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Adv Microb Physiol 2020 5;76:81-127. Epub 2020 Feb 5.

Department of Plant Pathology, Washington State University, Pullman, WA, United States; RAW Molecular Systems (RMS) LLC, Spokane, WA, United States; Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.

Absorbance measurements on intact chemolithotrophic microorganisms that respire aerobically on soluble iron are described that used a novel integrating cavity absorption meter to eliminate the effects of light scattering on the experimental results. Steady state kinetic measurements on ferric iron production by intact cells revealed that the Michaelis Menten equation described the initial rates of product formation for at least 8 different chemolithotrophic microorganisms in 6 phyla distributed equally among the archaea and the Gram negative and Gram positive eubacteria. Cell-monitored turnover measurements during aerobic respiration on soluble iron by the same 12 intact microorganisms revealed six different patterns of iron-dependent absorbance changes, suggesting that there may be at least six different sets of prosthetic groups and biomolecules that can accomplish aerobic respiration on soluble iron. Read More

Adv Microb Physiol 2020 17;76:41-79. Epub 2020 Feb 17.

Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.

Advances in optical microscopy are continually narrowing the chasm in our appreciation of biological organization between the molecular and cellular levels, but many practical problems are still limiting. Observation is always limited by the rapid dynamics of ultrastructural modifications of intracellular components, and often by cell motility: imaging of the unicellular protist parasite of ornamental fish, Spironucleus vortens, has proved challenging. Autofluorescence of nicotinamide nucleotides and flavins in the 400-580 nm region of the visible spectrum, is the most useful indicator of cellular redox state and hence vitality. Read More

Adv Microb Physiol 2020 11;76:129-186. Epub 2020 Feb 11.

Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia; Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia.

The synthetic s-triazines are abundant, nitrogen-rich, heteroaromatic compounds used in a multitude of applications including, herbicides, plastics and polymers, and explosives. Their presence in the environment has led to the evolution of bacterial catabolic pathways in bacteria that allow use of these anthropogenic chemicals as a nitrogen source that supports growth. Herbicidal s-triazines have been used since the mid-twentieth century and are among the most heavily used herbicides in the world, despite being withdrawn from use in some areas due to concern about their safety and environmental impact. Read More

Adv Microb Physiol 2020 16;76:1-39. Epub 2020 Apr 16.

Stress Adaptation and Metabolism Unit, Department of Microbiology, Institut Pasteur, Paris, France; ERL CNRS 6002, CNRS, Paris, France.

Iron sulfur (Fe-S) clusters rank among the most ancient and conserved prosthetic groups. Fe-S clusters containing proteins are present in most, if not all, organisms. Fe-S clusters containing proteins are involved in a wide range of cellular processes, from gene regulation to central metabolism, via gene expression, RNA modification or bioenergetics. Read More

Adv Microb Physiol 2019 10;75:69-135. Epub 2019 Oct 10.

Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.

Multihaem cytochromes c are widespread in nature where they perform numerous roles in diverse anaerobic metabolic pathways. This is achieved in two ways: multihaem cytochromes c display a remarkable diversity of ways to organize multiple hemes within the protein frame; and the hemes possess an intrinsic reactive versatility derived from diverse spin, redox and coordination states. Here we provide a brief survey of multihaem cytochromes c that have been characterized in the context of their metabolic role. Read More

Adv Microb Physiol 2019 12;75:53-67. Epub 2019 Jul 12.

Department of Organic and Inorganic Chemistry, Federal University of Ceara, Center for Sciences, Fortaleza, Ceara, Brazil.

The Escherichia coli operon dosCP, also called yddV-yddU, co-expresses two heme proteins, DosC and DosP, both of which are direct oxygen sensors but paradoxically have opposite effects on the levels of the second messenger c-di-GMP. DosC is a diguanylate cyclase that synthesizes c-di-GMP from GTP, whereas DosP is a phosphodiesterase that linearizes c-di-GMP to pGpG. Both proteins are associated with the large degradosome enzyme complex that regulates many bacterial genes post-transcriptionally by processing or degrading the corresponding RNAs. Read More

Adv Microb Physiol 2019 10;75:325-389. Epub 2019 Oct 10.

Department of Plant Sciences, University of Oxford, Oxford, United Kingdom.

Rhizobia are α- and β-proteobacteria that form a symbiotic partnership with legumes, fixing atmospheric dinitrogen to ammonia and providing it to the plant. Oxygen regulation is key in this symbiosis. Fixation is performed by an oxygen-intolerant nitrogenase enzyme but requires respiration to meet its high energy demands. Read More

Adv Microb Physiol 2019 5;75:279-323. Epub 2019 Jul 5.

Department of Microbiology, Cornell University, Ithaca, NY, United States.

Bacillus subtilis Spx is the prototype for a large family of redox-responsive transcription factors found in many bacteria, most notably those from the phylum Firmicutes. Unusually for a transcription factor, B. subtilis Spx protein modulates gene expression by binding as a monomer to the αCTD domain of RNA polymerase (RNAP), and only interacts with DNA during subsequent promoter engagement. Read More

Adv Microb Physiol 2019 23;75:233-277. Epub 2019 Aug 23.

Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.

Persulfide groups participate in a wide array of biochemical pathways and are chemically very versatile. The TusA protein has been identified as a central element supplying and transferring sulfur as persulfide to a number of important biosynthetic pathways, like molybdenum cofactor biosynthesis or thiomodifications in nucleosides of tRNAs. In recent years, it has furthermore become obvious that this protein is indispensable for the oxidation of sulfur compounds in the cytoplasm. Read More

Adv Microb Physiol 2019 10;75:205-231. Epub 2019 Oct 10.

Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.

Redox transformations of sulfur, involving dissimilatory and assimilatory oxidation and reduction reactions, occurs in water bodies and terrestrial environments worldwide, leading to dynamic cycling of this element throughout the biosphere. In cases where zero-valent (elemental) sulfur, sulfate and other oxidized forms are used as electron acceptor in (primarily) anaerobic microbial metabolisms, the end product is hydrogen sulfide (HS or HS, dependent on pH). While neutrophilic and alkalophilic sulfidogenic prokaryotes have been known for many decades, acid-tolerant and acidophilic strains and species have been isolated and characterized only in the past twenty or so years, even though evidence for sulfide generation on these environments was previously well documented. Read More

Adv Microb Physiol 2019 23;75:177-203. Epub 2019 Aug 23.

Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, Oeiras, Portugal.

The diversity and abundance of aromatic compounds in nature is crucial for proper metabolism in all biological systems, and also impacts greatly the development of many industrial processes. Naturally, understanding their catabolism becomes fundamental for many scientific fields of research, from clinical and environmental to technological. The genetic basis of the central pathways for the catabolism of aromatic compounds in fungi, particularly of benzene derivatives, remains however poorly understood largely overlooking their significance. Read More

Adv Microb Physiol 2019 10;75:137-175. Epub 2019 Oct 10.

Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany.

Biologically catalyzed nitrous oxide (NO, laughing gas) reduction to dinitrogen gas (N) is a desirable process in the light of ever-increasing atmospheric concentrations of this important greenhouse gas and ozone depleting substance. A diverse range of bacterial species produce the copper cluster-containing enzyme NO reductase (NosZ), which is the only known enzyme that converts NO to N. Based on phylogenetic analyses, NosZ enzymes have been classified into clade I or clade II and it has turned out that this differentiation is also applicable to nos gene clusters (NGCs) and some physiological traits of the corresponding microbial cells. Read More

Adv Microb Physiol 2019 5;75:1-51. Epub 2019 Jul 5.

Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.

Sulfoxides occur in biology as products of the S-oxygenation of small molecules as well as in peptides and proteins and their formation is often associated with oxidative stress and can affect biological function. In bacteria, sulfoxide damage can be reversed by different types of enzymes. Thioredoxin-dependent peptide methionine sulfoxide reductases (MSR proteins) repair oxidized methionine residues and are found in all Domains of life. Read More

Adv Microb Physiol 2019 4;74:97-141. Epub 2019 Mar 4.

Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands.

Bacteria thrive in virtually all environments. Like all other living organisms, bacteria may encounter various types of stresses, to which cells need to adapt. In this chapter, we describe how cells cope with stressful conditions and how this may lead to dramatic morphological changes. Read More

Adv Microb Physiol 2019 28;74:487-514. Epub 2019 Feb 28.

Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle/Saale, Germany.

Hydrogenases are metal-containing biocatalysts that reversibly convert protons and electrons to hydrogen gas. This reaction can contribute in different ways to the generation of the proton motive force (PMF) of a cell. One means of PMF generation involves reduction of protons on the inside of the cytoplasmic membrane, releasing H gas, which being without charge is freely diffusible across the cytoplasmic membrane, where it can be re-oxidized to release protons. Read More

Adv Microb Physiol 2019 28;74:465-486. Epub 2019 Feb 28.

Devonshire Centre for Biosystems Science & Engineering, School of Natural & Environmental Sciences, Newcastle University, Newcastle-Upon-Tyne NE1 7RU, England, United Kingdom.

Hydrogenase enzymes are currently under the international research spotlight due to emphasis on biologically produced hydrogen as one potential energy carrier to relinquish the requirement for 'fossil fuel' derived energy. Three major classes of hydrogenase exist in microbes all able to catalyze the reversible oxidation of dihydrogen to protons and electrons. These classes are defined by their active site metal content: [NiFe]-; [FeFe]- and [Fe]-hydrogenases. Read More

Adv Microb Physiol 2019 8;74:415-464. Epub 2019 Apr 8.

Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.

Bacteria display an array of enzymes to detoxify reactive oxygen species that cause damage to DNA and to other biomolecules leading to cell death. Hydrogen peroxide is one of these species, with endogenous and exogenous sources, such as lactic acid bacteria, oxidative burst of the immune system or chemical reactions at oxic-anoxic interfaces. The enzymes that detoxify hydrogen peroxide will be the focus of this review, with special emphasis on bacterial peroxidases that reduce hydrogen peroxide to water. Read More

Adv Microb Physiol 2019 22;74:331-414. Epub 2019 Apr 22.

Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal; University of Lisboa, Faculty of Sciences, BIOISI- Biosystems & Integrative Sciences Institute, Lisboa, Portugal.

The diversity of microbial cells is reflected in differences in cell size and shape, motility, mechanisms of cell division, pathogenicity or adaptation to different environmental niches. All these variations are achieved by the distinct metabolic strategies adopted by the organisms. The respiratory chains are integral parts of those strategies especially because they perform the most or, at least, most efficient energy conservation in the cell. Read More

Adv Microb Physiol 2019 8;74:239-329. Epub 2019 Mar 8.

Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK.

Campylobacter jejuni is a zoonotic Epsilonproteobacterium that grows in the gastrointestinal tract of birds and mammals, and is the most frequent cause of food-borne bacterial gastroenteritis worldwide. As an oxygen-sensitive microaerophile, C. jejuni has to survive high environmental oxygen tensions, adapt to oxygen limitation in the host intestine and resist host oxidative attack. Read More

Adv Microb Physiol 2019 4;74:191-238. Epub 2019 Mar 4.

Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Laboratory for Environmental Biotechnology, Station 6, CH-1015 Lausanne, Switzerland.

Organohalide respiration (OHR) is an anaerobic metabolism by which bacteria conserve energy with the use of halogenated compounds as terminal electron acceptors. Genes involved in OHR are organized in reductive dehalogenase (rdh) gene clusters and can be found in relatively high copy numbers in the genomes of organohalide-respiring bacteria (OHRB). The minimal rdh gene set is composed by rdhA and rdhB, encoding the catalytic enzyme involved in reductive dehalogenation and its putative membrane anchor, respectively. Read More

Adv Microb Physiol 2019 22;74:143-189. Epub 2019 Apr 22.

Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France.

Hydrogen metabolism plays a central role in sulfate-reducing bacteria of the Desulfovibrio genus and is based on hydrogenases that catalyze the reversible conversion of protons into dihydrogen. These metabolically versatile microorganisms possess a complex hydrogenase system composed of several enzymes of both [FeFe]- and [NiFe]-type that can vary considerably from one Desulfovibrio species to another. This review covers the molecular and physiological aspects of hydrogenases and H metabolism in Desulfovibrio but focuses particularly on our model bacterium Desulfovibrio fructosovorans. Read More

Adv Microb Physiol 2019 15;74:1-96. Epub 2019 May 15.

Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States.

The family Geobacteraceae, with its only valid genus Geobacter, comprises deltaproteobacteria ubiquitous in soil, sediments, and subsurface environments where metal reduction is an active process. Research for almost three decades has provided novel insights into environmental processes and biogeochemical reactions not previously known to be carried out by microorganisms. At the heart of the environmental roles played by Geobacter bacteria is their ability to integrate redox pathways and regulatory checkpoints that maximize growth efficiency with electron donors derived from the decomposition of organic matter while respiring metal oxides, particularly the often abundant oxides of ferric iron. Read More

Adv Microb Physiol 2018 20;73:77-122. Epub 2018 Jul 20.

Pulmonary Section, Denver Veterans Affairs Medical Center, Denver, CO, United States; Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora, CO, United States.

A growing body of research suggests bacterial metabolism and membrane bioenergetics affect the lethality of a broad spectrum of antibiotics. Electrochemical gradients spanning energy-transducing membranes are the foundation of the chemiosmotic hypothesis and are essential for life; accordingly, their dysfunction appears to be a critical factor in bacterial death. Proton flux across energy-transducing membranes is central for cellular homeostasis as vectorial proton translocation generates a proton motive force used for ATP synthesis, pH homeostasis, and maintenance of solute gradients. Read More

Adv Microb Physiol 2018 13;73:63-76. Epub 2018 Jul 13.

Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, United States. Electronic address:

Nitric oxide (NO) is an antimicrobial metabolite produced by immune cells to prohibit infection. Due to its reactivity, NO has numerous reaction routes available to it in biological systems with some leading to cellular damage and others producing innocuous compounds. Pathogens have evolved resistance mechanisms toward NO, and many of these take the form of enzymes that chemically passivate the molecule. Read More

Adv Microb Physiol 2018 20;73:171-220. Epub 2018 Jun 20.

Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy; Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy; Dipartimento di Biologia, Università Roma 3, Roma, Italy. Electronic address:

This review is an overview on marine bioactive peptides with promising activities for the development of alternative drugs to fight human pathologies. In particular, we focus on potentially prolific producers of peptides in microorganisms, including sponge-associated bacteria and marine photoautotrophs such as microalgae and cyanobacteria. Microorganisms are still poorly explored for drug discovery, even if they are highly metabolically plastic and potentially amenable to culturing. Read More

Adv Microb Physiol 2018 6;73:123-169. Epub 2018 Jul 6.

Department of Pathology and Infectious Disease, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom.

With the advent of the global antimicrobial resistance (AMR) crisis, our arsenal of effective antibiotics is diminishing. The widespread use and misuse of antibiotics in human and veterinary medicine, compounded by the lack of novel classes of antibiotic in the pharmaceutical pipeline, has left a hole in our antibiotic armamentarium. Thus, alternatives to traditional antibiotics are being investigated, including two major groups of antibacterial agents, which have been extensively studied, phytochemicals and metals. Read More

Adv Microb Physiol 2018 20;73:1-62. Epub 2018 Jun 20.

School of Medical Sciences, Inflammatory Response and Infection Susceptibility Centre (iRiSC), Örebro University, Örebro, Sweden. Electronic address:

Urinary tract infection (UTI) is one of the most common bacterial infections in humans, and the majority are caused by uropathogenic Escherichia coli (UPEC). The rising antibiotic resistance among UPEC and the frequent failure of antibiotics to effectively treat recurrent UTI and catheter-associated UTI motivate research on alternative ways of managing UTI. Abundant evidence indicates that the toxic radical nitric oxide (NO), formed by activation of the inducible nitric oxide synthase, plays an important role in host defence to bacterial infections, including UTI. Read More

Adv Microb Physiol 2018 ;72:xi

Adv Microb Physiol 2018 28;72:65-115. Epub 2018 Feb 28.

UT Southwestern Medical Center, Dallas, TX, United States. Electronic address:

Nitric oxide (NO) is a gaseous signalling molecule that plays diverse physiological functions including antimicrobial host defence. During microbial infection, NO is synthesized by inducible NO synthase (iNOS), which is expressed by host immune cells through the recognition of microbial pattern molecules. Therefore, sensing pathogens or their pattern molecules by pattern recognition receptors (PRRs), which are located at the cell surface, endosomal and phagosomal compartment, or in the cytosol, is key in inducing iNOS and eliciting antimicrobial host defence. Read More

Adv Microb Physiol 2018 2;72:29-63. Epub 2018 Mar 2.

Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan. Electronic address:

Nitric oxide (NO) is a cellular signalling molecule widely conserved among organisms, including microorganisms such as bacteria, yeasts, and fungi, and higher eukaryotes such as plants and mammals. NO is mainly produced by the activities of NO synthase (NOS) or nitrite reductase (NIR). There are several NO detoxification systems, including NO dioxygenase (NOD) and S-nitrosoglutathione reductase (GSNOR). Read More