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ISME Journal

Jonas S Madsen, Ole Hylling, Samuel Jacquiod, Sophia Pécastaings, Lars H Hansen, Leise Riber, Gisle Vestergaard, Søren J Sørensen
The second messenger cyclic diguanylate (c-di-GMP) is ubiquitously used by bacteria to modulate and shift between different phenotypes including motility, biofilm formation and virulence. Here we show that c-di-GMP-associated genes are widespread on plasmids and that enzymes that synthesize or degrade c-di-GMP are preferentially encoded on transmissible plasmids. Additionally, expression of enzymes that synthesize c-di-GMP was found to increase both biofilm formation and, interestingly, conjugative plasmid transfer rates...
June 13, 2018: ISME Journal
Víctor J Carrión, Viviane Cordovez, Olaf Tyc, Desalegn W Etalo, Irene de Bruijn, Victor C L de Jager, Marnix H Medema, Leo Eberl, Jos M Raaijmakers
Disease-suppressive soils are ecosystems in which plants suffer less from root infections due to the activities of specific microbial consortia. The characteristics of soils suppressive to specific fungal root pathogens are comparable to those of adaptive immunity in animals, as reported by Raaijmakers and Mazzola (Science 352:1392-3, 2016), but the mechanisms and microbial species involved in the soil suppressiveness are largely unknown. Previous taxonomic and metatranscriptome analyses of a soil suppressive to the fungal root pathogen Rhizoctonia solani revealed that members of the Burkholderiaceae family were more abundant and more active in suppressive than in non-suppressive soils...
June 13, 2018: ISME Journal
Tomo Aoyagi, Fumiaki Morishita, Yutaka Sugiyama, Daisuke Ichikawa, Daisuke Mayumi, Yoshitomo Kikuchi, Atsushi Ogata, Kenji Muraoka, Hiroshi Habe, Tomoyuki Hori
1,4-Dioxane is one of the most common and persistent artificial pollutants in petrochemical industrial wastewaters and chlorinated solvent groundwater plumes. Despite its possible biological treatment in natural environments, the identity and dynamics of the microorganisms involved are largely unknown. Here, we identified active and diverse 1,4-dioxane-degrading microorganisms from activated sludge by high-sensitivity stable isotope probing of rRNA. By rigorously analyzing 16S rRNA molecules in RNA density fractions of 13 C-labeled and unlabeled 1,4-dioxane treatments, we discovered 10 significantly 13 C-incorporating microbial species from the complex microbial community...
June 13, 2018: ISME Journal
Po-Nan Li, Jonathan Herrmann, Bradley B Tolar, Frédéric Poitevin, Rasika Ramdasi, John R Bargar, David A Stahl, Grant J Jensen, Christopher A Francis, Soichi Wakatsuki, Henry van den Bedem
Surface layers (S-layers) are two-dimensional, proteinaceous, porous lattices that form the outermost cell envelope component of virtually all archaea and many bacteria. Despite exceptional sequence diversity, S-layer proteins (SLPs) share important characteristics such as their ability to form crystalline sheets punctuated with nano-scale pores, and their propensity for charged amino acids, leading to acidic or basic isoelectric points. However, the precise function of S-layers, or the role of charged SLPs and how they relate to cellular metabolism is unknown...
June 13, 2018: ISME Journal
David M Needham, Erin B Fichot, Ellice Wang, Lyria Berdjeb, Jacob A Cram, Cédric G Fichot, Jed A Fuhrman
Short timescale observations are valuable for understanding microbial ecological processes. We assessed dynamics in relative abundance and potential activities by sequencing the small sub-unit ribosomal RNA gene (rRNA gene) and rRNA molecules (rRNA) of Bacteria, Archaea, and Eukaryota once to twice daily between March 2014 and May 2014 from the surface ocean off Catalina Island, California. Typically Ostreococcus, Braarudosphaera, Teleaulax, and Synechococcus dominated phytoplankton sequences (including chloroplasts) while SAR11, Sulfitobacter, and Fluviicola dominated non-phytoplankton Bacteria and Archaea...
June 13, 2018: ISME Journal
Sean M Kearney, Sean M Gibbons, Mathilde Poyet, Thomas Gurry, Kevin Bullock, Jessica R Allegretti, Clary B Clish, Eric J Alm
Endospore-formers in the human microbiota are well adapted for host-to-host transmission, and an emerging consensus points to their role in determining health and disease states in the gut. The human gut, more than any other environment, encourages the maintenance of endospore formation, with recent culture-based work suggesting that over 50% of genera in the microbiome carry genes attributed to this trait. However, there has been limited work on the ecological role of endospores and other stress-resistant cellular states in the human gut...
June 13, 2018: ISME Journal
Yuanyuan Xue, Huihuang Chen, Jun R Yang, Min Liu, Bangqin Huang, Jun Yang
Plankton communities normally consist of few abundant and many rare species, yet little is known about the ecological role of rare planktonic eukaryotes. Here we used a 18S ribosomal DNA sequencing approach to investigate the dynamics of rare planktonic eukaryotes, and to explore the co-occurrence patterns of abundant and rare eukaryotic plankton in a subtropical reservoir following a cyanobacterial bloom event. Our results showed that the bloom event significantly altered the eukaryotic plankton community composition and rare plankton diversity without affecting the diversity of abundant plankton...
June 13, 2018: ISME Journal
Sam Abraham, Roy N Kirkwood, Tanya Laird, Sugiyono Saputra, Tahlia Mitchell, Mohinder Singh, Benjamin Linn, Rebecca J Abraham, Stanley Pang, David M Gordon, Darren J Trott, Mark O'Dea
This study investigated the ecology, epidemiology and plasmid characteristics of extended-spectrum cephalosporin (ESC)-resistant E. coli in healthy pigs over a period of 4 years (2013-2016) following the withdrawal of ESCs. High carriage rates of ESC-resistant E. coli were demonstrated in 2013 (86.6%) and 2014 (83.3%), compared to 2015 (22%) and 2016 (8.5%). ESC resistance identified among E. coli isolates was attributed to the carriage of an IncI1 ST-3 plasmid (pCTXM1-MU2) encoding blaCTXM-1 . Genomic characterisation of selected E...
June 13, 2018: ISME Journal
Eric L Miller, Morten Kjos, Monica I Abrudan, Ian S Roberts, Jan-Willem Veening, Daniel E Rozen
Quorum sensing (QS), where bacteria secrete and respond to chemical signals to coordinate population-wide behaviors, has revealed that bacteria are highly social. Here, we investigate how diversity in QS signals and receptors can modify social interactions controlled by the QS system regulating bacteriocin secretion in Streptococcus pneumoniae, encoded by the blp operon (bacteriocin-like peptide). Analysis of 4096 pneumococcal genomes detected nine blp QS signals (BlpC) and five QS receptor groups (BlpH). Imperfect concordance between signals and receptors suggested widespread social interactions between cells, specifically eavesdropping (where cells respond to signals that they do not produce) and crosstalk (where cells produce signals that non-clones detect)...
June 13, 2018: ISME Journal
Merlin Sheldrake, Nicholas P Rosenstock, Scott Mangan, Daniel Revillini, Emma J Sayer, Pål Axel Olsson, Erik Verbruggen, Edmund V J Tanner, Benjamin L Turner, S Joseph Wright
Improved understanding of the nutritional ecology of arbuscular mycorrhizal (AM) fungi is important in understanding how tropical forests maintain high productivity on low-fertility soils. Relatively little is known about how AM fungi will respond to changes in nutrient inputs in tropical forests, which hampers our ability to assess how forest productivity will be influenced by anthropogenic change. Here we assessed the influence of long-term inorganic and organic nutrient additions and nutrient depletion on AM fungi, using two adjacent experiments in a lowland tropical forest in Panama...
June 13, 2018: ISME Journal
Dušan Veličković, Beverly J Agtuca, Sylwia A Stopka, Akos Vertes, David W Koppenaal, Ljiljana Paša-Tolić, Gary Stacey, Christopher R Anderton
In this study, the three-dimensional spatial distributions of a number of metabolites involved in regulating symbiosis and biological nitrogen fixation (BNF) within soybean root nodules were revealed using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). While many metabolites exhibited distinct spatial compartmentalization, some metabolites were asymmetrically distributed throughout the nodule (e.g., S-adenosylmethionine). These results establish a more complex metabolic view of plant-bacteria symbiosis (and BNF) within soybean nodules than previously hypothesized...
June 13, 2018: ISME Journal
Lin Zhang, Gu Feng, Stéphane Declerck
Cooperation is a prevalent phenomenon in nature and how it originates and maintains is a fundamental question in ecology. Many efforts have been made to understand cooperation between individuals in the same species, while the mechanisms enabling cooperation between different species are less understood. Here, we investigated under strict in vitro culture conditions if the exchange of carbon and phosphorus is pivotal to the cooperation between the arbuscular mycorrhizal fungus (AMF) Rhizophagus irregularis and the phosphate solubilizing bacterium (PSB) Rahnella aquatilis...
June 13, 2018: ISME Journal
Maitreyi Nagarkar, Peter D Countway, Yeong Du Yoo, Emy Daniels, Nicole J Poulton, Brian Palenik
High-throughput sequencing of ocean biomes has revealed vast eukaryotic microbial diversity, a significant proportion of which remains uncharacterized. Here we use a temporal approach to understanding eukaryotic diversity at the Scripps Pier, La Jolla, California, USA, via high-throughput amplicon sequencing of the 18S rRNA gene, the abundances of both Synechococcus and Synechococcus grazers, and traditional oceanographic parameters. We also exploit our ability to track operational taxonomic units (OTUs) temporally to evaluate the ability of 18S sequence-based OTU assignments to meaningfully reflect ecological dynamics...
June 13, 2018: ISME Journal
Majda Dzidic, Maria C Collado, Thomas Abrahamsson, Alejandro Artacho, Malin Stensson, Maria C Jenmalm, Alex Mira
Information on how the oral microbiome develops during early childhood and how external factors influence this ecological process is scarce. We used high-throughput sequencing to characterize bacterial composition in saliva samples collected at 3, 6, 12, 24 months and 7 years of age in 90 longitudinally followed children, for whom clinical, dietary and health data were collected. Bacterial composition patterns changed through time, starting with "early colonizers", including Streptococcus and Veillonella; other bacterial genera such as Neisseria settled after 1 or 2 years of age...
June 13, 2018: ISME Journal
Bosheng Chen, Kaiqian Du, Chao Sun, Arunprasanna Vimalanathan, Xili Liang, Yong Li, Baohong Wang, Xingmeng Lu, Lanjuan Li, Yongqi Shao
Bombyx mori, the domesticated silkworm, is of great importance as a silk producer and as a powerful experimental model for the basic and applied research. Similar to other animals, abundant microorganisms live inside the silkworm gut; however, surprisingly, the microbiota of this model insect has not been well characterized to date. Here, we comprehensively characterized the gut microbiota of the domesticated silkworm and its wild relatives. Comparative analyses with the mulberry-feeding moths Acronicta major and Diaphania pyloalis revealed a highly diverse but distinctive silkworm gut microbiota despite thousands of years of domestication, and stage-specific signatures in both total (DNA-based) and active (RNA-based) bacterial populations, dominated by the phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes...
June 12, 2018: ISME Journal
Sean A Crowe, Raymond P Cox, CarriAyne Jones, David A Fowle, J F Santibañez-Bustos, O Ulloa, Donald E Canfield
Here we present ecophysiological studies of the anaerobic sulfide oxidizers considered critical to cryptic sulfur cycling in oceanic oxygen minimum zones (OMZs). We find that HS- oxidation rates by microorganisms in the Chilean OMZ offshore from Dichato are sufficiently rapid (18 nM h-1 ), even at HS- concentrations well below 100 nM, to oxidize all sulfide produced during sulfate reduction in OMZs. Even at 100 nM, HS- is well below published half-saturation concentrations and we conclude that the sulfide-oxidizing bacteria in OMZs (likely the SUP05/ARTIC96BD lineage of the gammaproteobacteria) have high-affinity (>105  g-1 wet cells h-1 ) sulfur uptake systems...
June 8, 2018: ISME Journal
John Davison, Mari Moora, Maarja Öpik, Leho Ainsaar, Marc Ducousso, Inga Hiiesalu, Teele Jairus, Nancy Johnson, Philippe Jourand, Rein Kalamees, Kadri Koorem, Jean-Yves Meyer, Kersti Püssa, Ülle Reier, Meelis Pärtel, Marina Semchenko, Anna Traveset, Martti Vasar, Martin Zobel
Island biogeography theory is one of the most influential paradigms in ecology. That island characteristics, including remoteness, can profoundly modulate biological diversity has been borne out by studies of animals and plants. By contrast, the processes influencing microbial diversity in island systems remain largely undetermined. We sequenced arbuscular mycorrhizal (AM) fungal DNA from plant roots collected on 13 islands worldwide and compared AM fungal diversity on islands with existing data from mainland sites...
June 8, 2018: ISME Journal
Liping Hao, Simon Jon McIlroy, Rasmus Hansen Kirkegaard, Søren Michael Karst, Warnakulasuriya Eustace Yrosh Fernando, Hüsnü Aslan, Rikke Louise Meyer, Mads Albertsen, Per Halkjær Nielsen, Morten Simonsen Dueholm
Members of the candidate phylum Acetothermia are globally distributed and detected in various habitats. However, little is known about their physiology and ecological importance. In this study, an operational taxonomic unit belonging to Acetothermia was detected at high abundance in four full-scale anaerobic digesters by 16S rRNA gene amplicon sequencing. The first closed genome from this phylum was obtained by differential coverage binning of metagenomes and scaffolding with long nanopore reads. Genome annotation and metabolic reconstruction suggested an anaerobic chemoheterotrophic lifestyle in which the bacterium obtains energy and carbon via fermentation of peptides, amino acids, and simple sugars to acetate, formate, and hydrogen...
June 8, 2018: ISME Journal
Ryan Guillemette, Ryo Kaneko, Jessica Blanton, Jasmine Tan, Matthias Witt, Samantha Hamilton, Eric E Allen, Mónica Medina, Koji Hamasaki, Boris P Koch, Farooq Azam
Coral reef ecosystems are highly sensitive to microbial activities that result from dissolved organic matter (DOM) enrichment of their surrounding seawater. However, the response to particulate organic matter (POM) enrichment is less studied. In a microcosm experiment, we tested the response of bacterioplankton to a pulse of POM from the mass-spawning of Orbicella franksi coral off the Caribbean coast of Panama. Particulate organic carbon (POC), a proxy measurement for POM, increased by 40-fold in seawater samples collected during spawning; 68% degraded within 66 h...
June 8, 2018: ISME Journal
Erica Sterkenburg, Karina E Clemmensen, Alf Ekblad, Roger D Finlay, Björn D Lindahl
Symbiotic ectomycorrhizal fungi have received increasing attention as regulators of below-ground organic matter storage. They are proposed to promote organic matter accumulation by suppressing saprotrophs, but have also been suggested to play an active role in decomposition themselves. Here we show that exclusion of tree roots and associated ectomycorrhizal fungi in a boreal forest increased decomposition of surface litter by 11% by alleviating nitrogen limitation of saprotrophs-a "Gadgil effect"...
June 7, 2018: ISME Journal
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