scholarly journals Molybdenum-Based Diazotrophy in a Sphagnum Peatland in Northern Minnesota

2017 ◽  
Vol 83 (17) ◽  
Author(s):  
Melissa J. Warren ◽  
Xueju Lin ◽  
John C. Gaby ◽  
Cecilia B. Kretz ◽  
Max Kolton ◽  
...  
Keyword(s):  
Nitrogen Source ◽  
Environmental Parameters ◽  
Amplicon Sequencing ◽  
Peat Bog ◽  
Content Type ◽  
Environmental Controls ◽  
Low Concentrations ◽  
Activity Measurements ◽  
Microbial Group ◽  
Surface Peat

ABSTRACT Microbial N2 fixation (diazotrophy) represents an important nitrogen source to oligotrophic peatland ecosystems, which are important sinks for atmospheric CO2 and are susceptible to the changing climate. The objectives of this study were (i) to determine the active microbial group and type of nitrogenase mediating diazotrophy in an ombrotrophic Sphagnum-dominated peat bog (the S1 peat bog, Marcell Experimental Forest, Minnesota, USA); and (ii) to determine the effect of environmental parameters (light, O2, CO2, and CH4) on potential rates of diazotrophy measured by acetylene (C2H2) reduction and 15N2 incorporation. A molecular analysis of metabolically active microbial communities suggested that diazotrophy in surface peat was primarily mediated by Alphaproteobacteria (Bradyrhizobiaceae and Beijerinckiaceae). Despite higher concentrations of dissolved vanadium ([V] 11 nM) than molybdenum ([Mo] 3 nM) in surface peat, a combination of metagenomic, amplicon sequencing, and activity measurements indicated that Mo-containing nitrogenases dominate over the V-containing form. Acetylene reduction was only detected in surface peat exposed to light, with the highest rates observed in peat collected from hollows with the highest water contents. Incorporation of 15N2 was suppressed 90% by O2 and 55% by C2H2 and was unaffected by CH4 and CO2 amendments. These results suggest that peatland diazotrophy is mediated by a combination of C2H2-sensitive and C2H2-insensitive microbes that are more active at low concentrations of O2 and show similar activity at high and low concentrations of CH4. IMPORTANCE Previous studies indicate that diazotrophy provides an important nitrogen source and is linked to methanotrophy in Sphagnum-dominated peatlands. However, the environmental controls and enzymatic pathways of peatland diazotrophy, as well as the metabolically active microbial populations that catalyze this process, remain in question. Our findings indicate that oxygen levels and photosynthetic activity override low nutrient availability in limiting diazotrophy and that members of the Alphaproteobacteria (Rhizobiales) catalyze this process at the bog surface using the molybdenum-based form of the nitrogenase enzyme.

scholarly journals Molybdenum-based diazotrophy in aSphagnumpeatland in northern Minnesota

2017 ◽  
Author(s):  
Melissa J. Warren ◽  
Xueju Lin ◽  
John C. Gaby ◽  
Cecilia B. Kretz ◽  
Max Kolton ◽  
...  
Keyword(s):  
Nitrogen Source ◽  
Environmental Parameters ◽  
Amplicon Sequencing ◽  
Peat Bog ◽  
Environmental Controls ◽  
Activity Measurements ◽  
Microbial Group ◽  
Enzymatic Pathways ◽  
Surface Peat ◽  
Microbial N

AbstractMicrobial N2fixation (diazotrophy) represents an important nitrogen source to oligotrophic peatland ecosystems, which are important sinks for atmospheric CO2and susceptible to changing climate. The objectives of this study were: (i) to determine the active microbial group and type of nitrogenase mediating diazotrophy in a ombrotrophicSphagnum-dominated peat bog (the S1 peat bog, Marcell Experimental Forest, Minnesota, USA); and (ii) to determine the effect of environmental parameters (light, O2, CO2, CH4) on potential rates of diazotrophy measured by acetylene (C2H2) reduction and15N2incorporation. Molecular analysis of metabolically active microbial communities suggested that diazotrophy in surface peat was primarily mediated byAlphaproteobacteria(BradyrhizobiaceaeandBeijerinckiaceae). Despite higher dissolved vanadium (V; 11 nM) than molybdenum (Mo; 3 nM) in surface peat, a combination of metagenomic, amplicon sequencing and activity measurements indicated that Mo-containing nitrogenases dominate over the V-containing form. Acetylene reduction was only detected in surface peat exposed to light, with the highest rates observed in peat collected from hollows with the highest water content. Incorporation of15N2was suppressed 90% by O2and 55% by C2H2, and was unaffected by CH4and CO2amendments. These results suggest that peatland diazotrophy is mediated by a combination of C2H2- sensitive and C2H2- insensitive microbes that are more active at low O2and show similar activity at high and low CH4.ImportancePrevious studies indicate that diazotrophy provides an important nitrogen source and is linked to methanotrophy inSphagnum-dominated peatlands. However, the environmental controls and enzymatic pathways of peatland diazotrophy, as well as the metabolically active microbial populations that catalyze this process remain in question. Our findings indicate that oxygen levels and photosynthetic activity override low nutrient availability in limiting diazotrophy, and that members of theAlphaproteobacteria(Rhizobiales) catalyze this process at the bog surface using the molybdenum - based form of the nitrogenase enzyme.

scholarly journals PacBio Amplicon Sequencing Method To Measure Pilin Antigenic Variation Frequencies of Neisseria gonorrhoeae

mSphere ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Egon A. Ozer ◽  
Lauren L. Prister ◽  
Shaohui Yin ◽  
Billy H. Ward ◽  
Stanimir Ivanov ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Antigenic Variation ◽  
Amplicon Sequencing ◽  
Common Mechanism ◽  
Macrophage Infection ◽  
Gene Encoding ◽  
Transmitted Infection ◽  
Variable Regions ◽  
Content Type ◽  
Strain Fa1090

ABSTRACT Gene diversification is a common mechanism pathogens use to alter surface structures to aid in immune avoidance. Neisseria gonorrhoeae uses a gene conversion-based diversification system to alter the primary sequence of the gene encoding the major subunit of the pilus, pilE. Antigenic variation occurs when one of the nonexpressed 19 silent copies donates part of its DNA sequence to pilE. We have developed a method using Pacific Biosciences (PacBio) amplicon sequencing and custom software to determine pilin antigenic variation frequencies. The program analyzes 37 variable regions across the strain FA1090 1-81-S2 pilE gene and can be modified to determine sequence variation from other starting pilE sequences or other diversity generation systems. Using this method, we measured pilin antigenic variation frequencies for various derivatives of strain FA1090 and showed we can also analyze pilin antigenic variation frequencies during macrophage infection. IMPORTANCE Diversity generation systems are used by many unicellular organism to provide subpopulations of cell with different properties that are available when needed. We have developed a method using the PacBio DNA sequencing technology and a custom computer program to analyze the pilin antigenic variation system of the organism that is the sole cause of the sexually transmitted infection, gonorrhea.

scholarly journals Cervicovaginal Microbiome Composition Is Associated with Metabolic Profiles in Healthy Pregnancy

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Andrew Oliver ◽  
Brandon LaMere ◽  
Claudia Weihe ◽  
Stephen Wandro ◽  
Karen L. Lindsay ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Reproductive Health ◽  
Microbial Communities ◽  
Carbon Sources ◽  
Amplicon Sequencing ◽  
Vaginal Microbiome ◽  
Content Type ◽  
Healthy Women ◽  
Healthy Pregnancy ◽  
Tof Ms

ABSTRACT Microbes and their metabolic products influence early-life immune and microbiome development, yet remain understudied during pregnancy. Vaginal microbial communities are typically dominated by one or a few well-adapted microbes which are able to survive in a narrow pH range and are adapted to live on host-derived carbon sources, likely sourced from glycogen and mucin present in the vaginal environment. We characterized the cervicovaginal microbiomes of 16 healthy women throughout the three trimesters of pregnancy. Additionally, we analyzed saliva and urine metabolomes using gas chromatography-time of flight mass spectrometry (GC-TOF MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) lipidomics approaches for samples from mothers and their infants through the first year of life. Amplicon sequencing revealed most women had either a simple community with one highly abundant species of Lactobacillus or a more diverse community characterized by a high abundance of Gardnerella, as has also been previously described in several independent cohorts. Integrating GC-TOF MS and lipidomics data with amplicon sequencing, we found metabolites that distinctly associate with particular communities. For example, cervicovaginal microbial communities dominated by Lactobacillus crispatus have high mannitol levels, which is unexpected given the characterization of L. crispatus as a homofermentative Lactobacillus species. It may be that fluctuations in which Lactobacillus dominate a particular vaginal microbiome are dictated by the availability of host sugars, such as fructose, which is the most likely substrate being converted to mannitol. Overall, using a multi-“omic” approach, we begin to address the genetic and molecular means by which a particular vaginal microbiome becomes vulnerable to large changes in composition. IMPORTANCE Humans have a unique vaginal microbiome compared to other mammals, characterized by low diversity and often dominated by Lactobacillus spp. Dramatic shifts in vaginal microbial communities sometimes contribute to the presence of a polymicrobial overgrowth condition called bacterial vaginosis (BV). However, many healthy women lacking BV symptoms have vaginal microbiomes dominated by microbes associated with BV, resulting in debate about the definition of a healthy vaginal microbiome. Despite substantial evidence that the reproductive health of a woman depends on the vaginal microbiota, future therapies that may improve reproductive health outcomes are stalled due to limited understanding surrounding the ecology of the vaginal microbiome. Here, we use sequencing and metabolomic techniques to show novel associations between vaginal microbes and metabolites during healthy pregnancy. We speculate these associations underlie microbiome dynamics and may contribute to a better understanding of transitions between alternative vaginal microbiome compositions.

scholarly journals Factors Influencing the Microbial Composition of Metalworking Fluids and Potential Implications for Machine Operator's Lung

2011 ◽  
Vol 78 (1) ◽  
pp. 34-41 ◽  
Author(s):  
Jean-Benjamin Murat ◽  
Frédéric Grenouillet ◽  
Gabriel Reboux ◽  
Emmanuelle Penven ◽  
Adam Batchili ◽  
...  
Keyword(s):  
Metal Cutting ◽  
Hypersensitivity Pneumonitis ◽  
Environmental Parameters ◽  
Metalworking Fluids ◽  
Microbial Composition ◽  
Gram Positive ◽  
Gram Negative ◽  
Content Type ◽  
Kinetics Of

ABSTRACTHypersensitivity pneumonitis, also known as “machine operator's lung” (MOL), has been related to microorganisms growing in metalworking fluids (MWFs), especiallyMycobacterium immunogenum. We aimed to (i) describe the microbiological contamination of MWFs and (ii) look for chemical, physical, and environmental parameters associated with variations in microbiological profiles. We microbiologically analyzed 180 MWF samples from nonautomotive plants (e.g., screw-machining or metal-cutting plants) in the Franche-Comté region in eastern France and 165 samples from three French automotive plants in which cases of MOL had been proven. Our results revealed two types of microbial biomes: the first was from the nonautomotive industry, showed predominantly Gram-negative rods (GNR), and was associated with a low risk of MOL, and the second came from the automotive industry that was affected by cases of MOL and showed predominantly Gram-positive rods (GPR). Traces ofM. immunogenumwere sporadically detected in the first type, while it was highly prevalent in the automotive sector, with up to 38% of samples testing positive. The use of chromium, nickel, or iron was associated with growth of Gram-negative rods; conversely, growth of Gram-positive rods was associated with the absence of these metals. Synthetic MWFs were more frequently sterile than emulsions. Vegetable oil-based emulsions were associated with GNR, while mineral ones were associated with GPR. Our results suggest that metal types and the nature of MWF play a part in MWF contamination, and this work shall be followed by furtherin vitrosimulation experiments on the kinetics of microbial populations, focusing on the phenomena of inhibition and synergy.

Robot obstacle avoidance system using deep reinforcement learning

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Xiaojun Zhu ◽  
Yinghao Liang ◽  
Hanxu Sun ◽  
Xueqian Wang ◽  
Bin Ren
Keyword(s):  
Reinforcement Learning ◽  
Collision Avoidance ◽  
Obstacle Avoidance ◽  
Learning Algorithm ◽  
Optimal Path ◽  
Environmental Parameters ◽  
Working Environment ◽  
Content Type ◽  
Practical Applications ◽  
Human Operators

Purpose Most manufacturing plants choose the easy way of completely separating human operators from robots to prevent accidents, but as a result, it dramatically affects the overall quality and speed that is expected from human–robot collaboration. It is not an easy task to ensure human safety when he/she has entered a robot’s workspace, and the unstructured nature of those working environments makes it even harder. The purpose of this paper is to propose a real-time robot collision avoidance method to alleviate this problem. Design/methodology/approach In this paper, a model is trained to learn the direct control commands from the raw depth images through self-supervised reinforcement learning algorithm. To reduce the effect of sample inefficiency and safety during initial training, a virtual reality platform is used to simulate a natural working environment and generate obstacle avoidance data for training. To ensure a smooth transfer to a real robot, the automatic domain randomization technique is used to generate randomly distributed environmental parameters through the obstacle avoidance simulation of virtual robots in the virtual environment, contributing to better performance in the natural environment. Findings The method has been tested in both simulations with a real UR3 robot for several practical applications. The results of this paper indicate that the proposed approach can effectively make the robot safety-aware and learn how to divert its trajectory to avoid accidents with humans within the workspace. Research limitations/implications The method has been tested in both simulations with a real UR3 robot in several practical applications. The results indicate that the proposed approach can effectively make the robot be aware of safety and learn how to change its trajectory to avoid accidents with persons within the workspace. Originality/value This paper provides a novel collision avoidance framework that allows robots to work alongside human operators in unstructured and complex environments. The method uses end-to-end policy training to directly extract the optimal path from the visual inputs for the scene.

scholarly journals Environmental controls on the <i>Emiliania huxleyi</i> calcite mass

2014 ◽  
Vol 11 (8) ◽  
pp. 2295-2308 ◽  
Author(s):  
M. T. Horigome ◽  
P. Ziveri ◽  
M. Grelaud ◽  
K.-H. Baumann ◽  
G. Marino ◽  
...  
Keyword(s):  
Seawater Temperature ◽  
World Ocean ◽  
Environmental Parameters ◽  
Abundant Species ◽  
Emiliania Huxleyi ◽  
Ion Concentration ◽  
Carbonate Chemistry ◽  
Environmental Controls ◽  
Carbonate Ion ◽  
Phosphate Availability

Abstract. Although ocean acidification is expected to impact (bio) calcification by decreasing the seawater carbonate ion concentration, [CO32−], there is evidence of nonuniform response of marine calcifying plankton to low seawater [CO32−]. This raises questions about the role of environmental factors other than acidification and about the complex physiological responses behind calcification. Here we investigate the synergistic effect of multiple environmental parameters, including seawater temperature, nutrient (nitrate and phosphate) availability, and carbonate chemistry on the coccolith calcite mass of the cosmopolitan coccolithophore Emiliania huxleyi, the most abundant species in the world ocean. We use a suite of surface (late Holocene) sediment samples from the South Atlantic and southwestern Indian Ocean taken from depths lying above the modern lysocline (with the exception of eight samples that are located at or below the lysocline). The coccolith calcite mass in our results presents a latitudinal distribution pattern that mimics the main oceanographic features, thereby pointing to the potential importance of seawater nutrient availability (phosphate and nitrate) and carbonate chemistry (pH and pCO2) in determining coccolith mass by affecting primary calcification and/or the geographic distribution of E. huxleyi morphotypes. Our study highlights the importance of evaluating the combined effect of several environmental stressors on calcifying organisms to project their physiological response(s) in a high-CO2 world and improve interpretation of paleorecords.

scholarly journals Regulatory Effect of SlyA onrcsBExpression inSalmonella entericaSerovar Typhimurium

2018 ◽  
Vol 201 (4) ◽  
Author(s):  
María F. Ballesteros ◽  
Mónica F. Torrez Lamberti ◽  
Juan V. Farizano ◽  
María M. Pescaretti ◽  
Mónica A. Delgado
Keyword(s):  
Virulence Gene ◽  
Content Type ◽  
Virulence Gene Expression ◽  
Low Concentrations ◽  
Antagonistic Behavior ◽  
Serovar Typhimurium ◽  
Direct Binding ◽  
High Concentrations ◽  
Encoding Genes ◽  
Different Levels

ABSTRACTTheSalmonella entericaserovar Typhimurium RcsCDB system regulates the synthesis of colanic acid and the flagellum as well as the expression of virulence genes. We previously demonstrated that thercsC11mutant, which constitutively activates the RcsB regulator, attenuatesSalmonellavirulence in an animal model. This attenuated phenotype was also produced by deletion of theslyAgene. In this work, we investigated if this antagonistic behavior is produced by modulating the expression of both regulator-encoding genes. We demonstrated that SlyA overproduction negatively regulatesrcsBtranscription. A bioinformatics analysis enabled us to identify putative SlyA binding sites on both promoters, PrcsDBand PrcsB, which controlrcsBtranscriptional levels. We also determined that SlyA is able to recognize and bind to these predicted sites to modulate the activity of bothrcsBpromoters. According to these results, SlyA repressesrcsBtranscription by direct binding to specific sites located on thercsBpromoters, thus accounting for the attenuated/virulence antagonistic behaviors. Moreover, we showed that the opposite effect between both regulators also physiologically affects theSalmonellamotility phenotype. In this sense, we observed that under SlyA overproduction, PrcsBis repressed, and consequently, bacterial motility is increased. On the basis of these results, we suggest that during infection, the different RcsB levels produced act as a switch between the virulent and attenuated forms ofSalmonella. Thereby, we propose that higher concentrations of RcsB tilt the balance toward the attenuated form, while absence or low concentrations resulting from SlyA overproduction tilt the balance toward the virulent form.IMPORTANCEThe antagonistic behavior of RcsB and SlyA on virulence gene expression led us to hypothesize that there is interplay between both regulators in a regulatory network and these could be considered coordinators of this process. Here, we report that the SlyA virulence factor influences motility behavior by controllingrcsBtranscription from the PrcsBpromoter. We also demonstrate that SlyA negatively affects the expression of thercsBgene by direct binding to PrcsDBand PrcsBpromoters. We suggest that different levels of RcsB act as a switch between the virulent and attenuated forms ofSalmonella, where high concentrations of the regulator tend to tilt the balance toward the attenuated form and low concentrations or its absence tilt it toward the virulent form.

Environmental controls for underground coal gasification

2017 ◽  
Vol 232 (1) ◽  
pp. 47-55 ◽  
Author(s):  
CW Mallett
Keyword(s):  
Coal Gasification ◽  
Environmental Concern ◽  
Underground Coal Gasification ◽  
Transport Modelling ◽  
Pyrolysis Products ◽  
Groundwater Inflow ◽  
Gas Processing ◽  
Syngas Production ◽  
Environmental Controls ◽  
Low Concentrations

Effective environmental management of an underground coal gasification pilot has been demonstrated at Kogan in Queensland, Australia. It commenced with selection of a suitable site with a coal seam surrounded by impervious rocks that provided a gas seal for the gasifier and sufficient groundwater pressure to constrain lateral loss of gas and chemicals through coal fractures. Project infrastructure was specified to withstand the temperatures and pressures experienced during gasification and gas processing. During syngas production in the second gasifier, Panel 2, it was shown that all pyrolysis products of environmental concern were retained within the gasifier. This was achieved by maintaining continuous groundwater inflow into the gasifier cavity through control of the relative pressures of the gasifier and surrounding groundwater. In Panel 1, it was shown that when pyrolysis products migrated out of the cavity, they were quickly detected and by modifying relative pressures to increase groundwater inflow the original groundwater conditions were restored. Following production, the cavities were decommissioned and in Panel 2 steam cleaning of the cavity removed 92% of the chemical load from the cavity. As a result, relatively low concentrations of pyrolysis products remained in the cavity. Fate and transport modelling predicted that these products will not migrate into the regional groundwater and will naturally degrade within three decades.

scholarly journals A Mannose Family Phosphotransferase System Permease and Associated Enzymes Are Required for Utilization of Fructoselysine and Glucoselysine in Salmonella enterica Serovar Typhimurium

2015 ◽  
Vol 197 (17) ◽  
pp. 2831-2839 ◽  
Author(s):  
Katherine A. Miller ◽  
Robert S. Phillips ◽  
Paul B. Kilgore ◽  
Grady L. Smith ◽  
Timothy R. Hoover
Keyword(s):  
Nitrogen Source ◽  
Nitrogen Sources ◽  
Maillard Reaction Products ◽  
Reaction Products ◽  
Phosphotransferase System ◽  
Carbon And Nitrogen Sources ◽  
Content Type ◽  
Carbon And Nitrogen ◽  
Serovar Typhimurium ◽  
Food Borne Illness

ABSTRACTSalmonella entericserovar Typhimurium, a major cause of food-borne illness, is capable of using a variety of carbon and nitrogen sources. Fructoselysine and glucoselysine are Maillard reaction products formed by the reaction of glucose or fructose, respectively, with the ε-amine group of lysine. We report here thatS. Typhimurium utilizes fructoselysine and glucoselysine as carbon and nitrogen sources via a mannose family phosphotransferase (PTS) encoded bygfrABCD(glucoselysine/fructoselysine PTS components EIIA, EIIB, EIIC, and EIID; locus numbers STM14_5449 to STM14_5454 inS. Typhimurium 14028s). Genes coding for two predicted deglycases within thegfroperon,gfrEandgfrF, were required for growth with glucoselysine and fructoselysine, respectively. GfrF demonstrated fructoselysine-6-phosphate deglycase activity in a coupled enzyme assay. The biochemical and genetic analyses were consistent with a pathway in which fructoselysine and glucoselysine are phosphorylated at the C-6 position of the sugar by the GfrABCD PTS as they are transported across the membrane. The resulting fructoselysine-6-phosphate and glucoselysine-6-phosphate subsequently are cleaved by GfrF and GfrE to form lysine and glucose-6-phosphate or fructose-6-phosphate. Interestingly, althoughS. Typhimurium can use lysine derived from fructoselysine or glucoselysine as a sole nitrogen source, it cannot use exogenous lysine as a nitrogen source to support growth. Expression ofgfrABCDEFwas dependent on the alternative sigma factor RpoN (σ54) and an RpoN-dependent LevR-like activator, which we designated GfrR.IMPORTANCESalmonellaphysiology has been studied intensively, but there is much we do not know regarding the repertoire of nutrients these bacteria are able to use for growth. This study shows that a previously uncharacterized PTS and associated enzymes function together to transport and catabolize fructoselysine and glucoselysine. Knowledge of the range of nutrients thatSalmonellautilizes is important, as it could lead to the development of new strategies for reducing the load ofSalmonellain food animals, thereby mitigating its entry into the human food supply.

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