblages resulted from aged contamination by polycyclic aromatic hydrocarbons (PAHs) is of vital importance in successful in situ bioremediation treatments. Soil samples of three boreholes were collected at 12 different vertical depths. Overall, the dominating three-ring PAHs (76.2%) were closely related to distribution patterns of soil dehydrogenase activity, microbial cell numbers, and Shannon biodiversity index (H') of indigenous microorganisms. High-molecular-weight PAHs tend to yield more diverse communities...
March 15, 2018: Bioprocess and Biosystems Engineering
Cintia P J Rua, Louisi S de Oliveira, Adriana Froes, Diogo A Tschoeke, Ana Carolina Soares, Luciana Leomil, Gustavo B Gregoracci, Ricardo Coutinho, Eduardo Hajdu, Cristiane C Thompson, Roberto G S Berlinck, Fabiano L Thompson
Marine sponge holobionts harbor complex microbial communities whose members may be the true producers of secondary metabolites accumulated by sponges. Bromopyrrole alkaloids constitute a typical class of secondary metabolites isolated from sponges that very often display biological activities. Bromine incorporation into secondary metabolites can be catalyzed by either halogenases or haloperoxidases. The diversity of the metagenomes of sponge holobiont species containing bromopyrrole alkaloids (Agelas spp. and Tedania brasiliensis) as well as holobionts devoid of bromopyrrole alkaloids spanning in a vast biogeographic region (approx...
March 15, 2018: Microbial Ecology
Tonya L Ward, Maria Gloria Dominguez-Bello, Tim Heisel, Gabriel Al-Ghalith, Dan Knights, Cheryl A Gale
With the advent of next-generation sequencing and microbial community characterization, we are beginning to understand the key factors that shape early-life microbial colonization and associated health outcomes. Studies characterizing infant microbial colonization have focused mostly on bacteria in the microbiome and have largely neglected fungi (the mycobiome), despite their relevance to mucosal infections in healthy infants. In this pilot study, we characterized the skin, oral, and anal mycobiomes of infants over the first month of life ( n = 17) and the anal and vaginal mycobiomes of mothers ( n = 16) by internal transcribed spacer 2 (ITS2) amplicon sequencing...
May 2018: MSystems
Dan Zhu, Yong Ma, Sujuan Ding, Hongmei Jiang, Jun Fang
This study investigated the antioxidant capacity and intestinal bacteria community in a mouse model of DSS-induced colitis. Twenty mice were randomly assigned to two treatments: mice with colitis induced by 5% DSS (DSS group) and mice with colitis induced by 5% DSS that also received melatonin treatment (MEL group). The DSS group showed significantly less antioxidant capability than the MEL group, but the two groups did not differ significantly in terms of diversity index (Shannon and Simpson), bacterial culture abundance (Chao1 and ACE), and coverage (Good's coverage estimator)...
2018: BioMed Research International
Camila Carlos, Huan Fan, Cameron R Currie
Deconstructing the intricate matrix of cellulose, hemicellulose, and lignin poses a major challenge in biofuel production. In diverse environments in nature, some microbial communities, are able to overcome plant biomass recalcitrance. Identifying key degraders of each component of plant cell wall can help improve biological degradation of plant feedstock. Here, we sequenced the metagenome of lignocellulose-adapted microbial consortia sub-cultured on xylan and alkali lignin media. We observed a drastic shift on community composition after sub-culturing, independently of the original consortia...
2018: Frontiers in Microbiology
Kohei Tanaka, Darla K Zelenitsky, François Therrien, Yoshitsugu Kobayashi
Dinosaurs thrived and reproduced in various regions worldwide, including the Arctic. In order to understand their nesting in diverse or extreme environments, the relationships between nests, nesting environments, and incubation methods in extant archosaurs were investigated. Statistical analyses reveal that species of extant covered nesters (i.e., crocodylians and megapodes) preferentially select specific sediments/substrates as a function of their nesting style and incubation heat sources. Relationships between dinosaur eggs and the sediments in which they occur reveal that hadrosaurs and some sauropods (i...
March 15, 2018: Scientific Reports
Jialiang Xu, Huijun Wu, Zhiwei Wang, Fuping Zheng, Xin Lu, Zhenpeng Li, Qing Ren
Chinese rice wine (CRW) is the oldest kind of wine in China and is mainly fermented by wheat Qu and yeast with rice, millet, etc. This gives CRW a unique quality, but the flavor components are complex. Its formation is related to microorganisms, but the link between CRW and microorganisms is poorly understood. Here, we used two kinds of sorghum (JZ22 and JB3, of which JZ22 has a higher tannin content) as the raw materials to brew and determined the structural and functional dynamics of the microbiota by metagenomics and flavor analyses...
March 15, 2018: Scientific Reports
Aparna Chakkamadathil Rajeev, Nishi Sahu, Maushumi Deori, Suma Arun Dev, Vijay Pal Yadav, Ilora Ghosh
We report here targeted deep-sequencing metagenomic data that reveal a high level of diversity in the microbiota residing in the sediment of the Periyar River in a reserve forest of the Western Ghats. Of the 4,674 operational taxonomic units discovered, the dominant phyla represented were Proteobacteria (33.12%), Actinobacteria (14.58%), Acidobacteria (12.81%), and Bacteroidetes (9.89%).
March 15, 2018: Genome Announcements
Eloi Parladé, Andrea Hom-Diaz, Paqui Blánquez, Maira Martínez-Alonso, Teresa Vicent, Nuria Gaju
The use of microalgal consortia for urban wastewater treatment is an increasing trend, as it allows simultaneous nutrient removal and biomass production. Emerging contaminants proposed for the list of priority substances such as the hormone 17β-estradiol are commonly found in urban wastewater, and their removal using algal monocultures has been accomplished. Due to the inherent potential of algae-based systems, this study aimed to assess the capability of native photobioreactor biomass to remove 17β-estradiol under indoor and outdoor conditions...
March 3, 2018: Water Research
Heejung Kim, Dugin Kaown, Bernhard Mayer, Jin-Yong Lee, Kang-Kun Lee
Hyporheic zones are considered hot spots for numerically vast and phylogenetically diverse microbial communities. However, biogeochemical effects of hyporheic zones have rarely been investigated in detail because of the difficulty in accurately measuring denitrification in these zones. To date, little is known about the hydroecology of hyporheic zones. The effect of changes in hydraulic conditions on the community variations of indigenous microorganisms and water quality was examined based on the depth of the hyporheic zone...
March 12, 2018: Science of the Total Environment
Mariana Avalos, Gilles P van Wezel, Jos M Raaijmakers, Paolina Garbeva
Microorganisms represent a large and still resourceful pool for the discovery of novel compounds to combat antibiotic resistance in human and animal pathogens. The ability of microorganisms to produce structurally diverse volatile compounds has been known for decades, yet their biological functions and antimicrobial activities have only recently attracted attention. Various studies revealed that microbial volatiles can act as infochemicals in long-distance cross-kingdom communication as well as antimicrobials in competition and predation...
March 12, 2018: Current Opinion in Microbiology
Markus Basan
Elucidating strategies of resource allocation and metabolism is crucial for a better understanding of microbial phenotypes. In particular, uncovering the governing principles underlying these processes would be a crucial step for achieving a central aim of systems microbiology, which is to quantitatively predict phenotypes of microbial cells or entire populations in diverse conditions. Here, some of the key concepts for understanding cellular resource allocation and metabolism that have been suggested over the past years are reviewed...
March 12, 2018: Current Opinion in Microbiology
Alexander Gluschko, Marc Herb, Katja Wiegmann, Oleg Krut, Wolfram F Neiss, Olaf Utermöhlen, Martin Krönke, Michael Schramm
The intracellular pathogen Listeria monocytogenes (L.m.) is targeted by the autophagic machinery, but the molecular mechanisms involved and consequences for anti-listerial immunity remain enigmatic. Here, we demonstrate that L.m. infection of macrophages in vivo exclusively evokes LC3-associated phagocytosis (LAP), but not canonical autophagy, and that targeting of L.m. by LAP is required for anti-listerial immunity. The pathway leading to LAP induction in response to L.m. infection emanates from the β2 integrin Mac-1 (CR3, integrin αM β2 ), a receptor recognizing diverse microbial ligands...
March 14, 2018: Cell Host & Microbe
Joshua D Sackett, Desiree C Huerta, Brittany R Kruger, Scott D Hamilton-Brehm, Duane P Moser
Devils Hole is the sole natural habitat of the critically endangered Devils Hole pupfish (Cyprinodon diabolis). To establish a backup population, the Ash Meadows Fish Conservation Facility (AMFCF), a full-scale replica of the uppermost 6.7 m of Devils Hole, was constructed by management agencies in the mid-2010s. Despite rigorous efforts to mimic the bathymetric and physical details of the Devils Hole environment, the biogeochemistry and microbiology of the AMFCF refuge tank remain largely unaddressed. We evaluated water physicochemistry and employed Illumina DNA sequencing of 16S rRNA gene libraries to evaluate planktonic and benthic bacterial and archaeal community composition within their respective physicochemical contexts in Devils Hole and AMFCF on the same day...
2018: PloS One
Hanna Ferløv Schwensen, Carol Kan, Janet Treasure, Niels Høiby, Magnus Sjögren
PURPOSE: Anorexia nervosa (AN) is a poorly understood and often chronic condition. Deviations in the gut microbiota have been reported to influence the gut-brain axis in other disorders. Therefore, if present in AN, it may impact on symptoms and illness progression. A review of the gut microbiota studies in AN is presented. METHOD: A literature search on PubMed yielded 27 articles; 14 were selected and based on relevance, 9 articles were included. The findings were interpreted in the larger context of preclinical research and clinical observations...
March 14, 2018: Eating and Weight Disorders: EWD
Youfa Luo, Yonggui Wu, Hu Wang, Rongrong Xing, Zhilin Zheng, Jing Qiu, Lian Yang
This comparative field study examined the responses of bacterial community structure and diversity to the revegetation of zinc (Zn) smelting waste slag with eight plant species after 5 years. The microbial community structure of waste slag with and without vegetation was evaluated using high-throughput sequencing. The physiochemical properties of Zn smelting slag after revegetation with eight plant rhizospheres for 5 years were improved compared to those of bulk slag. Revegetation significantly increased the microbial community diversity in plant rhizospheres, and at the phylum level, Proteobacteria, Acidobacteria, and Bacteroidetes were notably more abundant in rhizosphere slags than those in bulk waste slag...
March 14, 2018: Environmental Science and Pollution Research International
Yehao Liu, Yongchun Li, Xiaomei Hua, Karin Müller, Hailong Wang, Tongyi Yang, Qiong Wang, Xin Peng, Mengcheng Wang, Yanjun Pang, Jinliang Qi, Yonghua Yang
Glyphosate is a non-selective organophosphate herbicide that is widely used in agriculture, but its effects on soil microbial communities are highly variable and often contradictory, especially for high dose applications. We applied glyphosate at two rates: the recommended rate of 50 mg active ingredient kg-1 soil and 10-fold this rate to simulate multiple glyphosate applications during a growing season. After 6 months, we investigated the effects on the composition of soil microbial community, the catabolic activity and the genetic diversity of the bacterial community using phospholipid fatty acids (PLFAs), community level catabolic profiles (CLCPs), and 16S rRNA denaturing gradient gel electrophoresis (DGGE)...
March 14, 2018: Environmental Science and Pollution Research International
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