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Roseovarius sp. strain MCTG156(2b) was isolated from a phytoplankton net sample collected on the west coast of Scotland and was selected based on its ability to degrade polycyclic aromatic hydrocarbons. Here, we present the genome sequence of this strain, which is 5,113,782 bp, with 5,142 genes and an average G+C content of 60.7%.
The conversion of biomass to biofuels presents a solution to one of the largest global challenges of our era, climate change. A critical part of this pipeline is the process of breaking down cellulosic sugars from plant matter to be used by microbes containing biosynthetic pathways that produce biofuels or bioproducts. In this inquiry-based course, students complete a research project that isolates cellulase-producing bacteria from samples collected from the environment. After obtaining isolates, the students characterize the production of cellulases. Students then amplify and sequence the 16S rRNA genes of confirmed cellulase producers and use bioinformatic methods to identify the bacterial isolates. Throughout the course, students learn about the process of generating biofuels and bioproducts through the deconstruction of cellulosic biomass to form monosaccharides from the biopolymers in plant matter. The program relies heavily on active learning and enables students to connect microbiology with issues of sustainability. In addition, it provides exposure to basic microbiology, molecular biology, and biotechnology laboratory techniques and concepts. The described activity was initially developed for the Introductory College Level Experience in Microbiology (iCLEM) program, a research-based immersive laboratory course at the US Department of Energy Joint BioEnergy Institute. Originally designed as an accelerated program for high-potential, low-income, high school students (11th–12th grade), this curriculum could also be implemented for undergraduate coursework in a research-intensive laboratory course at a two- or four-year college or university.
ABSTRACT Diet can influence the composition of the human microbiome, and yet relatively few dietary ingredients have been systematically investigated with respect to their impact on the functional potential of the microbiome. Dietary resistant starch (RS) has been shown to have health benefits, but we lack a mechanistic understanding of the metabolic processes that occur in the gut during digestion of RS. Here, we collected samples during a dietary crossover study with diets containing large or small amounts of RS. We determined the impact of RS on the gut microbiome and metabolic pathways in the gut, using a combination of “omics” approaches, including 16S rRNA gene sequencing, metaproteomics, and metabolomics. This multiomics approach captured changes in the abundance of specific bacterial species, proteins, and metabolites after a diet high in resistant starch (HRS), providing key insights into the influence of dietary interventions on the gut microbiome. The combined data showed that a high-RS diet caused an increase in the ratio of Firmicutes to Bacteroidetes , including increases in relative abundances of some specific members of the Firmicutes and concurrent increases in enzymatic pathways and metabolites involved in lipid metabolism in the gut. IMPORTANCE This work was undertaken to obtain a mechanistic understanding of the complex interplay between diet and the microorganisms residing in the intestine. Although it is known that gut microbes play a key role in digestion of the food that we consume, the specific contributions of different microorganisms are not well understood. In addition, the metabolic pathways and resultant products of metabolism during digestion are highly complex. To address these knowledge gaps, we used a combination of molecular approaches to determine the identities of the microorganisms in the gut during digestion of dietary starch as well as the metabolic pathways that they carry out. Together, these data provide a more complete picture of the function of the gut microbiome in digestion, including links between an RS diet and lipid metabolism and novel linkages between specific gut microbes and their metabolites and proteins produced in the gut.
Tetracyclines serve as broad-spectrum antibiotics to treat bacterial infections. The discovery of new tetracycline resistance genes has led to new questions about the underlying mechanisms of resistance, gene transfer, and their relevance to human health. We tracked changes in the abundance of a 55-kbp conjugative transposon (CTn214) carrying tetQ, a tetracycline resistance gene, within a Bacteroides fragilis metagenome-assembled genome derived from shotgun sequencing of microbial DNA extracted from the ileal pouch of a patient with ulcerative colitis. The mapping of metagenomic reads to CTn214 revealed the multi-copy nature of a 17,044-nt region containing tetQ in samples collected during inflammation and uninflamed visits. B. fragilis cultivars isolated from the same patient during periods of inflammation harbored CTn214 integrated into the chromosome or both a circular, multi-copy, extrachromosomal region of the CTn214 containing tetQ and the corresponding integrated form. The tetracycline-dependent mechanism for the transmission of CTn214 is nearly identical to a common conjugative transposon found in the genome of B. fragilis (CTnDOT), but the autonomously amplified nature of a circular 17,044-nt region of CTn214 that codes for tetQ and the integration of the same sequence in the linear chromosome within the same cell is a novel observation. Genome and transcriptome sequencing of B. fragilis cultivars grown under different concentrations of tetracycline and ciprofloxacin indicates that tetQ in strains containing the circular form remains actively expressed regardless of treatment, while the expression of tetQ in strains containing the linear form increases only in the presence of tetracycline.
Campylobacter jejuni is a common foodborne pathogen worldwide that is associated with high rates of morbidity and mortality among infants in low- to middle-income countries (LMICs). Human milk provides infants with an important source of nutrients and contains antimicrobial components for protection against infection. However, recent studies, including our own, have found significantly higher levels of Campylobacter in diarrheal stool samples collected from breastfed infants compared to non-breastfed infants in LMICs. We hypothesized that C. jejuni has unique strategies to resist the antimicrobial properties of human milk. Transcriptional profiling found human milk exposure induces genes associated with ribosomal function, iron acquisition, and amino acid utilization in C. jejuni strains 81–176 and 11168. However, unidentified proteinaceous components of human milk prevent bacterial growth. Evolving both C. jejuni isolates to survive in human milk resulted in mutations in genes encoding the acyl carrier protein (AcpP) and the major outer membrane porin (PorA). Introduction of the PorA/AcpP amino acid changes into the parental backgrounds followed by electron microscopy showed distinct membrane architectures, and the AcpP changes not only significantly improved growth in human milk, but also yielded cells surrounded with outer membrane vesicles. Analyses of the phospholipid and lipooligosaccharide (LOS) compositions suggest an imbalance in acyl chain distributions. For strain 11168, these changes protect both evolved and 11168ΔacpP G33R strains from bacteriophage infection and polymyxin killing. Taken together, this study provides insights into how C. jejuni may evolve to resist the bactericidal activity of human milk and flourish in the hostile environment of the gastrointestinal tract.
Operating biological nutrient removal (BNR) wastewater treatment plants with low dissolved oxygen (DO) conditions can reduce energy costs. We report on five metagenomes and 492 metagenome-assembled genomes (MAGs) obtained from samples collected at the Pomona water reclamation plant before and after a DO reduction from 3.5 to 0.7 mg/L.
Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty acid analysis, as well as functional processes of soil nitrification potential and CO 2 efflux. We demonstrated the critical role of soil type in determining microbial responses to land use changes at the continental level. Our findings underscore the inherent difficulty in generalizing ecosystem responses across landscapes and suggest that assessments of community feedback must take soil types into consideration. Soil types heavily influence ecological dynamics. It remains controversial to what extent soil types shape microbial responses to land management changes, largely due to lack of in-depth comparison across various soil types. Here, we collected samples from three major zonal soil types spanning from cold temperate to subtropical climate zones. We examined bacterial and fungal community structures, as well as microbial functional genes. Different soil types had distinct microbial biomass levels and community compositions. Five years of maize cropping (growing corn or maize) changed the bacterial community composition of the Ultisol soil type and the fungal composition of the Mollisol soil type but had little effect on the microbial composition of the Inceptisol soil type. Meanwhile, 5 years of fertilization resulted in soil acidification. Microbial compositions of the Mollisol and Ultisol, but not the Inceptisol, were changed and correlated ( P < 0.05) with soil pH. These results demonstrated the critical role of soil type in determining microbial responses to land management changes. We also found that soil nitrification potentials correlated with the total abundance of nitrifiers and that soil heterotrophic respiration correlated with the total abundance of carbon degradation genes, suggesting that changes in microbial community structure had altered ecosystem processes. Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty acid analysis, as well as functional processes of soil nitrification potential and CO 2 efflux. We demonstrated the critical role of soil type in determining microbial responses to land use changes at the continental level. Our findings underscore the inherent difficulty in generalizing ecosystem responses across landscapes and suggest that assessments of community feedback must take soil types into consideration.
The Snake River Plain of central Idaho represents the world’s best example of a mantle hotspot track impinging upon continental crust and provides a record of bimodal volcanism extending over 12 Ma to the present. Project Hotspot recovered almost 2 km of continuous drill core from the Kimama borehole, located in central Idaho on the axial volcanic zone. The Kimama drill core represents the most complete record of mafic volcanism along the Yellowstone–Snake River Plain hotspot track. A total of 432 basalt flow units, representing 183 basalt flows, 78 basalt flow groups, and 34 super groups, along with 42 sediment interbeds are recognized using volcanic facies observations, stratigraphic relationships, borehole geophysical logs, and paleosecular variation in magnetostratigraphy. Rhyolite and other non-basaltic volcanic materials were not encountered in the drill core. Ages for six basalt lava flows were determined by 40 Ar/ 39 Ar using incremental heating experiments. Paleomagnetic inclination was measured on over 1200 samples collected at roughly 2-m-depth intervals, yielding mean values of paleosecular variation between ±50° to ±70° in Kimama flow groups, close to the expected 61° axial dipole average for the Kimama borehole location. Twenty-three magnetic reversals were identified and correlated to dated geomagnetic chrons and subchrons and compared with the 40 Ar/ 39 Ar radiometric ages. A linear fit to 40 Ar/ 39 Ar dates, geomagnetic chron and subchron boundaries, and volcanogenic zircon U-Pb ages defines a mean accumulation rate of ~320 m/m.y. and extrapolates to a bottom hole age of 6.3 Ma. Average thicknesses of lithologic units increase from 2.7 m (sediment), 4 m (flow units), 10 m (flows), 23 m (flow groups), to 53 m (super groups). On average, one lava flow inundated the Kimama borehole location every 33 k.y. Intercalated sediments, ranging from 0.06 to 24.5 m thick, make up roughly 6% of the drill core and indicate lulls in local volcanic activity that may have lasted up to 77 k.y. Neutron and gamma-ray logs supplement observations from the drill cores: neutron logs document individual flow units through the contrast between massive flow interiors and more porous flow surfaces, and gamma-ray logs document the depth and thickness of sedimentary interbeds and high–K-Fe basalts. The 5.8 m.y. duration of basaltic volcanism in the Kimama drill core implies a steady rate of volcanism, indicating a relatively stable rate of mantle upflow along the lithosphere-mantle boundary in the wake of Yellowstone–Snake River Plain plume volcanism.
Isotope ratios of noble gases (He, Ne, Ar) were studied in samples collected by degassing of cores of water frozen over a glacier of Lake Vostok. The gases were collected into glass retorts during three days of degassing of cores, which have just been extracted from the borehole. Within the error, the isotope {sup 3}He/{sup 4}He ratios of 0.28 ± 0.08 R{sub A} (R{sub A} = 1.38 × 10{sup –6} is the ratio for air) correspond to those from [1]. The {sup 4}He/{sup 20}Ne and {sup 40}Ar/{sup 36}Ar ratios (12.4 ± 4.6 R{sub A} and 1.0074 ± 0.0023 R{sub A}, respectively) exceed their contents in air ({sup 4}He/{sup 20}Ne{sub A} = 0.29; {sup 40}Ar/{sup 36}Ar{sub A} = 298.6) and may indicate some contribution of terrigenous gas to the gaseous balance of the lake, as well as the high content of ancient ground waters in the lake. The {sup 3}He/{sup 4}He ratio of 0.28 R{sub A} means low mantle {sup 3}He flux typical of continental platforms far from active rift zones.
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A measurement of the inclusive WW+WZ diboson production cross section in proton-proton collisions is reported, based on events containing a leptonically decaying W boson and exactly two jets. The data sample, collected at sqrt(s) = 7 TeV with the CMS detector at the LHC, corresponds to an integrated luminosity of 5.0 inverse femtobarns. The measured value of the sum of the inclusive WW and WZ cross sections is sigma(pp to WW+WZ) = 68.9 +/- 8.7 (stat.) +/- 9.7 (syst.) +/- 1.5 (lum.) pb, consistent with the standard model prediction of 65.6 +/- 2.2 pb. This is the first measurement of WW+WZ production in pp collisions using this signature. No evidence for anomalous triple gauge couplings is found and upper limits are set on their magnitudes.
In addition jet activity in dijet events is measured using pp collisions at ATLAS at a centre-of-mass energy of 7TeV, for jets reconstructed using the anti-k t algorithm with radius parameter R=0.6. This is done using variables such as the fraction of dijet events without an additional jet in the rapidity interval bounded by the dijet subsystem and correlations between the azimuthal angles of the dijet s. They are presented, both with and without a veto on additional jet activity in the rapidity interval, as a function of the scalar average of the transverse momenta of the dijet s and of the rapidity interval size. The double differential dijet cross section is also measured as a function of the interval size and the azimuthal angle between the dijet s. These variables probe differences in the approach to resummation of large logarithms when performing QCD calculations. The data are compared to POWERHEG , interfaced to the PYTHIA 8 and HERWIG parton shower generators, as well as to HEJ with and without interfacing it to the ARIADNE parton shower generator. None of the theoretical predictions agree with the data across the full phase-space considered; however, POWERHEG + PYTHIA 8 and HEJ + ARIADNE are found to provide the best agreement with the data. These measurements use the full data sample collected with the ATLAS detector in 7TeV pp collisions at the LHC and correspond to integrated luminosities of 36.1pb –1 and 4.5fb –1 for data collected during 2010 and 2011, respectively.
This paper presents distributions of topological observables in inclusive three- and four-jet events produced in pp collisions at a centre-of-mass energy of 7TeV with a data sample collected by the CMS experiment corresponding to a luminosity of 5.1fb -1 . We corrected the distributions for detector effects, and compared with several event generators based on two- and multi-parton matrix elements at leading order. Thus, among the considered calculations, MADGRAPH interfaced with PYTHIA6displays the overall best agreement with data.
The large rate of multiple simultaneous proton–proton interactions, or pile-up, generated by the Large Hadron Collider in Run 1 required the development of many new techniques to mitigate the adverse effects of these conditions. This paper describes the methods employed in the ATLAS experiment to correct for the impact of pile-up on jet energy and jet shapes, and for the presence of spurious additional jets, with a primary focus on the large 20.3 fb -1 data sample collected at a centre-of-mass energy of $\sqrt{s}$ = 8TeV. The energy correction techniques that incorporate sophisticated estimates of the average pile-up energy density and tracking information are presented. Jet-to-vertex association techniques are discussed and projections of performance for the future are considered. Lastly, the extension of these techniques to mitigate the effect of pile-up on jet shapes using subtraction and grooming procedures is presented.
A search for heavy resonances with masses above 1 $\,\text {TeV}$ , decaying to final states containing a vector boson and a Higgs boson, is presented. The search considers hadronic decays of the vector boson, and Higgs boson decays to b quarks. The decay products are highly boosted, and each collimated pair of quarks is reconstructed as a single, massive jet. The analysis is performed using a data sample collected in 2016 by the CMS experiment at the LHC in proton-proton collisions at a center-of-mass energy of 13 $\,\text {TeV}$ , corresponding to an integrated luminosity of 35.9 $\,\text {fb}^{-1}$ . The data are consistent with the background expectation and are used to place limits on the parameters of a theoretical model with a heavy vector triplet. In the benchmark scenario with mass-degenerate $\mathrm{W^{'}}$ and $\mathrm{Z}' $ bosons decaying predominantly to pairs of standard model bosons, for the first time heavy resonances for masses as high as 3.3 $\,\text {TeV}$ are excluded at 95% confidence level, setting the most stringent constraints to date on such states decaying into a vector boson and a Higgs boson.
The nuclear modification factors of ${\mathrm {J}/\psi }$ and $\psi \text {(2S)}$ mesons are measured in $\text {PbPb}$ collisions at a centre-of-mass energy per nucleon pair of $\sqrt{\smash [b]{s_{_{\text {NN}}}}} = 5.02\,\text {Te}\text {V} $ . The analysis is based on $\text {PbPb}$ and $\mathrm {p}\mathrm {p}$ data samples collected by CMS at the LHC in 2015, corresponding to integrated luminosities of 464 $\,\mu \mathrm {b}^{-1}$ and 28 $\,\text {pb}^\text {-1}$ , respectively. The measurements are performed in the dimuon rapidity range of $|y | < 2.4$ as a function of centrality, rapidity, and transverse momentum ( $p_{\mathrm {T}}$ ) from $p_{\mathrm {T}} =3$ ${\,\text {Ge}\text {V}/}\text {c}$ in the most forward region and up to 50 ${\,\text {Ge}\text {V}/}\text {c}$ . Both prompt and nonprompt (coming from b hadron decays) ${\mathrm {J}/\psi }$ mesons are observed to be increasingly suppressed with centrality, with a magnitude similar to the one observed at $\sqrt{\smash [b]{s_{_{\text {NN}}}}} = 2.76\,\text {Te}\text {V} $ for the two ${\mathrm {J}/\psi }$ meson components. No dependence on rapidity is observed for either prompt or nonprompt ${\mathrm {J}/\psi }$ mesons. An indication of a lower prompt ${\mathrm {J}/\psi }$ meson suppression at $p_{\mathrm {T}} > 25$ ${\,\text {Ge}\text {V}/}\text {c}$ is seen with respect to that observed at intermediate $p_{\mathrm {T}}$ . The prompt $\psi \text {(2S)}$ meson yield is found to be more suppressed than that of the prompt ${\mathrm {J}/\psi }$ mesons in the entire $p_{\mathrm {T}}$ range.
We study bottomonium production in association with an η meson in e + e - annihilations near the Υ(5S), at a centre-of-mass energy of s√=10.866 GeV. The results are based on the 121.4 fb -1 data sample collected by the Belle experiment at the asymmetric-energy KEKB collider. Only the η meson is reconstructed and the missing-mass spectrum of η candidates is investigated. We observe the e + e - →ηΥ J (1D) process and find evidence for the e + e - →ηΥ(2S) process, while no significant signals of Υ(1S), hb(1P) , nor h b (2P) are found. Cross sections for the studied processes are reported.
The standard model (SM) production of four top quarks ($\text {t} {}{\overline{\text {t}}} \text {t} {}{\overline{\text {t}}} $) in proton–proton collisions is studied by the CMS Collaboration. The data sample, collected during the 2016–2018 data taking of the LHC, corresponds to an integrated luminosity of 137$\,\text {fb}^{-1}$ at a center-of-mass energy of 13$\,\text {TeV}$. The events are required to contain two same-sign charged leptons (electrons or muons) or at least three leptons, and jets. The observed and expected significances for the $\text {t} {}{\overline{\text {t}}} \text {t} {}{\overline{\text {t}}} $ signal are respectively 2.6 and 2.7 standard deviations, and the $\text {t} {}{\overline{\text {t}}} \text {t} {}{\overline{\text {t}}} $ cross section is measured to be $12.6^{+5.8}_{-5.2}\,\text {fb} $. The results are used to constrain the Yukawa coupling of the top quark to the Higgs boson, $y_{\text {t}}$, yielding a limit of $|y_{\text {t}}/y_{\text {t}}^{\mathrm {SM}} | < 1.7$ at $95\%$ confidence level, where $y_{\text {t}}^{\mathrm {SM}}$ is the SM value of $y_{\text {t}}$. They are also used to constrain the oblique parameter of the Higgs boson in an effective field theory framework, $\hat{H}<0.12$. Limits are set on the production of a heavy scalar or pseudoscalar boson in Type-II two-Higgs-doublet and simplified dark matter models, with exclusion limits reaching 350–470$\,\text {GeV}$ and 350–550$\,\text {GeV}$ for scalar and pseudoscalar bosons, respectively. Upper bounds are also set on couplings of the top quark to new light particles.