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ISME Journal

Alberto Scoma, Robert Heyer, Ridwan Rifai, Christian Dandyk, Ian Marshall, Frederiek-Maarten Kerckhof, Angeliki Marietou, Henricus T S Boshker, Filip J R Meysman, Kirsten G Malmos, Thomas Vosegaard, Pieter Vermeir, Ibrahim M Banat, Dirk Benndorf, Nico Boon
Petroleum hydrocarbons reach the deep-sea following natural and anthropogenic factors. The process by which they enter deep-sea microbial food webs and impact the biogeochemical cycling of carbon and other elements is unclear. Hydrostatic pressure (HP) is a distinctive parameter of the deep sea, although rarely investigated. Whether HP alone affects the assembly and activity of oil-degrading communities remains to be resolved. Here we have demonstrated that hydrocarbon degradation in deep-sea microbial communities is lower at native HP (10 MPa, about 1000 m below sea surface level) than at ambient pressure...
December 12, 2018: ISME Journal
E Gibbin, A Gavish, T Krueger, E Kramarsky-Winter, O Shapiro, R Guiet, L Jensen, A Vardi, A Meibom
Under homoeostatic conditions, the relationship between the coral Pocillopora damicornis and Vibrio coralliilyticus is commensal. An increase in temperature, or in the abundance of V. coralliilyticus, can turn this association pathogenic, causing tissue lysis, expulsion of the corals' symbiotic algae (genus Symbiodinium), and eventually coral death. Using a combination of microfluidics, fluorescence microscopy, stable isotopes, electron microscopy and NanoSIMS isotopic imaging, we provide insights into the onset and progression of V...
December 12, 2018: ISME Journal
David J Levy-Booth, Ian J W Giesbrecht, Colleen T E Kellogg, Thierry J Heger, David V D'Amore, Patrick J Keeling, Steven J Hallam, William W Mohn
The Pacific coastal temperate rainforest (PCTR) is a global hot-spot for carbon cycling and export. Yet the influence of microorganisms on carbon cycling processes in PCTR soil is poorly characterized. We developed and tested a conceptual model of seasonal microbial carbon cycling in PCTR soil through integration of geochemistry, micro-meteorology, and eukaryotic and prokaryotic ribosomal amplicon (rRNA) sequencing from 216 soil DNA and RNA libraries. Soil moisture and pH increased during the wet season, with significant correlation to net CO2 flux in peat bog and net CH4 flux in bog forest soil...
December 11, 2018: ISME Journal
César Nicolás, Tomas Martin-Bertelsen, Dimitrios Floudas, Johan Bentzer, Mark Smits, Tomas Johansson, Carl Troein, Per Persson, Anders Tunlid
Many trees form ectomycorrhizal symbiosis with fungi. During symbiosis, the tree roots supply sugar to the fungi in exchange for nitrogen, and this process is critical for the nitrogen and carbon cycles in forest ecosystems. However, the extents to which ectomycorrhizal fungi can liberate nitrogen and modify the soil organic matter and the mechanisms by which they do so remain unclear since they have lost many enzymes for litter decomposition that were present in their free-living, saprotrophic ancestors. Using time-series spectroscopy and transcriptomics, we examined the ability of two ectomycorrhizal fungi from two independently evolved ectomycorrhizal lineages to mobilize soil organic nitrogen...
December 11, 2018: ISME Journal
Andres Gutierrez-Rodriguez, Michael R Stukel, Adriana Lopes Dos Santos, Tristan Biard, Renate Scharek, Daniel Vaulot, Michael R Landry, Fabrice Not
Passive sinking of particulate organic matter (POM) is the main mechanism through which the biological pump transports surface primary production to the ocean interior. However, the contribution and variability of different biological sources to vertical export is not fully understood. Here, we use DNA metabarcoding of the 18S rRNA gene and particle interceptor traps (PITs) to characterize the taxonomic composition of particles sinking out of the photic layer in the California Current Ecosystem (CCE), a productive system with high export potential...
December 11, 2018: ISME Journal
Greta Reintjes, Carol Arnosti, B Fuchs, Rudolf Amann
Identifying the roles played by individual heterotrophic bacteria in the degradation of high molecular weight (HMW) substrates is critical to understanding the constraints on carbon cycling in the ocean. At five sites in the Atlantic Ocean, we investigated the processing of organic matter by tracking changes in microbial community composition as HMW polysaccharides were enzymatically hydrolysed over time. During this investigation, we discovered that a considerable fraction of heterotrophic bacteria uses a newly-identified 'selfish' mode of substrate processing...
December 7, 2018: ISME Journal
Hans K Carlson, Morgan N Price, Mark Callaghan, Alex Aaring, Romy Chakraborty, Hualan Liu, Jennifer V Kuehl, Adam P Arkin, Adam M Deutschbauer
In many environments, toxic compounds restrict which microorganisms persist. However, in complex mixtures of inhibitory compounds, it is challenging to determine which specific compounds cause changes in abundance and prevent some microorganisms from growing. We focused on a contaminated aquifer in Oak Ridge, Tennessee, USA that has large gradients of pH and widely varying concentrations of uranium, nitrate, and many other inorganic ions. In the most contaminated wells, the microbial community is enriched in the Rhodanobacter genus...
December 6, 2018: ISME Journal
Catharina Alves-de-Souza, Tatiane S Benevides, Mariângela Menezes, Christian Jeanthon, Laure Guillou
We report for the first time the in situ dynamics of a vampyrellid in a marine system. A high sampling frequency (twice-weekly) was applied in a tropical eutrophic lagoon (Rio de Janeiro, Brazil) for 5 years (2012-2016). The vampyrellid Hyalodiscus sp. specifically fed on the diatom Chaetoceros minimus during a short time window (~3 months), although the prey was intermittently detected as the dominant phytoplanktonic species over a longer period (~1 year). A classic Lotka-Volterra predator-prey dynamic was observed between the two partners, with a significant modification of the short-term oscillations of the prey...
December 6, 2018: ISME Journal
Phillipe M Rosado, Deborah C A Leite, Gustavo A S Duarte, Ricardo M Chaloub, Guillaume Jospin, Ulisses Nunes da Rocha, João P Saraiva, Francisco Dini-Andreote, Jonathan A Eisen, David G Bourne, Raquel S Peixoto
Although the early coral reef-bleaching warning system (NOAA/USA) is established, there is no feasible treatment that can minimize temperature bleaching and/or disease impacts on corals in the field. Here, we present the first attempts to extrapolate the widespread and well-established use of bacterial consortia to protect or improve health in other organisms (e.g., humans and plants) to corals. Manipulation of the coral-associated microbiome was facilitated through addition of a consortium of native (isolated from Pocillopora damicornis and surrounding seawater) putatively beneficial microorganisms for corals (pBMCs), including five Pseudoalteromonas sp...
December 5, 2018: ISME Journal
Shen Jean Lim, Brenton G Davis, Danielle E Gill, Jillian Walton, Erika Nachman, Annette Summers Engel, Laurie C Anderson, Barbara J Campbell
Lucinidae clams harbor gammaproteobacterial thioautotrophic gill endosymbionts that are environmentally acquired. Thioautotrophic lucinid symbionts are related to metabolically similar symbionts associated with diverse marine host taxa and fall into three distinct phylogenetic clades. Most studies on the lucinid-bacteria chemosymbiosis have been done with seagrass-dwelling hosts, whose symbionts belong to the largest phylogenetic clade. In this study, we examined the taxonomy and functional repertoire of bacterial endosymbionts at an unprecedented resolution from Phacoides pectinatus retrieved from mangrove-lined coastal sediments, which are underrepresented in chemosymbiosis studies...
December 5, 2018: ISME Journal
Zhichao Zhou, Yang Liu, Karen G Lloyd, Jie Pan, Yuchun Yang, Ji-Dong Gu, Meng Li
Marine Benthic Group D (MBG-D) archaea, discovered by 16S rRNA gene survey decades ago, are ecologically important, yet understudied and uncultured sedimentary archaea. In this study, a comprehensive meta-analysis based on the 16S rRNA genes of MBG-D archaea showed that MBG-D archaea are one of the most frequently found archaeal lineages in global sediment with widespread distribution and high abundance, including 16 subgroups in total. Interestingly, some subgroups show significant segregations toward salinity and methane seeps...
December 4, 2018: ISME Journal
Pascale Flury, Pilar Vesga, Ana Dominguez-Ferreras, Camille Tinguely, Cornelia I Ullrich, Regina G Kleespies, Christoph Keel, Monika Maurhofer
The discovery of insecticidal activity in root-colonizing pseudomonads, best-known for their plant-beneficial effects, raised fundamental questions about the ecological relevance of insects as alternative hosts for these bacteria. Since soil bacteria are limited in their inherent abilities of dispersal, insects as vectors might be welcome vehicles to overcome large distances. Here, we report on the transmission of the root-colonizing, plant-beneficial and insecticidal bacterium Pseudomonas protegens CHA0 from root to root by the cabbage root fly, Delia radicum...
November 30, 2018: ISME Journal
Antonio Cellini, Valentino Giacomuzzi, Irene Donati, Brian Farneti, Maria T Rodriguez-Estrada, Stefano Savioli, Sergio Angeli, Francesco Spinelli
Honeybees are well recognised for their key role in plant reproduction as pollinators. On the other hand, their activity may vector some pathogens, such as the bacterium Erwinia amylovora, the causative agent of fire blight disease in pomaceous plants. In this research, we evaluated whether honeybees are able to discriminate between healthy and E. amylovora-infected flowers, thus altering the dispersal of the pathogen. For this reason, honeybees were previously trained to forage either on inoculated or healthy (control) apple flower...
November 30, 2018: ISME Journal
Guibing Zhu, Shanyun Wang, Cheng Wang, Liguang Zhou, Siyan Zhao, Yixiao Li, Fangbai Li, Mike S M Jetten, Yonglong Lu, Lorenz Schwark
Water is essential for life on Earth, and an important medium for microbial energy and metabolism. Dormancy is a state of low metabolic activity upon unfavorable conditions. Many microorganisms can switch to a metabolically inactive state after water shortage, and recover once the environmental conditions become favorable again. Here, we resuscitated dormant anammox bacteria from dry terrestrial ecosystems after a resting period of >10 ka by addition of water without any other substrates. Isotopic-tracer analysis showed that water induced nitrate reduction yielding sufficient nitrite as substrate and energy for activating anammox bacteria...
November 30, 2018: ISME Journal
Carlos A Aguilar-Trigueros, Stefan Hempel, Jeff R Powell, William K Cornwell, Matthias C Rillig
Offspring size is a key trait for understanding the reproductive ecology of species, yet studies addressing the ecological meaning of offspring size have so far been limited to macro-organisms. We consider this a missed opportunity in microbial ecology and provide what we believe is the first formal study of offspring-size variation in microbes using reproductive models developed for macro-organisms. We mapped the entire distribution of fungal spore size in the arbuscular mycorrhizal (AM) fungi (subphylum Glomeromycotina) and tested allometric expectations of this trait to offspring (spore) output and body size...
November 30, 2018: ISME Journal
Ishay Ben-Zion, Shaul Pollak, Avigdor Eldar
Kin discrimination describes the differential interaction of organisms with kin versus non-kin. In microorganisms, many genetic loci act as effective kin-discrimination systems, such as kin-directed help and non-kin-directed harm. Another important example is facultative cooperation, where cooperators increase their investment in group-directed cooperation with the abundance of their kin in the group. Many of these kin-discrimination loci are highly diversified, yet it remains unclear what evolutionary mechanisms maintain this diversity, and how it is affected by population structure...
November 21, 2018: ISME Journal
Vicente I Fernandez, Yutaka Yawata, Roman Stocker
Aquatic environments harbor a great diversity of microorganisms, which interact with the same patchy, particulate, or diffuse resources by means of a broad array of physiological and behavioral adaptations, resulting in substantially different life histories and ecological success. To date, efforts to uncover and understand this diversity have not been matched by equivalent efforts to identify unifying frameworks that can provide a degree of generality and thus serve as a stepping stone to scale up microscale dynamics to predict their ecosystem-level consequences...
November 16, 2018: ISME Journal
Kristin M Rath, Noah Fierer, Daniel V Murphy, Johannes Rousk
Salinization is recognized as a threat to soil fertility worldwide. A challenge in understanding the effects of salinity on soil microbial communities is the fact that it can be difficult to disentangle the effects of salinity from those of other variables that may co-vary with salinity. Here we use a trait-based approach to identify direct effects of salinity on soil bacterial communities across two salinity gradients. Through dose-response relationships between salinity and bacterial growth, we quantified distributions of the trait salt tolerance within the communities...
November 16, 2018: ISME Journal
Wei Zhou, Kin-Hoe Chow, Elizabeth Fleming, Julia Oh
Mammalian hosts constantly interact with diverse exogenous microbes, but only a subset of the microbes manage to colonize due to selective colonization resistance exerted by host genetic factors as well as the native microbiota of the host. An important question in microbial ecology and medical science is if such colonization resistance can discriminate closely related microbial species, or even closely related strains of the same species. Using human-mouse fecal microbiota transplantation and metagenomic shotgun sequencing, we reconstructed colonization patterns of human fecal microbes in mice with different genotypes (C57BL6/J vs...
November 15, 2018: ISME Journal
Amanda N Shelton, Erica C Seth, Kenny C Mok, Andrew W Han, Samantha N Jackson, David R Haft, Michiko E Taga
The vitamin B12 family of cofactors known as cobamides are essential for a variety of microbial metabolisms. We used comparative genomics of 11,000 bacterial species to analyze the extent and distribution of cobamide production and use across bacteria. We find that 86% of bacteria in this data set have at least one of 15 cobamide-dependent enzyme families, but only 37% are predicted to synthesize cobamides de novo. The distribution of cobamide biosynthesis and use vary at the phylum level. While 57% of Actinobacteria are predicted to biosynthesize cobamides, only 0...
November 14, 2018: ISME Journal
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