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Environmental Microbiology

Yanjun Li, Shunwen Luo, Xiaojing Jia, Yuanye Zhu, Dongming Chen, Yabing Duan, Yiping Hou, Mingguo Zhou
Although the roles of introns have been much debated in eukaryotic organisms, none of them have been functionally characterized in Fusarium graminearum. In this study, we characterized the roles of introns in regulation of fungicide-sensitivity of F. graminearum. β2 tub, cyp51A and myosin-5 are important target genes of benzimidazoles, triazoles and cyanoacrylates, respectively. To explore the sensitivity regulation functions of introns in target genes, several detailed deletion studies were completed on the intronic regions of β2 tub, cyp51A, myosin-5...
July 21, 2017: Environmental Microbiology
Conor J Doyle, Paul W O'Toole, Paul D Cotter
Metagenomic-based analyses have the potential to revolutionise our understanding of the microbiology of food production and processing environments. By adopting such approaches it will be possible to more accurately determine sources of microbial contamination, identify critical control points for such contaminants, and select practices that optimise quality and safety. This mini-review will discuss the merits of adopting metagenostic-based approaches, highlight novel insights that they have provided to date and consider how they could be further implemented...
July 20, 2017: Environmental Microbiology
Timothy G Otten, Hans W Paerl, Theo W Dreher, Wim J Kimmerer, Alex E Parker
Harmful blooms of the cyanobacterium Microcystis sp. have become increasingly pervasive in the San Francisco Estuary Delta (USA) since the early 2000's and their rise has coincided with substantial decreases in several important fish species. We sought to investigate direct and indirect effects Microcystis blooms may have on the Delta food web. The Microcystis population was tracked for two years at six sites throughout the Delta using quantitative PCR. High-throughput amplicon sequencing and colony PCR sequencing revealed the presence of 10 different strains of Microcystis, including six different microcystin-producing strains...
July 20, 2017: Environmental Microbiology
Yutong Shi, Chengqian Pan, Kuiwu Wang, Xuegang Chen, Xiaodan Wu, Chen-Tung Arthur Chen, Bin Wu
Chemically mediated interactions have been hypothesized to be essential for ecosystem functioning as co-occurring organisms can influence the performance of each other by metabolic means. Here we present a co-culture device that allows co-culturing of microorganisms that are physically separated but can exchange chemical signals and metabolites. This setup was adopted to perform investigations on the secondary metabolisms of both a fungal-bacterial community and an actinomycetic-actinomycetic community. This study employed a metabolomics approach integrating LC-MS profiling, multivariate data analysis and molecular networking techniques...
July 17, 2017: Environmental Microbiology
Laura Moreno-Mesonero, Yolanda Moreno, José Luis Alonso, M Antonia Ferrús
Helicobacter pylori is one of the most concerning emerging waterborne pathogens. It has been suggested that it could survive in water inside free-living amoebae (FLA), but nobody has studied this relationship in the environment yet. Thus, we aimed to detect viable H. pylori cells from inside FLA in water samples. Sixty-nine wastewater and 31 drinking water samples were collected. FLA were purified and identified by PCR and sequencing. For exclusively detecting H. pylori inside FLA, samples were exposed to sodium hypochlorite and assayed by specific PMA-qPCR, DVC-FISH and culture...
July 14, 2017: Environmental Microbiology
Benoit Couvigny, Nicolas Lapaque, Lionel Rigottier-Gois, Alain Guillot, Sophie Chat, Thierry Meylheuc, Saulius Kulakauskas, Manfred Rohde, Michel-Yves Mistou, Pierre Renault, Joel Doré, Romain Briandet, Pascale Serror, Eric Guédon
Bacterial adhesion is a critical step for colonization of the host. The pioneer colonizer and commensal bacterium of the human gastrointestinal tract, Streptococcus salivarius, has strong adhesive properties but the molecular determinants of this adhesion remain uncharacterized. Serine-rich repeat (SRR) glycoproteins are a family of adhesins that fulfill an important role in adhesion. In general, Gram-positive bacterial genomes have a unique SRR glycoprotein-encoding gene. We demonstrate that S. salivarius expresses three large and glycosylated surface-exposed proteins - SrpA, SrpB and SrpC - that show characteristics of SRR glycoproteins and are secreted through the accessory SecA2/Y2 system...
July 11, 2017: Environmental Microbiology
Óscar Huertas-Rosales, Manuel Romero, Stephan Heeb, Manuel Espinosa-Urgel, Miguel Cámara, María Isabel Ramos-González
Expression of cfcR, encoding the only GGDEF/EAL response regulator in Pseudomonas putida, is transcriptionally regulated by RpoS, ANR and FleQ, and the functionality of CfcR as a diguanylate cyclase requires the multisensor CHASE3/GAF hybrid histidine kinase named CfcA. Here an additional level of cfcR control, operating post-transcriptionally via the RNA-binding proteins RsmA, RsmE and RsmI, is unraveled. Specific binding of the three proteins to an Rsm binding motif (5'CANGGANG3') encompassing the translational start codon of cfcR was confirmed...
July 5, 2017: Environmental Microbiology
Robert Wagner, Donatella Zona, Walter Oechel, David Lipson
While there is no doubt that biogenic methane production in the Arctic is an important aspect of global methane emissions, the relative roles of microbial community characteristics and soil environmental conditions in controlling Arctic methane emissions remains uncertain. Here, relevant methane-cycling microbial groups were investigated at two remote Arctic sites with respect to soil potential methane production (PMP). Percent abundances of methanogens and iron-reducing bacteria correlated with increased PMP, while methanotrophs correlated with decreased PMP...
July 5, 2017: Environmental Microbiology
Jing Liu, Sen-Miao Tong, Lei Qiu, Sheng-Hua Ying, Ming-Guang Feng
Filamentous fungi possess a large family of histidine kinases (HKs) classified to 11 distinct groups. Of those, only Group III (HK3) homologs in some fungi can sense osmotic, fungicidal and/or oxidative cues upstream of the signaling MAPK Hog1 cascade that usually governs two hallmark phenotypes, i.e., osmotolerance and dicarboximide/phenylpyrrole fungicide resistance. Here we examined functions of all eight HK groups with each possessing a single member in Beauveria bassiana. HK3 and HK8 (Group VIII) were evidently localized at hyphal cell periphery and had more functions in aerial conidiation and multiple stress responses than six other HKs...
July 5, 2017: Environmental Microbiology
Eulyn Pagaling, Kristin Vassileva, Catherine G Mills, Timothy Bush, Richard A Blythe, Jana Schwarz-Linek, Fiona Strathdee, Rosalind J Allen, Andrew Free
We studied in detail the reproducibility of community development in replicate nutrient-cycling microbial microcosms that were set up identically and allowed to develop under the same environmental conditions. Multiple replicate closed microcosms were constructed using pond sediment and water, enriched with cellulose and sulphate, and allowed to develop over several months under constant environmental conditions, after which their microbial communities were characterised using 16S rRNA gene sequencing. Our results show that initially similar microbial communities can follow alternative - yet stable - trajectories, diverging in time in a system size-dependent manner...
July 5, 2017: Environmental Microbiology
Jenifer B Walke, Matthew H Becker, Myra C Hughey, Meredith C Swartwout, Roderick V Jensen, Lisa K Belden
Some amphibian skin bacteria inhibit growth of a fungal amphibian pathogen, Batrachochytrium dendrobatidis (Bd), but it is unclear how dominant these anti-Bd bacteria are in skin communities. Using in vitro co-culture challenge assays, we quantified Bd inhibition by bacterial isolates collected from the skin of four amphibian species: bullfrogs, Eastern newts, spring peepers, and American toads. The 16S rRNA sequences for each isolate were matched to culture-independent amplicon sequences from the same individuals to assess inhibitory function versus relative abundance...
July 5, 2017: Environmental Microbiology
Jianming Yang, Liang Yin, Faith H Lessner, Ernesto S Nakayasu, Samuel H Payne, Kathryn R Fixen, Larry Gallagher, Caroline S Harwood
We used Tn-seq to identify genes essential for phototrophic growth by the purple bacterium Rhodopseudomonas palustris. We identified 167 genes required for anaerobic growth on acetate in light, 35 of which are annotated as photosynthesis genes. We verified the essentiality of many of these genes by analyzing the phenotypes of independently generated mutants that had altered pigmentation. We also identified three genes, two possibly involved in biogenesis of the membrane-bound photosynthetic apparatus and one for phosphadidylcholine biosynthesis, that were not known to be essential for phototrophic growth...
July 5, 2017: Environmental Microbiology
Andrea Campisano, Davide Albanese, Sohail Yousaf, Michael Pancher, Claudio Donati, Ilaria Pertot
Endophytic microorganisms asymptomatically colonise plant tissues. Exploring the assembly dynamics of bacterial endophytic communities is essential to understand the functioning of the plant holobiont and to optimise their possible use as biopesticides or plant biostimulants. We studied the variation in endophytic communities in above and below-ground organs in Vitis vinifera in the field. To understand the specific effect of temperature on endophytic communities, a separate experiment was set up where grapevine cuttings were grown under controlled conditions at three different temperatures...
June 27, 2017: Environmental Microbiology
Yimei Zhang, Xuli Gao, Manli Sun, Huiquan Liu, Jin-Rong Xu
The versatile functions of SR (serine/arginine-rich) proteins in pre-mRNA splicing and processing are modulated by reversible phosphorylation. Previous studies showed that FgPrp4, the only protein kinase among spliceosome components, is important for intron splicing and the FgSrp1 SR protein is phosphorylated at five conserved sites in Fusarium graminearum. In this study, we showed that the Fgsrp1 deletion mutant rarely produced conidia and caused only limited symptoms on wheat heads and corn silks. Deletion of FgSRP1 also reduced ascospore ejection and deoxynivalenol (DON) production...
June 27, 2017: Environmental Microbiology
Alexandra L McCully, Breah LaSarre, James B McKinlay
Nutrient cross-feeding can stabilize microbial mutualisms, including those important for carbon cycling in nutrient-limited anaerobic environments. It remains poorly understood how nutrient limitation within natural environments impacts mutualist growth, cross-feeding levels, and ultimately mutualism dynamics. We examined the effects of nutrient limitation within a mutualism using theoretical and experimental approaches with a synthetic anaerobic coculture pairing fermentative Escherichia coli and phototrophic Rhodopseudomonas palustris...
June 27, 2017: Environmental Microbiology
Nir Friedman, Elie Jami, Itzhak Mizrahi
Methanogenic archaea in the bovine rumen are responsible for the reduction of carbon molecules to methane, using various electron donors and driving the electron flow across the microbial food webs. Thus, methanogens play a key role in sustaining rumen metabolism and function. Research of rumen methanogenic archaea typically focuses on their composition and function in mature animals, while studies of early colonization and functional establishment remain scarce. Here, we investigated the metabolic potential and taxonomic composition of the methanogenic communities across different rumen developmental stages...
June 27, 2017: Environmental Microbiology
Antonia Johnston, Andrew T Crombie, Myriam El Khawand, Leanne Sims, Gregg Whited, Terry J McGenity, J Colin Murrell
Approximately one third of volatile organic compounds (VOCs) emitted to the atmosphere consists of isoprene, originating from the terrestrial and marine biosphere, with a profound effect on atmospheric chemistry. However, isoprene provides an abundant and largely unexplored source of carbon and energy for microbes. The potential for isoprene degradation in marine and estuarine samples from the Colne Estuary, UK, was investigated using DNA-Stable Isotope Probing (DNA-SIP). Analysis at two timepoints showed the development of communities dominated by Actinobacteria including members of the genera Mycobacterium, Rhodococcus, Microbacterium and Gordonia...
June 27, 2017: Environmental Microbiology
Pauline Basso, Pierre Wallet, Sylvie Elsen, Emmanuelle Soleilhac, Thomas Henry, Eric Faudry, Ina Attrée
Pathogenic bacteria secrete protein toxins that provoke apoptosis or necrosis of eukaryotic cells. Here, we developed a live-imaging method, based on incorporation of a DNA-intercalating dye into membrane-damaged host cells, to study the kinetics of primary bone marrow-derived macrophages (BMDMs) mortality induced by opportunistic pathogen Pseudomonas aeruginosa expressing either Type III Secretion System (T3SS) toxins or the pore-forming toxin, Exolysin (ExlA). We found that ExlA promotes the activation of Caspase-1 and maturation of interleukin-1β...
June 27, 2017: Environmental Microbiology
Merle Hirschmann, Florian Grundmann, Helge B Bode
Effective iron acquisition and fine-tuned intracellular iron storage systems are the main prerequisites for a successful host invasion by a pathogen. Bacteria have developed several different strategies to sequester this essential element from their environment, one relies on the secretion of low molecular weight compounds with high affinity for ferric iron, the so-called siderophores. Here we report hydroxamate siderophore structures produced by entomopathogenic bacteria of the species Xenorhabdus and Photorhabdus, which are known for their potential to produce bioactive natural products, required for their role as nematode symbiont and insect pathogen...
June 27, 2017: Environmental Microbiology
Bryndan P Durham, Stephen P Dearth, Shalabh Sharma, Shady A Amin, Christa B Smith, Shawn R Campagna, E Virginia Armbrust, Mary Ann Moran
The trophic linkage between marine bacteria and phytoplankton in the surface ocean is a key step in the global carbon cycle, with almost half of marine primary production transformed by heterotrophic bacterioplankton within hours to weeks of fixation. Early studies conceptualized this link as the passive addition and removal of organic compounds from a shared seawater reservoir. Here we analyzed transcript and intracellular metabolite patterns in a two-member model system and found that the presence of a heterotrophic bacterium induced a potential recognition cascade in a marine phytoplankton species that parallels better-understood vascular plant response systems...
June 19, 2017: Environmental Microbiology
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