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Environmental Microbiology Reports

Paul A Hoskisson, Lorena T Fernández-Martínez
The increase in availability of actinobacterial whole genome sequences has revealed huge numbers of specialised metabolite biosynthetic gene clusters, encoding a range of bioactive molecules such as antibiotics, antifungals, immunosuppressives and anticancer agents. Yet the majority of these clusters are not expressed under standard laboratory conditions in rich media conditions. Emerging data from studies of specialised metabolite biosynthesis suggest that the diversity of regulatory mechanisms is greater than previously thought and these act at multiple levels, through a range of signals such as nutrient limitation, intercellular signalling and competition with other organisms...
February 19, 2018: Environmental Microbiology Reports
Monica Conthe, Lea Wittorf, J Gijs Kuenen, Robbert Kleerebezem, Sara Hallin, Mark C M van Loosdrecht
Nitrous oxide (N2 O) reducing microorganisms may be key in the mitigation of N2 O emissions from managed ecosystems. However, there is still no clear understanding of the physiological and bioenergetic implications of microorganisms possessing either of the two N2 O reductase genes (nosZ), clade I and the more recently described clade II type nosZ. It has been suggested that organisms with nosZ clade II have higher growth yields and a lower affinity constant (Ks ) for N2 O. We compared N2 O reducing communities with different nosZI/nosZII ratios selected in chemostat enrichment cultures, inoculated with activated sludge, fed with N2 O as a sole electron acceptor and growth limiting factor, and acetate as electron donor...
February 19, 2018: Environmental Microbiology Reports
Christos Gougoulias, Andrew Meade, Liz J Shaw
An unresolved need in microbial ecology is methodology to enable quantitative analysis of in situ microbial substrate carbon use at the population level. Here, we evaluated if a novel combination of radiocarbon- labelled substrate tracing, Fluorescence in situ Hybridisation (FISH) and Fluorescence-Activated Cell Sorting (FACS) to sort the FISH-targeted population for quantification of incorporated radioactivity (14 C-FISH-FACS) can address this need. Our test scenario used FISH probe PSE1284 targeting Pseudomonas spp...
February 19, 2018: Environmental Microbiology Reports
Erik R Zinser
Hydrogen peroxide (HOOH) is a reactive oxygen species, derived from molecular oxygen, that is capable of damaging microbial cells. Surprisingly, the HOOH defense systems of some aerobes in the oxygenated marine environments are critically depleted, relative to model aerobes. For instance, the gene encoding catalase is absent in the numerically-dominant photosynthetic cyanobacterium, Prochlorococcus. Accordingly, Prochlorococcus is highly susceptible to HOOH when exposed as pure cultures. Pure cultures do not exist in the marine environment, however...
February 6, 2018: Environmental Microbiology Reports
Erik R Zinser
This review surveys the current state of knowledge of the concentrations, sources, and sinks of reactive oxygen species (ROS) in the ocean. Both abiotic and biotic factors contribute to ROS dynamics in seawater, and ROS can feature prominently in marine microbe-microbe interactions. The sun plays a key role in the production of ROS in the ocean, and consequently ROS concentrations are typically maximal in the sun-exposed surface. However, microbes can also contribute significantly to extracellular ROS. Production of superoxide is widespread within the microbial community, and may benefit the producers as antimicrobial agents, or, perhaps more generally, as a means of nutrient scavenging...
February 6, 2018: Environmental Microbiology Reports
Arthur Thompson, Marcus Fulde, Karsten Tedin
Only relatively recently has research on the metabolism of intracellular bacterial pathogens within their host cells begun to appear in the published literature. This reflects in part the experimental difficulties encountered in separating host metabolic processes from those of the resident pathogen. One of the most genetically tractable and thoroughly studied intracellular bacterial pathogen, Salmonella enterica serovar Typhimurium (S. Typhimurium), has been at the forefront of metabolic studies within eukaryotic host cells...
February 6, 2018: Environmental Microbiology Reports
Markus V Lindh, Brianne M Maillot, Craig R Smith, Matthew J Church
Deep-sea mining of commercially valuable polymetallic nodule fields will generate a seabed sediment plume into the water column. Yet, the response of bacterial communities, critical in regulating energy and matter fluxes in marine ecosystems, to such disturbances is unknown. Metacommunity theory, traditionally used in general ecology for macroorganisms, offers a mechanistic understanding on the relative role of spatial differences compared to local environmental conditions (habitat filtering) for community assembly...
February 6, 2018: Environmental Microbiology Reports
Yuichi Ueno, Emi Yoshida, Wakako Misumi, Eri Watando, Kenta Suzuki, Yuko Hirai, Masatoshi Okura, Makoto Osaki, Ken Katsuda, Daisuke Takamatsu
Paenibacillus larvae is the causative agent of American foulbrood (AFB), the most destructive disease of the honey bee brood. In this study, we investigated the population structure and antimicrobial susceptibility of Japanese P. larvae using 100 isolates isolated between 1993 and 2017 in 17 prefectures. Using repetitive-element PCR and multilocus sequence typing, isolates from diverse origins were classified into six genotypes, including the novel genotype ERIC II-ST24. Among these genotypes, ERIC I-ST15 is the most common in Japan, while ERIC II-ST10 isolates were found to be increasing during the 2010s...
February 2, 2018: Environmental Microbiology Reports
M Zimmermann, S Escrig, G Lavik, M M M Kuypers, A Meibom, M Ackermann, F Schreiber
Populations of genetically identical cells can display marked variation in phenotypic traits; such variation is termed phenotypic heterogeneity. Here we investigate the effect of substrate and electron donor limitation on phenotypic heterogeneity in N2 and CO2 fixation in the green sulphur bacterium Chlorobium phaeobacteroides. We grew populations in chemostats and batch cultures and used stable isotope labelling combined with nanometer-scale secondary ion mass spectrometry (NanoSIMS) to quantify phenotypic heterogeneity...
February 2, 2018: Environmental Microbiology Reports
Vanitha Mariappan, Jaikumar Thimma, Kumutha Malar Vellasamy, Esaki M Shankar, Jamuna Vadivelu
Physiological constituents in airway surface liquids (ASL) appear to impact the adherence and invasion potentials of Burkholderia pseudomallei contributing to recrudescent melioidosis. Here, we investigated the factors present in ASL that is likely to influence bacterial adhesion and invasion leading to improved understanding of bacterial pathogenesis. Six B.pseudomallei clinical isolates from different origins were used to investigate the ability of the bacteria to adhere and invade A549 human lung epithelial cells using a system that mimics the physiological ASL with different pH, NaCl, KCl, CaCl2 and glucose concentrations...
February 2, 2018: Environmental Microbiology Reports
Sophie Bouillet, Dallel Arabet, Cécile Jourlin-Castelli, Vincent Méjean, Chantal Iobbi-Nivol
Partner-Switching Systems (PSS) are widespread regulatory systems, each comprising a kinase-anti-σ, a phosphorylatable anti-σ antagonist and a phosphatase module. The anti-σ domain quickly sequesters or delivers the target σ factor according to the phosphorylation state of the anti-σ antagonist induced by environmental signals. The PSS components are proteins alone or merged to other domains probably to adapt to the input signals. PSS are involved in major cellular processes including stress response, sporulation, biofilm formation and pathogenesis...
February 2, 2018: Environmental Microbiology Reports
M Hüttener, A Prieto, S Aznar, M Dietrich, S Paytubi, A Juárez
In this report we show that bacterial plasmids that harbor the Tn10 transposon (i.e., the IncHI1 plasmid R27) modify expression of different Salmonella regulons responding to the presence of tetracycline (Tc) in the medium. By using as a model the Tc-dependent upregulation of the ibpAB operon (which belongs to the heat shock regulon), we have identified Tn10- tetA (coding for a Tc efflux pump) and adjacent tetC sequences as required for ibpAB upregulation. Characterization of transcripts in the tetAC region showed that tetA transcription can continue into tetC sequences, generating a long 3'UTR sequence, which can protect transcripts from RNA processing, thus increasing expression of TetA protein...
February 2, 2018: Environmental Microbiology Reports
Jason J Flowers, Matthew A Richards, Nitin Baliga, Birte Meyer, David A Stahl
A refined Desulfovibrio vulgaris Hildenborough flux balance analysis (FBA) model (iJF744) was developed, incorporating 1016 reactions that include 744 genes and 951 metabolites. A draft model was first developed through automatic model reconstruction using the ModelSeed Server and then curated based on existing literature. The curated model was further refined by incorporating three recently proposed redox reactions involving the Hdr-Flx and Qmo complexes and a lactate dehydrogenase (LdhAB, DVU 3027-3028) indicated by mutation and transcript analyses to serve electron transfer reactions central to syntrophic and respiratory growth...
January 26, 2018: Environmental Microbiology Reports
Sergio E Morales, Moana Meyer, Kim Currie, Federico Baltar
Ecotones are regarded as diversity hotspots in terrestrial systems, but it is unknown if this "ecotone effect" occurs in the marine environment. Oceanic fronts are widespread mesoscale features, present in the boundary between different water masses, and are arguably the best potential examples of ecotones in the ocean. Here we performed the first seasonal study along an oceanic front, combining 16S rRNA gene sequencing coupled with a high spatial resolution analysis of the physical properties of the water masses...
January 26, 2018: Environmental Microbiology Reports
Alireza Bolourian, Zahra Mojtahedi
Resistance to a drug and the suppression of inflammatory disorders with immunosuppressive drugs might have happened upon exposure to natural compounds during evolution. Streptomycetes are soil bacteria, but they produce therapeutic drugs. They have been reported to be the low-abundant members of mucosal microbiomes with a higher prevalence in nonhumans ingesting soil compared to humans. Their lower abundance in the human microbiome might be the representations of our current hygienic lifestyle. We suggest that the Streptomyces bacteria producing antiproliferative/immunosuppressive compounds (e...
January 26, 2018: Environmental Microbiology Reports
Blanca Perez-Sepulveda, Frances Pitt, An Ngoc N'Guyen, Morgane Ratin, Laurence Garczarek, Andrew Millard, David J Scanlan
Marine picocyanobacteria of the genus Synechococcus are ubiquitous phototrophs in oceanic systems. Consistent with these organisms occupying vast tracts of the nutrient impoverished ocean, most marine Synechococcus so far studied are monoploid i.e. contain a single chromosome copy. The exception is the oligoploid strain Synechococcus sp. WH7803, which on average possesses around 4 chromosome copies. Here, we set out to understand the role of resource availability (through nutrient deplete growth) and physical stressors (UV, exposure to low and high temperature) in regulating ploidy level in this strain...
January 12, 2018: Environmental Microbiology Reports
Mohammad Bahram, Dan Vanderpool, Mari Pent, Markus Hiltunen, Martin Ryberg
Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr...
January 12, 2018: Environmental Microbiology Reports
Monica Conthe, J Gijs Kuenen, Robbert Kleerebezem, Mark C M van Loosdrecht
N2 O is a potent greenhouse gas, but also a potent electron acceptor. In search of thermodynamically favorable - yet undescribed - metabolic pathways involving N2 O reduction, we set up a continuous microbial enrichment, inoculated with activated sludge, fed with N2 O as the sole electron acceptor and acetate as an electron donor. A nitrogen-free mineral medium was used with the intention of creating a selective pressure towards organisms that would use N2 O directly as source of nitrogen for cell synthesis...
January 12, 2018: Environmental Microbiology Reports
Cui-Jing Zhang, Manuel Delgado-Baquerizo, John E Drake, Peter B Reich, Mark G Tjoelker, David T Tissue, Jun-Tao Wang, Ji-Zheng He, Brajesh K Singh
Plant characteristics in different provenances within a single species may vary in response to climate change, which might alter soil microbial communities and ecosystem functions. We conducted a glasshouse experiment and grew seedlings of three provenances (temperate, subtropical and tropical origins) of a tree species (i.e. Eucalyptus tereticornis) at different growth temperatures (18, 21.5, 25, 28.5, 32 and 35.5°C) for 54 days. At the end of the experiment, bacterial and fungal community composition, diversity and abundance were characterized...
January 12, 2018: Environmental Microbiology Reports
G M Showalter, J W Deming
A variety of ecologically important processes are driven by bacterial motility and taxis, yet these basic bacterial behaviors remain understudied in cold habitats. Here we present a series of experiments designed to test the chemotactic ability of the model marine psychrophilic bacterium Colwellia psychrerythraea 34H, when grown at optimal temperature and salinity (8°C, 35 ppt) or its original isolation conditions (-1°C, 35 ppt), towards serine and mannose at temperatures from -8 to 27°C (above its upper growth temperature of 18°C), and at salinities of 15, 35 and 55 ppt (at 8 and -1°C)...
December 13, 2017: Environmental Microbiology Reports
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