Genetic engineering for enhanced productivity in bioelectrochemical systems.
Abstract A shift from petrochemical processes toward a bio-based economy is one of the most advocated developments for a sustainable future. To achieve this will require the biotechnological production of platform chemicals that can be further processed by chemical engineering. Bioelectrochemical systems (BESs) are a novel tool within the biotechnology field. In BESs, microbes serve as biocatalysts for the production of biofuels and value-added compounds, as well as for the production of electricity. Although the general feasibility of bioelectrochemical processes has been demonstrated in recent years, much resear...
Source: Advances in Applied Microbiology - May 26, 2020 Category: Microbiology Authors: Philipp LA, Edel M, Gescher J Tags: Adv Appl Microbiol Source Type: research

Advances in the control of phytopathogenic fungi that infect crops through their root system.
ez AM, Diez Galán A, Calvo-Peña C Abstract Productivity and economic sustainability of many herbaceous and woody crops are seriously threatened by numerous phytopathogenic fungi. While symptoms associated with phytopathogenic fungal infections of aerial parts (leaves, stems and fruits) are easily observable and therefore recognizable, allowing rapid or preventive action to control this type of infection, the effects produced by soil-borne fungi that infect plants through their root system are more difficult to detect. The fact that these fungi initiate infection and damage underground implies that th...
Source: Advances in Applied Microbiology - May 26, 2020 Category: Microbiology Authors: Coque JJR, Álvarez-Pérez JM, Cobos R, González-García S, Ibáñez AM, Diez Galán A, Calvo-Peña C Tags: Adv Appl Microbiol Source Type: research

Engineering transport systems for microbial production.
Abstract The rapid development in the field of metabolic engineering has enabled complex modifications of metabolic pathways to generate a diverse product portfolio. Manipulating substrate uptake and product export is an important research area in metabolic engineering. Optimization of transport systems has the potential to enhance microbial production of renewable fuels and chemicals. This chapter comprehensively reviews the transport systems critical for microbial production as well as current genetic engineering strategies to improve transport functions and thus production metrics. In addition, this chapter hig...
Source: Advances in Applied Microbiology - May 26, 2020 Category: Microbiology Authors: Onyeabor M, Martinez R, Kurgan G, Wang X Tags: Adv Appl Microbiol Source Type: research

Yeasts for low input winemaking: Microbial terroir and flavor differentiation.
Abstract Vitis vinifera flowers and grape fruits are one of the most interesting ecosystem niches for native yeasts development. There are more than a 100 yeast species and millions of strains that participate and contribute to design the microbial terroir. The wine terroir concept is understood when grape and wine micro-regions were delimited by different quality characteristics after humans had been growing vines for more than 10,000 years. Environmental conditions, such as climate, soil composition, water management, winds and air quality, altitude, fauna and flora and microbes, are considered part of the "...
Source: Advances in Applied Microbiology - May 26, 2020 Category: Microbiology Authors: Carrau F, Boido E, Ramey D Tags: Adv Appl Microbiol Source Type: research

Detection of the 'Big Five' mold killers of humans: Aspergillus, Fusarium, Lomentospora, Scedosporium and Mucormycetes.
Abstract Fungi are an important but frequently overlooked cause of morbidity and mortality in humans. Life-threatening fungal infections mainly occur in immunocompromised patients, and are typically caused by environmental opportunists that take advantage of a weakened immune system. The filamentous fungus Aspergillus fumigatus is the most important and well-documented mold pathogen of humans, causing a number of complex respiratory diseases, including invasive pulmonary aspergillosis, an often fatal disease in patients with acute leukemia or in immunosuppressed bone marrow or solid organ transplant recipients. Ho...
Source: Advances in Applied Microbiology - May 12, 2020 Category: Microbiology Authors: Thornton CR Tags: Adv Appl Microbiol Source Type: research

The versatility of Pseudomonas putida in the rhizosphere environment.
This article addresses the lifestyle of Pseudomonas and focuses on how Pseudomonas putida can be used as a model system for biotechnological processes in agriculture, and in the removal of pollutants from soils. In this chapter we aim to show how a deep analysis using genetic information and experimental tests has helped to reveal insights into the lifestyle of Pseudomonads. Pseudomonas putida is a Plant Growth Promoting Rhizobacteria (PGPR) that establishes commensal relationships with plants. The interaction involves a series of functions encoded by core genes which favor nutrient mobilization, prevention of pathogen dev...
Source: Advances in Applied Microbiology - May 12, 2020 Category: Microbiology Authors: Molina L, Segura A, Duque E, Ramos JL Tags: Adv Appl Microbiol Source Type: research

Glutathione: A powerful but rare cofactor among Actinobacteria.
Abstract Glutathione (γ-l-glutamyl-l-cysteinylglycine, GSH) is a powerful cellular redox agent. In nature only the l,l-form is common among the tree of life. It serves as antioxidant or redox buffer system, protein regeneration and activation by interaction with thiol groups, unspecific reagent for conjugation during detoxification, marker for amino acid or peptide transport even through membranes, activation or solubilization of compounds during degradative pathways or just as redox shuttle. However, the role of GSH production and utilization in bacteria is more complex and especially little is known for th...
Source: Advances in Applied Microbiology - May 12, 2020 Category: Microbiology Authors: Lienkamp AC, Heine T, Tischler D Tags: Adv Appl Microbiol Source Type: research

Bacteroidetes bacteria in the soil: Glycan acquisition, enzyme secretion, and gliding motility.
Abstract The secretion of extracellular enzymes by soil microbes is rate-limiting in the recycling of biomass. Fungi and bacteria compete and collaborate for nutrients in the soil, with wide ranging ecological impacts. Within soil microbiota, the Bacteroidetes tend to be a dominant phylum, just like in human and animal intestines. The Bacteroidetes thrive because of their ability to secrete diverse arrays of carbohydrate-active enzymes (CAZymes) that target the highly varied glycans in the soil. Bacteroidetes use an energy-saving system of genomic organization, whereby most of their CAZymes are grouped into Polysa...
Source: Advances in Applied Microbiology - May 12, 2020 Category: Microbiology Authors: Larsbrink J, McKee LS Tags: Adv Appl Microbiol Source Type: research

Anaerobic and hydrogenogenic carbon monoxide-oxidizing prokaryotes: Versatile microbial conversion of a toxic gas into an available energy.
Abstract Carbon monoxide (CO) is a gas that is toxic to various organisms including humans and even microbes; however, it has low redox potential, which can fuel certain microbes, namely, CO oxidizers. Hydrogenogenic CO oxidizers utilize an energy conservation system via a CO dehydrogenase/energy-converting hydrogenase complex to produce hydrogen gas, a zero emission fuel, by CO oxidation coupled with proton reduction. Biochemical and molecular biological studies using a few model organisms have revealed their enzymatic reactions and transcriptional response mechanisms using CO. Biotechnological studies for CO-dep...
Source: Advances in Applied Microbiology - May 12, 2020 Category: Microbiology Authors: Fukuyama Y, Inoue M, Omae K, Yoshida T, Sako Y Tags: Adv Appl Microbiol Source Type: research

Microalgae for biofuel production.
Abstract Microalgae have been used commercially since the 1950s and 1960s, particularly in the Far East for human health foods and in the United States for wastewater treatment. Initial attempts to produce bulk chemicals such as biofuels from microalgae were not successful, despite commercially favorable conditions during the 1970s oil crisis. However, research initiatives at this time, many using extremophilic microalgae and cyanobacteria (e.g., Dunaliella and Spirulina), did solve many problems and clearly identified biomass productivity and harvesting as the two main constraints stopping microalgae producing bu...
Source: Advances in Applied Microbiology - November 4, 2019 Category: Microbiology Authors: Gilmour DJ Tags: Adv Appl Microbiol Source Type: research

Research progress on the basic helix-loop-helix transcription factors of Aspergillus species.
Abstract Basic helix-loop-helix (bHLH) proteins belong to a superfamily of transcription factors, and they are widely distributed in eukaryotic organisms. Members of the bHLH protein family can form homodimers or heterodimers with themselves or other family members, and they often play bifunctional roles as activators and repressors to uniquely regulate the transcription of downstream target genes. The bHLH transcription factors are usually involved in developmental processes, including cellular proliferation and differentiation. Therefore, these transcription factors often play crucial roles in regulating growth,...
Source: Advances in Applied Microbiology - November 4, 2019 Category: Microbiology Authors: Wang BT, Yu XY, Zhu YJ, Zhuang M, Zhang ZM, Jin L, Jin FJ Tags: Adv Appl Microbiol Source Type: research

Advances in yeast alcoholic fermentations for the production of bioethanol, beer and wine.
Basso TO Abstract Yeasts have a long-standing relationship with humankind that has widened in recent years to encompass production of diverse foods, beverages, fuels and medicines. Here, key advances in the field of yeast fermentation applied to alcohol production, which represents the predominant product of industrial biotechnology, will be presented. More specifically, we have selected industries focused in producing bioethanol, beer and wine. In these bioprocesses, yeasts from the genus Saccharomyces are still the main players, with Saccharomyces cerevisiae recognized as the preeminent industrial ethanologen. ...
Source: Advances in Applied Microbiology - November 4, 2019 Category: Microbiology Authors: Eliodório KP, Cunha GCGE, Müller C, Lucaroni AC, Giudici R, Walker GM, Alves SL, Basso TO Tags: Adv Appl Microbiol Source Type: research

Azotobacters as biofertilizer.
Abstract Azotobacters have been used as biofertilizer since more than a century. Azotobacters fix nitrogen aerobically, elaborate plant hormones, solubilize phosphates and also suppress phytopathogens or reduce their deleterious effect. Application of wild type Azotobacters results in better yield of cereals like corn, wheat, oat, barley, rice, pearl millet and sorghum, of oil seeds like mustard and sunflower, of vegetable crops like tomato, eggplant, carrot, chillies, onion, potato, beans and sugar beet, of fruits like mango and sugar cane, of fiber crops like jute and cotton and of tree like oak. In addition to ...
Source: Advances in Applied Microbiology - September 11, 2019 Category: Microbiology Authors: Das HK Tags: Adv Appl Microbiol Source Type: research

Application of model systems to study adaptive responses of Mycobacterium tuberculosis during infection and disease.
We describe mechanisms that tubercle bacteria use to resuscitate from these non-replicating conditions, together with phenotypic heterogeneity in terms of culturabiliy of M. tuberculosis in sputum. Transcriptional changes in M. tuberculosis that allow for adaptation of the organism to the lung environment are also summarized. Finally, given the emerging importance of the microbiome in various infectious diseases, we provide a description of how the lung and gut microbiome affect susceptibility to TB infection and response to treatment. Consideration of these collective aspects will enhance the understanding of basic metabo...
Source: Advances in Applied Microbiology - September 11, 2019 Category: Microbiology Authors: Gordhan BG, Peters J, Kana BD Tags: Adv Appl Microbiol Source Type: research

The role of microorganisms in soy sauce production.
Abstract Soy sauce is a salty condiment commonly used in Eastern Asia that is made from soy beans with varying amounts of wheat or no wheat at all. It is known as shoyu in Japan, chiang-yu (or -yi) in China, kecup in Indonesia, kunjang in Korea, toyo in The Philippines, and see-ieu in Thailand (Beuchat, 1985; Djien, 1982; Fukushima, 1989). It provides flavor in an otherwise bland diet, and nutritionally it provides salt (NaCl) and predigested proteins in a diet that is traditionally protein poor. It has been made for centuries on a small scale in many towns and villages in Asia, but since 1950, particularly in Jap...
Source: Advances in Applied Microbiology - September 11, 2019 Category: Microbiology Authors: O'toole DK Tags: Adv Appl Microbiol Source Type: research

Biological oxidation of iron sulfides.
Abstract The biological oxidation of minerals and ores, called bioleaching, has been studied for the last decades to solubilize metals and recover them. In particular, iron sulfides are the most studied ores for an optimum extraction of different metals, such as copper or zinc. The use of chemolithotrophic bacteria, as Acidothiobacillus ferrooxidans, to oxidize both iron and sulfur species in aerobic conditions and at acidic pH shows promising results. In the field of heritage preservation, the development of "green" treatments is more and more studied. Waterlogged archeological wood presents an accumula...
Source: Advances in Applied Microbiology - May 29, 2019 Category: Microbiology Authors: Monachon M, Albelda-Berenguer M, Joseph E Tags: Adv Appl Microbiol Source Type: research

Mucoid switch in Burkholderia cepacia complex bacteria: Triggers, molecular mechanisms and implications in pathogenesis.
Abstract Bacteria produce a vast range of exopolysaccharides (EPSs) to thrive in diverse environmental niches and often display a mucoid phenotype in solid media. One such exopolysaccharide, cepacian, is produced by bacteria of the genus Burkholderia and is of interest due to its role in pathogenesis associated with lung infections in cystic fibrosis (CF) patients. Cepacian is a repeat-unit polymer that has been implicated in biofilm formation, immune system evasion, interaction with host cells, resistance against antimicrobials, and virulence. Its biosynthesis proceeds through the Wzy-dependent polymerization and...
Source: Advances in Applied Microbiology - May 29, 2019 Category: Microbiology Authors: Ferreira MR, Gomes SC, Moreira LM Tags: Adv Appl Microbiol Source Type: research

Phenotypic instability in fungi.
Abstract Fungi are prone to phenotypic instability, that is, the vegetative phase of these organisms, be they yeasts or molds, undergoes frequent switching between two or more behaviors, often with different morphologies, but also sometime having different physiologies without any obvious morphological outcome. In the context of industrial utilization of fungi, this can have a negative impact on the maintenance of strains and/or on their productivity. Instabilities have been shown to result from various mechanisms, either genetic or epigenetic. This chapter will review different types of instabilities and discuss ...
Source: Advances in Applied Microbiology - May 29, 2019 Category: Microbiology Authors: Silar P Tags: Adv Appl Microbiol Source Type: research

Microbes associated with fresh produce: Sources, types and methods to reduce spoilage and contamination.
Abstract Global food security remains one of the most important challenges that needs to be addressed to ensure the increasing demand for food of the fast growing human population is satisfied. Fruits and vegetables comprise an essential component of a healthy balanced diet as they are the major source of both macro- and micronutrients. They are particularly important for communities in developing countries whose nutrition often relies solely on a plant-based diet. Recent advances in agriculture and food processing technologies have facilitated production of fresh, nutritious and safe food for consumers. However, ...
Source: Advances in Applied Microbiology - May 29, 2019 Category: Microbiology Authors: Kaczmarek M, Avery SV, Singleton I Tags: Adv Appl Microbiol Source Type: research

Toward rational selection criteria for selection of probiotics in pigs.
e M Abstract An accurate understanding of properties of probiotics is a prerequisite for selecting probiotic organisms for use in swine production. This review aims to review selection criteria for probiotic organism in swine. The systematically investigated ecological history rather than the source of isolates should be regarded as the natural origin of probiotic strains, which helps to correct the inconsistencies arising from incorrect identification of the source. Moreover, in vivo studies are suggested as follow-up assessment to validate the characteristics of probiotic predicted by in vitro experiments. In ad...
Source: Advances in Applied Microbiology - May 29, 2019 Category: Microbiology Authors: Wang W, Gänzle M Tags: Adv Appl Microbiol Source Type: research

Role and regulation of the stress activated sigma factor sigma B ( σB) in the saprophytic and host-associated life stages of Listeria monocytogenes.
Role and regulation of the stress activated sigma factor sigma B (σB) in the saprophytic and host-associated life stages of Listeria monocytogenes. Adv Appl Microbiol. 2019;106:1-48 Authors: Dorey A, Marinho C, Piveteau P, O'Byrne C Abstract The stress activated sigma factor sigma B (σB) plays a pivotal role in allowing the food-borne bacterial pathogen Listeria monocytogenes to modulate its transcriptional landscape in order to survive in a variety of harsh environments both outside and within the host. While we have a comparatively good understanding of the systems under the control of t...
Source: Advances in Applied Microbiology - February 27, 2019 Category: Microbiology Authors: Dorey A, Marinho C, Piveteau P, O'Byrne C Tags: Adv Appl Microbiol Source Type: research

Nitrogen cycling during wastewater treatment.
Abstract Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrog...
Source: Advances in Applied Microbiology - February 27, 2019 Category: Microbiology Authors: Holmes DE, Dang Y, Smith JA Tags: Adv Appl Microbiol Source Type: research

Siderophores: From natural roles to potential applications.
Abstract Siderophores are secondary metabolites produced by different organisms in order to scavenge iron from their surrounding environment making this essential element available to the cell. Presenting high affinity for ferric iron, siderophores are secreted out to form soluble ferric complexes that can be taken up by the organisms. Siderophores present complex chemistry that allows them to form the strongest iron-chelating complexes. Interest in this field is always up to date and new siderophores are found with new roles and applications. For example, siderophores participate to the mobilization of iron and o...
Source: Advances in Applied Microbiology - February 27, 2019 Category: Microbiology Authors: Albelda-Berenguer M, Monachon M, Joseph E Tags: Adv Appl Microbiol Source Type: research

Oxalic acid, a molecule at the crossroads of bacterial-fungal interactions.
Abstract Oxalic acid is the most ubiquitous and common low molecular weight organic acid produced by living organisms. Oxalic acid is produced by fungi, bacteria, plants, and animals. The aim of this review is to give an overview of current knowledge about the microbial cycling of oxalic acid through ecosystems. Here we review the production and degradation of oxalic acid, as well as its implications in the metabolism for fungi, bacteria, plants, and animals. Indeed, fungi are well known producers of oxalic acid, while bacteria are considered oxalic acid consumers. However, this framework may need to be modified, ...
Source: Advances in Applied Microbiology - February 27, 2019 Category: Microbiology Authors: Palmieri F, Estoppey A, House GL, Lohberger A, Bindschedler S, Chain PSG, Junier P Tags: Adv Appl Microbiol Source Type: research

Bacterial spores, from ecology to biotechnology.
Abstract The production of a highly specialized cell structure called a spore is a remarkable example of a survival strategy displayed by bacteria in response to challenging environmental conditions. The detailed analysis and description of the process of sporulation in selected model organisms have generated a solid background to understand the cellular processes leading to the formation of this specialized cell. However, much less is known regarding the ecology of spore-formers. This research gap needs to be filled as the feature of resistance has important implications not only on the survival of spore-formers ...
Source: Advances in Applied Microbiology - February 27, 2019 Category: Microbiology Authors: Paul C, Filippidou S, Jamil I, Kooli W, House GL, Estoppey A, Hayoz M, Junier T, Palmieri F, Wunderlin T, Lehmann A, Bindschedler S, Vennemann T, Chain PSG, Junier P Tags: Adv Appl Microbiol Source Type: research

The Genus Macrococcus: An Insight Into Its Biology, Evolution, and Relationship With Staphylococcus.
Abstract The Gram-positive genus Macrococcus is composed of eight species that are evolutionarily closely related to species of the Staphylococcus genus. In contrast to Staphylococcus species, species of Macrococcus are generally regarded to be avirulent in their animal hosts. Recent reports on Macrococcus have focused on the presence of novel methicillin resistance genes in Macrococcus caseolyticus and Macrococcus canis, with the discovery of the first plasmid-encoded methicillin resistance gene in clinical Staphylococcus aureus of probable macrococcal origin generating further interest in these organisms. Furthe...
Source: Advances in Applied Microbiology - October 23, 2018 Category: Microbiology Authors: Mazhar S, Hill C, McAuliffe O Tags: Adv Appl Microbiol Source Type: research

Diversity-Function Relationships in Natural, Applied, and Engineered Microbial Ecosystems.
Abstract The connection between ecosystem function and taxonomic diversity has been of interest and relevance to macroecologists for decades. After many years of lagging behind due to the difficulty of assigning both taxonomy and function to poorly distinguishable microscopic cells, microbial ecology now has access to a suite of powerful molecular tools which allow its practitioners to generate data relating to diversity and function of a microbial community on an unprecedented scale. Instead, the problem facing today's microbial ecologists is coupling the ease of generation of these datasets with the formulation ...
Source: Advances in Applied Microbiology - October 23, 2018 Category: Microbiology Authors: Free A, McDonald MA, Pagaling E Tags: Adv Appl Microbiol Source Type: research

Epigenetic and Posttranslational Modifications in Regulating the Biology of Aspergillus Species.
This article describes the advances in typical DNA and protein modifications in the genus Aspergillus, focusing on methylation, acetylation, phosphorylation, ubiquitination, sumoylation, and neddylation. PMID: 30342722 [PubMed - in process] (Source: Advances in Applied Microbiology)
Source: Advances in Applied Microbiology - October 23, 2018 Category: Microbiology Authors: Nie X, Li B, Wang S Tags: Adv Appl Microbiol Source Type: research

Electrochemical Bioreactor Technology for Biocatalysis and Microbial Electrosynthesis.
Abstract Two seemingly distinct fields, industrial biocatalysis and microbial electrosynthesis, can be viewed together through the lens of electrochemical bioreactor technology in order to highlight the challenges that exist in creating a versatile platform technology for use in chemical and biological applications. Industrial biocatalysis applications requiring NAD(P)H to perform redox transformations often necessitate convoluted coupled-enzyme regeneration systems to regenerate reduced cofactor, NAD(P)H from oxidized cofactor, NAD(P). Renewed interest in continuously recycling the cofactor via electrochemical re...
Source: Advances in Applied Microbiology - October 23, 2018 Category: Microbiology Authors: Morrison C, Heitmann E, Armiger W, Dodds D, Koffas M Tags: Adv Appl Microbiol Source Type: research

Enhancing Yeast Alcoholic Fermentations.
Abstract The production of ethanol by yeast fermentation represents the largest of all global biotechnologies. Consequently, the yeast Saccharomyces cerevisiae is the world's premier industrial microorganism, which is responsible not only for the production of alcoholic beverages, including beer, wine, and distilled spirits, but also for the billions of liters of bioethanol produced annually for use as a renewable transportation fuel. Although humankind has exploited the fermentative activities of yeasts for millennia, many aspects of alcohol fermentation remain poorly understood. This chapter will review some of ...
Source: Advances in Applied Microbiology - October 23, 2018 Category: Microbiology Authors: Walker GM, Walker RSK Tags: Adv Appl Microbiol Source Type: research

Salmonella Cold Stress Response: Mechanisms and Occurrence in Foods.
Abstract Since bacteria in foods often encounter various cold environments during food processing, such as chilling, cold chain distribution, and cold storage, lower temperatures can become a major stress environment for foodborne pathogens. Bacterial responses in stressful environments have been considered in the past, but now the importance of stress responses at the molecular level is becoming recognized. Documenting how bacterial changes occur at the molecular level may help to achieve the in-depth understanding of stress responses, to predict microbial fate when they encounter cold temperatures, and to design...
Source: Advances in Applied Microbiology - August 27, 2018 Category: Microbiology Authors: Ricke SC, Dawoud TM, Kim SA, Park SH, Kwon YM Tags: Adv Appl Microbiol Source Type: research

Enhancement of Metallosphaera sedula Bioleaching by Targeted Recombination and Adaptive Laboratory Evolution.
Abstract Thermophilic and lithoautotrophic archaea such as Metallosphaera sedula occupy acidic, metal-rich environments and are used in biomining processes. Biotechnological approaches could accelerate these processes and improve metal recovery by biomining organisms, but systems for genetic manipulation in these organisms are currently lacking. To gain a better understanding of the interplay between metal resistance, autotrophy, and lithotrophic metabolism, a genetic system was developed for M. sedula and used to evaluate parameters governing the efficiency of copper bioleaching. Additionally, adaptive laboratory...
Source: Advances in Applied Microbiology - August 27, 2018 Category: Microbiology Authors: McCarthy S, Ai C, Blum P Tags: Adv Appl Microbiol Source Type: research

Applications of Microbial Processes in Geotechnical Engineering.
Abstract Over the last 10-15 years, a new field of "biogeotechnics" has emerged as geotechnical engineers seek to find ground improvement technologies which have the potential to be lower carbon, more ecologically friendly, and more cost-effective than existing practices. This review summarizes the developments which have occurred in this new field, outlining in particular the microbial processes which have been shown to be most promising for altering the hydraulic and mechanical responses of soils and rocks. Much of the research effort in this new field has been focused on microbially induced carbonate ...
Source: Advances in Applied Microbiology - August 27, 2018 Category: Microbiology Authors: El Mountassir G, Minto JM, van Paassen LA, Salifu E, Lunn RJ Tags: Adv Appl Microbiol Source Type: research

Ecology of Contaminant Biotransformation in the Mycosphere: Role of Transport Processes.
We describe the characteristics of the mycosphere as a unique and highly dynamic bacterial habitat and a hot spot for contaminant biotransformation. In particular, we emphasize the role of the mycosphere for (i) bacterial dispersal and colonization of subsurface interfaces and new habitats, (ii) matter transport processes and contaminant bioaccessibility, and (iii) the functional stability of microbial ecosystems when exposed to environmental fluctuations such as stress or disturbances. Adopting concepts from ecological theory, the chapter disentangles bacterial-fungal impacts on contaminant biotransformation in a systemic...
Source: Advances in Applied Microbiology - August 27, 2018 Category: Microbiology Authors: Worrich A, Wick LY, Banitz T Tags: Adv Appl Microbiol Source Type: research

Antimicrobial Resistance in Campylobacter Species: Mechanisms and Genomic Epidemiology.
Abstract The Campylobacter genus is a large and diverse group of Gram-negative bacteria that are known to colonize humans and other mammals, birds, reptiles, and shellfish. While it is now recognized that several emerging Campylobacter species can be associated with human disease, two species, C. jejuni and C. coli, are responsible for the vast majority of bacterial gastroenteritis in humans worldwide. Infection with C. jejuni, in particular, has also been associated with a number of extragastrointestinal manifestations and autoimmune conditions, most notably Guillain-Barré syndrome. The antimicrobial drugs...
Source: Advances in Applied Microbiology - June 21, 2018 Category: Microbiology Authors: Whitehouse CA, Zhao S, Tate H Tags: Adv Appl Microbiol Source Type: research

Modeling Bacteria-Phage Interactions and Its Implications for Phage Therapy.
Abstract Bacteriophages are more abundant than any other organism on our planet. The interaction of bacteriophages and bacteria and their coevolution is well known. In this chapter, we describe various aspects of modeling such systems and their dynamics. We explore their interaction in: (i) liquid media, which leads to well-mixed populations and (ii) solid media, where their interaction is spatially restricted. Such modeling, when used in conjunction with experiments would not only shed deep insight into the underlying dynamics but also provide useful clues toward potential therapeutic applications. PMID: 299...
Source: Advances in Applied Microbiology - June 21, 2018 Category: Microbiology Authors: Sinha S, Grewal RK, Roy S Tags: Adv Appl Microbiol Source Type: research

Bacterial Anaerobic Synthesis Gas (Syngas) and CO2+H2 Fermentation.
e P Abstract Anaerobic bacterial gas fermentation gains broad interest in various scientific, social, and industrial fields. This microbial process is carried out by a specific group of bacterial strains called acetogens. All these strains employ the Wood-Ljungdahl pathway but they belong to different taxonomic groups. Here we provide an overview of the metabolism of acetogens and naturally occurring products. Characteristics of 61 strains were summarized and selected acetogens described in detail. Acetobacterium woodii, Clostridium ljungdahlii, and Moorella thermoacetica serve as model organisms. Results of appro...
Source: Advances in Applied Microbiology - June 21, 2018 Category: Microbiology Authors: Bengelsdorf FR, Beck MH, Erz C, Hoffmeister S, Karl MM, Riegler P, Wirth S, Poehlein A, Weuster-Botz D, Dürre P Tags: Adv Appl Microbiol Source Type: research

Biofilm: A Hotspot for Emerging Bacterial Genotypes.
Abstract Bacteria have the ability to adapt to changing environments through rapid evolution mediated by modification of existing genetic information, as well as by horizontal gene transfer (HGT). This makes bacteria a highly successful life form when it comes to survival. Unfortunately, this genetic plasticity may result in emergence and dissemination of antimicrobial resistance and virulence genes, and even the creation of multiresistant "superbugs" which may pose serious threats to public health. As bacteria commonly reside in biofilms, there has been an increased interest in studying these phenomena ...
Source: Advances in Applied Microbiology - June 21, 2018 Category: Microbiology Authors: Nesse LL, Simm R Tags: Adv Appl Microbiol Source Type: research

Microbial Source Tracking of Cronobacter spp.
Abstract Being able to track bacterial pathogens is essential for epidemiological purposes as well as monitoring in-house production facilities. Common bacterial pathogens, such as Salmonella serovars, are already been well defined, and their detection methods are very advanced. However, this will not be the case for emergent bacterial pathogens, as was the case for Cronobacter. The clinical significance of the organism is due to its association with rare sporadic infections in adults, and severe life-threatening outbreaks of necrotizing enterocolitis and meningitis in newborn babies. The main recognized route of ...
Source: Advances in Applied Microbiology - June 21, 2018 Category: Microbiology Authors: Forsythe S Tags: Adv Appl Microbiol Source Type: research

Twenty-Five Years of Investigating the Universal Stress Protein: Function, Structure, and Applications.
Abstract Since the initial discovery of universal stress protein A (UspA) 25 years ago, remarkable advances in molecular and biochemical technologies have revolutionized our understanding of biology. Many studies using these technologies have focused on characterization of the uspA gene and Usp-type proteins. These studies have identified the conservation of Usp-like proteins across bacteria, archaea, plants, and even some invertebrate animals. Regulation of these proteins under diverse stresses has been associated with different stress-response genes including spoT and relA in the stringent response and the dosR ...
Source: Advances in Applied Microbiology - April 25, 2018 Category: Microbiology Authors: Vollmer AC, Bark SJ Tags: Adv Appl Microbiol Source Type: research

Spore Germination of Pathogenic Filamentous Fungi.
Abstract Fungi, algae, plants, protozoa, and bacteria are all known to form spores, especially hardy and ubiquitous propagation structures that are also often the infectious agents of diseases. Spores can survive for thousands of years, frozen in the permafrost (Kochkina et al., 2012), with the oldest viable spores extracted after 250 million years from salt crystals (Vreeland, Rosenzweig, & Powers, 2000). Their resistance to high levels of UV, desiccation, pressure, heat, and cold enables the survival of spores in the harshest conditions (Setlow, 2016). For example, Bacillus subtilis spores can survive and re...
Source: Advances in Applied Microbiology - April 25, 2018 Category: Microbiology Authors: Sephton-Clark PCS, Voelz K Tags: Adv Appl Microbiol Source Type: research

Host Sensing by Pathogenic Fungi.
Abstract The ability to cause disease extends from the ability to grow within the host environment. The human host provides a dynamic environment to which fungal pathogens must adapt to in order to survive. The ability to grow under a particular condition (i.e., the ability to grow at mammalian body temperature) is considered a fitness attribute and is essential for growth within the human host. On the other hand, some environmental conditions activate signaling mechanisms resulting in the expression of virulence factors, which aid pathogenicity. Therefore, pathogenic fungi have evolved fitness and virulence attri...
Source: Advances in Applied Microbiology - April 25, 2018 Category: Microbiology Authors: Sherrington SL, Kumwenda P, Kousser C, Hall RA Tags: Adv Appl Microbiol Source Type: research

Fungal Genomes and Genotyping.
Abstract The availability of complete fungal genomes is expanding rapidly and is offering an extensive and accurate view of this "kingdom." The scientific milestone of free access to more than 1000 fungal genomes of different species was reached, and new and stimulating projects have meanwhile been released. The "1000 Fungal Genomes Project" represents one of the largest sequencing initiative regarding fungal organisms trying to fill some gaps on fungal genomics. Presently, there are 329 fungal families with at least one representative genome sequenced, but there is still a large number of fung...
Source: Advances in Applied Microbiology - April 25, 2018 Category: Microbiology Authors: Araujo R, Sampaio-Maia B Tags: Adv Appl Microbiol Source Type: research

Fungi in Deep Subsurface Environments.
Abstract The igneous crust of the oceans and the continents represents the major part of Earth's lithosphere and has recently been recognized as a substantial, yet underexplored, microbial habitat. While prokaryotes have been the focus of most investigations, microeukaryotes have been surprisingly neglected. However, recent work acknowledges eukaryotes, and in particular fungi, as common inhabitants of the deep biosphere, including the deep igneous provinces. The fossil record of the subseafloor igneous crust, and to some extent the continental bedrock, establishes fungi or fungus-like organisms as inhabitants of ...
Source: Advances in Applied Microbiology - April 25, 2018 Category: Microbiology Authors: Ivarsson M, Bengtson S, Drake H, Francis W Tags: Adv Appl Microbiol Source Type: research

Sodium Chloride Does Not Ensure Microbiological Safety of Foods: Cases and Solutions.
Abstract Addition of salt or salt-containing water to food is one of the oldest and most effective preservation methods in history; indeed, salt-cured foods are generally recognized as microbiologically safe due to their high salinity. However, a number of microbiological risks remain. The microbiological hazards and risks associated with salt-cured foods must be addressed more in-depth as they are likely to be underestimated by previous studies. This review examined a number of scientific reports and articles about the microbiological safety of salt-cured foods, which included salted, brined, pickled, and/or mari...
Source: Advances in Applied Microbiology - October 21, 2017 Category: Microbiology Authors: Kim NH, Cho TJ, Rhee MS Tags: Adv Appl Microbiol Source Type: research

Uranium Bioreduction and Biomineralization.
The objective of this review is to provide an understanding of recent developments in these two fields in relation to relevant microorganisms, mechanisms, influential factors, and obstacles. PMID: 29050665 [PubMed - in process] (Source: Advances in Applied Microbiology)
Source: Advances in Applied Microbiology - October 21, 2017 Category: Microbiology Authors: Wufuer R, Wei Y, Lin Q, Wang H, Song W, Liu W, Zhang D, Pan X, Gadd GM Tags: Adv Appl Microbiol Source Type: research

The Contribution of Bacteriophages to the Biology and Virulence of Pathogenic Clostridia.
Abstract Bacteriophages are key players in the evolution of most bacteria. Temperate phages have been associated with virulence of some of the deadliest pathogenic bacteria. Among the most notorious cases, the genes encoding the botulinum neurotoxin produced by Clostridium botulinum types C and D and the α-toxin (TcnA) produced by Clostridium novyi are both encoded within prophage genomes. Clostridium difficile is another important human pathogen and the recent identification of a complete binary toxin locus (CdtLoc) carried on a C. difficile prophage raises the potential for horizontal transf...
Source: Advances in Applied Microbiology - October 21, 2017 Category: Microbiology Authors: Fortier LC Tags: Adv Appl Microbiol Source Type: research

Toward  Genome-Based Metabolic Engineering in Bacteria.
Toward Genome-Based Metabolic Engineering in Bacteria. Adv Appl Microbiol. 2017;101:49-82 Authors: Oesterle S, Wuethrich I, Panke S Abstract Prokaryotes modified stably on the genome are of great importance for production of fine and commodity chemicals. Traditional methods for genome engineering have long suffered from imprecision and low efficiencies, making construction of suitable high-producer strains laborious. Here, we review the recent advances in discovery and refinement of molecular precision engineering tools for genome-based metabolic engineering in bacteria for chemical production, w...
Source: Advances in Applied Microbiology - October 21, 2017 Category: Microbiology Authors: Oesterle S, Wuethrich I, Panke S Tags: Adv Appl Microbiol Source Type: research

Microbial Transformation of Iodine: From Radioisotopes to Iodine Deficiency.
Abstract Iodine is a biophilic element that is important for human health, both as an essential component of several thyroid hormones and, on the other hand, as a potential carcinogen in the form of radioiodine generated by anthropogenic nuclear activity. Iodine exists in multiple oxidation states (-1, 0, +1, +3, +5, and +7), primarily as molecular iodine (I2), iodide (I(-)), iodate [Formula: see text] , or organic iodine (org-I). The mobility of iodine in the environment is dependent on its speciation and a series of redox, complexation, sorption, precipitation, and microbial reactions. Over the last 15years...
Source: Advances in Applied Microbiology - October 21, 2017 Category: Microbiology Authors: Yeager CM, Amachi S, Grandbois R, Kaplan DI, Xu C, Schwehr KA, Santschi PH Tags: Adv Appl Microbiol Source Type: research

Current Interventions for Controlling Pathogenic Escherichia coli.
Abstract This review examined scientific reports and articles published from 2007 to 2016 regarding the major environmental sources of pathogenic Escherichia coli and the routes by which they enter the human gastrointestinal tract. The literature describes novel techniques used to combat pathogenic E. coli transmitted to humans from livestock and agricultural products, food-contact surfaces in processing environments, and food products themselves. Although prevention before contamination is always the best "intervention," many studies aim to identify novel chemical, physical, and biological techniqu...
Source: Advances in Applied Microbiology - July 25, 2017 Category: Microbiology Authors: Kim NH, Cho TJ, Rhee MS Tags: Adv Appl Microbiol Source Type: research