scholarly journals Bioenergetic Aspects of Halophilism

1999 ◽  
Vol 63 (2) ◽  
pp. 334-348 ◽  
Author(s):  
Aharon Oren
Keyword(s):  
Free Energy ◽  
Compatible Solutes ◽  
Methanogenic Archaea ◽  
Energetic Cost ◽  
Salt Adaptation ◽  
Energy Yield ◽  
Dissimilatory Sulfate Reduction ◽  
Fermentative Bacteria ◽  
Osmotic Solutes ◽  
Dissimilatory Metabolism

SUMMARY Examinination of microbial diversity in environments of increasing salt concentrations indicates that certain types of dissimilatory metabolism do not occur at the highest salinities. Examples are methanogenesis for H2 + CO2 or from acetate, dissimilatory sulfate reduction with oxidation of acetate, and autotrophic nitrification. Occurrence of the different metabolic types is correlated with the free-energy change associated with the dissimilatory reactions. Life at high salt concentrations is energetically expensive. Most bacteria and also the methanogenic archaea produce high intracellular concentrations of organic osmotic solutes at a high energetic cost. All halophilic microorganisms expend large amounts of energy to maintain steep gradients of NA+ and K+ concentrations across their cytoplasmic membrane. The energetic cost of salt adaptation probably dictates what types of metabolism can support life at the highest salt concentrations. Use of KCl as an intracellular solute, while requiring far-reaching adaptations of the intracellular machinery, is energetically more favorable than production of organic-compatible solutes. This may explain why the anaerobic halophilic fermentative bacteria (order Haloanaerobiales) use this strategy and also why halophilic homoacetogenic bacteria that produce acetate from H2 + CO2 exist whereas methanogens that use the same substrates in a reaction with a similar free-energy yield do not.

SAMPL6 Octanol-Water Partition Coefficients from Alchemical Free Energy Calculations with MBIS Atomic Charges

2019 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Electron Density ◽  
Free Energy Calculations ◽  
Basis Set ◽  
Energetic Cost ◽  
Atomic Charges ◽  
Free Energies ◽  
Energy Calculations ◽  
Alchemical Free Energy ◽  
Alchemical Free Energy Calculations

In molecular modeling the description of the interactions between molecules forms the basis for a correct prediction of macroscopic observables. Here, we derive atomic charges from the implicitly polarized electron density of eleven molecules in the SAMPL6 challenge using the Hirshfeld-I and Minimal Basis Set Iterative Stockholder(MBIS) partitioning method. These atomic charges combined with other parameters in the GAFF force field and different water/octanol models were then used in alchemical free energy calculations to obtain hydration and solvation free energies, which after correction for the polarization cost, result in the blind prediction of the partition coefficient. From the tested partitioning methods and water models the S-MBIS atomic charges with the TIP3P water model presented the smallest deviation from the experiment. Conformational dependence of the free energies and the energetic cost associated with the polarization of the electron density are discussed.

The contribution of fermentative bacteria and methanogenic archaea to azo dye reduction by a thermophilic anaerobic consortium

2006 ◽  
Vol 39 (1) ◽  
pp. 38-46 ◽  
Author(s):  
André B. dos Santos ◽  
Marta P. de Madrid ◽  
Frank A.M. de Bok ◽  
Alfons J.M. Stams ◽  
Jules B. van Lier ◽  
...  
Keyword(s):  
Azo Dye ◽  
Methanogenic Archaea ◽  
Fermentative Bacteria ◽  
Dye Reduction ◽  
Anaerobic Consortium

scholarly journals Inertial-range kinetic turbulence in pressure-anisotropic astrophysical plasmas

2015 ◽  
Vol 81 (5) ◽  
Author(s):  
M. W. Kunz ◽  
A. A. Schekochihin ◽  
C. H. K. Chen ◽  
I. G. Abel ◽  
S. C. Cowley
Keyword(s):  
Solar Wind ◽  
Free Energy ◽  
Distribution Function ◽  
Low Frequency ◽  
Energetic Cost ◽  
Astrophysical Plasmas ◽  
Order Unity ◽  
Quantitative Measurements ◽  
Maxwellian Plasma ◽  
Field Lines

A theoretical framework for low-frequency electromagnetic (drift-)kinetic turbulence in a collisionless, multi-species plasma is presented. The result generalises reduced magnetohydrodynamics (RMHD) and kinetic RMHD (Schekochihinet al.,Astrophys. J. Suppl. Ser., vol. 182, 2009, pp. 310–377) to the case where the mean distribution function of the plasma is pressure-anisotropic and different ion species are allowed to drift with respect to each other – a situation routinely encountered in the solar wind and presumably ubiquitous in hot dilute astrophysical plasmas such as the intracluster medium. Two main objectives are achieved. First, in a non-Maxwellian plasma, the relationships between fluctuating fields (e.g. the Alfvén ratio) are order-unity modified compared to the more commonly considered Maxwellian case, and so a quantitative theory is developed to support quantitative measurements now possible in the solar wind. Beyond these order-unity corrections, the main physical feature of low-frequency plasma turbulence survives the generalisation to non-Maxwellian distributions: Alfvénic and compressive fluctuations are energetically decoupled, with the latter passively advected by the former; the Alfvénic cascade is fluid, satisfying RMHD equations (with the Alfvén speed modified by pressure anisotropy and species drifts), whereas the compressive cascade is kinetic and subject to collisionless damping (and for a bi-Maxwellian plasma splits into three independent collisionless cascades). Secondly, the organising principle of this turbulence is elucidated in the form of a conservation law for the appropriately generalised kinetic free energy. It is shown that non-Maxwellian features in the distribution function reduce the rate of phase mixing and the efficacy of magnetic stresses, and that these changes influence the partitioning of free energy amongst the various cascade channels. As the firehose or mirror instability thresholds are approached, the dynamics of the plasma are modified so as to reduce the energetic cost of bending magnetic-field lines or of compressing/rarefying them. Finally, it is shown that this theory can be derived as a long-wavelength limit of non-Maxwellian slab gyrokinetics.

scholarly journals Identification of a Salt-Induced Primary Transporter for Glycine Betaine in the Methanogen Methanosarcina mazei Gö1

2002 ◽  
Vol 68 (5) ◽  
pp. 2133-2139 ◽  
Author(s):  
M. Roeßler ◽  
K. Pflüger ◽  
H. Flach ◽  
T. Lienard ◽  
G. Gottschalk ◽  
...  
Keyword(s):  
Glycine Betaine ◽  
Northern Blot Analysis ◽  
Compatible Solutes ◽  
Gene Organization ◽  
Compatible Solute ◽  
Salt Adaptation ◽  
Methanosarcina Mazei ◽  
Transport Studies ◽  
Uptake Activity ◽  
Transport Device

ABSTRACT The salt adaptation of the methanogenic archaeon Methanosarcina mazei Gö1 was studied at the physiological and molecular levels. The freshwater organism M. mazei Gö1 was able to adapt to salt concentrations up to 1 M, and the addition of the compatible solute glycine betaine to the growth medium facilitated adaptation to higher salt concentrations. Transport studies with cell suspensions revealed a salt-induced glycine betaine uptake activity in M. mazei Gö1, and inhibitor studies argue for a primary transport device. Analysis of the genome of M. mazei Gö1 identified a homolog of known primary glycine betaine transporters. This gene cluster was designated Ota (osmoprotectant transporter A). Its sequence and gene organization are very similar to those of the glycine betaine transporter OpuA of Bacillus subtilis. Northern blot analysis of otaC revealed a salt-dependent transcription of this gene. Ota is the first identified salt-induced transporter for compatible solutes in Archaea.

scholarly journals Methanogenic Granules Are Replicated, Whole Microbial Communities With Reproducible Responses To Environmental Cues

2020 ◽  
Author(s):  
Anna Christine Trego ◽  
Sarah O'Sullivan ◽  
Simon Mills ◽  
Estefania Porca ◽  
Christopher Quince ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Size Fraction ◽  
Methanogenic Archaea ◽  
Organic Content ◽  
Environmental Cues ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Methanogenic Activity ◽  
Fermentative Bacteria

Abstract Background In this study, individual anaerobic granular biofilms were used as true community replicates to assess whole-microbial-community responses to environmental cues. The aggregates originated from three different biomass sources, i.e. three different engineered biological wastewater treatment systems, were each size-separated into three fractions – small, medium and large – and characterised according to organic matter concentrations and rates of methanogenic activity. Differences in the microbial community structure of each size fraction from each source were determined using 16S rRNA gene sequencing. Subsequently, single granules from the large size fraction of one of the sources were separately subjected controlled environmental cues in novel micro batch reactors (mBRs). Results Organic content, methanogenic activity, and microbial community were significantly different between the three size fractions, with diversity trajectories replicated across the three sludge sources – indicating a potential development model as granules age. Individual large granules from one of these sources were statistically identical with respect to the structure of the active community based on cDNA analysis. It was observed that the active microbial community of individual granules, at the depth of 16S rRNA sequencing, produced reproducible responses to environmental conditions. While each condition resulted in the up-regulation of particular OTUs and clades, the core microbiome, consisting of many fermentative bacteria along with methanogenic archaea, namely, Methanosarcina and Methanobacterium , persisted. Conclusions At this level, single anaerobic granules can be considered highly-replicated whole-ecosystems, opening the door to high-throughput studies in Microbial Ecology.

SAMPL6 Octanol-Water Partition Coefficients from Alchemical Free Energy Calculations with MBIS Atomic Charges

2019 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Electron Density ◽  
Free Energy Calculations ◽  
Basis Set ◽  
Energetic Cost ◽  
Atomic Charges ◽  
Free Energies ◽  
Energy Calculations ◽  
Alchemical Free Energy ◽  
Alchemical Free Energy Calculations

In molecular modeling the description of the interactions between molecules forms the basis for a correct prediction of macroscopic observables. Here, we derive atomic charges from the implicitly polarized electron density of eleven molecules in the SAMPL6 challenge using the Hirshfeld-I and Minimal Basis Set Iterative Stockholder(MBIS) partitioning method. These atomic charges combined with other parameters in the GAFF force field and different water/octanol models were then used in alchemical free energy calculations to obtain hydration and solvation free energies, which after correction for the polarization cost, result in the blind prediction of the partition coefficient. From the tested partitioning methods and water models the S-MBIS atomic charges with the TIP3P water model presented the smallest deviation from the experiment. Conformational dependence of the free energies and the energetic cost associated with the polarization of the electron density are discussed.

scholarly journals Lysine-2,3-Aminomutase and β-Lysine Acetyltransferase Genes of Methanogenic Archaea Are Salt Induced and Are Essential for the Biosynthesis of Nε-Acetyl-β-Lysine and Growth at High Salinity

2003 ◽  
Vol 69 (10) ◽  
pp. 6047-6055 ◽  
Author(s):  
K. Pflüger ◽  
S. Baumann ◽  
G. Gottschalk ◽  
W. Lin ◽  
H. Santos ◽  
...  
Keyword(s):  
Compatible Solutes ◽  
Methanogenic Archaea ◽  
Methanosarcina Barkeri ◽  
Methanosarcina Acetivorans ◽  
Methanococcus Maripaludis ◽  
Methanosarcina Mazei ◽  
Lysine Acetyltransferase ◽  
And Function ◽  
High Degree ◽  
Lysine Synthesis

ABSTRACT The compatible solute N ε-acetyl-β-lysine is unique to methanogenic archaea and is produced under salt stress only. However, the molecular basis for the salt-dependent regulation of N ε-acetyl-β-lysine formation is unknown. Genes potentially encoding lysine-2,3-aminomutase (ablA) and β-lysine acetyltransferase (ablB), which are assumed to catalyze N ε-acetyl-β-lysine formation from α-lysine, were identified on the chromosomes of the methanogenic archaea Methanosarcina mazei Gö1, Methanosarcina acetivorans, Methanosarcina barkeri, Methanococcus jannaschii, and Methanococcus maripaludis. The order of the two genes was identical in the five organisms, and the deduced proteins were very similar, indicating a high degree of conservation of structure and function. Northern blot analysis revealed that the two genes are organized in an operon (termed the abl operon) in M. mazei Gö1. Expression of the abl operon was strictly salt dependent. The abl operon was deleted in the genetically tractable M. maripaludis. Δabl mutants of M. maripaludis no longer produced N ε-acetyl-β-lysine and were incapable of growth at high salt concentrations, indicating that the abl operon is essential for N ε-acetyl-β-lysine synthesis. These experiments revealed the first genes involved in the biosynthesis of compatible solutes in methanogens.

scholarly journals Syntrophic Growth on Formate: a New Microbial Niche in Anoxic Environments

2008 ◽  
Vol 74 (19) ◽  
pp. 6126-6131 ◽  
Author(s):  
Jan Dolfing ◽  
Bo Jiang ◽  
Anne M. Henstra ◽  
Alfons J. M. Stams ◽  
Caroline M. Plugge
Keyword(s):  
Experimental Evidence ◽  
Pure Culture ◽  
Narrow Range ◽  
Methanogenic Archaea ◽  
Anoxic Environments ◽  
Fermentative Bacteria ◽  
Thermodynamic Limits ◽  
Substrate Concentrations ◽  
Syntrophic Associations

ABSTRACT Anaerobic syntrophic associations of fermentative bacteria and methanogenic archaea operate at the thermodynamic limits of life. The interspecies transfer of electrons from formate or hydrogen as a substrate for the methanogens is key. Contrary requirements of syntrophs and methanogens for growth-sustaining product and substrate concentrations keep the formate and hydrogen concentrations low and within a narrow range. Since formate is a direct substrate for methanogens, a niche for microorganisms that grow by the conversion of formate to hydrogen plus bicarbonate—or vice versa—may seem unlikely. Here we report experimental evidence for growth on formate by syntrophic communities of (i) Moorella sp. strain AMP in coculture with a thermophilic hydrogen-consuming Methanothermobacter species and of (ii) Desulfovibrio sp. strain G11 in coculture with a mesophilic hydrogen consumer, Methanobrevibacter arboriphilus AZ. In pure culture, neither Moorella sp. strain AMP, nor Desulfovibrio sp. strain G11, nor the methanogens grow on formate alone. These results imply the existence of a previously unrecognized microbial niche in anoxic environments.

scholarly journals A joint reaction coordinate for computing the free energy landscape of pore nucleation and pore expansion in lipid membranes

2020 ◽  
Author(s):  
Jochen S. Hub
Keyword(s):  
Free Energy ◽  
Lipid Membranes ◽  
Pore Formation ◽  
Energy Landscape ◽  
Potential Of Mean Force ◽  
Conformational Space ◽  
Energetic Cost ◽  
Free Energy Landscape ◽  
Pore Nucleation ◽  
Pore Expansion

AbstractTopological transitions of membranes, such as pore formation or membrane fusion, play key roles in biology, biotechnology, and in medical applications. Calculating the related free energy landscapes has been complicated by the fact that such processes involve a sequence of transitions along highly distinct directions in conformational space, making it difficult to define good reaction coordinates (RCs) for the overall process. In this study, we present a new RC capable of driving both pore nucleation and pore expansion in lipid membranes. The potential of mean force (PMF) along the RC computed with molecular dynamics (MD) simulations provides a comprehensive view on the free-energy landscape of pore formation, including a barrier for pore nucleation, the size, free energy, and metastability of the open pore, and the energetic cost for further pore expansion against the line tension of the pore rim. We illustrate the RC by quantifying the effects (i) of simulation system size and (ii) of the addition of dimethyl sulfoxide (DMSO) on the free energy landscape of pore formation. PMF calculations along the RC provide mechanistic and energetic understanding of pore formation, hence they will be useful to rationalize the effects of membrane-active peptides, electric fields, and membrane composition on transmembrane pores.

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