Kinopus chlorellivorus gen. nov., sp. nov.(Vampyrellida, Rhizaria), a new algivorous protist predator isolated from large-scale outdoor cultures of Chlorella sorokiniana

Physical Review C

We report systematic measurements of dielectron (e+ e−) invariant-mass M e e spectra at midrapidity in Au+ Au collisions at s N N= 27, 39, and 62.4 GeV taken with the STAR detector at the Relativistic Heavy Ion Collider. For all energies studied, a significant excess yield of dielectrons is observed in the low-mass region (0.40< M e e< 0.75 MeV/c 2) compared to hadronic cocktail simulations at freeze-out. Models that include an in-medium broadening of the ρ-meson spectral function consistently describe the observed excess. In addition, we report acceptance-corrected dielectron-excess spectra for Au+ Au collisions at midrapidity (| y e e|< 1) in the 0–80% centrality bin for each collision energy. The integrated excess yields for 0.4< M e e< 0.75 GeV/c 2, normalized by the charged particle multiplicity at midrapidity, are compared with previously published measurements for Au+ Au at s N N 1= 19.6 and 200 GeV …

The European Physical Journal C

A search for dark matter in the form of strongly interacting massive particles (SIMPs) using the CMS detector at the LHC is presented. The SIMPs would be produced in pairs that manifest themselves as pairs of jets without tracks. The energy fraction of jets carried by charged particles is used as a key discriminator to suppress efficiently the large multijet background, and the remaining background is estimated directly from data. The search is performed using proton–proton collision data corresponding to an integrated luminosity of 16.1, collected with the CMS detector in 2016. No significant excess of events is observed above the expected background. For the simplified dark matter model under consideration, SIMPs with masses up to 100 are excluded and further sensitivity is explored towards higher masses.

Applied and Environmental Microbiology

The large-scale culture of low-cost algal biomass can be significantly affected by microbial grazing on the algae. To minimize the impact, it is necessary to manage the predators. In this study, we describe a new genus and species of vampyrellid amoeba, Kinopus chlorellivorus, which caused the loss of Chlorella sorokiniana in large-scale cultures. We assigned it to the family Leptophryidae (Vampyrellida) based on morphology and small-subunit (SSU) rRNA gene sequence comparisons. Using transmission electron microscopy, we found spherical lucent inclusions, which have not been reported for any leptophryids or other vampyrellids. The gene sequence of SSU rRNA did not match any recognized genera or species and contained four characteristic regions. K. chlorellivorus preys on algae by engulfment. Laboratory feeding experiments confirmed that its grazing rate was as high as 131 Chlorella cells day−1 …

Physics Letters B

Jets containing a prompt J/ψ meson are studied in lead-lead collisions at a nucleon-nucleon center-of-mass energy of 5.02 TeV, using the CMS detector at the LHC. Jets are selected to be in the transverse momentum range of 30< p T< 40 GeV. The J/ψ yield in these jets is evaluated as a function of the jet fragmentation variable z, the ratio of the J/ψ p T to the jet p T. The nuclear modification factor, R AA, is then derived by comparing the yield in lead-lead collisions to the corresponding expectation based on proton-proton data, at the same nucleon-nucleon center-of-mass energy. The suppression of the J/ψ yield shows a dependence on z, indicating that the interaction of the J/ψ with the quark-gluon plasma formed in heavy ion collisions depends on the fragmentation that gives rise to the J/ψ meson.

Nature Physics

Mesons comprising a beauty quark and strange quark can oscillate between particle () and antiparticle () flavour eigenstates, with a frequency given by the mass difference between heavy and light mass eigenstates, Δms. Here we present a measurement of Δms using π+ decays produced in proton–proton collisions collected with the LHCb detector at the Large Hadron Collider. The oscillation frequency is found to be Δms = 17.7683 ± 0.0051 ± 0.0032 ps−1, where the first uncertainty is statistical and the second is systematic. This measurement improves on the current Δms precision by a factor of two. We combine this result with previous LHCb measurements to determine Δms = 17.7656 ± 0.0057 ps−1, which is the legacy measurement of the original LHCb detector.

Physical review letters

Multiparticle azimuthal correlations of prompt D 0 mesons are measured in Pb-Pb collisions at a nucleon-nucleon center-of-mass energy of s NN= 5.02 TeV. For the first time, a four-particle cumulant method is used to extract the second Fourier coefficient of the azimuthal distribution (v 2) of D 0 mesons as a function of event centrality and the D 0 transverse momentum. The ratios of the four-particle v 2 values to previously measured two-particle cumulant results provide direct experimental access to event-by-event fluctuations of charm quark azimuthal anisotropies. These ratios are also found to be comparable to those of inclusive charged particles in the event. However, hints of deviations are seen in the most central and peripheral collisions. To investigate the origin of flow fluctuations in the charm sector, these measurements are compared to a model implementing fluctuations of charm quark energy loss via …

Physical review letters

The B c+ meson is observed for the first time in heavy ion collisions. Data from the CMS detector are used to study the production of the B c+ meson in lead-lead (Pb-Pb) and proton-proton (p p) collisions at a center-of-mass energy per nucleon pair of s N N= 5.02 TeV, via the B c+→(J/ψ→ μ+ μ−) μ+ ν μ decay. The B c+ nuclear modification factor, derived from the Pb-Pb–to–p p ratio of production cross sections, is measured in two bins of the trimuon transverse momentum and of the Pb-Pb collision centrality. The B c+ meson is shown to be less suppressed than quarkonia and most of the open heavy-flavor mesons, suggesting that effects of the hot and dense nuclear matter created in heavy ion collisions contribute to its production. This measurement sets forth a promising new probe of the interplay of suppression and enhancement mechanisms in the production of heavy-flavor mesons in the quark-gluon plasma.

Physics Letters B

A search for W γ resonances in the mass range between 0.7 and 6.0 TeV is presented. The W boson is reconstructed via its hadronic decays, with the final-state products forming a single large-radius jet, owing to a high Lorentz boost of the W boson. The search is based on proton-proton collision data at s= 13 TeV, corresponding to an integrated luminosity of 137 fb− 1, collected with the CMS detector at the LHC in 2016–2018. The W γ mass spectrum is parameterized with a smoothly falling background function and examined for the presence of resonance-like signals. No significant excess above the predicted background is observed. Model-specific upper limits at 95% confidence level on the product of the cross section and branching fraction to the W γ channel are set. Limits for narrow resonances and for resonances with an intrinsic width equal to 5% of their mass, for spin-0 and spin-1 hypotheses, range …

Quaternary International

During the past several decades, the paleoecology of the Mammuthus-Coelodonta Faunal Complex in the Palearctic has been thoroughly explored, especially using stable isotope analysis. Numerous studies have documented high ecological plasticity and regional heterogeneities for this fauna. However, very limited attention has focused on Northeast Asia, at the southeastern edge of the distribution of the mammoth steppe biome. In the present study, we undertook radiocarbon dating, zooarchaeology by mass spectrometry (ZooMS), and stable isotope analysis on the fossil faunas from Yanjiagang Paleolithic site, Northeast (NE) China, and from the Geographical Society Cave in the nearby Russian Far East, to explore the paleoecology of this fauna in this middle-latitude region. Isotopic (δ13C, δ15N) data from these two sites suggested that the woolly mammoth (Mammuthus primigenius) was a grazer feeding on …

Quaternary International

The giant short-faced hyena, Pachycrocuta brevirostris, was the largest and most spectacular bone-cracking hyena that ever existed. Although already extinct long ago, it was extensively distributed across Eurasia during the Early and Middle Pleistocene. P. brevirostris is remarkable for a series of iconic craniodental adaptations in sway with a commitment to scavenging off carcasses of other large herbivores, such as the powerfully built skull and massive premolars, yet the most eye-catching aspect is the enormous size as emphasized by its vernacular name. The largest hitherto known skull of this species is the holotype from Sainzelles in Auvergne, France, discovered over a century ago. We hereby report a new discovery from Jinyuan Cave in Dalian, China, which slightly surpasses the holotype in craniodental dimension, posing a new record in Pachycrocuta body size. Three skull fragments of the same individual …

Physics Letters B

Measurements of the second Fourier harmonic coefficient (v 2) of the azimuthal distributions of prompt and nonprompt D 0 mesons produced in p p and p Pb collisions are presented. Nonprompt D 0 mesons come from beauty hadron decays. The data samples are collected by the CMS experiment at nucleon-nucleon center-of-mass energies of 13 and 8.16 TeV, respectively. In high multiplicity p p collisions, v 2 signals for prompt charm hadrons are reported for the first time, and are found to be comparable to those for light-flavor hadron species over a transverse momentum (p T) range of 2–6 GeV. Compared at similar event multiplicities, the prompt D 0 meson v 2 values in p p and p Pb collisions are similar in magnitude. The v 2 values for open beauty hadrons are extracted for the first time via nonprompt D 0 mesons in p Pb collisions. For p T in the range of 2–5 GeV, the results suggest that v 2 for nonprompt D 0 …

Journal of High Energy Physics

A search is presented for new particles produced at the LHC in proton-proton collisions at= 13 TeV, using events with energetic jets and large missing transverse momentum. The analysis is based on a data sample corresponding to an integrated luminosity of 101 fb− 1, collected in 2017–2018 with the CMS detector. Machine learning techniques are used to define separate categories for events with narrow jets from initial-state radiation and events with large-radius jets consistent with a hadronic decay of a W or Z boson. A statistical combination is made with an earlier search based on a data sample of 36 fb− 1, collected in 2016. No significant excess of events is observed with respect to the standard model background expectation determined from control samples in data. The results are interpreted in terms of limits on the branching fraction of an invisible decay of the Higgs boson, as well as constraints on …

The European Physical Journal C

The Deep Underground Neutrino Experiment (DUNE), a 40-kton underground liquid argon time projection chamber experiment, will be sensitive to the electron-neutrino flavor component of the burst of neutrinos expected from the next Galactic core-collapse supernova. Such an observation will bring unique insight into the astrophysics of core collapse as well as into the properties of neutrinos. The general capabilities of DUNE for neutrino detection in the relevant few- to few-tens-of-MeV neutrino energy range will be described. As an example, DUNE’s ability to constrain the spectral parameters of the neutrino burst will be considered.

Eur. Phys. J. C

A search is performed for heavy neutrinos in the decay of a W boson into two muons and a jet. The data set corresponds to an integrated luminosity of approximately 3. 0 fb− 1 of proton–proton collision data at centre-of-mass energies of 7 and 8 TeV collected with the LHCb experiment. Both same-sign and opposite-sign muons in the final state are considered. Data are found to be consistent with the expected background. Upper limits on the coupling of a heavy neutrino with the Standard Model neutrino are set at 95% confidence level in the heavy-neutrino mass range from 5 to 50 GeV/c2. These are of the order of 10− 3 for lepton-number-conserving decays and of the order of 10− 4 for lepton-number-violating heavy-neutrino decays.

Physical Review D

A search for C P violation in charmless three-body Ξ b−→ p K− K− decays is performed using p p collision data recorded with the LHCb detector, corresponding to integrated luminosities of 1 fb− 1 at a center-of-mass energy s= 7 TeV, 2 fb− 1 at s= 8 TeV and 2 fb− 1 at s= 13 TeV. A good description of the phase-space distribution is obtained with an amplitude model containing contributions from Σ (1385), Λ (1405), Λ (1520), Λ (1670), Σ (1775) and Σ (1915) resonances. The model allows for C P-violation effects, which are found to be consistent with zero. The branching fractions of Ξ b−→ Σ (1385) K−, Ξ b−→ Λ (1405) K−, Ξ b−→ Λ (1520) K−, Ξ b−→ Λ (1670) K−, Ξ b−→ Σ (1775) K− and Ξ b−→ Σ (1915) K− decays are also reported. In addition, an upper limit is placed on the product of ratios of Ω b− and Ξ b− fragmentation fractions and the Ω b−→ p K− K− and Ξ b−→ p K− K− branching fractions.

Quaternary International

Recently, rich fossiliferous deposits dated to the late Cenozoic have been discovered from Jinyuan Cave at Luotuo Hill, an extremely large-sized cave site situated within in the Dalian Puwan Economic Zone of Dalian Municipality, Liaoning Province in Northeast China. Abundant and diverse vertebrate fossils unearthed from different fossiliferous layers of Jinyuan Cave, a site of enormous size with a sedimentary thickness of over 40 m and its deposits can be roughly divided into three fossiliferous deposit units, altogether containing six fossiliferous layers belonging to different ages from the Late Pliocene to the Middle Pleistocene. Based on a combination of biostratigraphic and geochronological evidence, the fossil assemblages from Jinyuan Cave can be divided into three successive faunas that span the Late Cenozoic (ca. 3.60–0.35 Ma): the Wanghai fauna from upper faunal unit (Middle Pleistocene, 0.78–0.35 …

Physical Review C

Event-by-event long-range correlations of azimuthal anisotropy Fourier coefficients (v n) in 8.16 TeV p Pb data, collected by the CMS experiment at the CERN Large Hadron Collider, are extracted using a subevent four-particle cumulant technique applied to very low multiplicity events. Each combination of four charged particles is selected from either two, three, or four distinct subevent regions of a pseudorapidity range from− 2.4 to 2.4 of the CMS tracker, and with transverse momentum between 0.3 and 3.0 GeV. Using the subevent cumulant technique, correlations between v n of different orders are measured as functions of particle multiplicity and compared to the standard cumulant method without subevents over a wide event multiplicity range. At high multiplicities, the v 2 and v 3 coefficients exhibit an anticorrelation; this behavior is observed consistently using various methods. The v 2 and v 4 correlation strength …

Science Bulletin

First evidence of a structure in the J/ψ Λ invariant mass distribution is obtained from an amplitude analysis of Ξ b-→ J/ψ Λ K-decays. The observed structure is consistent with being due to a charmonium pentaquark with strangeness with a significance of 3.1 σ including systematic uncertainties and look-elsewhere effect. Its mass and width are determined to be 4458.8±2.9-1.1+ 4.7 MeV and 17.3±6.5-5.7+ 8.0 MeV, respectively, where the quoted uncertainties are statistical and systematic. The structure is also consistent with being due to two resonances. In addition, the narrow excited Ξ-states, Ξ 1690-and Ξ 1820-, are seen for the first time in a Ξ b-decay, and their masses and widths are measured with improved precision. The analysis is performed using pp collision data corresponding to a total integrated luminosity of 9 fb-1, collected with the LHCb experiment at centre-of-mass energies of 7, 8 and 13 TeV.

Physical Review Letters

We present an angular analysis of the B+→ K*+(→ K S 0 π+) μ+ μ− decay using 9 fb− 1 of p p collision data collected with the LHCb experiment. For the first time, the full set of C P-averaged angular observables is measured in intervals of the dimuon invariant mass squared. Local deviations from standard model predictions are observed, similar to those in previous LHCb analyses of the isospin-partner B 0→ K* 0 μ+ μ− decay. The global tension is dependent on which effective couplings are considered and on the choice of theory nuisance parameters.

Applied and Environmental Microbiology

Acinetobacter baumannii, an important pathogen known for its widespread antibiotic resistance, has been the focus of extensive research within its genus, primarily involving clinical isolates. Consequently, data on environmental A. baumannii and other Acinetobacter species remain limited. Here, we utilized Illumina and Nanopore sequencing to analyze the genomes of 10 Acinetobacter isolates representing 6 different species sourced from aquatic environments in South Australia. All 10 isolates were phylogenetically distinct compared to clinical and other non-clinical Acinetobacter strains, often tens of thousands of single-nucleotide polymorphisms from their nearest neighbors. Despite the genetic divergence, we identified pdif modules (sections of mobilized DNA) carrying clinically important antimicrobial resistance genes in species other than A. baumannii, including carbapenemase oxa58, tetracycline …

Applied and Environmental Microbiology

Lignocellulose is a renewable but complex material exhibiting high recalcitrance to enzymatic hydrolysis, which is attributed, in part, to the presence of covalent linkages between lignin and polysaccharides in the plant cell wall. Glucuronoyl esterases from carbohydrate esterase family 15 (CE15) have been proposed as an aid in reducing this recalcitrance by cleaving ester bonds found between lignin and glucuronoxylan. In the Bacteroidota phylum, some species organize genes related to carbohydrate metabolism in polysaccharide utilization loci (PULs) which encode all necessary proteins to bind, deconstruct, and respond to a target glycan. Bioinformatic analyses identified CE15 members in some PULs that appear to not target the expected glucuronoxylan. Here, five CE15 members from such PULs were investigated with the aim of gaining insights on their biological roles. The selected targets were …

Applied and Environmental Microbiology

The build-up of formaldehyde, a highly reactive molecule is cytotoxic and must be eliminated for the organism’s survival. Formaldehyde detoxification system is found in nearly all organisms including both pathogenic and non-pathogenic mycobacteria. MscR, a formaldehyde dehydrogenase from Mycobacterium smegmatis (Msm), is an indispensable part of this system and forms a bicistronic operon with its downstream uncharacterized gene, fmh. We here show that Fmh, a putative metallo-beta-lactamase, is essential in tolerating higher amounts of formaldehyde when co-overexpressed with mscR in vivo. Our NMR studies indicate that MscR, along with Fmh, enhances formate production through a mycothiol (MSH)-dependent pathway, emphasizing the importance of Fmh in detoxifying formaldehyde. Although another aldehyde dehydrogenase, MSMEG_1543, induces upon formaldehyde addition, it is not involved …

Applied and Environmental Microbiology

The coronavirus disease 2019 pandemic illustrates the importance of understanding the behavior and control of human pathogenic viruses in the environment. Exposure via water (drinking, bathing, and recreation) is a known route of transmission of viruses to humans, but the literature is relatively void of studies on the persistence of many viruses, especially coronaviruses, in water and their susceptibility to chlorine disinfection. To fill that knowledge gap, we evaluated the persistence and free chlorine disinfection of human coronavirus OC43 (HCoV-OC43) and its surrogates, murine hepatitis virus (MHV) and porcine transmissible gastroenteritis virus (TGEV), in drinking water and laboratory buffer using cell culture methods. The decay rate constants of human coronavirus and its surrogates in water varied, depending on virus and water matrix. In drinking water without disinfectant addition, MHV showed the largest …

Applied and Environmental Microbiology

The novel genus Aquibium that lacks nitrogenase was recently reclassified from the Mesorhizobium genus. The genomes of Aquibium species isolated from water were smaller and had higher GC contents than those of Mesorhizobium species. Six Mesorhizobium species lacking nitrogenase were found to exhibit low similarity in the average nucleotide identity values to the other 24 Mesorhizobium species. Therefore, they were classified as the non-N2-fixing Mesorhizobium lineage (N-ML), an evolutionary intermediate species. The results of our phylogenomic analyses and the loss of Rhizobiales-specific fur/mur indicated that Mesorhizobium species may have evolved from Aquibium species through an ecological transition. Halotolerant and alkali-resistant Aquibium and Mesorhizobium microcysteis belonging to N-ML possessed many tripartite ATP-independent periplasmic transporter and sodium/proton …

Applied and Environmental Microbiology

Adding trace calcium peroxide and magnetite into a semi-continuous digester is a new method to effectively improve the anaerobic digestion of food waste. However, the microbial mechanism in this system has not been fully explored. Metaproteomics further revealed that the most active and significantly regulated genus u_p_Chloroflexi had formed a good cooperative relationship with Methanomicrobiales and Methanothrix in the system. u_p_Chloroflexi decomposed more organic compounds into CO2, acetate, amino acids, and other substances by alternating between short aerobic-anaerobic respiration. It perceived and adapted to the surrounding environment by producing biofilm, extracellular enzymes, and accelerating substrate transport, formed a respiratory barrier, and enhanced iron transport capacity by using highly expressed cytochrome C. The methanogens formed reactive oxygen species scavengers …

Applied and Environmental Microbiology

Bifidobacterium breve, one of the main bifidobacterial species colonizing the human gastrointestinal tract in early life, has received extensive attention for its purported beneficial effects on human health. However, exploration of the mode of action of such beneficial effects exerted by B. breve is cumbersome due to the lack of effective genetic tools, which limits its synthetic biology application. The widespread presence of CRISPR-Cas systems in the B. breve genome makes endogenous CRISPR-based gene editing toolkits a promising tool. This study revealed that Type I-C CRISPR-Cas systems in B. breve can be divided into two groups based on the amino acid sequences encoded by cas gene clusters. Deletion of the gene coding uracil phosphoribosyl-transferase (upp) was achieved in five B. breve strains from both groups using this system. In addition, translational termination of uracil phosphoribosyl-transferase …

Applied and Environmental Microbiology

The degree of cyclization, or ring index (RI), in archaeal glycerol dibiphytanyl glycerol tetraether (GDGT) lipids was long thought to reflect homeoviscous adaptation to temperature. However, more recent experiments show that other factors (e.g., pH, growth phase, and energy flux) can also affect membrane composition. The main objective of this study was to investigate the effect of carbon and energy metabolism on membrane cyclization. To do so, we cultivated Acidianus sp. DS80, a metabolically flexible and thermoacidophilic archaeon, on different electron donor, acceptor, and carbon source combinations (S0/Fe3+/CO2, H2/Fe3+/CO2, H2/S0/CO2, or H2/S0/glucose). We show that differences in energy and carbon metabolism can result in over a full unit of change in RI in the thermoacidophile Acidianus sp. DS80. The patterns in RI correlated with the normalized electron transfer rate between the electron donor …

Applied and Environmental Microbiology

In this study, we conducted an in-depth analysis to characterize potential Acanthamoeba castellanii (Ac) proteins capable of recognizing fungal β-1,3-glucans. Ac specifically anchors curdlan or laminarin, indicating the presence of surface β-1,3-glucan-binding molecules. Using optical tweezers, strong adhesion of laminarin- or curdlan-coated beads to Ac was observed, highlighting their adhesive properties compared to controls (characteristic time τ of 46.9 and 43.9 s, respectively). Furthermore, Histoplasma capsulatum (Hc) G217B, possessing a β-1,3-glucan outer layer, showed significant adhesion to Ac compared to a Hc G186 strain with an α-1,3-glucan outer layer (τ of 5.3 s vs τ 83.6 s). The addition of soluble β-1,3-glucan substantially inhibited this adhesion, indicating the involvement of β-1,3-glucan recognition. Biotinylated β-1,3-glucan-binding proteins from Ac exhibited higher binding to Hc G217B …

Applied and Environmental Microbiology

Anti-viral surface coatings are under development to prevent viral fomite transmission from high-traffic touch surfaces in public spaces. Copper’s anti-viral properties have been widely documented, but the anti-viral mechanism of copper surfaces is not fully understood. We screened a series of metal and metal oxide surfaces for anti-viral activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease (COVID-19). Copper and copper oxide surfaces exhibited superior anti-SARS-CoV-2 activity; however, the level of anti-viral activity was dependent on the composition of the carrier solution used to deliver virus inoculum. We demonstrate that copper ions released into solution from test surfaces can mediate virus inactivation, indicating a copper ion dissolution-dependent anti-viral mechanism. The level of anti-viral activity is, however, not dependent on the …

Applied and Environmental Microbiology

Aquaculture provides a rich resource of high-quality protein; however, the production is challenged by emerging pathogens such as Vibrio crassostreae. While probiotic bacteria have been proposed as a sustainable solution to reduce pathogen load in aquaculture, their application requires a comprehensive assessment across the aquaculture food chain. The purpose of this study was to determine the antagonistic effect of the potential probiotic bacterium Phaeobacter piscinae against the emerging fish pathogen V. crassostreae in aquaculture feed algae that can be an entry point for pathogens in fish and shellfish aquaculture. P. piscinae strain S26 produces the antibacterial compound tropodithietic acid (TDA). In a plate-based assay, P. piscinae S26 was equally to more effective than the well-studied Phaeobacter inhibens DSM17395 in its inhibition of the fish pathogens Vibrio anguillarum 90-11-286 and V …

Applied and Environmental Microbiology

Clostridioides difficile represents a major burden to public health. As a well-known nosocomial pathogen whose occurrence is highly associated with antibiotic treatment, most examined C. difficile strains originated from clinical specimen and were isolated under selective conditions employing antibiotics. This suggests a significant bias among analyzed C. difficile strains, which impedes a holistic view on this pathogen. In order to support extensive isolation of C. difficile strains from environmental samples, we designed a detection PCR that targets the hpdBCA-operon and thereby identifies low abundances of C. difficile in environmental samples. This operon encodes the 4-hydroxyphenylacetate decarboxylase, which catalyzes the production of the antimicrobial compound para-cresol. Amplicon-based analyses of diverse environmental samples demonstrated that the designed PCR is highly specific for C. difficile …

Applied and Environmental Microbiology

Fungi have the capacity to assimilate a diverse range of both inorganic and organic sulfur compounds. It has been recognized that all sulfur sources taken up by fungi are in soluble forms. In this study, we present evidence that fungi can utilize gaseous carbonyl sulfide (COS) for the assimilation of a sulfur compound. We found that the filamentous fungus Trichoderma harzianum strain THIF08, which has constitutively high COS-degrading activity, was able to grow with COS as the sole sulfur source. Cultivation with 34S-labeled COS revealed that sulfur atom from COS was incorporated into intracellular metabolites such as glutathione and ergothioneine. COS degradation by strain THIF08, in which as much of the moisture derived from the agar medium as possible was removed, indicated that gaseous COS was taken up directly into the cell. Escherichia coli transformed with a COS hydrolase (COSase) gene, which is …

Applied and Environmental Microbiology

Expulsions of virus-laden aerosols or droplets from the oral and nasal cavities of an infected host are an important source of onward respiratory virus transmission. However, the presence of infectious influenza virus in the oral cavity during infection has not been widely considered, and thus, little work has explored the environmental persistence of influenza virus in oral cavity expulsions. Using the ferret model, we detected infectious virus in the nasal and oral cavities, suggesting that the virus can be expelled into the environment from both anatomical sites. We also assessed the stability of two influenza A viruses (H1N1 and H3N2) in droplets of human saliva or respiratory mucus over a range of relative humidities. We observed that influenza virus infectivity decays rapidly in saliva droplets at intermediate relative humidity, while viruses in airway surface liquid droplets retain infectivity. Virus inactivation was not …

Applied and Environmental Microbiology

Penicillin-binding proteins (PBPs) play critical roles in cell wall construction, cell shape maintenance, and bacterial replication. Bacteria maintain a diversity of PBPs, indicating that despite their apparent functional redundancy, there is differentiation across the PBP family. Apparently-redundant proteins can be important for enabling an organism to cope with environmental stressors. In this study, we evaluated the consequence of environmental pH on PBP enzymatic activity in Bacillus subtilis. Our data show that a subset of PBPs in B. subtilis change activity levels during alkaline shock and that one PBP isoform is rapidly modified to generate a smaller protein (i.e., PBP1a to PBP1b). Our results indicate that a subset of the PBPs are favored for growth under alkaline conditions, while others are readily dispensable. Indeed, we found that this phenomenon could also be observed in Streptococcus pneumoniae, implying …

Applied and Environmental Microbiology

Plasmid conjugation is a key facilitator of horizontal gene transfer (HGT), and plasmids encoding antibiotic resistance drive the increasing prevalence of antibiotic resistance. In natural, engineered, and clinical environments, bacteria often grow in protective biofilms. Therefore, a better understanding of plasmid transfer in biofilms is needed. Our aim was to investigate plasmid transfer in a biofilm-adapted wrinkly colony mutant of Xanthomonas retroflexus (XRw) with enhanced matrix production and reduced motility. We found that XRw biofilms had an increased uptake of the broad host-range IncP-1ϵ plasmid pKJK5 compared to the wild type (WT). Proteomics revealed fewer flagellar-associated proteins in XRw, suggesting that flagella were responsible for reducing plasmid uptake. This was confirmed by the higher plasmid uptake of non-flagellated fliM mutants of the X. retroflexus wrinkly mutant as well as the wild …

Applied and Environmental Microbiology

Biodesulfurization (BD) systems that treat sour gas employ mixtures of haloalkaliphilic sulfur-oxidizing bacteria to convert sulfide to elemental sulfur. In the past years, these systems have seen major technical innovations that have led to changes in microbial community composition. Different studies have identified and discussed the microbial communities in both traditional and improved systems. However, these studies do not identify metabolically active community members and merely focus on members’ presence/absence. Therefore, their results cannot confirm the activity and role of certain bacteria in the BD system. To investigate the active community members, we determined the microbial communities of six different runs of a pilot-scale BD system. 16S rRNA gene-based amplicon sequencing was performed using both DNA and RNA. A comparison of the DNA- and RNA-based sequencing results identified …

Applied and environmental microbiology

The generation of nitrite by the oral microbiota is believed to contribute to healthy cardiovascular function, with oral nitrate reduction to nitrite associated with systemic blood pressure regulation. There is the potential to manipulate the composition or activities of the oral microbiota to a higher nitrate-reducing state through nitrate supplementation. The current study examined microbial community composition and enzymatic responses to nitrate supplementation in sessile oral microbiota grown in continuous culture. Nitrate reductase (NaR) activity and nitrite concentrations were not significantly different to tongue-derived inocula in model biofilms. These were generally dominated by Streptococcus spp., initially, and a single nitrate supplementation resulted in the increased relative abundance of the nitrate-reducing genera Veillonella, Neisseria, and Proteus spp. Nitrite concentrations increased concomitantly and …

Applied and Environmental Microbiology

The coronavirus disease 2019 pandemic illustrates the importance of understanding the behavior and control of human pathogenic viruses in the environment. Exposure via water (drinking, bathing, and recreation) is a known route of transmission of viruses to humans, but the literature is relatively void of studies on the persistence of many viruses, especially coronaviruses, in water and their susceptibility to chlorine disinfection. To fill that knowledge gap, we evaluated the persistence and free chlorine disinfection of human coronavirus OC43 (HCoV-OC43) and its surrogates, murine hepatitis virus (MHV) and porcine transmissible gastroenteritis virus (TGEV), in drinking water and laboratory buffer using cell culture methods. The decay rate constants of human coronavirus and its surrogates in water varied, depending on virus and water matrix. In drinking water without disinfectant addition, MHV showed the largest …

Applied and Environmental Microbiology

Application of organic fertilizers is an important strategy for sustainable agriculture. The biological source of organic fertilizers determines their specific functional characteristics, but few studies have systematically examined these functions or assessed their health risk to soil ecology. To fill this gap, we analyzed 16S rRNA gene amplicon sequencing data from 637 soil samples amended with plant- and animal-derived organic fertilizers (hereafter plant fertilizers and animal fertilizers). Results showed that animal fertilizers increased the diversity of soil microbiome, while plant fertilizers maintained the stability of soil microbial community. Microcosm experiments verified that plant fertilizers were beneficial to plant root development and increased carbon cycle pathways, while animal fertilizers enriched nitrogen cycle pathways. Compared with animal fertilizers, plant fertilizers harbored a lower abundance of risk factors …