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ISME Journal

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https://www.readbyqxmd.com/read/28106881/phylogenomics-of-rhodobacteraceae-reveals-evolutionary-adaptation-to-marine-and-non-marine-habitats
#1
Meinhard Simon, Carmen Scheuner, Jan P Meier-Kolthoff, Thorsten Brinkhoff, Irene Wagner-Döbler, Marcus Ulbrich, Hans-Peter Klenk, Dietmar Schomburg, Jörn Petersen, Markus Göker
Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic environments and are often mutualists of eukaryotes. As 'Roseobacter clade', these 'roseobacters' are assumed to be monophyletic, but non-marine Rhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling and its effect on phylogenetic stability, and investigated relationships between marine versus non-marine habitat, evolutionary origin and genomic adaptations...
January 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/28106880/discovery-of-anaerobic-lithoheterotrophic-haloarchaea-ubiquitous-in-hypersaline-habitats
#2
Dimitry Y Sorokin, Enzo Messina, Francesco Smedile, Pawel Roman, Jaap S Sinninghe Damsté, Sergio Ciordia, Maria Carmen Mena, Manuel Ferrer, Peter N Golyshin, Ilya V Kublanov, Nazar I Samarov, Stepan V Toshchakov, Violetta La Cono, Michail M Yakimov
Hypersaline anoxic habitats harbour numerous novel uncultured archaea whose metabolic and ecological roles remain to be elucidated. Until recently, it was believed that energy generation via dissimilatory reduction of sulfur compounds is not functional at salt saturation conditions. Recent discovery of the strictly anaerobic acetotrophic Halanaeroarchaeum compels to change both this assumption and the traditional view on haloarchaea as aerobic heterotrophs. Here we report on isolation and characterization of a novel group of strictly anaerobic lithoheterotrophic haloarchaea, which we propose to classify as a new genus Halodesulfurarchaeum...
January 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/28106879/bacterial-community-segmentation-facilitates-the-prediction-of-ecosystem-function-along-the-coast-of-the-western-antarctic-peninsula
#3
Jeff S Bowman, Linda A Amaral-Zettler, Jeremy J Rich, Catherine M Luria, Hugh W Ducklow
Bacterial community structure can be combined with observations of ecophysiological data to build predictive models of microbial ecosystem function. These models are useful for understanding how function might change in response to a changing environment. Here we use five spring-summer seasons of bacterial community structure and flow cytometry data from a productive coastal site along the western Antarctic Peninsula to construct models of bacterial production (BP), an ecosystem function that heterotrophic bacteria provide...
January 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/28094796/the-evolution-of-no-cost-resistance-at-sub-mic-concentrations-of-streptomycin-in-streptomyces-coelicolor
#4
Sanne Westhoff, Tim Marijn van Leeuwe, Omar Qachach, Zheren Zhang, Gilles Philippus van Wezel, Daniel Eric Rozen
At the high concentrations used in medicine, antibiotics exert strong selection on bacterial populations for the evolution of resistance. However, these lethal concentrations may not be representative of the concentrations bacteria face in soil, a recognition that has led to questions of the role of antibiotics in soil environments as well as the dynamics of resistance evolution during sublethal challenge. Here we examine the evolution of resistance to sub-minimal inhibitory concentrations (sub-MIC) of streptomycin in the filamentous soil bacterium Streptomyces coelicolor...
January 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/28094795/impacts-of-chemical-gradients-on-microbial-community-structure
#5
Jianwei Chen, Anna Hanke, Halina E Tegetmeyer, Ines Kattelmann, Ritin Sharma, Emmo Hamann, Theresa Hargesheimer, Beate Kraft, Sabine Lenk, Jeanine S Geelhoed, Robert L Hettich, Marc Strous
Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the 'redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat...
January 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/28085158/new-insights-into-marine-group-iii-euryarchaeota-from-dark-to-light
#6
Jose M Haro-Moreno, Francisco Rodriguez-Valera, Purificación López-García, David Moreira, Ana-Belen Martin-Cuadrado
Marine Euryarchaeota remain among the least understood major components of marine microbial communities. Marine group II Euryarchaeota (MG-II) are more abundant in surface waters (4-20% of the total prokaryotic community), whereas marine group III Euryarchaeota (MG-III) are generally considered low-abundance members of deep mesopelagic and bathypelagic communities. Using genome assembly from direct metagenome reads and metagenomic fosmid clones, we have identified six novel MG-III genome sequence bins from the photic zone (Epi1-6) and two novel bins from deep-sea samples (Bathy1-2)...
January 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/28085157/temperature-is-a-key-factor-in-micromonas-virus-interactions
#7
David Demory, Laure Arsenieff, Nathalie Simon, Christophe Six, Fabienne Rigaut-Jalabert, Dominique Marie, Pei Ge, Estelle Bigeard, Stéphan Jacquet, Antoine Sciandra, Olivier Bernard, Sophie Rabouille, Anne-Claire Baudoux
The genus Micromonas comprises phytoplankton that show among the widest latitudinal distributions on Earth, and members of this genus are recurrently infected by prasinoviruses in contrasted thermal ecosystems. In this study, we assessed how temperature influences the interplay between the main genetic clades of this prominent microalga and their viruses. The growth of three Micromonas strains (Mic-A, Mic-B, Mic-C) and the stability of their respective lytic viruses (MicV-A, MicV-B, MicV-C) were measured over a thermal range of 4-32...
January 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/28085156/divergent-functional-isoforms-drive-niche-specialisation-for-nutrient-acquisition-and-use-in-rumen-microbiome
#8
Francesco Rubino, Ciara Carberry, Sinéad M Waters, David Kenny, Matthew S McCabe, Christopher J Creevey
Many microbes in complex competitive environments share genes for acquiring and utilising nutrients, questioning whether niche specialisation exists and if so, how it is maintained. We investigated the genomic signatures of niche specialisation in the rumen microbiome, a highly competitive, anaerobic environment, with limited nutrient availability determined by the biomass consumed by the host. We generated individual metagenomic libraries from 14 cows fed an ad libitum diet of grass silage and calculated functional isoform diversity for each microbial gene identified...
January 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/28085155/shift-in-fungal-communities-and-associated-enzyme-activities-along-an-age-gradient-of-managed-pinus-sylvestris-stands
#9
Julia Kyaschenko, Karina E Clemmensen, Andreas Hagenbo, Erik Karltun, Björn D Lindahl
Forestry reshapes ecosystems with respect to tree age structure, soil properties and vegetation composition. These changes are likely to be paralleled by shifts in microbial community composition with potential feedbacks on ecosystem functioning. Here, we assessed fungal communities across a chronosequence of managed Pinus sylvestris stands and investigated correlations between taxonomic composition and extracellular enzyme activities. Not surprisingly, clear-cutting had a negative effect on ectomycorrhizal fungal abundance and diversity...
January 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/28085154/genomic-reconstruction-of-multiple-lineages-of-uncultured-benthic-archaea-suggests-distinct-biogeochemical-roles-and-ecological-niches
#10
C S Lazar, B J Baker, K W Seitz, A P Teske
Genomic bins belonging to multiple archaeal lineages were recovered from distinct redox regimes in sediments of the White Oak River estuary. The reconstructed archaeal genomes were identified as belonging to the rice cluster subgroups III and V (RC-III, RC-V), the Marine Benthic Group D (MBG-D), and a newly described archaeal class, the Theionarchaea. The metabolic capabilities of these uncultured archaea were inferred and indicated a common capability for extracellular protein degradation, supplemented by other pathways...
January 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/28072422/the-fitness-costs-and-trade-off-shapes-associated-with-the-exclusion-of-nine-antibiotics-by-ompf-porin-channels
#11
Katherine Phan, Thomas Ferenci
The trade-off relationship between antibiotic exclusion and nutrient access across the Gram-negative outer membrane is determined by structural constraints in porin channels. The precise nutritional cost of exclusion is unknown for different antibiotics, as are the shapes of the nutrition-susceptibility trade-off. Using a library of 10 engineered isogenic Escherichia coli strains with structural modifications of OmpF porin expressed at a constant level, susceptibilities were measured for nine antibiotics and the nutritional fitness costs estimated by competitions in chemostats...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28072421/on-the-ecosystemic-network-of-saliva-in-healthy-young-adults
#12
Egija Zaura, Bernd W Brandt, Andrei Prodan, Maarten Joost Teixeira de Mattos, Sultan Imangaliyev, Jolanda Kool, Mark J Buijs, Ferry Lpw Jagers, Nienke L Hennequin-Hoenderdos, Dagmar E Slot, Elena A Nicu, Maxim D Lagerweij, Marleen M Janus, Marcela M Fernandez-Gutierrez, Evgeni Levin, Bastiaan P Krom, Henk S Brand, Enno Ci Veerman, Michiel Kleerebezem, Bruno G Loos, G A van der Weijden, Wim Crielaard, Bart Jf Keijser
A dysbiotic state is believed to be a key factor in the onset of oral disease. Although oral diseases have been studied for decades, our understanding of oral health, the boundaries of a healthy oral ecosystem and ecological shift toward dysbiosis is still limited. Here, we present the ecobiological heterogeneity of the salivary ecosystem and relations between the salivary microbiome, salivary metabolome and host-related biochemical salivary parameters in 268 healthy adults after overnight fasting. Gender-specific differences in the microbiome and metabolome were observed and were associated with salivary pH and dietary protein intake...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28072420/where-less-may-be-more-how-the-rare-biosphere-pulls-ecosystems-strings
#13
Alexandre Jousset, Christina Bienhold, Antonis Chatzinotas, Laure Gallien, Angélique Gobet, Viola Kurm, Kirsten Küsel, Matthias C Rillig, Damian W Rivett, Joana F Salles, Marcel G A van der Heijden, Noha H Youssef, Xiaowei Zhang, Zhong Wei, W H Gera Hol
Rare species are increasingly recognized as crucial, yet vulnerable components of Earth's ecosystems. This is also true for microbial communities, which are typically composed of a high number of relatively rare species. Recent studies have demonstrated that rare species can have an over-proportional role in biogeochemical cycles and may be a hidden driver of microbiome function. In this review, we provide an ecological overview of the rare microbial biosphere, including causes of rarity and the impacts of rare species on ecosystem functioning...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28072419/an-acid-tolerant-ammonia-oxidizing-%C3%AE-proteobacterium-from-soil
#14
Masahito Hayatsu, Kanako Tago, Ikuo Uchiyama, Atsushi Toyoda, Yong Wang, Yumi Shimomura, Takashi Okubo, Futoshi Kurisu, Yuhei Hirono, Kunihiko Nonaka, Hiroko Akiyama, Takehiko Itoh, Hideto Takami
Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, occurs in a wide range of acidic soils. However, the ammonia-oxidizing bacteria (AOB) that have been isolated from soil to date are acid-sensitive. Here we report the isolation and characterization of an acid-adapted AOB from an acidic agricultural soil. The isolated AOB, strain TAO100, is classified within the Gammaproteobacteria based on phylogenetic characteristics. TAO100 can grow in the pH range of 5-7.5 and survive in highly acidic conditions until pH 2 by forming cell aggregates...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28072418/microbial-community-dynamics-in-inferno-crater-lake-a-thermally-fluctuating-geothermal-spring
#15
Laura Ward, Michael W Taylor, Jean F Power, Bradley J Scott, Ian R McDonald, Matthew B Stott
Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40-60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28060364/single-cell-transcriptomics-of-small-microbial-eukaryotes-limitations-and-potential
#16
Zhenfeng Liu, Sarah K Hu, Victoria Campbell, Avery O Tatters, Karla B Heidelberg, David A Caron
Single-cell transcriptomics is an emerging research tool that has huge untapped potential in the study of microbial eukaryotes. Its application has been tested in microbial eukaryotes 50 μm or larger, and it generated transcriptomes similar to those obtained from culture-based RNA-seq. However, microbial eukaryotes have a wide range of sizes and can be as small as 1 μm. Single-cell RNA-seq was tested in two smaller protists (8 and 15 μm). Transcript recovery rate was much lower and randomness in observed gene expression levels was much higher in single-cell transcriptomes than those derived from bulk cultures of cells...
January 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28060363/genomic-repertoire-of-the-woeseiaceae-jtb255-cosmopolitan-and-abundant-core-members-of-microbial-communities-in-marine-sediments
#17
Marc Mußmann, Petra Pjevac, Karen Krüger, Stefan Dyksma
To date, very little is known about the bacterial core community of marine sediments. Here we study the environmental distribution, abundance and ecogenomics of the gammaproteobacterial Woeseiaceae/JTB255 marine benthic group. A meta-analysis of published work shows that the Woeseiaceae/JTB255 are ubiquitous and consistently rank among the most abundant 16S rRNA gene sequences in diverse marine sediments. They account for up to 22% of bacterial amplicons and 6% of total cell counts in European and Australian coastal sediments...
January 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28060362/cheating-fosters-species-co-existence-in-well-mixed-bacterial-communities
#18
Anne Leinweber, R Fredrik Inglis, Rolf Kümmerli
Explaining the enormous biodiversity observed in bacterial communities is challenging because ecological theory predicts that competition between species occupying the same niche should lead to the exclusion of less competitive community members. Competitive exclusion should be particularly strong when species compete for a single limiting resource or live in unstructured habitats that offer no refuge for weaker competitors. Here, we describe the 'cheating effect', a form of intra-specific competition that can counterbalance between-species competition, thereby fostering biodiversity in unstructured habitats...
January 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28045459/faecalibacterium-prausnitzii-from-microbiology-to-diagnostics-and-prognostics
#19
Mireia Lopez-Siles, Sylvia H Duncan, L Jesús Garcia-Gil, Margarita Martinez-Medina
There is an increasing interest in Faecalibacterium prausnitzii, one of the most abundant bacterial species found in the gut, given its potentially important role in promoting gut health. Although some studies have phenotypically characterized strains of this species, it remains a challenge to determine which factors have a key role in maintaining the abundance of this bacterium in the gut. Besides, phylogenetic analysis has shown that at least two different F. prausnitzii phylogroups can be found within this species and their distribution is different between healthy subjects and patients with gut disorders...
January 3, 2017: ISME Journal
https://www.readbyqxmd.com/read/28045458/bacteria-isolated-from-lung-modulate-asthma-susceptibility-in-mice
#20
Aude Remot, Delphyne Descamps, Marie-Louise Noordine, Abdelhak Boukadiri, Elliot Mathieu, Véronique Robert, Sabine Riffault, Bart Lambrecht, Philippe Langella, Hamida Hammad, Muriel Thomas
Asthma is a chronic, non-curable, multifactorial disease with increasing incidence in industrial countries. This study evaluates the direct contribution of lung microbial components in allergic asthma in mice. Germ-Free and Specific-Pathogen-Free mice display similar susceptibilities to House Dust Mice-induced allergic asthma, indicating that the absence of bacteria confers no protection or increased risk to aeroallergens. In early life, allergic asthma changes the pattern of lung microbiota, and lung bacteria reciprocally modulate aeroallergen responsiveness...
January 3, 2017: ISME Journal
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