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ISME Journal

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https://www.readbyqxmd.com/read/29053151/highly-structured-prokaryote-communities-exist-within-the-skeleton-of-coral-colonies
#1
Vanessa R Marcelino, Madeleine Jh van Oppen, Heroen Verbruggen
Physiological performance, disease and bleaching prevalence are often patchy within individual coral colonies. These responses are largely influenced by coral-associated microbes, but how the coral microbiome changes over small spatial scales has never been quantified before. We performed a high-resolution quantification of the spatial scale of microbial species turnover (β-diversity) within skeletons of boulder-forming Porites corals. We found very strong prokaryotic species turnover across spatial scales ranging from 4 mm to 2 m within individual colonies, possibly resulting from dispersal limitation and microbial interactions...
October 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/29053150/dispersal-alters-bacterial-diversity-and-composition-in-a-natural-community
#2
Michaeline B N Albright, Jennifer B H Martiny
Dispersal is central to the evolution and maintenance of microbial diversity. Quantifying microbial dispersal and its role in shaping communities remains a challenge, however. Here, we manipulated a bacterial community's dispersal rate in a grassland ecosystem and test whether this altered diversity and composition. We constructed bags of two nylon mesh sizes that allowed more or less bacterial movement and filled them with an edible or inedible substrate, irradiated plant litter or nylon sheets. We measured changes in bacterial abundance (using flow cytometry) and composition (using 16S amplicon sequencing) in the bags weekly over 5 months...
October 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/29053149/recent-expansion-of-heat-activated-retrotransposons-in-the-coral-symbiont-symbiodinium-microadriaticum
#3
Jit Ern Chen, Guoxin Cui, Xin Wang, Yi Jin Liew, Manuel Aranda
Rising sea surface temperature is the main cause of global coral reef decline. Abnormally high temperatures trigger the breakdown of the symbiotic association between corals and their photosynthetic symbionts in the genus Symbiodinium. Higher genetic variation resulting from shorter generation times has previously been proposed to provide increased adaptability to Symbiodinium compared to the host. Retrotransposition is a significant source of genetic variation in eukaryotes and some transposable elements are specifically expressed under adverse environmental conditions...
October 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/29053148/stress-response-of-a-marine-ammonia-oxidizing-archaeon-informs-physiological-status-of-environmental-populations
#4
Wei Qin, Shady A Amin, Rachel A Lundeen, Katherine R Heal, Willm Martens-Habbena, Serdar Turkarslan, Hidetoshi Urakawa, Kyle C Costa, Erik L Hendrickson, Tony Wang, David Ac Beck, Sonia M Tiquia-Arashiro, Fred Taub, Andrew D Holmes, Neeraja Vajrala, Paul M Berube, Todd M Lowe, James W Moffett, Allan H Devol, Nitin S Baliga, Daniel J Arp, Luis A Sayavedra-Soto, Murray Hackett, E Virginia Armbrust, Anitra E Ingalls, David A Stahl
High representation by ammonia-oxidizing archaea (AOA) in marine systems is consistent with their high affinity for ammonia, efficient carbon fixation, and copper (Cu)-centric respiratory system. However, little is known about their response to nutrient stress. We therefore used global transcriptional and proteomic analyses to characterize the response of a model AOA, Nitrosopumilus maritimus SCM1, to ammonia starvation, Cu limitation and Cu excess. Most predicted protein-coding genes were transcribed in exponentially growing cells, and of ~74% detected in the proteome, ~6% were modified by N-terminal acetylation...
October 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/29053147/dispersal-timing-determines-the-importance-of-priority-effects-in-bacterial-communities
#5
Pavel Svoboda, Eva S Lindström, Omneya Ahmed Osman, Silke Langenheder
The order and timing of species arrival during community assembly can have long term effects on community structure due to priority effects. The importance of such processes in complex bacterial communities where dispersal involves mixing of entire communities is currently not known. Here we used a transplant experiment with two bacterioplankton communities of different origin (freshwater and brackish). Sterile medium of each origin was initially inoculated with a bacterial community of different ('alien') origin, followed by dispersal of the respective 'home' community at different time points after initial inoculation...
October 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/29053146/the-plant-circadian-clock-influences-rhizosphere-community-structure-and-function
#6
Charley J Hubbard, Marcus T Brock, Linda Ta van Diepen, Loïs Maignien, Brent E Ewers, Cynthia Weinig
Plants alter chemical and physical properties of soil, and thereby influence rhizosphere microbial community structure. The structure of microbial communities may in turn affect plant performance. Yet, outside of simple systems with pairwise interacting partners, the plant genetic pathways that influence microbial community structure remain largely unknown, as are the performance feedbacks of microbial communities selected by the host plant genotype. We investigated the role of the plant circadian clock in shaping rhizosphere community structure and function...
October 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/29053145/geometagenomics-illuminates-the-impact-of-agriculture-on-the-distribution-and-prevalence-of-plant-viruses-at-the-ecosystem-scale
#7
Pauline Bernardo, Tristan Charles-Dominique, Mohamed Barakat, Philippe Ortet, Emmanuel Fernandez, Denis Filloux, Penelope Hartnady, Tony A Rebelo, Stephen R Cousins, François Mesleard, Damien Cohez, Nicole Yavercovski, Arvind Varsani, Gordon W Harkins, Michel Peterschmitt, Carolyn M Malmstrom, Darren P Martin, Philippe Roumagnac
Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plant-associated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France)...
October 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/29053144/uncultivated-microbes-in-need-of-their-own-nomenclature
#8
Aharon Oren, George M Garrity
No abstract text is available yet for this article.
October 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/29039844/soil-microbial-diversity-drives-the-priming-effect-along-climate-gradients-a-case-study-in-madagascar
#9
Kanto Razanamalala, Tantely Razafimbelo, Pierre-Alain Maron, Lionel Ranjard, Nicolas Chemidlin, Mélanie Lelièvre, Samuel Dequiedt, Volaniaina H Ramaroson, Claire Marsden, Thierry Becquer, Jean Trap, Eric Blanchart, Laetitia Bernard
The priming effect in soil is proposed to be generated by two distinct mechanisms: 'stoichiometric decomposition' and/or 'nutrient mining' theories. Each mechanism has its own dynamics, involves its own microbial actors, and targets different soil organic matter (SOM) pools. The present study aims to evaluate how climatic parameters drive the intensity of each priming effect generation mechanism via the modification of soil microbial and physicochemical properties. Soils were sampled in the center of Madagascar, along climatic gradients designed to distinguish temperature from rainfall effects...
October 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/29039843/acetoclastic-methanosaeta-are-dominant-methanogens-in-organic-rich-antarctic-marine-sediments
#10
Stephanie A Carr, Florence Schubotz, Robert B Dunbar, Christopher T Mills, Robert Dias, Roger E Summons, Kevin W Mandernack
Despite accounting for the majority of sedimentary methane, the physiology and relative abundance of subsurface methanogens remain poorly understood. We combined intact polar lipid and metagenome techniques to better constrain the presence and functions of methanogens within the highly reducing, organic-rich sediments of Antarctica's Adélie Basin. The assembly of metagenomic sequence data identified phylogenic and functional marker genes of methanogens and generated the first Methanosaeta sp. genome from a deep subsurface sedimentary environment...
October 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/29028006/polymorphism-of-antibiotic-inactivating-enzyme-driven-by-ecology-expands-the-environmental-resistome
#11
Dae-Wi Kim, Cung Nawl Thawng, Jung-Hye Choi, Kihyun Lee, Chang-Jun Cha
The environmental resistome has been recognized as the origin and reservoir of antibiotic resistance genes and considered to be dynamic and ever expanding. In this study, a targeted gene sequencing approach revealed that the polymorphic diversity of the aminoglycoside-inactivating enzyme AAC(6')-Ib was ecological niche-specific. AAC(6')-Ib-cr, previously known as a clinical variant, was prevalent in various soils and the intestines of chickens and humans, suggesting that this variant might not have arisen from adaptive mutations in the clinic but instead originated from the environment...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29028005/microbiome-and-infectivity-studies-reveal-complex-polyspecies-tree-disease-in-acute-oak-decline
#12
Sandra Denman, James Doonan, Emma Ransom-Jones, Martin Broberg, Sarah Plummer, Susan Kirk, Kelly Scarlett, Andrew R Griffiths, Maciej Kaczmarek, Jack Forster, Andrew Peace, Peter N Golyshin, Francis Hassard, Nathan Brown, John G Kenny, James E McDonald
Decline-diseases are complex and becoming increasingly problematic to tree health globally. Acute Oak Decline (AOD) is characterized by necrotic stem lesions and galleries of the bark-boring beetle, Agrilus biguttatus, and represents a serious threat to oak. Although multiple novel bacterial species and Agrilus galleries are associated with AOD lesions, the causative agent(s) are unknown. The AOD pathosystem therefore provides an ideal model for a systems-based research approach to address our hypothesis that AOD lesions are caused by a polymicrobial complex...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29028004/geobiological-feedbacks-and-the-evolution-of-thermoacidophiles
#13
Daniel R Colman, Saroj Poudel, Trinity L Hamilton, Jeff R Havig, Matthew J Selensky, Everett L Shock, Eric S Boyd
Oxygen-dependent microbial oxidation of sulfur compounds leads to the acidification of natural waters. How acidophiles and their acidic habitats evolved, however, is largely unknown. Using 16S rRNA gene abundance and composition data from 72 hot springs in Yellowstone National Park, Wyoming, we show that hyperacidic (pH<3.0) hydrothermal ecosystems are dominated by a limited number of archaeal lineages with an inferred ability to respire O2. Phylogenomic analyses of 584 existing archaeal genomes revealed that hyperacidophiles evolved independently multiple times within the Archaea, each coincident with the emergence of the ability to respire O2, and that these events likely occurred in the recent evolutionary past...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29028003/bacterial-secretion-of-d-arginine-controls-environmental-microbial-biodiversity
#14
Laura Alvarez, Alena Aliashkevich, Miguel A de Pedro, Felipe Cava
Bacteria face tough competition in polymicrobial communities. To persist in a specific niche, many species produce toxic extracellular effectors to interfere with the growth of nearby microbes. These effectors include the recently reported non-canonical D-amino acids (NCDAAs). In Vibrio cholerae, the causative agent of cholera, NCDAAs control cell wall integrity in stationary phase. Here, an analysis of the composition of the extracellular medium of V. cholerae revealed the unprecedented presence of D-Arg. Compared with other D-amino acids, D-Arg displayed higher potency and broader toxicity in terms of the number of bacterial species affected...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29028002/cyanophage-encoded-lipid-desaturases-oceanic-distribution-diversity-and-function
#15
Sheila Roitman, Ellen Hornung, José Flores-Uribe, Itai Sharon, Ivo Feussner, Oded Béjà
Cyanobacteria are among the most abundant photosynthetic organisms in the oceans; viruses infecting cyanobacteria (cyanophages) can alter cyanobacterial populations, and therefore affect the local food web and global biochemical cycles. These phages carry auxiliary metabolic genes (AMGs), which rewire various metabolic pathways in the infected host cell, resulting in increased phage fitness. Coping with stress resulting from photodamage appears to be a central necessity of cyanophages, yet the overall mechanism is poorly understood...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29028001/soil-protist-communities-form-a-dynamic-hub-in-the-soil-microbiome
#16
Wu Xiong, Alexandre Jousset, Sai Guo, Ida Karlsson, Qingyun Zhao, Huasong Wu, George A Kowalchuk, Qirong Shen, Rong Li, Stefan Geisen
Soil microbes are essential for soil fertility. However, most studies focus on bacterial and/or fungal communities, while the top-down drivers of this microbiome composition, protists, remain poorly understood. Here, we investigated how soil amendments affect protist communities and inferred potential interactions with bacteria and fungi. Specific fertilization treatments impacted both the structure and function of protist communities. Organic fertilizer amendment strongly reduced the relative abundance of plant pathogenic protists and increased bacterivorous and omnivorous protists...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29028000/influence-of-resistance-breeding-in-common-bean-on-rhizosphere-microbiome-composition-and-function
#17
Lucas William Mendes, Jos M Raaijmakers, Mattias de Hollander, Rodrigo Mendes, Siu Mui Tsai
The rhizosphere microbiome has a key role in plant growth and health, providing a first line of defense against root infections by soil-borne pathogens. Here, we investigated the composition and metabolic potential of the rhizobacterial community of different common bean (Phaseolus vulgaris) cultivars with variable levels of resistance to the fungal root pathogen Fusarium oxysporum (Fox). For the different bean cultivars grown in two soils with contrasting physicochemical properties and microbial diversity, rhizobacterial abundance was positively correlated with Fox resistance...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29027999/a-population-genomics-approach-shows-widespread-geographical-distribution-of-cryptic-genomic-forms-of-the-symbiotic-fungus-rhizophagus-irregularis
#18
Romain Savary, Frédéric G Masclaux, Tania Wyss, Germain Droh, Joaquim Cruz Corella, Ana Paula Machado, Joseph B Morton, Ian R Sanders
Arbuscular mycorrhizal fungi (AMF; phylum Gomeromycota) associate with plants forming one of the most successful microbe-plant associations. The fungi promote plant diversity and have a potentially important role in global agriculture. Plant growth depends on both inter- and intra-specific variation in AMF. It was recently reported that an unusually large number of AMF taxa have an intercontinental distribution, suggesting long-distance gene flow for many AMF species, facilitated by either long-distance natural dispersal mechanisms or human-assisted dispersal...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29027998/temporal-dynamics-of-uncultured-viruses-a-new-dimension-in-viral-diversity
#19
Ksenia Arkhipova, Timofey Skvortsov, John P Quinn, John W McGrath, Christopher Cr Allen, Bas E Dutilh, Yvonne McElarney, Leonid A Kulakov
Recent work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bacterial populations and environmental variables. We reconstructed 8950 complete and partial viral genomes, the majority of which were not persistent in the lake throughout the year, but instead continuously succeeded each other...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29027997/microdiversification-in-genome-streamlined-ubiquitous-freshwater-actinobacteria
#20
Stefan M Neuenschwander, Rohit Ghai, Jakob Pernthaler, Michaela M Salcher
Actinobacteria of the acI lineage are the most abundant microbes in freshwater systems, but there are so far no pure living cultures of these organisms, possibly because of metabolic dependencies on other microbes. This, in turn, has hampered an in-depth assessment of the genomic basis for their success in the environment. Here we present genomes from 16 axenic cultures of acI Actinobacteria. The isolates were not only of minute cell size, but also among the most streamlined free-living microbes, with extremely small genome sizes (1...
October 13, 2017: ISME Journal
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