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ISME Journal

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https://www.readbyqxmd.com/read/28534880/a-tale-of-two-risks-smoking-diabetes-and-the-subgingival-microbiome
#1
Sukirth M Ganesan, Vinayak Joshi, Megan Fellows, Shareef M Dabdoub, Haikady N Nagaraja, Benjamin O'Donnell, Neeta Rohit Deshpande, Purnima S Kumar
Although smoking and diabetes have been established as the only two risk factors for periodontitis, their individual and synergistic impacts on the periodontal microbiome are not well studied. The present investigation analyzed 2.7 million 16S sequences from 175 non-smoking normoglycemic individuals (controls), smokers, diabetics and diabetic smokers with periodontitis as well as periodontally healthy controls, smokers and diabetics to assess subgingival bacterial biodiversity and co-occurrence patterns. The microbial signatures of periodontally healthy smokers, but not diabetics, were highly aligned with the disease-associated microbiomes of their respective cohorts...
May 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28534879/epibionts-dominate-metabolic-functional-potential-of-trichodesmium-colonies-from-the-oligotrophic-ocean
#2
Kyle R Frischkorn, Mónica Rouco, Benjamin A S Van Mooy, Sonya T Dyhrman
Trichodesmium is a genus of marine diazotrophic colonial cyanobacteria that exerts a profound influence on global biogeochemistry, by injecting 'new' nitrogen into the low nutrient systems where it occurs. Colonies of Trichodesmium ubiquitously contain a diverse assemblage of epibiotic microorganisms, constituting a microbiome on the Trichodesmium host. Metagenome sequences from Trichodesmium colonies were analyzed along a resource gradient in the western North Atlantic to examine microbiome community structure, functional diversity and metabolic contributions to the holobiont...
May 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28534878/successive-range-expansion-promotes-diversity-and-accelerates-evolution-in-spatially-structured-microbial-populations
#3
Felix Goldschmidt, Roland R Regoes, David R Johnson
Successive range expansions occur within all domains of life, where one population expands first (primary expansion) and one or more secondary populations then follow (secondary expansion). In general, genetic drift reduces diversity during range expansion. However, it is not clear whether the same effect applies during successive range expansion, mainly because the secondary population must expand into space occupied by the primary population. Here we used an experimental microbial model system to show that, in contrast to primary range expansion, successive range expansion promotes local population diversity...
May 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28534877/light-enhances-the-growth-rates-of-natural-populations-of-aerobic-anoxygenic-phototrophic-bacteria
#4
Isabel Ferrera, Olga Sánchez, Eva Kolářová, Michal Koblížek, Josep M Gasol
Aerobic anoxygenic phototrophic (AAP) bacteria are microorganisms that can harvest light energy using bacteriochlorophyll a to supplement their predominantly organotrophic metabolism. Growth enhancement by light has repeatedly been demonstrated in laboratory experiments with AAP isolates. However, the ecological advantage of light utilization is unclear, as it has never been proven in the natural environment. Here, we conducted manipulation experiments in the NW Mediterranean and found that AAP bacteria display high growth rates which are controlled to a large extent by intense grazing pressure and phosphorous availability...
May 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28534876/alpine-soil-carbon-is-vulnerable-to-rapid-microbial-decomposition-under-climate-cooling
#5
Linwei Wu, Yunfeng Yang, Shiping Wang, Haowei Yue, Qiaoyan Lin, Yigang Hu, Zhili He, Joy D Van Nostrand, Lauren Hale, Xiangzhen Li, Jack A Gilbert, Jizhong Zhou
As climate cooling is increasingly regarded as important natural variability of long-term global warming trends, there is a resurging interest in understanding its impact on biodiversity and ecosystem functioning. Here, we report a soil transplant experiment from lower to higher elevations in a Tibetan alpine grassland to simulate the impact of cooling on ecosystem community structure and function. Three years of cooling resulted in reduced plant productivity and microbial functional potential (for example, carbon respiration and nutrient cycling)...
May 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28524871/in-situ-light-responses-of-the-proteorhodopsin-bearing-antarctic-sea-ice-bacterium-psychroflexus-torques
#6
David J Burr, Andrew Martin, Elizabeth W Maas, Ken G Ryan
Proteorhodopsin (PR) is a wide-spread protein found in many marine prokaryotes. PR allows for the potential conversion of solar energy to ATP, possibly assisting in cellular growth and survival during periods of high environmental stress. PR utilises either blue or green light through a single amino acid substitution. We incubated the PR-bearing bacterium Psychroflexus torquis 50 cm deep within Antarctic sea ice for 13 days, exposing cultures to diurnal fluctuations in light and temperature. Enhanced growth occurred most prominently in cultures incubated under irradiance levels of ∼50 μmol photons m(-2) s(-1), suggesting PR provides a strong selective advantage...
May 19, 2017: ISME Journal
https://www.readbyqxmd.com/read/28524870/autotrophic-and-heterotrophic-acquisition-of-carbon-and-nitrogen-by-a-mixotrophic-chrysophyte-established-through-stable-isotope-analysis
#7
Ramon Terrado, Alexis L Pasulka, Alle A-Y Lie, Victoria J Orphan, Karla B Heidelberg, David A Caron
Collectively, phagotrophic algae (mixotrophs) form a functional continuum of nutritional modes between autotrophy and heterotrophy, but the specific physiological benefits of mixotrophic nutrition differ among taxa. Ochromonas spp. are ubiquitous chrysophytes that exhibit high nutritional flexibility, although most species generally fall towards the heterotrophic end of the mixotrophy spectrum. We assessed the sources of carbon and nitrogen in Ochromonas sp. strain BG-1 growing mixotrophically via short-term stable isotope probing...
May 19, 2017: ISME Journal
https://www.readbyqxmd.com/read/28524869/characterising-and-predicting-cyanobacterial-blooms-in-an-8-year-amplicon-sequencing-time-course
#8
Nicolas Tromas, Nathalie Fortin, Larbi Bedrani, Yves Terrat, Pedro Cardoso, David Bird, Charles W Greer, B Jesse Shapiro
Cyanobacterial blooms occur in lakes worldwide, producing toxins that pose a serious public health threat. Eutrophication caused by human activities and warmer temperatures both contribute to blooms, but it is still difficult to predict precisely when and where blooms will occur. One reason that prediction is so difficult is that blooms can be caused by different species or genera of cyanobacteria, which may interact with other bacteria and respond to a variety of environmental cues. Here we used a deep 16S amplicon sequencing approach to profile the bacterial community in eutrophic Lake Champlain over time, to characterise the composition and repeatability of cyanobacterial blooms, and to determine the potential for blooms to be predicted based on time course sequence data...
May 19, 2017: ISME Journal
https://www.readbyqxmd.com/read/28524868/diabetes-associated-microbiota-in-fa-fa-rats-is-modified-by-roux-en-y-gastric-bypass
#9
Tulika Arora, Florian Seyfried, Neil G Docherty, Valentina Tremaroli, Carel W le Roux, Rosie Perkins, Fredrik Bäckhed
Roux-en-Y gastric bypass (RYGB) and duodenal jejunal bypass (DJB), two different forms of bariatric surgery, are associated with improved glucose tolerance, but it is not clear whether the gut microbiota contributes to this effect. Here we used fa/fa rats as a model of impaired glucose tolerance to investigate whether (i) the microbiota varies between fa/fa and nondiabetic fa/+ rats; (ii) the microbiota of fa/fa rats is affected by RYGB and/or DJB; and (iii) surgically induced microbiota alterations contribute to glucose metabolism...
May 19, 2017: ISME Journal
https://www.readbyqxmd.com/read/28524867/fundamental-differences-in-diversity-and-genomic-population-structure-between-atlantic-and-pacific-prochlorococcus
#10
Nadav Kashtan, Sara E Roggensack, Jessie W Berta-Thompson, Maor Grinberg, Ramunas Stepanauskas, Sallie W Chisholm
The Atlantic and Pacific Oceans represent different biogeochemical regimes in which the abundant marine cyanobacterium Prochlorococcus thrives. We have shown that Prochlorococcus populations in the Atlantic are composed of hundreds of genomically, and likely ecologically, distinct coexisting subpopulations with distinct genomic backbones. Here we ask if differences in the ecology and selection pressures between the Atlantic and Pacific are reflected in the diversity and genomic composition of their indigenous Prochlorococcus populations...
May 19, 2017: ISME Journal
https://www.readbyqxmd.com/read/28524866/succession-in-the-petroleum-reservoir-microbiome-through-an-oil-field-production-lifecycle
#11
Adrien Vigneron, Eric B Alsop, Bartholomeus P Lomans, Nikos C Kyrpides, Ian M Head, Nicolas Tsesmetzis
Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system...
May 19, 2017: ISME Journal
https://www.readbyqxmd.com/read/28509910/convergence-of-gut-microbiotas-in-the-adaptive-radiations-of-african-cichlid-fishes
#12
Laura Baldo, Joan Lluís Pretus, Joan Lluís Riera, Zuzana Musilova, Arnold Roger Bitja Nyom, Walter Salzburger
Ecoevolutionary dynamics of the gut microbiota at the macroscale level, that is, in across-species comparisons, are largely driven by ecological variables and host genotype. The repeated explosive radiations of African cichlid fishes in distinct lakes, following a dietary diversification in a context of reduced genetic diversity, provide a natural setup to explore convergence, divergence and repeatability in patterns of microbiota dynamics as a function of the host diet, phylogeny and environment. Here we characterized by 16S rRNA amplicon sequencing the gut microbiota of 29 cichlid species from two distinct lakes/radiations (Tanganyika and Barombi Mbo) and across a broad dietary and phylogenetic range...
May 16, 2017: ISME Journal
https://www.readbyqxmd.com/read/28509909/experimental-evolution-and-the-dynamics-of-adaptation-and-genome-evolution-in-microbial-populations
#13
Richard E Lenski
Evolution is an on-going process, and it can be studied experimentally in organisms with rapid generations. My team has maintained 12 populations of Escherichia coli in a simple laboratory environment for >25 years and 60 000 generations. We have quantified the dynamics of adaptation by natural selection, seen some of the populations diverge into stably coexisting ecotypes, described changes in the bacteria's mutation rate, observed the new ability to exploit a previously untapped carbon source, characterized the dynamics of genome evolution and used parallel evolution to identify the genetic targets of selection...
May 16, 2017: ISME Journal
https://www.readbyqxmd.com/read/28509908/microbial-contributions-to-the-persistence-of-coral-reefs
#14
Nicole S Webster, Thorsten B H Reusch
On contemplating the adaptive capacity of reef organisms to a rapidly changing environment, the microbiome offers significant and greatly unrecognised potential. Microbial symbionts contribute to the physiology, development, immunity and behaviour of their hosts, and can respond very rapidly to changing environmental conditions, providing a powerful mechanism for acclimatisation and also possibly rapid evolution of coral reef holobionts. Environmentally acquired fluctuations in the microbiome can have significant functional consequences for the holobiont phenotype upon which selection can act...
May 16, 2017: ISME Journal
https://www.readbyqxmd.com/read/28498373/genomic-exploration-of-individual-giant-ocean-viruses
#15
William H Wilson, Ilana C Gilg, Mohammad Moniruzzaman, Erin K Field, Sergey Koren, Gary R LeCleir, Joaquín Martínez Martínez, Nicole J Poulton, Brandon K Swan, Ramunas Stepanauskas, Steven W Wilhelm
Viruses are major pathogens in all biological systems. Virus propagation and downstream analysis remains a challenge, particularly in the ocean where the majority of their microbial hosts remain recalcitrant to current culturing techniques. We used a cultivation-independent approach to isolate and sequence individual viruses. The protocol uses high-speed fluorescence-activated virus sorting flow cytometry, multiple displacement amplification (MDA), and downstream genomic sequencing. We focused on 'giant viruses' that are readily distinguishable by flow cytometry...
May 12, 2017: ISME Journal
https://www.readbyqxmd.com/read/28498372/comparative-transcriptomics-analyses-reveal-the-conservation-of-an-ancestral-infectious-strategy-in-two-bacteriophage-genera
#16
Bob G Blasdel, Anne Chevallereau, Marc Monot, Rob Lavigne, Laurent Debarbieux
Although the evolution of tailed bacteriophages has increasingly been better understood through comparisons of their DNA sequences, the functional consequences of this evolution on phage infectious strategies have remained unresolved. In this study, we comprehensively compared the transcriptional strategies of two related myoviruses, PAK_P3 and PAK_P4, infecting the same Pseudomonas aeruginosa host strain. Outside of the conservation of their structural clusters, their highly syntenic genomes display only limited DNA similarity...
May 12, 2017: ISME Journal
https://www.readbyqxmd.com/read/28475180/multi-stability-and-the-origin-of-microbial-community-types
#17
Didier Gonze, Leo Lahti, Jeroen Raes, Karoline Faust
The study of host-associated microbial community composition has suggested the presence of alternative community types. We discuss three mechanisms that could explain these observations. The most commonly invoked mechanism links community types to a response to environmental change; alternatively, community types were shown to emerge from interactions between members of local communities sampled from a metacommunity. Here, we emphasize multi-stability as a third mechanism, giving rise to different community types in the same environmental conditions...
May 5, 2017: ISME Journal
https://www.readbyqxmd.com/read/28463234/denitrifying-community-in-coastal-sediments-performs-aerobic-and-anaerobic-respiration-simultaneously
#18
Hannah K Marchant, Soeren Ahmerkamp, Gaute Lavik, Halina E Tegetmeyer, Jon Graf, Judith M Klatt, Moritz Holtappels, Eva Walpersdorf, Marcel M M Kuypers
Nitrogen (N) input to the coastal oceans has increased considerably because of anthropogenic activities, however, concurrent increases have not occurred in open oceans. It has been suggested that benthic denitrification in sandy coastal sediments is a sink for this N. Sandy sediments are dynamic permeable environments, where electron acceptor and donor concentrations fluctuate over short temporal and spatial scales. The response of denitrifiers to these fluctuations are largely unknown, although previous observations suggest they may denitrify under aerobic conditions...
May 2, 2017: ISME Journal
https://www.readbyqxmd.com/read/28452997/not-just-browsing-an-animal-that-grazes-phyllosphere-microbes-facilitates-community-heterogeneity
#19
Richard O'Rorke, Leah Tooman, Kapono Gaughen, Brenden S Holland, Anthony S Amend
Although grazers have long been recognized as top-down architects of plant communities, animal roles in determining microbial community composition have seldom been examined, particularly in aboveground systems. To determine the extent to which an animal can shape microbial communities, we conducted a controlled mesocosm study in situ to see if introducing mycophageous tree snails changed phyllosphere fungal community composition relative to matched control mesocosms. Fungal community composition and change was determined by Illumina sequencing of DNA collected from leaf surfaces before snails were introduced, daily for 3 days and weekly for 6 weeks thereafter...
April 28, 2017: ISME Journal
https://www.readbyqxmd.com/read/28440802/genetic-hurdles-limit-the-arms-race-between-prochlorococcus-and-the-t7-like-podoviruses-infecting-them
#20
Daniel A Schwartz, Debbie Lindell
Phages and hosts coexist in nature with a high degree of population diversity. This is often explained through coevolutionary models, such as the arms race or density-dependent fluctuating selection, which differ in assumptions regarding the emergence of phage mutants that overcome host resistance. Previously, resistance in the abundant marine cyanobacterium, Prochlorococcus, was found to occur frequently. However, little is known about the ability of phages to overcome this resistance. Here we report that, in some cases, T7-like cyanophage mutants emerge to infect resistant Prochlorococcus strains...
April 25, 2017: ISME Journal
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