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FEMS Microbiology Ecology

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https://www.readbyqxmd.com/read/28645188/temporal-variation-of-the-microbiome-is-dependent-on-body-region-in-a-wild-mammal-tamiasciurus-hudsonicus
#1
Colleen B Bobbie, Nadia C S Mykytczuk, Albrecht I Schulte-Hostedde
Microbial communities are increasingly being recognized as important to host health in wild mammals, but how these communities are characterized can have important consequences on the results of these studies. Previous research has explored temporal variation in microbial communities in humans and lab mammals, but few have investigated how microbiomes fluctuate in wild populations and none have examined the temporal dynamics of these fluctuations in different body regions on a wild mammal. Using Illumina MiSeq sequencing of the V3-V4 16S rRNA gene regions, we characterized the buccal and gut microbiomes of wild North American red squirrels, Tamiasciurus hudsonicus, to measure changes in these two microbiomes over short (< 2 weeks), medium (2-4 weeks) and long (> 1 month) term sampling periods...
June 22, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28645185/soil-prokaryotic-communities-in-chernobyl-waste-disposal-trench-t22-are-modulated-by-organic-matter-and-radionuclide-contamination
#2
Nicolas Theodorakopoulos, Laureline Février, Mohamed Barakat, Philippe Ortet, Richard Christen, Laurie Piette, Sviatoslav Levchuk, Karine Beaugelin-Seiller, Claire Sergeant, Catherine Berthomieu, Virginie Chapon
After the Chernobyl nuclear power plant accident in 1986, contaminated soils, vegetation from the Red Forest, and other radioactive debris were buried within trenches. In this area, trench T22 has long been a pilot site for the study of radionuclide migration in soil. Here, we used 454 pyrosequencing of 16S rRNA genes to obtain a comprehensive view of the bacterial and archaeal diversity in soils collected inside and in the vicinity of the trench T22 and to investigate the impact of radioactive waste disposal on prokaryotic communities...
June 22, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28645183/in-defense-of-bacillus-thuringiensis-the-safest-and-most-successful-microbial-insecticide-available-to-humanity-a-response-to-efsa
#3
Ben Raymond, Brian A Federici
The Bacillus cereus group contains vertebrate pathogens such as Bacillus anthracis and Bacillus cereus and the invertebrate pathogen Bacillus thuringiensis. Microbial biopesticides based on B. thuringiensis (Bt) are widely recognized as being among the safest and least environmentally damaging insecticidal products available. Nevertheless, a recent food poisoning incident prompted a European Food Safety Authority review which argued that B. thuringiensis poses a health risk equivalent to B. cereus, a causative agent of diarrhoea...
June 22, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28645159/genomic-characterization-of-two-novel-sar11-isolates-from-the-red-sea-including-the-first-strain-of-the-sar11-ib-clade
#4
Francy Jimenez-Infante, David Kamanda Ngugi, Manikandan Vinu, Jochen Blom, Intikhab Alam, Vladimir B Bajic, Ulrich Stingl
The SAR11 clade (Pelagibacterales) is a diverse group that forms a monophyletic clade within the Alphaproteobacteria, and constitutes up to one third of all prokaryotic cells in the photic zone of most oceans. Pelagibacterales are very abundant in the warm and highly saline surface waters of the Red Sea, raising the question of adaptive traits of SAR11 populations in this water body and warmer oceans through the world. In this study, two pure cultures were successfully obtained from surface waters on the Red Sea, one isolate of subgroup Ia and one of the previously uncultured SAR11 Ib lineage...
June 22, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28637338/complex-interactions-between-potentially-pathogenic-opportunistic-and-resident-bacteria-emerge-during-infection-on-a-reef-building-coral
#5
Sarah A Gignoux-Wolfsohn, Felicia M Aronson, Steven V Vollmer
Increased bacterial diversity on diseased corals can obscure disease etiology and complicate our understanding of pathogenesis. To untangle microbes that may cause white band disease signs from microbes responding to disease, we inoculated healthy Acropora cervicornis corals with an infectious dose from visibly diseased corals. We sampled these dosed corals and healthy controls over time for sequencing of the bacterial 16S region. Endozoicomonas were associated with healthy fragments from 4/10 colonies, dominating microbiomes before dosing and decreasing over time only in corals that displayed disease signs, suggesting a role in disease resistance...
June 15, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28637304/effects-of-alternative-electron-acceptors-on-the-activity-and-community-structure-of-methane-producing-and-consuming-microbes-in-the-sediments-of-two-shallow-boreal-lakes
#6
Antti J Rissanen, Anu Karvinen, Hannu Nykänen, Sari Peura, Marja Tiirola, Anita Mäki, Paula Kankaala
The role of anaerobic CH4 oxidation in controlling lake sediment CH4 emissions remains unclear. Therefore, we tested how relevant EAs (SO42-, NO3-, Fe3+, Mn4+, O2) affect CH4 production and oxidation in the sediments of two shallow boreal lakes. The changes induced to microbial communities by the addition of Fe3+ and Mn4+ were studied using next-generation sequencing targeting the 16S rRNA and methyl-coenzyme M reductase (mcrA) genes and mcrA transcripts. Putative anaerobic CH4 oxidizing archaea (ANME-2D) and bacteria (NC 10) were scarce (up to 3...
June 15, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28582549/changes-in-bacterial-community-after-application-of-three-different-herbicides
#7
Jéssica Aparecida Silva Moretto, Lucas Miguel Altarugio, Pedro Avelino Andrade, Ana Lúcia Fachin, Fernando Dini Andreote, Eliana Guedes Stehling
The native soil microbiota is very important to maintain the quality of that environment, but with the intensive use of agrochemicals, changes in microbial biomass and formation of large quantities of toxic waste were observed in soil, groundwater and surface water. Thereby, the goal of the present study was to evaluate if the selective pressure exerted by the presence of the herbicides atrazine, diuron and 2,4-Dchanges the bacterial community structure of an agricultural soil, using Denaturing Gradient Gel Electrophoresis (DGGE) technique...
June 4, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28582517/stress-responsively-modulated-ymdab-clsc-operon-plays-a-role-in-biofilm-formation-and-apramycin-susceptibility-in-escherichia-coli
#8
Moonjeong Kim, Kwang-Sun Kim
The YmdB protein, an inhibitor of biofilm formation and an inducer of apramycin susceptibility in Escherichia coli (E. coli), is part of a putative operon. However, transcription of this operon and its subsequent effects on biological pathways has not been fully studied. Here, we characterized the operon in terms of promoter activity, transcription, and function. Promoter activity assays identified two new growth- and cold-shock-responsive upstream (PymdA) and inner (PclsC) promoters, respectively. Moreover, investigation of the operon-derived transcripts identified different polycistronic transcripts harboring multiple heterogeneous 3' ends...
June 4, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28582504/cytochrome-p450-enzyme-rosc-catalyzes-a-multistep-oxidation-reaction-to-form-the-non-active-compound-20-carboxyrosamicin
#9
Yohei Iizaka, Rina Takeda, Yuki Senzaki, Atsushi Fukumoto, Yojiro Anzai
The cytochrome P450 enzyme RosC catalyzes a two-step, hydroxylation and alcohol oxidation, oxidation reaction to form the C-20 formyl group in the biosynthesis of a 16-membered macrolide antibiotic rosamicin produced by Micromonospora rosaria IFO13697. RosC is presumed to be involved in the formation of 20-carboxyrosamicin because it has been isolated from the culture broth of M. rosaria. Here, we confirmed that RosC has catalytic activity, with Escherichia coli expressing RosC converting rosamicin into 20-carboxyrosamicin...
June 4, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28575426/evolution-of-microbial-communities-growing-with-carbon-monoxide-hydrogen-and-carbon-dioxide
#10
Sofia Esquivel-Elizondo, Anca G Delgado, Rosa Krajmalnik-Brown
Microbial anaerobic conversion of carbon monoxide (CO) and syngas (mainly composed of CO, CO2 and H2) leads to the production of important industrial products, such as acetate and ethanol. The composition of CO- and syngas-converting microbial communities, and the microbial interactions involved are still largely unknown. The main objectives of this study were 1) to understand the effects of CO, CO2 and H2 on the structure and function of a CO-consuming microbial community, and 2) to identify key carboxidotrophs in the mixed culture...
May 29, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28575320/high-throughput-sequencing-of-microbial-eukaryotes-in-lake-baikal-reveals-ecologically-differentiated-communities-and-novel-evolutionary-radiations
#11
Zhenzhen Yi, Cedric Berney, Hanna Hartikainen, Shazia Mahamdallie, Michelle Gardner, Jens Boenigk, Thomas Cavalier-Smith, David Bass
We performed high throughput 18S rDNA V9 region sequencing analyses of micro-eukaryote communities at seven sites with depths ranging from 0-1450 m in the southern part of Lake Baikal. We show that micro-eukaryotic diversity differed according to water column depth and sediment depth. Chrysophytes and perkinsids were diverse in subsurface samples, novel radiations of petalomonads and Ichthyobodo relatives were found in benthic samples, and a broad range of divergent OTUs were detected in deep sub-benthic samples...
May 29, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28541458/microbiome-analysis-of-a-disease-affecting-the-deep-sea-sponge-geodia-barretti
#12
Heidi M Luter, Raymond J Bannister, Steve Whalan, Tina Kutti, Mari-Carmen Pineda, Nicole S Webster
Reports of sponge disease are becoming increasingly frequent, although almost all instances involve shallow-water, tropical species. Here, we describe the first disease affecting the deep-water sponge, Geodia barretti. The disease is characterised by brown/black discolouration of the sponge tissue, extensive levels of tissue disintegration and increased levels of fouling. Disease prevalence was quantified using video survey transects conducted between 100 and 220 meters in Korsfjorden, Norway and the microbial communities of healthy and diseased sponges were compared using 16S rRNA gene sequencing...
May 24, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28520877/abundance-and-molecular-diversity-of-thraustochytrids-in-coastal-waters-of-southern-china
#13
Ying Liu, Purnima Singh, Yuanmei Liang, Jingjing Li, Ningdong Xie, Zhiquan Song, Maurycy Daroch, Keming Leng, Zackary I Johnson, Guangyi Wang
Thraustochytrids are unicellular fungi-like (heterotrophic) marine protists and have long been considered to play an important role in the biogeochemical cycles of the coastal oceans. However, the significance of their ecological functions and diversity in marine ecosystems remain largely unknown. In this report, we examined the spatial and temporal variations of planktonic thraustochytrids, their relationship with other environmental factors, and their diversity in the subtropical coastal waters of China. The abundance of planktonic thraustochytrids ranged from 2...
May 18, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28498986/sequence-of-inoculation-influences-the-nature-of-exopolymeric-substances-eps-and-biofilm-formation-in-azotobacter-chroococcum-and-trichoderma-viride
#14
Kulandaivelu Velmourougane, Radha Prasanna, Shashi Bala Singh, Rajesh Kumar, Supradip Saha
Extracellular polymeric substances (EPS) are important structural components of biofilms. In the present study, the EPS in biofilms developed using two agriculturally beneficial organisms- Azotobacter chroococcum (Az) and Trichoderma viride (Tv) were quantified and characterised. Time course experiments were undertaken to optimize the EPS yield of biofilm samples resulting from coculture and staggered inoculation. The EPS produced during biofilm formation was found to differ quantitatively and qualitatively in individual cultures (Az alone, Tv alone), and in treatments differing in the sequence of inoculation of bacterium and fungus (Az+Tv coculture, staggered inoculation of Az followed by Tv-Az-Tv, or Tv followed by Az-Tv-Az)...
May 11, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28449125/saccharomyces-cerevisiae-accumulates-gapdh-derived-peptides-on-its-cell-surface-that-induce-death-of-non-saccharomyces-yeasts-by-cell-to-cell-contact
#15
Patrícia Branco, Varongsiri Kemsawasd, Lara Santos, Mário Diniz, Jorge Caldeira, Maria Gabriela Almeida, Nils Arneborg, Helena Albergaria
During wine fermentations Saccharomyces cerevisiae starts to excrete into the growth medium antimicrobial peptides (AMPs) that induce death of non-Saccharomyces yeasts at the end of exponential growth phase (24-48 h). Those AMPs were found to derive from the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH). On the other hand, the early death of non-Saccharomyces yeasts during wine fermentations was also found to be mediated by a cell-to-cell contact mechanism. Since GAPDH is a cell wall-associated protein in S...
April 25, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28531284/different-abundance-and-correlational-patterns-exist-between-total-and-presumed-pathogenic-vibrio-vulnificus-and-v-parahaemolyticus-in-shellfish-and-waters-along-the-north-carolina-coast
#16
Tiffany C Williams, Brett A Froelich, Britney Phippen, Patricia Fowler, Rachel T Noble, James D Oliver
Monitoring of Vibrio vulnificus and V. parahaemolyticus abundance is pertinent due to the ability of these species to cause disease in humans through aquatic vectors. Previously, we performed a multiyear investigation tracking Vibrio spp. levels in five sites along the southeastern North Carolina coast. From February 2013 to October 2015, total V. vulnificus and V. parahaemolyticus abundance was measured in water, oysters and clams. In the current study, pathogenic subpopulations were identified in these isolates using molecular markers, revealing that 5...
June 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28531262/biogeography-of-cryoconite-bacterial-communities-on-glaciers-of-the-tibetan-plateau
#17
Yongqin Liu, Trista J Vick-Majors, John C Priscu, Tandong Yao, Shichang Kang, Keshao Liu, Ziyuang Cong, Jingbo Xiong, Yang Li
Cryoconite holes, water-filled pockets containing biological and mineralogical deposits that form on glacier surfaces, play important roles in glacier mass balance, glacial geochemistry and carbon cycling. The presence of cryoconite material decreases surface albedo and accelerates glacier mass loss, a problem of particular importance in the rapidly melting Tibetan Plateau. No studies have addressed the microbial community composition of cryoconite holes and their associated ecosystem processes on Tibetan glaciers...
June 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28505366/bacterioplankton-assemblages-in-coastal-ponds-reflect-the-influence-of-hydrology-and-geomorphological-setting
#18
Megan J Huggett, Christopher R J Kavazos, Rachele Bernasconi, Robert Czarnik, Pierre Horwitz
The factors that shape microbial community assembly in aquatic ecosystems have been widely studied; yet it is still unclear how distinct communities within a connected landscape influence one another. Coastal lakes are recipients of, and thus are connected to, both marine and terrestrial environments. Thus, they may host microbial assemblages that reflect the relative degree of influence by, and connectivity to, either system. In order to address this idea, we interrogated microbial community diversity at 49 sites in seven ponds in two seasons in the Lake MacLeod basin, a system fed by seawater flowing inland through underground karst...
June 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28505340/members-of-microvirga-and-bradyrhizobium-genera-are-native-endosymbiotic-bacteria-nodulating-lupinus-luteus-in-northern-tunisian-soils
#19
Abdelhakim Msaddak, Mokhtar Rejili, David Durán, Luis Rey, Juan Imperial, Jose Manuel Palacios, Tomas Ruiz-Argüeso, Mohamed Mars
The genetic diversity of bacterial populations nodulating Lupinus luteus (yellow lupine) in Northern Tunisia was examined. Phylogenetic analyses of 43 isolates based on recA and gyrB partial sequences grouped them in three clusters, two of which belong to genus Bradyrhizobium (41 isolates) and one, remarkably, to Microvirga (2 isolates), a genus never previously described as microsymbiont of this lupine species. Representatives of the three clusters were analysed in-depth by multilocus sequence analysis of five housekeeping genes (rrs, recA, glnII, gyrB and dnaK)...
June 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28498948/community-composition-and-assembly-processes-of-the-free-living-and-particle-attached-bacteria-in-taihu-lake
#20
Dayong Zhao, Huimin Xu, Jin Zeng, Xinyi Cao, Rui Huang, Feng Shen, Zhongbo Yu
Although previous studies have compared the diversity and community composition of free-living (FL) and particle-attached (PA) bacterial groups in marine ecosystems, few studies have focused on the FL and PA bacterial communities in large and shallow eutrophic lakes. Furthermore, the assembly processes of the FL and PA bacterial communities have not been investigated. To illustrate the differences between PA (≥5.0 μm) and FL (0.22-5.0 μm) bacterial communities, samples were collected from 13 different sites in Taihu Lake, China...
June 1, 2017: FEMS Microbiology Ecology
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