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ISME Journal

Frédéric De Meyer, Bram Danneels, Tessa Acar, Rado Rasolomampianina, Mamy Tiana Rajaonah, Vololoniaina Jeannoda, Aurelien Carlier
Various plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves in what is commonly referred to as leaf nodule symbiosis. We describe here a highly specific symbiosis between a wild yam species from Madagascar, Dioscorea sansibarensis and bacteria of the species Orrella dioscoreae. Using whole-genome sequencing of plastids and bacteria from wild-collected samples, we show phylogenetic patterns consistent with a dominant vertical mode of transmission of the symbionts...
March 15, 2019: ISME Journal
Lanlan Cai, Bo B Jørgensen, Curtis A Suttle, Maoqiu He, Barry A Cragg, Nianzhi Jiao, Rui Zhang
Viruses are ubiquitous and cause significant mortality in marine bacterial and archaeal communities. Little is known about the role of viruses in the sub-seafloor biosphere, which hosts a large fraction of all microbes on Earth. We quantified and characterized viruses in sediments from the Baltic Sea. The results show that the Baltic Sea sub-seafloor biosphere harbors highly abundant viruses with densities up to 1.8 × 1010 viruses cm-3 . High potential viral production down to 37 meters below seafloor in ca...
March 15, 2019: ISME Journal
Liam P Shaw, Hassan Bassam, Chris P Barnes, A Sarah Walker, Nigel Klein, Francois Balloux
Treatment with antibiotics is one of the most extreme perturbations to the human microbiome. Even standard courses of antibiotics dramatically reduce the microbiome's diversity and can cause transitions to dysbiotic states. Conceptually, this is often described as a 'stability landscape': the microbiome sits in a landscape with multiple stable equilibria, and sufficiently strong perturbations can shift the microbiome from its normal equilibrium to another state. However, this picture is only qualitative and has not been incorporated in previous mathematical models of the effects of antibiotics...
March 15, 2019: ISME Journal
François Thomas, Erwan Corre, Aurélie Cébron
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. 13 C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in 13 C-SIP incubations compared to 12 C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil...
March 14, 2019: ISME Journal
Sherlynette Pérez Castro, Elsa E Cleland, Robert Wagner, Risha Al Sawad, David A Lipson
Significant gaps in our understanding of how global change drivers interact to affect the resistance and functioning of microbial communities hinders our ability to model ecosystem responses and feedbacks to co-occurring global stressors. Here, we investigated the effects of extreme drought and exotic plants, two of the most significant threats to Mediterranean-type ecosystems, on soil microbial community composition and carbon metabolic genes within a four-year field rainfall manipulation experiment. We combined measurements of bulk microbial and soil properties with high-throughput microbial community analyses to elucidate microbial responses and microbial-mediated alterations to carbon cycling...
March 14, 2019: ISME Journal
Zahra F Islam, Paul R F Cordero, Joanna Feng, Ya-Jou Chen, Sean K Bay, Thanavit Jirapanjawat, Roslyn M Gleadow, Carlo R Carere, Matthew B Stott, Eleonora Chiri, Chris Greening
Most aerobic bacteria exist in dormant states within natural environments. In these states, they endure adverse environmental conditions such as nutrient starvation by decreasing metabolic expenditure and using alternative energy sources. In this study, we investigated the energy sources that support persistence of two aerobic thermophilic strains of the environmentally widespread but understudied phylum Chloroflexi. A transcriptome study revealed that Thermomicrobium roseum (class Chloroflexia) extensively remodels its respiratory chain upon entry into stationary phase due to nutrient limitation...
March 14, 2019: ISME Journal
Dineshkumar Kandasamy, Jonathan Gershenzon, Martin N Andersson, Almuth Hammerbacher
Insects have mutualistic symbioses with a variety of microorganisms. However, the chemical signals that maintain these insect-microbe relationships are poorly known compared to those from insect-plant symbioses. The spruce bark beetle, Ips typographus, the most destructive forest pest in Europe, has a symbiotic relationship with several fungi that are believed to contribute to its successful invasion of Norway spruce. Here we tested the hypothesis that volatile organic compounds (VOCs) emitted from fungal symbionts could be cues for bark beetles to recognize and distinguish among members of its microbial community...
March 14, 2019: ISME Journal
Eria A Rebollar, Tiffany Bridges, Myra C Hughey, Daniel Medina, Lisa K Belden, Reid N Harris
Chytridiomycosis, caused by the pathogen Batrachochytrium dendrobatidis (Bd), has led to population declines and extinctions of frog species around the world. While it is known that symbiotic skin bacteria can play a protective role against pathogens, it is not known how these defensive bacteria are integrated into the bacterial community on amphibian skin. In this study, we used 16S rRNA gene amplicon sequencing, culturing and Bd inhibition bioassays to characterize the communities of skin bacteria on three Neotropical frog species that persist in a Bd-infected area in Panama and determined the abundance and integration of anti-Bd bacteria into the community...
March 13, 2019: ISME Journal
Elizabeth M Fones, Daniel R Colman, Emily A Kraus, Daniel B Nothaft, Saroj Poudel, Kaitlin R Rempfert, John R Spear, Alexis S Templeton, Eric S Boyd
Hydration of ultramafic rock during the geologic process of serpentinization can generate reduced substrates that microorganisms may use to fuel their carbon and energy metabolisms. However, serpentinizing environments also place multiple constraints on microbial life by generating highly reduced hyperalkaline waters that are limited in dissolved inorganic carbon. To better understand how microbial life persists under these conditions, we performed geochemical measurements on waters from a serpentinizing environment and subjected planktonic microbial cells to metagenomic and physiological analyses...
March 12, 2019: ISME Journal
Amy R Smith, Brandon Kieft, Ryan Mueller, Martin R Fisk, Olivia U Mason, Radu Popa, Frederick S Colwell
Earth's largest aquifer ecosystem resides in igneous oceanic crust, where chemosynthesis and water-rock reactions provide the carbon and energy that support an active deep biosphere. The Calvin Cycle is the predominant carbon fixation pathway in cool, oxic, crust; however, the energy and carbon metabolisms in the deep thermal basaltic aquifer are poorly understood. Anaerobic carbon fixation pathways such as the Wood-Ljungdahl pathway, which uses hydrogen (H2 ) and CO2 , may be common in thermal aquifers since water-rock reactions can produce H2 in hydrothermal environments and bicarbonate is abundant in seawater...
March 12, 2019: ISME Journal
Samiran Banerjee, Florian Walder, Lucie Büchi, Marcel Meyer, Alain Y Held, Andreas Gattinger, Thomas Keller, Raphael Charles, Marcel G A van der Heijden
Root-associated microbes play a key role in plant performance and productivity, making them important players in agroecosystems. So far, very few studies have assessed the impact of different farming systems on the root microbiota and it is still unclear whether agricultural intensification influences the structure and complexity of microbial communities. We investigated the impact of conventional, no-till, and organic farming on wheat root fungal communities using PacBio SMRT sequencing on samples collected from 60 farmlands in Switzerland...
March 8, 2019: ISME Journal
Lucy C Stewart, Christopher K Algar, Caroline S Fortunato, Benjamin I Larson, Joseph J Vallino, Julie A Huber, David A Butterfield, James F Holden
The size and biogeochemical impact of the subseafloor biosphere in oceanic crust remain largely unknown due to sampling limitations. We used reactive transport modeling to estimate the size of the subseafloor methanogen population, volume of crust occupied, fluid residence time, and nature of the subsurface mixing zone for two low-temperature hydrothermal vents at Axial Seamount. Monod CH4 production kinetics based on chemostat H2 availability and batch-culture Arrhenius growth kinetics for the hyperthermophile Methanocaldococcus jannaschii and thermophile Methanothermococcus thermolithotrophicus were used to develop and parameterize a reactive transport model, which was constrained by field measurements of H2 , CH4 , and metagenome methanogen concentration estimates in 20-40 °C hydrothermal fluids...
March 6, 2019: ISME Journal
Dianming Wu, Marcus A Horn, Thomas Behrendt, Stefan Müller, Jingsong Li, Jeff A Cole, Baohua Xie, Xiaotang Ju, Guo Li, Michael Ermel, Robert Oswald, Janine Fröhlich-Nowoisky, Peter Hoor, Chunsheng Hu, Min Liu, Meinrat O Andreae, Ulrich Pöschl, Yafang Cheng, Hang Su, Ivonne Trebs, Bettina Weber, Matthias Sörgel
Nitrous acid (HONO) is a precursor of the hydroxyl radical (OH), a key oxidant in the degradation of most air pollutants. Field measurements indicate a large unknown source of HONO during the day time. Release of nitrous acid (HONO) from soil has been suggested as a major source of atmospheric HONO. We hypothesize that nitrite produced by biological nitrate reduction in oxygen-limited microzones in wet soils is a source of such HONO. Indeed, we found that various contrasting soil samples emitted HONO at high water-holding capacity (75-140%), demonstrating this to be a widespread phenomenon...
March 4, 2019: ISME Journal
David Scheidweiler, Hannes Peter, Paraskevi Pramateftaki, Pietro de Anna, Tom J Battin
Biofilms regulate critical processes in porous ecosystems. However, the biophysical underpinnings of the ecological success of these biofilms are poorly understood. Combining experiments with fluidic devices, sequencing and modeling, we reveal that architectural plasticity enhances space exploitation by multispecies biofilms in porous environments. Biofilms consistently differentiated into an annular base biofilm coating the grains and into streamers protruding from the grains into the pore space. Although different flow-related processes governed the differentiation of these architectures, both BB and streamers were composed of similar bacterial assemblages...
March 4, 2019: ISME Journal
Annemieke Smet, Koji Yahara, Mirko Rossi, Alfred Tay, Steffen Backert, Armin Ensser, James G Fox, Bram Flahou, Richard Ducatelle, Freddy Haesebrouck, Jukka Corander
The original version of this Article contained an error in the presentation of the author Armin Ensser, which was incorrectly given as Ensser Armin. The correct author list is as follows.
February 28, 2019: ISME Journal
Cristiana Callieri, Violeta Slabakova, Nina Dzhembekova, Nataliya Slabakova, Elisaveta Peneva, Pedro J Cabello-Yeves, Andrea Di Cesare, Ester M Eckert, Roberto Bertoni, Gianluca Corno, Michaela M Salcher, Lyudmila Kamburska, Filippo Bertoni, Snejana Moncheva
The Black Sea is the largest meromictic sea with a reservoir of anoxic water extending from 100 to 1000 m depth. These deeper layers are characterised by a poorly understood fluorescence signal called "deep red fluorescence", a chlorophyll a- (Chl a) like signal found in deep dark oceanic waters. In two cruises, we repeatedly found up to 103 cells ml-1 of picocyanobacteria at 750 m depth in these waters and isolated two phycoerythrin-rich Synechococcus sp. strains (BS55D and BS56D). Tests on BS56D revealed its high adaptability, involving the accumulation of Chl a in anoxic/dark conditions and its capacity to photosynthesise when re-exposed to light...
February 28, 2019: ISME Journal
Xiaoqian Yu, Martin F Polz, Eric J Alm
How the diversity of organisms competing for or sharing resources influences community function is an important question in ecology but has rarely been explored in natural microbial communities. These generally contain large numbers of species making it difficult to disentangle how the effects of different interactions scale with diversity. Here, we show that changing diversity affects measures of community function in relatively simple communities but that increasing richness beyond a threshold has little detectable effect...
February 26, 2019: ISME Journal
Yuichiro Kashiyama, Akiko Yokoyama, Takashi Shiratori, Sebastian Hess, Fabrice Not, Charles Bachy, Andres Gutierrez-Rodriguez, Jun Kawahara, Toshinobu Suzaki, Masami Nakazawa, Takahiro Ishikawa, Moe Maruyama, Mengyun Wang, Man Chen, Yingchun Gong, Kensuke Seto, Maiko Kagami, Yoko Hamamoto, Daiske Honda, Takahiro Umetani, Akira Shihongi, Motoki Kayama, Toshiki Matsuda, Junya Taira, Akinori Yabuki, Masashi Tsuchiya, Yoshihisa Hirakawa, Akane Kawaguchi, Mami Nomura, Atsushi Nakamura, Noriaki Namba, Mitsufumi Matsumoto, Tsuyoshi Tanaka, Tomoko Yoshino, Rina Higuchi, Akihiro Yamamoto, Tadanobu Maruyama, Aika Yamaguchi, Akihiro Uzuka, Shinya Miyagishima, Goro Tanifuji, Masanobu Kawachi, Yusuke Kinoshita, Hitoshi Tamiaki
Extant eukaryote ecology is primarily sustained by oxygenic photosynthesis, in which chlorophylls play essential roles. The exceptional photosensitivity of chlorophylls allows them to harvest solar energy for photosynthesis, but on the other hand, they also generate cytotoxic reactive oxygen species. A risk of such phototoxicity of the chlorophyll must become particularly prominent upon dynamic cellular interactions that potentially disrupt the mechanisms that are designed to quench photoexcited chlorophylls in the phototrophic cells...
February 26, 2019: ISME Journal
Keith Bouma-Gregson, Matthew R Olm, Alexander J Probst, Karthik Anantharaman, Mary E Power, Jillian F Banfield
Blooms of planktonic cyanobacteria have long been of concern in lakes, but more recently, harmful impacts of riverine benthic cyanobacterial mats been recognized. As yet, we know little about how various benthic cyanobacteria are distributed in river networks, or how environmental conditions or other associated microbes in their consortia affect their biosynthetic capacities. We performed metagenomic sequencing for 22 Oscillatoriales-dominated (Cyanobacteria) microbial mats collected across the Eel River network in Northern California and investigated factors associated with anatoxin-a producing cyanobacteria...
February 26, 2019: ISME Journal
Daniel S Jones, Gabriel M Walker, Nathan W Johnson, Carl P J Mitchell, Jill K Coleman Wasik, Jake V Bailey
Methylmercury (MeHg) is a bioaccumulative neurotoxin that is produced by certain anaerobic microorganisms, but the abundance and importance of different methylating populations in the environment is not well understood. We combined mercury geochemistry, hgcA gene cloning, rRNA methods, and metagenomics to compare microbial communities associated with MeHg production in two sulfate-impacted lakes on Minnesota's Mesabi Iron Range. The two lakes represent regional endmembers among sulfate-impacted sites in terms of their dissolved sulfide concentrations and MeHg production potential...
February 26, 2019: ISME Journal
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