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ISME Journal

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https://www.readbyqxmd.com/read/29222444/diazotroph-diversity-and-nitrogen-fixation-in-the-coral-stylophora-pistillata-from-the-great-barrier-reef
#1
Michael P Lesser, Kathleen M Morrow, Sabrina M Pankey, Sam H C Noonan
Diazotrophs, both Bacteria and Archaea, capable of fixing nitrogen (N2), are present in the tissues and mucous, of corals and can supplement the coral holobiont nitrogen budget with fixed nitrogen (N) in the form of ammonia (NH3). Stylophora pistillata from Heron Island on the Great Barrier Reef collected at 5 and 15 m, and experimentally manipulated in the laboratory, showed that the rates of net photosynthesis, steady state quantum yields of photosystem II (PSII) fluorescence (∆F v/F m') and calcification varied based on irradiance as expected...
December 8, 2017: ISME Journal
https://www.readbyqxmd.com/read/29222443/metabolic-versatility-of-small-archaea-micrarchaeota-and-parvarchaeota
#2
Lin-Xing Chen, Celia Méndez-García, Nina Dombrowski, Luis E Servín-Garcidueñas, Emiley A Eloe-Fadrosh, Bao-Zhu Fang, Zhen-Hao Luo, Sha Tan, Xiao-Yang Zhi, Zheng-Shuang Hua, Esperanza Martinez-Romero, Tanja Woyke, Li-Nan Huang, Jesús Sánchez, Ana Isabel Peláez, Manuel Ferrer, Brett J Baker, Wen-Sheng Shu
Small acidophilic archaea belonging to Micrarchaeota and Parvarchaeota phyla are known to physically interact with some Thermoplasmatales members in nature. However, due to a lack of cultivation and limited genomes on hand, their biodiversity, metabolisms, and physiologies remain largely unresolved. Here, we obtained 39 genomes from acid mine drainage (AMD) and hot spring environments around the world. 16S rRNA gene based analyses revealed that Parvarchaeota were only detected in AMD and hot spring habitats, while Micrarchaeota were also detected in others including soil, peat, hypersaline mat, and freshwater, suggesting a considerable higher diversity and broader than expected habitat distribution for this phylum...
December 8, 2017: ISME Journal
https://www.readbyqxmd.com/read/29222442/contrasting-patterns-of-genome-level-diversity-across-distinct-co-occurring-bacterial-populations
#3
Sarahi L Garcia, Sarah L R Stevens, Benjamin Crary, Manuel Martinez-Garcia, Ramunas Stepanauskas, Tanja Woyke, Susannah G Tringe, Siv G E Andersson, Stefan Bertilsson, Rex R Malmstrom, Katherine D McMahon
To understand the forces driving differentiation and diversification in wild bacterial populations, we must be able to delineate and track ecologically relevant units through space and time. Mapping metagenomic sequences to reference genomes derived from the same environment can reveal genetic heterogeneity within populations, and in some cases, be used to identify boundaries between genetically similar, but ecologically distinct, populations. Here we examine population-level heterogeneity within abundant and ubiquitous freshwater bacterial groups such as the acI Actinobacteria and LD12 Alphaproteobacteria (the freshwater sister clade to the marine SAR11) using 33 single-cell genomes and a 5-year metagenomic time series...
December 8, 2017: ISME Journal
https://www.readbyqxmd.com/read/29208946/the-enigmatic-sar202-cluster-up-close-shedding-light-on-a-globally-distributed-dark-ocean-lineage-involved-in-sulfur-cycling
#4
Maliheh Mehrshad, Francisco Rodriguez-Valera, Mohammad Ali Amoozegar, Purificación López-García, Rohit Ghai
The dark ocean microbiota represents the unknown majority in the global ocean waters. The SAR202 cluster belonging to the phylum Chloroflexi was the first microbial lineage discovered to specifically inhabit the aphotic realm, where they are abundant and globally distributed. The absence of SAR202 cultured representatives is a significant bottleneck towards understanding their metabolic capacities and role in the marine environment. In this work, we use a combination of metagenome-assembled genomes from deep-sea datasets and publicly available single-cell genomes to construct a genomic perspective of SAR202 phylogeny, metabolism and biogeography...
December 5, 2017: ISME Journal
https://www.readbyqxmd.com/read/29192905/microbial-life-on-a-sand-grain-from-bulk-sediment-to-single-grains
#5
David Probandt, Thilo Eickhorst, Andreas Ellrott, Rudolf Amann, Katrin Knittel
Globally, marine surface sediments constitute a habitat for estimated 1.7 × 1028 prokaryotes. For benthic microbial community analysis, usually, several grams of sediment are processed. In this study, we made the step from bulk sediments to single sand grains to address the microbial community directly in its micro-habitat: the individual bacterial diversity on 17 sand grains was analyzed by 16S ribosomal RNA gene sequencing and visualized on sand grains using catalyzed reporter deposition fluorescence in situ hybridization...
December 1, 2017: ISME Journal
https://www.readbyqxmd.com/read/29192904/specific-substrate-driven-changes-in-human-faecal-microbiota-composition-contrast-with-functional-redundancy-in-short-chain-fatty-acid-production
#6
Nicole Reichardt, Maren Vollmer, Grietje Holtrop, Freda M Farquharson, Daniel Wefers, Mirko Bunzel, Sylvia H Duncan, Janice E Drew, Lynda M Williams, Graeme Milligan, Thomas Preston, Douglas Morrison, Harry J Flint, Petra Louis
The diet provides carbohydrates that are non-digestible in the upper gut and are major carbon and energy sources for the microbial community in the lower intestine, supporting a complex metabolic network. Fermentation produces the short-chain fatty acids (SCFAs) acetate, propionate and butyrate, which have health-promoting effects for the human host. Here we investigated microbial community changes and SCFA production during in vitro batch incubations of 15 different non-digestible carbohydrates, at two initial pH values with faecal microbiota from three different human donors...
December 1, 2017: ISME Journal
https://www.readbyqxmd.com/read/29192903/rare-symbionts-may-contribute-to-the-resilience-of-coral-algal-assemblages
#7
Maren Ziegler, Víctor M Eguíluz, Carlos M Duarte, Christian R Voolstra
The association between corals and photosynthetic dinoflagellates (Symbiodinium spp.) is the key to the success of reef ecosystems in highly oligotrophic environments, but it is also their Achilles' heel due to its vulnerability to local stressors and the effects of climate change. Research during the last two decades has shaped a view that coral host-Symbiodinium pairings are diverse, but largely exclusive. Deep sequencing has now revealed the existence of a rare diversity of cryptic Symbiodinium assemblages within the coral holobiont, in addition to one or a few abundant algal members...
December 1, 2017: ISME Journal
https://www.readbyqxmd.com/read/29171840/what-intrinsic-and-extrinsic-factors-explain-the-stoichiometric-diversity-of-aquatic-heterotrophic-bacteria
#8
Casey M Godwin, James B Cotner
The elemental content of microbial communities is dependent upon the physiology of constituent populations, yet ecological stoichiometry has made slow progress toward identifying predictors of how species and strains change the elemental content of their biomass in response to the stoichiometry of elements in resources. We asked whether the elemental content of aquatic bacteria, especially flexibility in elemental content, could be predicted by their phylogeny, maximum growth rate or lake productivity. We examined 137 isolates using chemostats and found that strains differed substantially in how the carbon:nitrogen:phosphorus ratios (C:N:P) in their biomass responded to P-sufficient and P-limiting conditions...
November 24, 2017: ISME Journal
https://www.readbyqxmd.com/read/29160864/clonal-expansion-behind-a-marine-diatom-bloom
#9
Maria Valeria Ruggiero, Domenico D'Alelio, Maria Immacolata Ferrante, Mariano Santoro, Laura Vitale, Gabriele Procaccini, Marina Montresor
Genetic diversity is what selection acts on, thus shaping the adaptive potential of populations. We studied micro-evolutionary patterns of the key planktonic diatom Pseudo-nitzschia multistriata at a long-term sampling site over 2 consecutive years by genotyping isolates with 22 microsatellite markers. We show that both sex and vegetative growth interplay in shaping intraspecific diversity. We document a brief but massive demographic and clonal expansion driven by strains of the same mating type. The analysis of an extended data set (6 years) indicates that the genetic fingerprint of P...
November 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/29135971/build-your-own-soil-exploring-microfluidics-to-create-microbial-habitat-structures
#10
Kristin Aleklett, E Toby Kiers, Pelle Ohlsson, Thomas S Shimizu, Victor Ea Caldas, Edith C Hammer
Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats.The ISME Journal advance online publication, 14 November 2017; doi:10.1038/ismej.2017.184.
November 14, 2017: ISME Journal
https://www.readbyqxmd.com/read/29135970/metabolic-shift-at-the-class-level-sheds-light-on-adaptation-of-methanogens-to-oxidative-environments
#11
Zhe Lyu, Yahai Lu
Methanogens have long been considered strictly anaerobic and oxygen-sensitive microorganisms, but their ability to survive oxygen stress has also been documented. Indeed, methanogens have been found in oxidative environments, and antioxidant genes have been detected in their genomes. How methanogens adapt to oxidative environments, however, remain poorly understood. Here, we systematically predicted and annotated antioxidant features from representative genomes across six well-established methanogen orders...
November 14, 2017: ISME Journal
https://www.readbyqxmd.com/read/29125597/phage-mobility-is-a-core-determinant-of-phage-bacteria-coexistence-in-biofilms
#12
Matthew Simmons, Knut Drescher, Carey D Nadell, Vanni Bucci
Many bacteria are adapted for attaching to surfaces and for building complex communities, termed biofilms. The biofilm mode of life is predominant in bacterial ecology. So too is the exposure of bacteria to ubiquitous viral pathogens, termed bacteriophages. Although biofilm-phage encounters are likely to be common in nature, little is known about how phages might interact with biofilm-dwelling bacteria. It is also unclear how the ecological dynamics of phages and their hosts depend on the biological and physical properties of the biofilm environment...
November 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/29125596/contrasting-the-relative-importance-of-species-sorting-and-dispersal-limitation-in-shaping-marine-bacterial-versus-protist-communities
#13
Wenxue Wu, Hsiao-Pei Lu, Akash Sastri, Yi-Chun Yeh, Gwo-Ching Gong, Wen-Chen Chou, Chih-Hao Hsieh
A central challenge in microbial ecology is to understand the underlying mechanisms driving community assembly, particularly in the continuum of species sorting and dispersal limitation. However, little is known about the relative importance of species sorting and dispersal limitation in shaping marine microbial communities; especially, how they are related to organism types/traits and water depth. Here, we used variation partitioning and null model analysis to compare mechanisms driving bacterial and protist metacommunity dynamics at the basin scale in the East China Sea, based on MiSeq paired-end sequencing of 16S ribosomal DNA (rDNA) and 18S rDNA, respectively, in surface, deep chlorophyll maximum and bottom layers...
November 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/29099492/characterization-of-ecologically-diverse-viruses-infecting-co-occurring-strains-of-cosmopolitan-hyperhalophilic-bacteroidetes
#14
Judith Villamor, María Dolores Ramos-Barbero, Pedro González-Torres, Toni Gabaldón, Ramón Rosselló-Móra, Inmaculada Meseguer, Manuel Martínez-García, Fernando Santos, Josefa Antón
Hypersaline environments close to saturation harbor the highest density of virus-like particles reported for aquatic systems as well as low microbial diversity. Thus, they offer unique settings for studying virus-host interactions in nature. However, no viruses have been isolated so far infecting the two most abundant inhabitants of these systems (that is, the euryarchaeon Haloquadratum walsbyi and the bacteroidetes Salinibacter ruber). Here, using three different co-occurring strains, we have isolated eight viruses infecting the ubiquitous S...
November 3, 2017: ISME Journal
https://www.readbyqxmd.com/read/29099491/the-bacterium-wolbachia-exploits-host-innate-immunity-to-establish-a-symbiotic-relationship-with-the-dengue-vector-mosquito-aedes-aegypti
#15
Xiaoling Pan, Andrew Pike, Deepak Joshi, Guowu Bian, Michael J McFadden, Peng Lu, Xiao Liang, Fengrui Zhang, Alexander S Raikhel, Zhiyong Xi
A host's immune system plays a central role in shaping the composition of the microbiota and, in return, resident microbes influence immune responses. Symbiotic associations of the maternally transmitted bacterium Wolbachia occur with a wide range of arthropods. It is, however, absent from the dengue and Zika vector mosquito Aedes aegypti in nature. When Wolbachia is artificially forced to form symbiosis with this new mosquito host, it boosts the basal immune response and enhances the mosquito's resistance to pathogens, including dengue, Zika virus and malaria parasites...
November 3, 2017: ISME Journal
https://www.readbyqxmd.com/read/29099490/a-dynamic-microbial-community-with-high-functional-redundancy-inhabits-the-cold-oxic-subseafloor-aquifer
#16
Benjamin J Tully, C Geoff Wheat, Brain T Glazer, Julie A Huber
The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups...
November 3, 2017: ISME Journal
https://www.readbyqxmd.com/read/29087380/electron-carriers-in-microbial-sulfate-reduction-inferred-from-experimental-and-environmental-sulfur-isotope-fractionations
#17
Christine B Wenk, Boswell A Wing, Itay Halevy
Dissimilatory sulfate reduction (DSR) has been a key process influencing the global carbon cycle, atmospheric composition and climate for much of Earth's history, yet the energy metabolism of sulfate-reducing microbes remains poorly understood. Many organisms, particularly sulfate reducers, live in low-energy environments and metabolize at very low rates, requiring specific physiological adaptations. We identify one such potential adaptation-the electron carriers selected for survival under energy-limited conditions...
October 31, 2017: ISME Journal
https://www.readbyqxmd.com/read/29087379/changes-in-bacterioplankton-community-structure-during-early-lake-ontogeny-resulting-from-the-retreat-of-the-greenland-ice-sheet
#18
Hannes Peter, Erik Jeppesen, Luc De Meester, Ruben Sommaruga
Retreating glaciers and ice sheets are among the clearest signs of global climate change. One consequence of glacier retreat is the formation of new meltwater-lakes in previously ice-covered terrain. These lakes provide unique opportunities to understand patterns in community organization during early lake ontogeny. Here, we analyzed the bacterial community structure and diversity in six lakes recently formed by the retreat of the Greenland Ice Sheet (GrIS). The lakes represented a turbidity gradient depending on their past and present connectivity to the GrIS meltwaters...
October 31, 2017: ISME Journal
https://www.readbyqxmd.com/read/29087378/the-impact-of-elevated-co2-on-prochlorococcus-and-microbial-interactions-with-helper-bacterium-alteromonas
#19
Gwenn Mm Hennon, J Jeffrey Morris, Sheean T Haley, Erik R Zinser, Alexander R Durrant, Elizabeth Entwistle, Terje Dokland, Sonya T Dyhrman
Prochlorococcus is a globally important marine cyanobacterium that lacks the gene catalase and relies on 'helper' bacteria such as Alteromonas to remove reactive oxygen species. Increasing atmospheric CO2 decreases the need for carbon concentrating mechanisms and photorespiration in phytoplankton, potentially altering their metabolism and microbial interactions even when carbon is not limiting growth. Here, Prochlorococcus (VOL4, MIT9312) was co-cultured with Alteromonas (strain EZ55) under ambient (400 p...
October 31, 2017: ISME Journal
https://www.readbyqxmd.com/read/29087377/degradation-of-hydrogen-peroxide-at-the-ocean-s-surface-the-influence-of-the-microbial-community-on-the-realized-thermal-niche-of-prochlorococcus
#20
Lanying Ma, Benjamin C Calfee, J Jeffrey Morris, Zackary I Johnson, Erik R Zinser
Prochlorococcus, the smallest and most abundant phytoplankter in the ocean, is highly sensitive to hydrogen peroxide (HOOH), and co-occurring heterotrophs such as Alteromonas facilitate the growth of Prochlorococcus by scavenging HOOH. Temperature is also a major influence on Prochlorococcus abundance and distribution in the ocean, and studies in other photosynthetic organisms have shown that HOOH and temperature extremes can act together as synergistic stressors. To address potential synergistic effects of temperature and HOOH on Prochlorococcus growth, high- and low-temperature-adapted representative strains were cultured at ecologically relevant concentrations under a range of HOOH concentrations and temperatures...
October 31, 2017: ISME Journal
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