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Environmental Microbiology

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https://read.qxmd.com/read/30773816/integrated-mobile-genetic-elements-in-thaumarchaeota
#1
Mart Krupovic, Kira S Makarova, Yuri I Wolf, Sofia Medvedeva, David Prangishvili, Patrick Forterre, Eugene V Koonin
To explore the diversity of mobile genetic elements (MGE) associated with archaea of the phylum Thaumarchaeota, we exploited the property of most MGE to integrate into the genomes of their hosts. Integrated MGE (iMGE) were identified in 20 thaumarchaeal genomes amounting to 2 Mbp of mobile thaumarchaeal DNA. These iMGE group into five major classes: (i) proviruses, (ii) casposons, (iii) insertion sequence-like transposons, (iv) integrative-conjugative elements, and (v) cryptic integrated elements. The majority of the iMGE belong to the latter category and might represent novel families of viruses or plasmids...
February 17, 2019: Environmental Microbiology
https://read.qxmd.com/read/30773801/coping-with-low-water-activities-and-osmotic-stress-in-acinetobacter-baumannii-significance-current-status-and-perspectives
#2
REVIEW
Sabine Zeidler, Volker Müller
Multidrug resistant (MDR) pathogens are one of the most pressing challenges of contemporary health care. Acinetobacter baumannii takes a predominant position, emphasized in 2017 by the World Health Organization. The increasing emergence of MDR strains strengthens the demand for new antimicrobials. Possible targets for such compounds might be proteins involved in resistance against low water activity environments, since A. baumannii is known for its pronounced resistance against desiccation stress. Despite the importance of desiccation resistance for persistence of this pathogen in hospitals, comparable studies and precise data on this topic are rare and the mechanisms involved are largely unknown...
February 17, 2019: Environmental Microbiology
https://read.qxmd.com/read/30773777/viral-and-bacterial-community-responses-to-stimulated-fe-iii-bioreduction-during-simulated-subsurface-bioremediation
#3
Xiaolong Liang, Jie Zhuang, Frank E Löffler, Yingyue Zhang, Jennifer DeBruyn, Steven Wilhelm, Sean M Schaeffer, Mark Radosevich
The delivery of fermentable substrate(s) to subsurface environments stimulates Fe(III)-bioreduction and achieves detoxification of organic/inorganic contaminants. Though much research has been conducted on the microbiology of such engineered systems at lab and field scales, little attention has been given to the phage-host interactions and virus community dynamics in these environments. The objective was to determine the responses of soil bacterial communities and viral assemblages to stimulated anaerobic Fe(III)-bioreduction following electron donor (e...
February 17, 2019: Environmental Microbiology
https://read.qxmd.com/read/30773776/the-y233-gatekeeper-of-dmpr-modulates-effector-responsive-transcriptional-control-of-%C3%AF-54-rna-polymerase
#4
Henrik Seibt, Uwe H Sauer, Victoria Shingler
DmpR is the obligate transcriptional activator of genes involved in (methyl)phenol catabolism by Pseudomonas putida. DmpR belongs to the AAA+ class of mechano-transcriptional regulators that employ ATP-hydrolysis to engage and remodel σ54 -RNA polymerase to allow transcriptional initiation. Previous work has established that binding of phenolic effectors by DmpR is a prerequisite to relieve inter-domain repression and allow ATP-binding to trigger transition to its active multimeric conformation, and further that a structured inter-domain linker between the effector- and ATP-binding domains is involved in coupling these processes...
February 17, 2019: Environmental Microbiology
https://read.qxmd.com/read/30773773/a-novel-approach-to-investigate-hypoxic-microenvironment-during-rice-colonization-by-magnaporthe-oryzae
#5
Hyunjung Chung, Seongbeom Kim, Ki-Tae Kim, Bae-Geun Hwang, Hye-Jeong Kim, Sang-Joon Lee, Yong-Hwan Lee
Because molecular oxygen functions as the final acceptor of electrons during aerobic respiration and a substrate for diverse enzymatic reactions, eukaryotes employ various mechanisms to maintain cellular homeostasis under varying oxygen concentration. Human fungal pathogens change the expression of genes involved in virulence and oxygen-required metabolisms such as ergosterol (EGR) synthesis when they encounter oxygen limitation (hypoxia) during infection. The oxygen level in plant tissues also fluctuates, potentially creating hypoxic stress to pathogens during infection...
February 17, 2019: Environmental Microbiology
https://read.qxmd.com/read/30761723/microdiversity-and-temporal-dynamics-of-marine-bacterial-dimethylsulfoniopropionate-genes
#6
Brent Nowinski, Jessie Motard-Côté, Marine Landa, Christina M Preston, Christopher A Scholin, James M Birch, Ronald P Kiene, Mary Ann Moran
Dimethylsulfoniopropionate (DMSP) is an abundant organic sulfur metabolite produced by many phytoplankton species and degraded by bacteria via two distinct pathways with climate-relevant implications. We assessed the diversity and abundance of bacteria possessing these pathways in the context of phytoplankton community composition over a three-week time period spanning September - October, 2014 in Monterey Bay, CA. The dmdA gene from the DMSP demethylation pathway dominated the DMSP gene pool and was harbored mostly by members of the alphaproteobacterial SAR11 clade and secondarily by the Roseobacter group, particularly during the second half of the study...
February 14, 2019: Environmental Microbiology
https://read.qxmd.com/read/30761716/baseline-characterisation-of-aerobic-hydrocarbon-degrading-microbial-communities-in-deep-sea-sediments-of-the-great-australian-bight-australia
#7
Jodie van de Kamp, Sharon E Hook, Alan Williams, Jason E Tanner, Levente Bodrossy
Exploratory drilling for deep-sea oil and gas resources is planned for the Great Australian Bight (GAB). There is scant knowledge of the region's benthic ecosystems and no baseline information of the region's indigenous oil degrading bacteria. To address this knowledge gap, we used next generation sequencing (NGS) of three marker genes (alkB, c23o and pmoA) to detect and characterise the microbial communities capable of aerobic hydrocarbon degradation. Unique, highly novel microbial communities capable of degrading hydrocarbons occur in surface sediments at depths between 200 and 2800 m...
February 14, 2019: Environmental Microbiology
https://read.qxmd.com/read/30761715/increased-algicidal-activity-of-aeromonas-veronii-in-response-to-microcystis-aeruginosa-inter-species-crosstalk-and-secondary-metabolites-synergism
#8
Gad Weiss, Dimitry Kovalerchick, Judy Lieman-Hurwitz, Omer Murik, Roberto De Philippis, Shmuel Carmeli, Assaf Sukenik, Aaron Kaplan
Toxic Microcystis spp. blooms constitute a serious threat to water quality worldwide. Aeromonas veronii was isolated from Microcystis sp. colonies collected in Lake Kinneret. Spent Aeromonas media inhibits the growth of Microcystis aeruginosa MGK isolated from Lake Kinneret. The inhibition was much stronger when Aeromonas growth medium contained spent media from MGK suggesting that Aeromonas recognized its presence and produced secondary metabolites that inhibit Microcystis growth. Fractionations of the crude extract and analyses of the active fractions identified several secondary metabolites including lumichrome in Aeromonas media...
February 14, 2019: Environmental Microbiology
https://read.qxmd.com/read/30761714/ecological-implications-of-gene-regulation-by-tfox-and-tfoy-among-diverse-vibrio-species
#9
Lisa C Metzger, Noémie Matthey, Candice Stoudmann, Esther J Collas, Melanie Blokesch
Bacteria of the genus Vibrio are common members of aquatic environments where they compete with other prokaryotes and defend themselves against grazing predators. A macromolecular protein complex called the type VI secretion system (T6SS) is used for both purposes. Previous research showed that the sole T6SS of the human pathogen V. cholerae is induced by extracellular (chitin) or intracellular (low c-di-GMP levels) cues and that these cues lead to distinctive signalling pathways for which the proteins TfoX and TfoY serve as master regulators...
February 14, 2019: Environmental Microbiology
https://read.qxmd.com/read/30735001/nitrification-inhibitors-effectively-target-n-2-o-producing-nitrosospira-spp-in-tropical-soil
#10
Noriko A Cassman, Johnny R Soares, Agata Pijl, Késia S Lourenço, Johannes A van Veen, Heitor Cantarella, Eiko E Kuramae
The nitrification inhibitors (NIs) 3,4-dimethylpyrazole (DMPP) and dicyandiamide (DCD) can effectively reduce N2 O emissions; however, which species are targeted and the effect of these NIs on the microbial nitrifier community is still unclear. Here we identified the ammonia oxidizing bacteria (AOB) species linked to N2 O emissions and evaluated the effects of urea and urea with DCD and DMPP on the nitrifying community in a 258-day field experiment under sugarcane. Using an amoA AOB amplicon sequencing approach and mining a previous dataset of 16S rRNA sequences, we characterized the most likely N2 O-producing AOB as a Nitrosospira spp...
February 8, 2019: Environmental Microbiology
https://read.qxmd.com/read/30724449/dietary-polysaccharides-fermentation-potentials-of-a-primitive-gut-ecosystem
#11
Lydia Zeibich, Oliver Schmidt, Harold L Drake
The alimentary canal of the earthworm is representative of primitive gut ecosystems, and gut fermenters capable of degrading ingested biomass-derived polysaccharides might contribute to the environmental impact and survival of this terrestrial invertebrate. Thus, this study evaluated the postulation that gut microbiota of the model earthworm Lumbricus terrestris ferment diverse biomass-derived polysaccharides. Structural polysaccharides (e.g., cellulose, chitin) had marginal impact on fermentation in anoxic gut content treatments...
February 6, 2019: Environmental Microbiology
https://read.qxmd.com/read/30724443/long-term-fertilization-regimes-change-soil-nitrification-potential-by-impacting-active-autotrophic-ammonia-oxidizers-and-nitrite-oxidizers-as-assessed-by-dna-stable-isotope-probing
#12
Yali Kong, Ning Ling, Chao Xue, Huan Chen, Yang Ruan, Junjie Guo, Chen Zhu, Min Wang, Qirong Shen, Shiwei Guo
Chemoautotrophic ammonia-oxidizers and nitrite-oxidizers are responsible for a significant amount of soil nitrate production. The identity and composition of these active nitrifiers in soils under different long-term fertilization regimes remain largely under-investigated. Based on that soil nitrification potential significantly decreased in soils with chemical fertilization (CF) and increased in soils with organic fertilization (OF), a microcosm experiment with DNA stable isotope probing was further conducted to clarify the active nitrifiers...
February 6, 2019: Environmental Microbiology
https://read.qxmd.com/read/30724442/marine-synechococcus-isolates-representing-globally-abundant-genomic-lineages-demonstrate-a-unique-evolutionary-path-of-genome-reduction-without-a-decrease-in-gc-content
#13
Michael D Lee, Nathan A Ahlgren, Joshua D Kling, Nathan G Walworth, Gabrielle Rocap, Mak A Saito, David A Hutchins, Eric A Webb
Synechococcus, a genus of unicellular cyanobacteria found throughout the global surface ocean, is a large driver of Earth's carbon cycle. Developing a better understanding of its diversity and distributions is an ongoing effort in biological oceanography. Here we introduce 12 new draft genomes of marine Synechococcus isolates spanning five clades and utilize ~100 environmental metagenomes largely sourced from the TARA Oceans project to assess the global distributions of the genomic lineages they and other reference genomes represent...
February 6, 2019: Environmental Microbiology
https://read.qxmd.com/read/30724441/high-diversity-and-rapid-spatial-turnover-of-integron-gene-cassettes-in-soil
#14
Timothy M Ghaly, Jemma L Geoghegan, John Alroy, Michael R Gillings
Integrons are genetic elements that promote rapid adaptation in bacteria by capturing exogenous, mobile gene cassettes. Recently, a subset of gene cassettes has facilitated the global spread of antibiotic resistance. However, outside clinical settings, very little is known about their diversity and spatial ecology. To address this question, we sequenced integron gene cassettes from soils sampled across Australia and Antarctica. We recovered 44,970 open reading frames that encoded 27,215 unique proteins, representing an order of magnitude more cassettes than previous sequencing efforts...
February 6, 2019: Environmental Microbiology
https://read.qxmd.com/read/30724440/transcriptomic-analysis-reveals-the-relationship-of-melanization-to-growth-and-resistance-to-gamma-radiation-in-cryptococcus-neoformans
#15
Zachary Schultzhaus, Amy Chen, Seongwon Kim, Igor Shuryak, Melody Chang, Zheng Wang
The pathogenic fungus Cryptococcus neoformans produces melanin within its cell wall for infection and resistance against external stresses such as exposure to UV, temperature fluctuations, and reactive oxygen species. It has been reported that melanin may also protect cells from ionizing radiation damage, against which C. neoformans is extremely resistant. This has tagged melanin as a potential radioprotective biomaterial. Here, we report the effect of melanin on the transcriptomic response of C. neoformans to gamma radiation...
February 6, 2019: Environmental Microbiology
https://read.qxmd.com/read/30724439/prokaryotic-and-viral-community-structure-in-the-singular-chaotropic-salt-lake-salar-de-uyuni
#16
María Dolores Ramos-Barbero, José M Martínez, Cristina Almansa, Nuria Rodríguez, Judith Villamor, María Gomariz, Cristina Escudero, Sergio Rubin, Josefa Antón, Manuel Martínez-García, Ricardo Amils
Salar de Uyuni (SdU) is the largest hypersaline salt flat and the highest lithium reservoir on Earth. In addition to extreme temperatures and high UV irradiance, SdU has high concentrations of chaotropic salts which can be important factors in controlling microbial diversity. Here, for the first time we characterize the viral diversity of this hypersaline environment during the two seasons, as well as the physicochemical characteristics and the prokaryotic communities of the analyzed samples. Most of the selected samples showed a peculiar physicochemical composition and prokaryotic diversity, mostly different from each other even for samples from locations in close proximity or the same season...
February 6, 2019: Environmental Microbiology
https://read.qxmd.com/read/30724438/spatial-separation-of-anaerobic-ammonium-oxidation-and-nitrite-dependent-anaerobic-methane-oxidation-in-permeable-riverbeds
#17
Li-Dong Shen, Liao Ouyang, Yizhu Zhu, Mark Trimmer
Anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) play important roles in nitrogen and carbon cycling in fresh waters but we do not know how these two processes compete for their common electron acceptor, nitrite. Here, we investigated the spatial distribution of anammox and n-damo across a range of permeable riverbed sediments. Anammox activity and gene abundance were detected in both gravel and sandy riverbeds and showed a simple, common vertical distribution pattern, while the patterns in n-damo were more complex and n-damo activity was confined to the more reduced, sandy riverbeds...
February 6, 2019: Environmental Microbiology
https://read.qxmd.com/read/30724437/an-evaluation-of-primers-for-detecting-denitrifiers-via-their-functional-genes
#18
Yanjun Ma, Julie L Zilles, Angela D Kent
Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality, and climate change. Denitrification, in particular, impacts socio-environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups...
February 6, 2019: Environmental Microbiology
https://read.qxmd.com/read/30702193/transcriptional-regulation-of-fatty-acid-cis-trans-isomerization-in-the-solvent-tolerant-soil-bacterium-pseudomonas-putida-f1
#19
Tatiana Kondakova, John E Cronan
One key to the success of Pseudomonas spp. is their ability to reside in the hostile environments. Pseudomonas spp. possess a cis-trans isomerase (Cti) an enzyme that converts the cis-unsaturated fatty acids of the membrane lipids to their trans-isomers to rigidify the membrane and thereby resist stresses. Whereas the posttranslational Cti regulation has been previously reported, transcriptional cti regulation remains to be studied in more details. Here, we have studied cti transcriptional regulation in the solvent-tolerant strain P...
January 31, 2019: Environmental Microbiology
https://read.qxmd.com/read/30702191/bacteria-and-micro-eukaryotes-are-differentially-segregated-in-sympatric-wastewater-microhabitats
#20
Yossi Cohen, Zohar Pasternak, Julia Johnke, Alfred Abed-Rabbo, Ariel Kushmaro, Antonis Chatzinotas, Edouard Jurkevitch
Wastewater purification is mostly performed in activated sludge reactors by bacterial and micro-eukaryotic communities, populating organic flocs and a watery liquor. While there are numerous molecular community studies of the bacterial fraction, those on micro-eukaryotes are rare. We performed a year-long parallel 16S rRNA gene and 18S rRNA-gene based analysis of the bacterial and of the micro-eukaryote communities, respectively, of physically separated flocs and particle-free liquor samples from three WWTPs...
January 31, 2019: Environmental Microbiology
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