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FEMS Microbiology Ecology

Mincheol Kim, Ji Young Jung, Dominique Laffly, Hye Young Kwon, Yoo Kyung Lee
Primary succession after glacier retreat has been widely studied in plant communities, but bacterial succession is still poorly understood. In particular, few studies of microbial succession have been performed in the Arctic. We investigated the shifts in bacterial community structure and soil physicochemical properties along a successional gradient in a 100-year glacier foreland of the High Arctic. Multivariate analyses revealed that time after glacier retreat played a key role in associated bacterial community structure during succession...
October 17, 2016: FEMS Microbiology Ecology
Joost T P Verhoeven, Alana N Kavanagh, Suzanne C Dufour
The Cladorhizidae is a unique family of carnivorous marine sponges characterized by either the absence or reduction of the aquiferous system and by the presence of specialized structures to trap and digest mesoplanktonic prey. Previous studies have postulated a key role of host-associated bacteria in enabling carnivory in this family of sponges. In this study, we employed high-throughput Illumina based sequencing to identify the bacterial community associated with four individuals of the deep-sea sponge Chondrocladia grandis sampled in the Gulf of Maine...
October 17, 2016: FEMS Microbiology Ecology
Sabine A Ragot, Michael A Kertesz, Éva Mészáros, Emmanuel Frossard, Else K Bünemann
Alkaline phosphatases such as PhoD and PhoX are important genes in organic phosphorus cycling in soil. We identified the key organisms harboring the phoD and phoX gene in soil and explored the relationships between environmental factors and the phoD- and phoX-harboring community structures across three land-uses located in arid to temperate climates on two continents using 454-sequencing. phoD was investigated using recently published primers, and new primers were designed to study phoX in soil. phoD was found in 1 archaeal, 13 bacterial and 2 fungal phyla, and phoX in 1 archaeal and 16 bacterial phyla...
October 12, 2016: FEMS Microbiology Ecology
Pauline D Scanlan, Anna M Bischofberger, Alex R Hall
Although experiments indicate that the abiotic environment plays an important role in bacterial interactions with their parasitic viruses (bacteriophages or phages), it is not yet clear how exposure to compounds present in nature alters the impact of phages on bacterial growth and evolution. To address this question we exposed Escherichia coli K12 MG1655, in combination with three lytic phages, to various substances that natural and clinical microbial populations are likely to encounter: bile salts (present in mammalian gastrointestinal tracts), sodium dodecyl sulfate (SDS, a common surfactant in cleaning and hygiene products), and four antibiotics (present at variable concentrations in natural and clinical environments)...
October 12, 2016: FEMS Microbiology Ecology
Caroline Fromont, Markus Riegler, James M Cook
While obligate primary (P-) endosymbionts usually co-speciate with their insect hosts, less is known about co-diversification of secondary (S-) endosymbionts that are generally considered facultative. Typically, insects of the superfamily Psylloidea harbour one P- (Carsonella) and at least one S-endosymbiont, thought to compensate for Carsonella genome reduction. Most co-diversification studies have used phylogenies of psyllids and their endosymbionts across and within host families or genera, but few have explored patterns within species...
October 3, 2016: FEMS Microbiology Ecology
Danilo Tosta Souza, Diego Bonaldo Genuário, Fabio Sérgio Paulino Silva, Camila Cristiane Pansa, Vanessa Nessner Kavamura, Fernando Coreixas Moraes, Rodrigo Gouvea Taketani, Itamar Soares Melo
Bacterial communities associated with sponges are influenced by environmental factors; however, some degree of genetic influence of the host on the microbiome is also expected. In this work, 16S rRNA gene amplicon sequencing revealed diverse bacterial phylotypes based on the phylogenies of three tropical sponges (Aplysina fulva, Aiolochroia crassa and Chondrosia collectrix). Despite their sympatric occurrence, the studied sponges presented different bacterial compositions that differed from those observed in seawater...
October 3, 2016: FEMS Microbiology Ecology
Xiaobao Li, Nanxi Lu, Hannah R Brady, Aaron I Packman
Proteus mirabilis and Pseudomonas aeruginosa are common pathogens that often form biofilms together in catheter-associated urinary tract infections (CAUTI). However, the interactions between these two species in biofilms are largely unknown. P. mirabilis induces ureolytic biomineralization that substantially modifies key biofilm properties including morphology, persistence, and recalcitrance to antimicrobial therapy. These processes are well known to complicate CAUTI, but the consequences for colonization and persistence of P...
October 2, 2016: FEMS Microbiology Ecology
M Sagova-Mareckova, M Omelka, J Kopecky
The severity of common scab (CS) of potatoes was correlated with multiple environmental factors. This study aimed in separating the effect of factors related to local conditions from those correlated to the disease development at all studied sites using a mathematical adjustment of the variables' means for site and field. The experiment was conducted at two sites differing in soil conditions, where a field with low disease severity occurs next to one with high severity. Three cultivars susceptible to CS were grown in four replicates on each field...
September 29, 2016: FEMS Microbiology Ecology
R Piredda, M P Tomasino, A M D'Erchia, C Manzari, G Pesole, M Montresor, W H C F Kooistra, D Sarno, A Zingone
We tracked temporal changes in protist diversity at the Long Term Ecological Research (LTER)-MC site in the Gulf of Naples (Mediterranean Sea) on eight dates in 2011 using a metabarcoding approach. The ILLUMINA analysis of the V4 and V9 fragments of the 18S rDNA produced 869,522 and 1,410,071 sequences resulting in 6,517 and 6,519 OTUs, respectively. Marked compositional variations were recorded across the year, with less than 2% of OTUs shared among all samples and similar patterns for the two marker tags...
September 26, 2016: FEMS Microbiology Ecology
Alexander J Reisinger, Peter M Groffman, Emma J Rosi-Marshall
Nitrogen (N) pollution of freshwater, estuarine, and marine ecosystems is widespread and has numerous environmental and economic impacts. A portion of this excess N comes from urban watersheds comprised of natural and engineered ecosystems which can alter downstream N export. Studies of urban N cycling have focused on either specific ecosystems or on watershed-scale mass balances. Comparisons of specific N transformations across ecosystems are required to contextualize rates from individual studies. Here we reviewed urban N cycling in terrestrial, aquatic, and engineered ecosystems, and compared N processing in these urban ecosystem types to native reference ecosystems...
September 21, 2016: FEMS Microbiology Ecology
Matheus A P Cipriano, Manoeli Lupatini, Lucilene Lopes-Santos, Márcio J da Silva, Luiz F W Roesh, Suzete A L Destéfano, Sueli S Freitas, Eiko E Kuramae
Plant growth promoting rhizobacteria (PGPR) are well described and recommended for several crops worldwide. However, one of the most common problems in PGPR research is the difficulty in obtaining reproducible results. Furthermore, few studies have evaluated plant growth promotion and soil microbial community composition due to bacterial inoculation under field conditions. Here we evaluated the effect of 54 Pseudomonas strains on lettuce (Lactuca sativa) growth. The 12 most promising strains were phylogenetically and physiologically characterized for plant growth-promoting traits including phosphate solubilization, hormone production and antagonism to pathogen compounds and their effect on plant growth under farm field conditions...
September 21, 2016: FEMS Microbiology Ecology
Sudeep Perumbakkam, Henry D Hunt, Hans H Cheng
Marek's disease (MD) is an important neoplastic disease of chickens caused by Marek's disease virus (MDV), a highly oncogenic alphaherpesvirus. In this study using two chicken lines, one resistant and another susceptible to MD, splenic T cells and cecal microbiome were profiled to gain a better understanding of primary differences in these lines. The percent of splenic CD4(+) T cells were similar regardless of MDV challenge status in both bird lines. In contrast, CD8αα profiles were different (P < 0.005) between chicken lines under naïve status and under MDV challenge, suggesting that CD8αα T cells play a key role in mediating MDV infection...
September 7, 2016: FEMS Microbiology Ecology
Leonardo Di Meglio, Fernando Santos, María Gomariz, Cristina Almansa, Cristina López, Josefa Antón, Débora Nercessian
A seasonal sampling was carried out in three Argentinian salterns: Salitral Negro (SN), Colorada Grande (CG) and Guatraché (G), aimed to analyze abiotic parameters and microbial diversity and dynamics. Microbial assemblages were correlated to environmental factors by statistical analyses. Principal-Component-Analysis of environmental data grouped SN and CG, separately from G samples, owing to its higher pH values and sulfate concentration. Differences in microbial assemblages were also found. Many archaeal sequences belonged to uncultured members of Haloquadratum and Haloquadratum-related genera, with different environmental optima...
September 7, 2016: FEMS Microbiology Ecology
A Vaksmaa, C Lüke, T van Alen, G Valè, E Lupotto, Msm Jetten, K F Ettwig
In order to mitigate methane emissions from paddy fields, it is important to understand the sources and sinks. Most paddy fields are heavily fertilized with nitrite and nitrate which can be used as electron acceptors by anaerobic methanotrophs. Here we show that slurry incubations of Italian paddy field soil with nitrate and (13)C-labelled methane have the potential for nitrate-dependent anaerobic oxidation of methane (79.9. nmol g(-1) dw d(-1)). Community analysis based on 16S rRNA amplicon sequencing and qPCR of the water-logged soil and the rhizosphere showed that AOM-associated archaea (AAA), including Methanoperedens nitroreducens, comprised 9% (bulk soil) and 1% (rhizosphere) of all archaeal reads...
August 24, 2016: FEMS Microbiology Ecology
Maria V Orlova, Sergey V Tarlachkov, Galina A Dubinina, Elena V Belousova, Maria N Tutukina, Margarita Y Grabovich
Diazotrophic Alphaproteobacteria of the genus Azospirillum are usually organotrophs, although some strains of Azospirillum lipoferum are capable of hydrogen-dependent autotrophic growth. Azospirillum thiophilum strain was isolated from a mineral sulfide spring, a biotope highly unusual for azospirilla. Here, the metabolic pathways utilized by A. thiophilum were revealed based on comprehensive analysis of its genomic organization, together with physiological and biochemical approaches. The A. thiophilum genome contained all the genes encoding the enzymes of carbon metabolism via glycolysis, tricarboxylic acid cycle and glyoxylate cycle...
December 2016: FEMS Microbiology Ecology
Joicye Hernández-Zulueta, Rubén Araya, Ofelia Vargas-Ponce, Leopoldo Díaz-Pérez, Alma P Rodríguez-Troncoso, Janja Ceh, Eduardo Ríos-Jara, Fabián A Rodríguez-Zaragoza
Bacterial assemblages associated with the hermatypic corals Pocillopora damicornis and P. verrucosa, the surrounding seawater and the sediment at six coral reef sites in the north section of the Tropical Eastern Pacific were assessed using MiSeq Illumina sequencing of the V4 region of the 16S rDNA. The bacterial microbiota in both coral species, seawater and sediment were stable to seasonal variations. Bacterial assemblages between the same substrates were not significantly different from each other in the six sites sampled...
December 2016: FEMS Microbiology Ecology
Joseph F Miceli, César I Torres, Rosa Krajmalnik-Brown
Fermentation is a key process in many anaerobic environments. Varying the concentration of electron donor fed to a fermenting community is known to shift the distribution of products between hydrogen, fatty acids and alcohols. Work to date has focused mainly on the fermentation of glucose, and how the microbial community structure is affected has not been explored. We fed ethanol, lactate, glucose, sucrose or molasses at 100 me- eq. L(-1), 200 me- eq. L(-1) or 400 me- eq. L(-1) to batch-fed cultures with fermenting, methanogenic communities...
December 2016: FEMS Microbiology Ecology
Rocel Amor Ortega, Alexander Mahnert, Christian Berg, Henry Müller, Gabriele Berg
The plant microbiome is a key determinant of plant health. Less is known about the phyllosphere microbiota and its driving factors in built environments. To study the variability of the microbiome in relation to plant genotype and climate under different controlled conditions, we investigated 14 phylogenetically diverse plant species grown in the greenhouses of the Botanical Garden in Graz (Austria). All investigated plants showed specific bacterial abundances of up to 10(6) CFU cm(-2) on their leaves. Bacterial diversity (H('): 2...
December 2016: FEMS Microbiology Ecology
Ben J J Lugtenberg, John R Caradus, Linda J Johnson
This minireview highlights the importance of endophytic fungi for sustainable agriculture and horticulture production. Fungal endophytes play a key role in habitat adaptation of plants resulting in improved plant performance and plant protection against biotic and abiotic stresses. They encode a vast variety of novel secondary metabolites including volatile organic compounds. In addition to protecting plants against pathogens and pests, selected fungal endophytes have been used to remove animal toxicities associated with fungal endophytes in temperate grasses, to create corn and rice plants that are tolerant to a range of biotic and abiotic stresses, and for improved management of post-harvest control...
December 2016: FEMS Microbiology Ecology
Simone Gwosdz, Julia M West, David Jones, Jana Rakoczy, Kay Green, Tom Barlow, Marco Blöthe, Karon Smith, Michael Steven, Martin Krüger
Impacts of long-term CO2 exposure on environmental processes and microbial populations of near-surface soils are poorly understood. This near-surface long-term CO2 injection study demonstrated that soil microbiology and geochemistry is influenced more by seasonal parameters than elevated CO2 Soil samples were taken during a 3-year field experiment including sampling campaigns before, during and after 24 months of continuous CO2 injection. CO2 concentrations within CO2-injected plots increased up to 23% during the injection period...
December 2016: FEMS Microbiology Ecology
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