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FEMS Microbiology Ecology

Dong Han Choi, Sung Min An, Eun Chan Yang, Howon Lee, JaeSeol Shim, JinYong Jeong, Jae Hoon Noh
To understand prokaryotic responses during a spring bloom in offshore shelf waters, prokaryotic parameters were measured daily at a station located in the middle of the East China Sea over a 6-week period from March 25 to May 19. The site experienced a phytoplankton bloom in late April, triggering changes in prokaryotic abundance and production after a lag of approximately 1 week. Before the bloom, changes in prokaryotic composition were small. Both during the bloom and in the post-bloom period, successive changes among bacterial groups were apparent...
July 13, 2018: FEMS Microbiology Ecology
Rachelle E Beattie, Michael Walsh, Mercedes Cecilia Cruz, L Rex McAliley, Laurel Dodgen, Wei Zheng, Krassimira R Hristova
Kewaunee County, Wisconsin is an agricultural area dominated by concentrated animal feeding operations and manure fertilized cropland. The objective of this study was to characterize chemical and antibiotic resistance gene (ARG) profiles of 20 surface water locations in Kewaunee County to better understand relationships between agricultural contamination and ARG abundance over one year. Surface water (n = 101) and bed sediment (n = 93) were collected from 20 sites during five timepoints between July 2016 and May 2017...
July 13, 2018: FEMS Microbiology Ecology
David J Nusbaum, Fengzhu Sun, Jie Ren, Zifan Zhu, Natalie Ramsy, Nicholas Pervolarakis, Sachin Kunde, Whitney England, Bei Gao, Oliver Fiehn, Sonia Michail, Katrine Whiteson
Ulcerative colitis is a chronic inflammatory disease of the colon that carries a significant disease burden in children. Therefore, new therapeutic approaches are being explored to help children living with this disease. Fecal microbiota transplantation (FMT) has been successful in some children with ulcerative colitis. However, the mechanism of its therapeutic effect in this patient population is not well understood. To characterize changes in gut microbial and metabolomic profiles after FMT, we performed 16S rRNA gene sequencing, shotgun metagenomic sequencing, virome analysis, and untargeted metabolomics by gas chromatography-time of flight-mass spectrometry on stool samples collected before and after FMT from four children with ulcerative colitis who responded to this treatment...
July 13, 2018: FEMS Microbiology Ecology
Joe D Taylor, Kimberley E Bird, Claire E Widdicome, Michael Cunliffe
Seawater contains dissolved 'free' DNA (dDNA) that is part of a larger <0.2 μm pool of DNA (D-DNA) including viruses and uncharacterised bound DNA. Previous studies have shown that bacterioplankton readily degrade dDNA and culture-based approaches have identified several potential dDNA-utilising taxa. This study characterised the seasonal variation in D-DNA concentrations at Station L4, a coastal marine observatory in the Western English Channel, and linked changes in concentration to cognate physicochemical and biological factors...
July 13, 2018: FEMS Microbiology Ecology
Yuping Zhang, Christian Jewett, John Gilley, Shannon L Bartelt-Hunt, Daniel D Snow, Laurie Hodges, Xu Li
Reclaimed wastewater is increasingly used as a source of irrigation water in croplands. The enteric pathogens in reclaimed wastewater may accumulate in soil and plants and cause food safety concerns. The objective of this study was to determine the effects of irrigation water containing Salmonella on the microbial communities in the rhizosphere and in the root of lettuce. The effects were also examined with three variables (soil texture, lettuce cultivar, and harvest time) in a factorial design. Analyses on the 16S rRNA gene sequences show that the microbial communities in the root were significantly different from those in the rhizosphere, although ∼80% of the microbes in the root originated from the rhizosphere...
July 13, 2018: FEMS Microbiology Ecology
Marek Stibal, Carsten Suhr Jacobsen, Max M Häggblom
No abstract text is available yet for this article.
July 11, 2018: FEMS Microbiology Ecology
Lourdes Macías-Rodríguez, Araceli Guzmán-Gómez, Perla García-Juárez, Hexon Angel Contreras-Cornejo
Several species of Trichoderma promote plant growth and help in defense against root pathogens. The role of root-exuded carbohydrates as chemo-attractive stimuli for Trichoderma colonization is attracting considerable interest. In this project, we studied the interaction between Trichoderma atroviride and tomato (Lycopersicon esculentum L. cv. Río Grande) plants in 2 different stages, before and during root colonization. In addition, the biocontrol capacity of T. atroviride against the phytopathogen Phytophthora cinnamomi in a tripartite interaction system was examined...
July 11, 2018: FEMS Microbiology Ecology
Lloyd D Potts, Luis J Perez Calderon, Evangelia Gontikaki, Lehanne Keith, Cécile Gubry-Rangin, James A Anderson, Ursula Witte
Oil reserves in deep-sea sediments are currently subject to intense exploration, with associated risks of oil spills. Previous research suggests that microbial communities from deep-sea sediment (>1000 m) can degrade hydrocarbons, but have a lower degradation ability than shallow (<200 m) communities, probably due to in situ temperature. This study aimed to assess the effect of marine origin on microbial hydrocarbon (HC) degradation potential while separating the influence of temperature, and to characterise associated HC-degrading bacterial communities...
June 30, 2018: FEMS Microbiology Ecology
S Heß, T U Berendonk, D Kneis
River sediments are regarded as hot spots of bacterial density and activity. Moreover, high bacterial densities and biofilm formation are known to promote horizontal gene transfer, the latter playing a vital role in the spread of antimicrobial resistance. It can thus be hypothesized that sediments act as a reservoir of antibiotic resistant bacteria (ARB) and resistance genes (ARGs), particularly in rivers receiving microbes and drug residues from treated sewage. We analyzed the phenotypic susceptibility of 782 Escherichia coli isolates against 24 antimicrobials and we measured the relative abundances of five ARGs in water and sediment extracts of a small stream...
June 30, 2018: FEMS Microbiology Ecology
Patricia M Valdespino-Castillo, Daniel Cerqueda-García, Ana Cecilia Espinosa, Silvia Batista, Martín Merino-Ibarra, Neslihan Tas, Rocío J Alcántara-Hernández, Luisa I Falcón
Maritime Antarctica has shown the highest increase in temperature in the Southern Hemisphere. Under this scenario, biogeochemical cycles may be altered, resulting in rapid environmental change for Antarctic biota. Microbes, that drive biogeochemical cycles often form biofilms or microbial mats in continental meltwater environments. Limnetic microbial mats from the Fildes Peninsula were studied using high-throughput 16S rRNA gene sequencing. Mat samples were collected from fifteen meltwater stream sites, comprising a natural gradient from ultraoligotrophic glacier flows to meltwater streams exposed to anthropogenic activities...
June 30, 2018: FEMS Microbiology Ecology
Šárka Angst, Petr Baldrian, Lenka Harantová, Tomáš Cajthaml, Jan Frouz
Small twigs represent a substantial input of organic carbon into forest soils, but potential influencing factors on their decomposition have rarely been investigated. Here, we studied potential effects of twig size on decomposition and associated composition and activity of microbial communities during decomposition. Because the surface area for microbial colonization and the volume of accessible substrate increase with decreasing twig-size, we hypothesized that twig size affects both, microbial community and decomposition rate...
June 28, 2018: FEMS Microbiology Ecology
Xikun Liu, Yang Wu, Fernanda P Wilson, Ke Yu, Carly Lintner, Alison M Cupples, Timothy E Mattes
Vinyl chloride (VC), a known human carcinogen, is often formed in groundwater by incomplete reductive dechlorination of chlorinated ethenes. An integrated microbial ecology approach involving bacterial enrichments and isolations, carbon stable-isotope probing (SIP), and metagenome and genome sequencing was applied to ethene-fed groundwater microcosms that rapidly transitioned to aerobic growth on VC. Actinobacteria, Proteobacteria and Bacteroidetes dominated the microbial communities in ethene- and VC-grown cultures...
June 26, 2018: FEMS Microbiology Ecology
Minna Männistö, Jaana Vuosku, Sari Stark, Karita Saravesi, Marko Suokas, Annamari Markkola, Françoise Martz, Pasi Rautio
The northern regions are experiencing considerable changes in winter climate leading to more frequent warm periods, rain-on-snow events and reduced snow pack diminishing the insulation properties of snow cover and increasing soil frost and freeze-thaw cycles. In this study, we investigated how the lack of snow cover, formation of ice encasement and snow compaction affect the size, structure and activities of soil bacterial and fungal communities. Contrary to our hypotheses, snow manipulation treatments over one winter had limited influence on microbial community structure, bacterial or fungal copy numbers or enzyme activities...
June 23, 2018: FEMS Microbiology Ecology
Margarita Lopez-Fernandez, Elias Broman, Stephanie Turner, Xiaofen Wu, Stefan Bertilsson, Mark Dopson
The deep biosphere is the largest 'bioreactor' on earth and microbes inhabiting this biome profoundly influence global nutrient and energy cycles. An important question for deep biosphere microbiology is whether or not specific populations are viable. To address this, we used quantitative PCR and high throughput 16S rRNA gene sequencing of total and viable cells (i.e. with an intact cellular membrane) from three groundwaters with different ages and chemical constituents. There were no statistically significant differences in 16S rRNA gene abundances and microbial diversity between total and viable communities...
June 19, 2018: FEMS Microbiology Ecology
Anja Kamp, Caitlin Petro, Hans Røy, Susanne Nielsen, Pedro Carvalho, Peter Stief, Andreas Schramm
Intracellular nitrate is an important electron acceptor in oxygen-deficient aquatic environments, either for the nitrate-storing microbes themselves, or for ambient microbial communities through nitrate leakage. This study links the spatial distribution of intracellular nitrate with the abundance and identity of nitrate-storing microbes in sediments of the Bornholm Basin, an environmental showcase for severe hypoxia. Intracellular nitrate (up to 270 nmol cm-3 sediment) was detected at all 18 stations along a 35-km transect through the basin and typically extended as deep as 1...
June 19, 2018: FEMS Microbiology Ecology
Alireza Bolourian, Zahra Mojtahedi
Inflammation contributes to colon cancer initiation. The disease along with allergy and autoimmunity has been on the rise in Western and more recently in developing countries. This shared rise may imply a shared cause. Streptomycetes are known as soil residents and produce numerous antiproliferative, anti-inflammatory/immunosuppressive compounds, e.g. rapamycin and tacrolimus. Recently, Streptomyces has been shown in gut microbiome with a lower prevalence in humans than nonhumans whose microbiomes might be more representative of past humans' in a hunter-gatherer and farming environment...
June 14, 2018: FEMS Microbiology Ecology
Helena Osterholz, David L Kirchman, Jutta Niggemann, Thorsten Dittmar
Relationships between bacterial community and dissolved organic matter (DOM) include microbial uptake, transformation and secretion, all of which influence DOM composition. In this study, we explore diversity and similarity metrics of dissolved organic molecules (Fourier-transform ion cyclotron resonance mass spectrometry) and bacterial communities (tag-sequencing of 16S rRNA genes) along the salinity gradient of the Delaware Estuary (USA). We found that even though mixing, discharge and seasonal changes explained most of the variation in DOM and bacterial communities, there was still a relationship, albeit weak, between the composition of DOM and bacterial communities in the estuary...
June 14, 2018: FEMS Microbiology Ecology
Clara Ruiz-González, Esther Archambault, Isabelle Laforest-Lapointe, Paul A Del Giorgio, Steven W Kembel, Christian Messier, Charles A Nock, Beatrix E Beisner
Freshwater bacterioplankton communities are influenced by the inputs of material and bacteria from the surrounding landscape, yet few studies have investigated how different terrestrial inputs affect bacterioplankton. We examined whether the addition of soils collected under various tree species combinations differentially influences lake bacterial communities. Lake water was incubated for 6 days following addition of five different soils. We assessed the taxonomic composition (16S rRNA gene sequencing) and metabolic activity (Biolog Ecoplates) of lake bacteria with and without soil addition, and compared these to initial soil communities...
June 14, 2018: FEMS Microbiology Ecology
Valentina Maggini, Elisangela Miceli, Camilla Fagorzi, Isabel Maida, Marco Fondi, Elena Perrin, Alessio Mengoni, Patrizia Bogani, Carolina Chiellini, Stefano Mocali, Arturo Fabiani, Francesca Decorosi, Luciana Giovannetti, Fabio Firenzuoli, Renato Fani
A key factor in the study of plant-microbes interaction is the composition of plant microbiota, but little is known about the factors determining its functional and taxonomic organization. Here we investigated the possible forces driving the assemblage of bacterial endophytic and rhizospheric communities, isolated from two congeneric medicinal plants, Echinacea purpurea (L.) Moench and Echinacea angustifolia (DC) Heller, grown in the same soil, by analyzing bacterial strains (isolated from three different compartments, i...
June 14, 2018: FEMS Microbiology Ecology
Eric M Bottos, David W Kennedy, Elvira B Romero, Sarah J Fansler, Joseph M Brown, Lisa M Bramer, Rosalie K Chu, Malak M Tfaily, Janet K Jansson, James C Stegen
Understanding drivers of permafrost microbial community composition is critical for understanding permafrost microbiology and predicting ecosystem responses to thaw. We hypothesize that permafrost communities are shaped by physical constraints imposed by prolonged freezing, and exhibit spatial distributions that reflect dispersal limitation and selective pressures associated these physical constraints. To test this, we characterized patterns of environmental variation and microbial community composition in permafrost across an Alaskan boreal forest landscape...
June 14, 2018: FEMS Microbiology Ecology
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