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FEMS Microbiology Ecology

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
Igor S Pessi, Yannick Lara, Benoit Durieu, Pedro de C Maalouf, Elie Verleyen, Annick Wilmotte
The terrestrial Antarctic Realm has recently been divided into 16 Antarctic Conservation Biogeographic Regions (ACBRs) based on environmental properties and the distribution of biota. Despite their prominent role in the primary production and nutrient cycling in Antarctic lakes, cyanobacteria were only poorly represented in the biological dataset used to delineate these ACBRs. Here we provide a first high-throughput sequencing (HTS) insight into the spatial distribution of benthic cyanobacterial communities in Antarctic lakes located in four distinct, geographically distant ACBRs and covering a range of limnological conditions...
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
Morgan Petrovich, Binh Chu, Dorothy Wright, Jim Griffin, Maryam Elfeki, Brian T Murphy, Rachel Poretsky, George Wells
Wastewater treatment plants (WWTPs) are known to harbor antibiotic resistance genes (ARGs) that are disseminated into the environment via effluent. However, few studies have compared abundance, mobilization, and selective pressures for ARGs in WWTPs as a function of variations in secondary treatment bioprocesses. We used shotgun metagenomics to provide a comprehensive analysis of ARG composition, relationship to mobile genetic elements, and co-occurrences with antibiotic production genes (APGs) throughout two full-scale municipal WWTPs, one of which employs biofilm-based secondary treatment and another that uses a suspended growth system...
March 9, 2018: FEMS Microbiology Ecology
Isabelle Raymond-Bouchard, Jacqueline Goordial, Yevgen Zolotarov, Jennifer Ronholm, Martina Stromvik, Corien Bakermans, Lyle G Whyte
Permafrost accounts for 27% of all soil ecosystems and harbors diverse microbial communities. Our understanding of microorganisms in permafrost, their activities and adaptations, remains limited. Using five subzero-growing (cryophilic) permafrost bacteria, we examined features of cold adaptation through comparative genomic analyses with mesophilic relatives. The cryophiles possess genes associated with cold adaptation, including cold shock proteins, RNA helicases, and oxidative stress and carotenoid synthesis enzymes...
March 8, 2018: FEMS Microbiology Ecology
Sophie de Vries, Janina K von Dahlen, Anika Schnake, Sarah Ginschel, Barbara Schulz, Laura E Rose
Phytophthora infestans is a devastating pathogen of tomato and potato. It readily overcomes resistance genes and applied agrochemicals and hence even today causes large yield losses. Fungal endophytes provide a largely unexplored avenue of control of Phytophthora infestans. Not only do endophytes produce a wide array of bioactive metabolites, they may also directly compete with and defeat pathogens in planta. Here, we tested twelve fungal endophytes isolated from different plant species in vitro for their production of metabolites with anti- Phytophthora activity...
March 8, 2018: FEMS Microbiology Ecology
Muhe Diao, Jef Huisman, Gerard Muyzer
Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) drive major transformations in the sulfur cycle, and play vital roles in oxic-anoxic transitions in lakes and coastal waters. However, information on the succession of these sulfur bacteria in seasonally stratified lakes using molecular biological techniques is scarce. Here, we used 16S rRNA gene amplicon sequencing to study the spatio-temporal dynamics of sulfur bacteria during oxic-anoxic regime shifts in Lake Vechten. Oxygen and sulfate were mixed throughout the water column in winter and early spring...
March 8, 2018: FEMS Microbiology Ecology
Nadine Graupner, Manfred Jensen, Christina Bock, Sabina Marks, Sven Rahmann, Daniela Beisser, Jens Boenigk
Shifts in the nutritional mode between phototrophy, mixotrophy and heterotrophy are a widespread phenomenon in the evolution of eukaryotic diversity. The transition between nutritional modes is particularly pronounced in chrysophytes and occurred independently several times through parallel evolution. Thus, chrysophytes provide a unique opportunity for studying the molecular basis of nutritional diversification and of the accompanying pathway reduction and degradation of plastid structures. In order to analyze the succession in switching the nutritional mode from mixotrophy to heterotrophy, we compared the transcriptome of the mixotrophic Poterioochromonas malhamensis with the transcriptomes of three obligate heterotrophic species of Ochromonadales...
March 6, 2018: FEMS Microbiology Ecology
Géraldine Florence Buttet, Alexandra Marie Murray, Tobias Goris, Mélissa Burion, Biao Jin, Massimo Rolle, Christof Holliger, Julien Maillard
Two anaerobic bacterial consortia, each harboring a distinct Sulfurospirillum population, were derived from a ten year old consortium, SL2, previously characterized for the stepwise dechlorination of tetrachloroethene (PCE) to cis-dichloroethene (cis-DCE) via accumulation of trichloroethene (TCE). Population SL2-1 dechlorinated PCE to TCE exclusively, while SL2-2 produced cis-DCE from PCE without substantial TCE accumulation. The reasons explaining the long-term coexistence of the populations were investigated...
March 6, 2018: FEMS Microbiology Ecology
Rippin Martin, Lange Sebastian, Sausen Nicole, Becker Burkhard
Biological soil crusts (BSCs) are amalgamations of autotrophic, heterotrophic and saprotrophic organisms. In the Polar Regions, these unique communities occupy essential ecological functions such as primary production, nitrogen fixation and ecosystem engineering. Here we present the first molecular survey of BSCs from the Arctic and Antarctica focused on both eukaryotes and prokaryotes as well as passive and active biodiversity. Considering sequence abundance, Bryophyta is among the most abundant taxa in all analyzed BSCs suggesting that they were in a late successional stage...
March 4, 2018: FEMS Microbiology Ecology
Jenni Hultman, Manu Tamminen, Katariina Pärnänen, Johannes Cairns, Antti Karkman, Marko Virta
Wastewater treatment plants (WWTPs) collect wastewater from various sources for a multi-step treatment process. By mixing a large variety of bacteria and promoting their proximity, WWTPs constitute potential hotspots for the emergence of antibiotic resistant bacteria. Concerns have been expressed regarding the potential of WWTPs to spread antibiotic resistance genes from environmental reservoirs to human pathogens.We utilized epicPCR (Emulsion, Paired Isolation and Concatenation PCR) to detect the bacterial hosts of antibiotic resistance genes in two WWTPs...
March 4, 2018: FEMS Microbiology Ecology
Anne-Mari Luhtanen, Eeva Eronen-Rasimus, Hanna M Oksanen, Jean-Louis Tison, Bruno Delille, Gerhard S Dieckmann, Janne-Markus Rintala, Dennis H Bamford
Viruses are recognized as important actors in ocean ecology and biogeochemical cycles, but many details are not yet understood. We participated in a winter expedition to the Weddell Sea, Antarctica, to isolate viruses and to measure virus-like particle abundance (flow cytometry) in sea ice. We isolated 59 bacterial strains and the first four Antarctic sea-ice viruses known (PANV1, PANV2, OANV1, and OANV2), which grow in bacterial hosts belonging to the typical sea-ice genera Paraglaciecola and Octadecabacter...
February 22, 2018: FEMS Microbiology Ecology
Tina Šantl-Temkiv, Ulrich Gosewinkel, Piotr Starnawski, Mark Lever, Kai Finster
The Arctic is undergoing dramatic climatic changes that cause profound transformations in its terrestrial ecosystems and consequently in the microbial communities that inhabit them. The assembly of these communities is affected by aeolian deposition. However, the abundance, diversity, sources, and activity of airborne microorganisms in the Arctic are poorly understood. We studied bacteria in the atmosphere over southwest Greenland and found that the diversity of bacterial communities correlated positively with air temperature and negatively with relative humidity...
February 22, 2018: FEMS Microbiology Ecology
Aurèle Vuillemin, Daniel Ariztegui, Fabian Horn, Jens Kallmeyer, William D Orsi
For decades, microbial community composition in subseafloor sediments has been the focus of extensive studies. In deep lacustrine sediments however, the taxonomic composition of microbial communities remains undercharacterized. Greater knowledge on microbial diversity in lacustrine sediments would improve our understanding of how environmental factors, and resulting selective pressures, shape subsurface biospheres in marine and freshwater sediments. Using high-throughput sequencing of 16S rRNA genes across high resolution climate intervals covering the last 50,000 years in Laguna Potrok Aike, Argentina, we identified changes in microbial populations in response to both past environmental conditions and geochemical changes of the sediment during burial...
February 20, 2018: FEMS Microbiology Ecology
A F C Leonard, X L Yin, T Zhang, M Hui, W H Gaze
Background: Antimicrobial resistance and the spread of antibiotic resistance genes (ARGs) poses a threat to human health. Community-acquired infections resistant to treatment with first-line antibiotics are increasing, and there are few studies investigating environmental exposures and transmission. Aim: To develop a novel targeted metagenomic method to quantify the abundance and diversity of ARGs in a faecal indicator bacterium, and to estimate human exposure to resistant bacteria in a natural environment...
February 19, 2018: FEMS Microbiology Ecology
Kathleen M Morrow, Abbey Rose Tedford, M Sabrina Pankey, Michael P Lesser
Symbiotic associations with subcuticular bacteria (SCB) have been identified and studied in many echinoderms, including the SCB of the brooding brittle star, Amphipholis squamata. Previous studies on the SCB of A. squamata placed the isolated bacterium, designated as AS1, in the genus Vibrio (Gammaproteobacteria), but subsequent studies suggested that the SCB of echinoderms belong to the Alphaproteobacteria. This study examines the taxonomic composition of SCB associated with A. squamata from the Northwest Atlantic using the 16S rRNA gene and next generation sequencing (NGS)...
February 19, 2018: FEMS Microbiology Ecology
Birgit Wolters, Samuel J A Jacquiod, Søren J Sørensen, Arum Widyasari-Mehta, Tina B Bech, Robert Kreuzig, Kornelia Smalla
Organic soil fertilizers, such as livestock manure and biogas digestate, frequently contain bacteria carrying resistance genes (RGs) to antimicrobial substances and mobile genetic elements (MGEs). The effects of different fertilizers (inorganic, manure, digestate) on RG and MGE abundance and microbial community composition were investigated in a field plot experiment. The relative abundances of RGs [sul1, sul2, tet(A), tet(M), tet(Q), tet(W), qacEΔ1/qacE] and MGEs [intI1, intI2, IncP-1, IncP-1ε and LowGC plasmids] in total community (TC)-DNA from organic fertilizers, bulk soil and maize rhizosphere were quantified by qPCR before/after fertilization and prior to maize harvest...
February 16, 2018: FEMS Microbiology Ecology
Song-Can Chen, Gui-Lan Duan, Kai Ding, Fu-Yi Huang, Yong-Guan Zhu
Identifying functional microorganisms involved in the degradation of high-molecular-mass polycyclic aromatic hydrocarbons (HMM-PAHs) in agricultural soil environments could assist in developing bioremediation strategies for soil PAH-contamination. Active populations of HMM-PAHs degraders in agricultural soils are currently poorly understood. In this study, we identified aerobic pyrene-degrading bacteria in agricultural and industrial soils by 13C-pyrene incubations followed by DNA stable isotope probing (DNA-SIP) and high-throughput sequencing...
February 15, 2018: FEMS Microbiology Ecology
C J Williamson, A M Anesio, J Cook, A Tedstone, E Poniecka, A Holland, D Fagan, M Tranter, M L Yallop
It is fundamental to understand the development of Zygnematophycean (Streptophyte) micro-algal blooms within Greenland Ice Sheet (GrIS) supraglacial environments, given their potential to significantly impact both physical (melt) and chemical (carbon and nutrient cycling) surface characteristics. Here we report on a space-for-time assessment of a GrIS ice-algal bloom, achieved by sampling an ∼ 85 km transect spanning the south-western GrIS bare ice zone during the 2016 ablation season. Cell abundances ranged from 0 to 1...
February 10, 2018: FEMS Microbiology Ecology
Michelle J Chua, Richard L Campen, Lindsay Wahl, Joseph J Grzymski, Jill A Mikucki
Antarctic subice environments are diverse, underexplored microbial habitats. Here we describe the ecophysiology and annotated genome of a Marinobacter strain isolated from a cold, saline, iron-rich subglacial outflow of the Taylor Glacier, Antarctica. This strain (BF04_CF4) grows fastest at neutral pH (range 6-10), is psychrophilic (range: 0-20°C), moderately halophilic (range: 0.8-15% NaCl), and hosts genes encoding potential low temperature and high salt adaptations. The predicted proteome suggests it utilizes fewer charged amino acids than a mesophilic Marinobacter strain...
February 10, 2018: FEMS Microbiology Ecology
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