scholarly journals Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Elizabeth A. McDaniel ◽  
Benjamin D. Peterson ◽  
Sarah L. R. Stevens ◽  
Patricia Q. Tran ◽  
Karthik Anantharaman ◽  
...  
Keyword(s):  
Phylogenetic Diversity ◽  
Large Scale ◽  
Carbon Fixation ◽  
Anaerobic Bacteria ◽  
Inorganic Mercury ◽  
Metal Resistance ◽  
Metabolic Flexibility ◽  
Metabolic Diversity ◽  
Content Type ◽  
Methylmercury Production

ABSTRACT Methylmercury is a potent bioaccumulating neurotoxin that is produced by specific microorganisms that methylate inorganic mercury. Methylmercury production in diverse anaerobic bacteria and archaea was recently linked to the hgcAB genes. However, the full phylogenetic and metabolic diversity of mercury-methylating microorganisms has not been fully unraveled due to the limited number of cultured experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury-methylating microorganisms by hgcAB identification in publicly available isolate genomes and metagenome-assembled genomes (MAGs) as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known and that hgcAB distribution among genomes is most likely due to several independent horizontal gene transfer events. The microorganisms we identified possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. We identified 111 putative mercury methylators in a set of previously published permafrost metatranscriptomes and demonstrated that different methylating taxa may contribute to hgcA expression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify putative methylators based upon hgcAB presence and describe their putative functions in the environment. IMPORTANCE Accurately assessing the production of bioaccumulative neurotoxic methylmercury by characterizing the phylogenetic diversity, metabolic functions, and activity of methylators in the environment is crucial for understanding constraints on the mercury cycle. Much of our understanding of methylmercury production is based on cultured anaerobic microorganisms within the Deltaproteobacteria, Firmicutes, and Euryarchaeota. Advances in next-generation sequencing technologies have enabled large-scale cultivation-independent surveys of diverse and poorly characterized microorganisms from numerous ecosystems. We used genome-resolved metagenomics and metatranscriptomics to highlight the vast phylogenetic and metabolic diversity of putative mercury methylators and their depth-discrete activities in thawing permafrost. This work underscores the importance of using genome-resolved metagenomics to survey specific putative methylating populations of a given mercury-impacted ecosystem.

scholarly journals Expanded Phylogenetic Diversity and Metabolic Flexibility of Microbial Mercury Methylation

2020 ◽  
Author(s):  
Elizabeth A. McDaniel ◽  
Benjamin Peterson ◽  
Sarah L.R. Stevens ◽  
Patricia Q. Tran ◽  
Karthik Anantharaman ◽  
...  
Keyword(s):  
Phylogenetic Diversity ◽  
Large Scale ◽  
Carbon Fixation ◽  
Inorganic Mercury ◽  
Metal Resistance ◽  
Anthropogenic Sources ◽  
Metabolic Flexibility ◽  
Mercury Methylation ◽  
Metabolic Diversity ◽  
Methylmercury Production

ABSTRACTMethylmercury is a potent, bioaccumulating neurotoxin that is produced by specific microorganisms by methylation of inorganic mercury released from anthropogenic sources. The hgcAB genes were recently discovered to be required for microbial methylmercury production in diverse anaerobic bacteria and archaea. However, the full phylogenetic and metabolic diversity of mercury methylating microorganisms has not been fully explored due to the limited number of cultured, experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury methylating microorganisms identified by hgcA sequence identity from publicly available isolate genomes and metagenome-assembled genomes (MAGs), as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known, and the distribution of hgcA is most likely due to several independent horizontal gene transfer events. Identified methylating microorganisms possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. Using a metatranscriptomic survey of a thawing permafrost gradient from which we identified 111 putative mercury methylators, we demonstrate that specific methylating populations may contribute to hgcA expression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify methylators based upon hgcA presence and describe their putative functions in the environment.IMPORTANCESpecific anaerobic microorganisms among the Deltaproteobacteria, Firmicutes, and Euryarchaeota have been shown to produce the bioaccumulating neurotoxin methylmercury. Accurately assessing the sources of microbial methylmercury production in the context of phylogenetic identification, metabolic guilds, and activity in the environment is crucial for understanding the constraints and effects of mercury impacted sites. Advances in next-generation sequencing technologies have enabled large-scale, cultivation-independent surveys of diverse and poorly characterized microorganisms of numerous ecosystems. We used genome-resolved metagenomics and metatranscriptomics to highlight the vast phylogenetic and metabolic diversity of putative mercury methylators, and their depth-discrete activities in the environment. This work underscores the importance of using genome-resolved metagenomics to survey specific putative methylating populations of a given mercury-impacted ecosystem.

scholarly journals A Targetron-Recombinase System for Large-Scale Genome Engineering of Clostridia

mSphere ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Tristan Cerisy ◽  
William Rostain ◽  
Audam Chhun ◽  
Magali Boutard ◽  
Marcel Salanoubat ◽  
...  
Keyword(s):  
Large Scale ◽  
Genome Engineering ◽  
Genome Structure ◽  
Anaerobic Bacteria ◽  
Cre Recombinase ◽  
Fluorescent Reporter ◽  
Content Type ◽  
Genomic Deletions ◽  
Cassette Exchange ◽  
Clostridium Phytofermentans

ABSTRACT Clostridia are a group of Gram-positive anaerobic bacteria of medical and industrial importance for which limited genetic methods are available. Here, we demonstrate an approach to make large genomic deletions and insertions in the model Clostridium phytofermentans by combining designed group II introns (targetrons) and Cre recombinase. We apply these methods to delete a 50-gene prophage island by programming targetrons to position markerless lox66 and lox71 sites, which mediate deletion of the intervening 39-kb DNA region using Cre recombinase. Gene expression and growth of the deletion strain showed that the prophage genes contribute to fitness on nonpreferred carbon sources. We also inserted an inducible fluorescent reporter gene into a neutral genomic site by recombination-mediated cassette exchange (RMCE) between genomic and plasmid-based tandem lox sites bearing heterospecific spacers to prevent intracassette recombination. These approaches generally enable facile markerless genome engineering in clostridia to study their genome structure and regulation. IMPORTANCE Clostridia are anaerobic bacteria with important roles in intestinal and soil microbiomes. The inability to experimentally modify the genomes of clostridia has limited their study and application in biotechnology. Here, we developed a targetron-recombinase system to efficiently make large targeted genomic deletions and insertions using the model Clostridium phytofermentans. We applied this approach to reveal the importance of a prophage to host fitness and introduce an inducible reporter by recombination-mediated cassette exchange.

scholarly journals In Vitro Activity of Omadacycline, a New Tetracycline Analog, and Comparators against Clostridioides difficile

2020 ◽  
Vol 64 (8) ◽  
Author(s):  
Khurshida Begum ◽  
Eugénie Bassères ◽  
Julie Miranda ◽  
Chris Lancaster ◽  
Anne J. Gonzales-Luna ◽  
...  
Keyword(s):  
Large Scale ◽  
Anaerobic Bacteria ◽  
Oral Antibiotic ◽  
Content Type ◽  
Microdilution Method ◽  
Clostridioides Difficile ◽  
Broth Microdilution Method ◽  
Time Kill ◽  
Further Development

ABSTRACT Omadacycline is a potent aminomethylcycline with in vitro activity against Gram-positive, Gram-negative, and anaerobic bacteria. Preliminary data demonstrated that omadacycline has in vitro activity against Clostridioides difficile; however, large-scale in vitro studies have not been done. The purpose of this study was to assess the in vitro susceptibility of omadacycline and comparators on a large biobank of clinical C. difficile isolates. In vitro C. difficile susceptibility to omadacycline and comparators (fidaxomicin, metronidazole, and vancomycin) was assessed using the broth microdilution method. Minimum bactericidal concentrations (MBCs) and time-kill assays were assessed for pharmacodynamics analysis, and whole-genome sequencing was performed in a subset of isolates to assess distribution of MICs and resistance determinants. Two hundred fifty clinical C. difficile isolates collected between 2015 and 2018 were tested for in vitro susceptibility of omadacycline and comparators. Ribotypes included F001 (n = 5), F002 (n = 56), F014-020 (n = 66), F017 (n = 8), F027 (n = 53), F106 (n = 45), and F255 (n = 17). Omadacycline demonstrated potent in vitro activity with an MIC range of 0.016 to 0.13 μg/ml, an MIC50 of 0.031 μg/ml, and an MIC90 of 0.031 μg/ml. No difference was observed for omadacycline MIC50 and MIC90 values stratified by ribotype, disease severity, or vancomycin susceptibility. Bactericidal activity was confirmed in time-kill studies. No difference was observed in MIC based on C. difficile phylogeny. Further development of omadacycline as an intravenous and oral antibiotic directed toward C. difficile infection is warranted.

scholarly journals Systems Analysis of NADH Dehydrogenase Mutants Reveals Flexibility and Limits of Pseudomonas taiwanensis VLB120’s Metabolism

2020 ◽  
Vol 86 (11) ◽  
Author(s):  
Salome C. Nies ◽  
Robert Dinger ◽  
Yan Chen ◽  
Gossa G. Wordofa ◽  
Mette Kristensen ◽  
...  
Keyword(s):  
Respiratory Chain ◽  
Large Scale ◽  
Nadh Dehydrogenase ◽  
Metabolic Flexibility ◽  
Second Phase ◽  
Content Type ◽  
Depth Analysis ◽  
Nadh Dehydrogenases ◽  
The Impact

ABSTRACT Obligate aerobic organisms rely on a functional electron transport chain for energy conservation and NADH oxidation. Because of this essential requirement, the genes of this pathway are likely constitutively and highly expressed to avoid a cofactor imbalance and energy shortage under fluctuating environmental conditions. We here investigated the essentiality of the three NADH dehydrogenases of the respiratory chain of the obligate aerobe Pseudomonas taiwanensis VLB120 and the impact of the knockouts of corresponding genes on its physiology and metabolism. While a mutant lacking all three NADH dehydrogenases seemed to be nonviable, the single or double knockout mutant strains displayed no, or only a weak, phenotype. Only the mutant deficient in both type 2 dehydrogenases showed a clear phenotype with biphasic growth behavior and a strongly reduced growth rate in the second phase. In-depth analyses of the metabolism of the generated mutants, including quantitative physiological experiments, transcript analysis, proteomics, and enzyme activity assays revealed distinct responses to type 2 and type 1 dehydrogenase deletions. An overall high metabolic flexibility enables P. taiwanensis to cope with the introduced genetic perturbations and maintain stable phenotypes, likely by rerouting of metabolic fluxes. This metabolic adaptability has implications for biotechnological applications. While the phenotypic robustness is favorable in large-scale applications with inhomogeneous conditions, the possible versatile redirecting of carbon fluxes upon genetic interventions can thwart metabolic engineering efforts. IMPORTANCE While Pseudomonas has the capability for high metabolic activity and the provision of reduced redox cofactors important for biocatalytic applications, exploitation of this characteristic might be hindered by high, constitutive activity of and, consequently, competition with the NADH dehydrogenases of the respiratory chain. The in-depth analysis of NADH dehydrogenase mutants of Pseudomonas taiwanensis VLB120 presented here provides insight into the phenotypic and metabolic response of this strain to these redox metabolism perturbations. This high degree of metabolic flexibility needs to be taken into account for rational engineering of this promising biotechnological workhorse toward a host with a controlled and efficient supply of redox cofactors for product synthesis.

scholarly journals Energetics and Application of Heterotrophy in Acetogenic Bacteria

2016 ◽  
Vol 82 (14) ◽  
pp. 4056-4069 ◽  
Author(s):  
Kai Schuchmann ◽  
Volker Müller
Keyword(s):  
Anaerobic Bacteria ◽  
Metabolic Flexibility ◽  
Strictly Anaerobic ◽  
Autotrophic Growth ◽  
Content Type ◽  
Anoxic Environments ◽  
Acetogenic Bacteria ◽  
Heterotrophic Metabolism ◽  
Global Carbon ◽  
Substrate Spectrum

ABSTRACTAcetogenic bacteria are a diverse group of strictly anaerobic bacteria that utilize the Wood-Ljungdahl pathway for CO2fixation and energy conservation. These microorganisms play an important part in the global carbon cycle and are a key component of the anaerobic food web. Their most prominent metabolic feature is autotrophic growth with molecular hydrogen and carbon dioxide as the substrates. However, most members also show an outstanding metabolic flexibility for utilizing a vast variety of different substrates. In contrast to autotrophic growth, which is hardly competitive, metabolic flexibility is seen as a key ability of acetogens to compete in ecosystems and might explain the almost-ubiquitous distribution of acetogenic bacteria in anoxic environments. This review covers the latest findings with respect to the heterotrophic metabolism of acetogenic bacteria, including utilization of carbohydrates, lactate, and different alcohols, especially in the model acetogenAcetobacterium woodii. Modularity of metabolism, a key concept of pathway design in synthetic biology, together with electron bifurcation, to overcome energetic barriers, appears to be the basis for the amazing substrate spectrum. At the same time, acetogens depend on only a relatively small number of enzymes to expand the substrate spectrum. We will discuss the energetic advantages of coupling CO2reduction to fermentations that exploit otherwise-inaccessible substrates and the ecological advantages, as well as the biotechnological applications of the heterotrophic metabolism of acetogens.

Financial distress determinants among SMEs: empirical evidence from Sweden

2020 ◽  
Vol 47 (3) ◽  
pp. 547-560 ◽  
Author(s):  
Darush Yazdanfar ◽  
Peter Öhman
Keyword(s):  
Financial Crisis ◽  
Financial Distress ◽  
Large Scale ◽  
Global Financial Crisis ◽  
Binary Logistic Regression ◽  
Data Availability ◽  
Cross Sectional ◽  
Data Set ◽  
Content Type ◽  
The Global Financial Crisis

PurposeThe purpose of this study is to empirically investigate determinants of financial distress among small and medium-sized enterprises (SMEs) during the global financial crisis and post-crisis periods.Design/methodology/approachSeveral statistical methods, including multiple binary logistic regression, were used to analyse a longitudinal cross-sectional panel data set of 3,865 Swedish SMEs operating in five industries over the 2008–2015 period.FindingsThe results suggest that financial distress is influenced by macroeconomic conditions (i.e. the global financial crisis) and, in particular, by various firm-specific characteristics (i.e. performance, financial leverage and financial distress in previous year). However, firm size and industry affiliation have no significant relationship with financial distress.Research limitationsDue to data availability, this study is limited to a sample of Swedish SMEs in five industries covering eight years. Further research could examine the generalizability of these findings by investigating other firms operating in other industries and other countries.Originality/valueThis study is the first to examine determinants of financial distress among SMEs operating in Sweden using data from a large-scale longitudinal cross-sectional database.

scholarly journals Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities

2021 ◽  
Vol 97 (3) ◽  
Author(s):  
Constantinos Xenophontos ◽  
Martin Taubert ◽  
W Stanley Harpole ◽  
Kirsten Küsel
Keyword(s):  
Bacterial Communities ◽  
Species Interactions ◽  
Phylogenetic Diversity ◽  
Molecular Mechanisms ◽  
Linear Models ◽  
Theory Development ◽  
Metabolic Diversity ◽  
Community Functioning ◽  
Metabolic Functions ◽  
Independent Effects

ABSTRACT Quantifying the relative contributions of microbial species to ecosystem functioning is challenging, because of the distinct mechanisms associated with microbial phylogenetic and metabolic diversity. We constructed bacterial communities with different diversity traits and employed exoenzyme activities (EEAs) and carbon acquisition potential (CAP) from substrates as proxies of bacterial functioning to test the independent effects of these two aspects of biodiversity. We expected that metabolic diversity, but not phylogenetic diversity would be associated with greater ecological function. Phylogenetically relatedness should intensify species interactions and coexistence, therefore amplifying the influence of metabolic diversity. We examined the effects of each diversity treatment using linear models, while controlling for the other, and found that phylogenetic diversity strongly influenced community functioning, positively and negatively. Metabolic diversity, however, exhibited negative or non-significant relationships with community functioning. When controlling for different substrates, EEAs increased along with phylogenetic diversity but decreased with metabolic diversity. The strength of diversity effects was related to substrate chemistry and the molecular mechanisms associated with each substrate's degradation. EEAs of phylogenetically similar groups were strongly affected by within-genus interactions. These results highlight the unique flexibility of microbial metabolic functions that must be considered in further ecological theory development.

The dialectics of authoring expansive learning: tracing the long tail of a Change Laboratory

2016 ◽  
Vol 28 (4) ◽  
pp. 245-262 ◽  
Author(s):  
Annalisa Sannino ◽  
Yrjö Engeström ◽  
Johanna Lahikainen
Keyword(s):  
Large Scale ◽  
Scale Transformation ◽  
Dialectical Tensions ◽  
Content Type ◽  
Organization Model ◽  
Expansive Learning ◽  
Conceptual Argument ◽  
University Library ◽  
Dialectical Process ◽  
Cultural Historical Activity

Purpose The paper aims to examine organizational authoring understood as a longitudinal, material and dialectical process of transformation efforts. The following questions are asked: To which extent can a Change Laboratory intervention help practitioners author their own learning? Are the authored outcomes of a Change Laboratory intervention futile if a workplace subsequently undergoes large-scale organizational transformations? Does the expansive learning authored in a Change Laboratory intervention survive large-scale organizational transformations, and if so, why does it survive and how? Design/methodology/approach The paper develops a conceptual argument based on cultural–historical activity theory. The conceptual argument is grounded in the examination of a case of eight years of change efforts in a university library, including a Change Laboratory (CL) intervention. Follow-up interview data are used to discuss and illuminate our argument in relation to the three research questions. Findings The idea of knotworking constructed in the CL process became a “germ cell” that generates novel solutions in the library activity. A large-scale transformation from the local organization model developed in the CL process to the organization model of the entire university library was not experienced as a loss. The dialectical tension between the local and global models became a source of movement driven by the emerging expansive object. Practitioners are modeling their own collective future competences, expanding them both in socio-spatial scope and interactive depth. Originality/value The article offers an expanded view of authorship, calling attention to material changes and practical change actions. The dialectical tensions identified serve as heuristic guidelines for future studies and interventions.

Dynamic output feedback control for nonlinear large-scale interconnected systems

2020 ◽  
Vol 39 (4) ◽  
pp. 801-821
Author(s):  
Ezzeddine Touti ◽  
Ali Sghaier Tlili ◽  
Muhannad Almutiry
Keyword(s):  
Decentralized Control ◽  
Output Feedback ◽  
Large Scale ◽  
Optimization Problem ◽  
Lyapunov Theory ◽  
Interconnected Systems ◽  
Dynamic Output Feedback ◽  
Content Type ◽  
Dynamic Output ◽  
Control Scheme

Purpose This paper aims to focus on the design of a decentralized observation and control method for a class of large-scale systems characterized by nonlinear interconnected functions that are assumed to be uncertain but quadratically bounded. Design/methodology/approach Sufficient conditions, under which the designed control scheme can achieve the asymptotic stabilization of the augmented system, are developed within the Lyapunov theory in the framework of linear matrix inequalities (LMIs). Findings The derived LMIs are formulated under the form of an optimization problem whose resolution allows the concurrent computation of the decentralized control and observation gains and the maximization of the nonlinearity coverage tolerated by the system without becoming unstable. The reliable performances of the designed control scheme, compared to a distinguished decentralized guaranteed cost control strategy issued from the literature, are demonstrated by numerical simulations on an extensive application of a three-generator infinite bus power system. Originality/value The developed optimization problem subject to LMI constraints is efficiently solved by a one-step procedure to analyze the asymptotic stability and to synthesize all the control and observation parameters. Therefore, such a procedure enables to cope with the conservatism and suboptimal solutions procreated by optimization problems based on iterative algorithms with multi-step procedures usually used in the problem of dynamic output feedback decentralized control of nonlinear interconnected systems.

scholarly journals Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment

Diversity ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 234 ◽  
Author(s):  
Eric A. Griffin ◽  
Joshua G. Harrison ◽  
Melissa K. McCormick ◽  
Karin T. Burghardt ◽  
John D. Parker
Keyword(s):  
Phylogenetic Diversity ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Spatial Scales ◽  
Fungal Endophytes ◽  
Fungal Endophyte ◽  
Tree Diversity ◽  
Trophic Levels ◽  
Community Diversity ◽  
And Function

Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.

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