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Advances in Applied Microbiology

B Sampaio-Maia, L Simões-Silva, M Pestana, R Araujo, I J Soares-Silva
Chronic kidney disease (CKD) is estimated to affect nearly 500 million people worldwide and cardiovascular (CV) disease is a major cause of death in this population. However, therapeutic interventions targeting traditional CV risks are not effective at lowering the incidence of CV events or at delaying the progression of the disease in CKD patients. In recent years, disturbances of normal gut microbiome were recognized in the pathogenesis of diverse chronic diseases. Gut dysbiosis is being unraveled in CKD and pointed as a nontraditional risk factor for CV risk and CKD progression...
2016: Advances in Applied Microbiology
A J Hay, J Zhu
Colonization of a human host with a commensal microbiota has a complex interaction in which bacterial communities provide numerous health benefits to the host. An equilibrium between host and microbiota is kept in check with the help of biliary secretions by the host. Bile, composed primarily of bile salts, promotes digestion. It also provides a barrier between host and bacteria. After bile salts are synthesized in the liver, they are stored in the gallbladder to be released after food intake. The set of host-secreted bile salts is modified by the resident bacteria...
2016: Advances in Applied Microbiology
H A Crosby, J Kwiecinski, A R Horswill
The human commensal bacterium Staphylococcus aureus can cause a wide range of infections ranging from skin and soft tissue infections to invasive diseases like septicemia, endocarditis, and pneumonia. Muticellular organization almost certainly contributes to S. aureus pathogenesis mechanisms. While there has been considerable focus on biofilm formation and its role in colonizing prosthetic joints and indwelling devices, less attention has been paid to nonsurface-attached group behavior like aggregation and clumping...
2016: Advances in Applied Microbiology
N Wallace, A Zani, E Abrams, Y Sun
Bacterial enteric pathogens are responsible for a tremendous amount of foodborne illnesses every year through the consumption of contaminated food products. During their transit from contaminated food sources to the host gastrointestinal tract, these pathogens are exposed and must adapt to fluctuating oxygen levels to successfully colonize the host and cause diseases. However, the majority of enteric infection research has been conducted under aerobic conditions. To raise awareness of the importance in understanding the impact of oxygen, or lack of oxygen, on enteric pathogenesis, we describe in this review the metabolic and physiological responses of nine bacterial enteric pathogens exposed to environments with different oxygen levels...
2016: Advances in Applied Microbiology
Y Morono, F Inagaki
Over the past few decades, the subseafloor biosphere has been explored by scientific ocean drilling to depths of about 2.5km below the seafloor. Although organic-rich anaerobic sedimentary habitats in the ocean margins harbor large numbers of microbial cells, microbial populations in ultraoligotrophic aerobic sedimentary habitats in the open ocean gyres are several orders of magnitude less abundant. Despite advances in cultivation-independent molecular ecological techniques, exploring the low-biomass environment remains technologically challenging, especially in the deep subseafloor biosphere...
2016: Advances in Applied Microbiology
I S Druzhinina, C P Kubicek
The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) has properties of an efficient cell factory for protein production that is exploited by the enzyme industry, particularly with respect to cellulase and hemicellulase formation. Under conditions of industrial fermentations it yields more than 100g secreted protein L(-1). Consequently, T. reesei has been intensively studied in the 20th century. Most of these investigations focused on the biochemical characteristics of its cellulases and hemicellulases, on the improvement of their properties by protein engineering, and on enhanced enzyme production by recombinant strategies...
2016: Advances in Applied Microbiology
R Alegria Terrazas, C Giles, E Paterson, S Robertson-Albertyn, S Cesco, T Mimmo, Y Pii, D Bulgarelli
A major challenge facing agriculture in the 21st century is the need to increase the productivity of cultivated land while reducing the environmentally harmful consequences of mineral fertilization. The microorganisms thriving in association and interacting with plant roots, the plant microbiota, represent a potential resource of plant probiotic function, capable of conjugating crop productivity with sustainable management in agroecosystems. However, a limited knowledge of the organismal interactions occurring at the root-soil interface is currently hampering the development and use of beneficial plant-microbiota interactions in agriculture...
2016: Advances in Applied Microbiology
A Schmalenberger, A Fox
Soil amendments with biochar to improve soil fertility and increase soil carbon stocks have received some high-level attention. Physical and chemical analyses of amended soils and biochars from various feedstocks are reported, alongside some evaluations of plant growth promotion capabilities. Fewer studies investigated the soil microbiota and their potential to increase cycling and mobilization of nutrients in biochar-amended soils. This review is discussing the latest findings in the bacterial contribution to cycling and mobilizing nitrogen, phosphorus, and sulfur in biochar-amended soils and potential contributions to plant growth promotion...
2016: Advances in Applied Microbiology
Deepika Kumari, Xin-Yi Qian, Xiangliang Pan, Varenyam Achal, Qianwei Li, Geoffrey Michael Gadd
Rapid urbanization and industrialization resulting from growing populations contribute to environmental pollution by toxic metals and radionuclides which pose a threat to the environment and to human health. To combat this threat, it is important to develop remediation technologies based on natural processes that are sustainable. In recent years, a biomineralization process involving ureolytic microorganisms that leads to calcium carbonate precipitation has been found to be effective in immobilizing toxic metal pollutants...
2016: Advances in Applied Microbiology
M Itävaara, H Salavirta, K Marjamaa, T Ruskeeniemi
Fractures in the deep subsurface of Earth's crust are inhabited by diverse microbial communities that participate in biogeochemical cycles of the Earth. Life on Earth, which arose c. 3.5-4.0 billion years ago, reaches down at least 5 km in the crust. Deep mines, caves, and boreholes have provided scientists with opportunities to sample deep subsurface microbiomes and to obtain information on the species diversity and functions. A wide variety of bacteria, archaea, eukaryotes, and viruses are now known to reside in the crust, but their functions are still largely unknown...
2016: Advances in Applied Microbiology
Jan Nešvera, Lenka Rucká, Miroslav Pátek
Phenol and its derivatives (alkylphenols, halogenated phenols, nitrophenols) are natural or man-made aromatic compounds that are ubiquitous in nature and in human-polluted environments. Many of these substances are toxic and/or suspected of mutagenic, carcinogenic, and teratogenic effects. Bioremediation of the polluted soil and water using various bacteria has proved to be a promising option for the removal of these compounds. In this review, we describe a number of peripheral pathways of aerobic and anaerobic catabolism of various natural and xenobiotic phenolic compounds, which funnel these substances into a smaller number of central catabolic pathways...
2015: Advances in Applied Microbiology
Nancy I López, M Julia Pettinari, Pablo I Nikel, Beatriz S Méndez
Bacterial polyhydroxyalkanoates (PHAs) are isotactic polymers that play a critical role in central metabolism, as they act as dynamic reservoirs of carbon and reducing equivalents. These polymers have a number of technical applications since they exhibit thermoplastic and elastomeric properties, making them attractive as a replacement of oil-derived materials. PHAs are accumulated under conditions of nutritional imbalance (usually an excess of carbon source with respect to a limiting nutrient, such as nitrogen or phosphorus)...
2015: Advances in Applied Microbiology
Penny R Hirsch, Tim H Mauchline
Nitrogen is crucial for living cells, and prior to the introduction of mineral N fertilizer, fixation of atmospheric N2 by diverse prokaryotes was the primary source of N in all ecosystems. Microorganisms drive the N cycle starting with N2 fixation to ammonia, through nitrification in which ammonia is oxidized to nitrate and denitrification where nitrate is reduced to N2 to complete the cycle, or partially reduced to generate the greenhouse gas nitrous oxide. Traditionally, agriculture has relied on rotations that exploited N fixed by symbiotic rhizobia in leguminous plants, and recycled wastes and manures that microbial activity mineralized to release ammonia or nitrate...
2015: Advances in Applied Microbiology
Ruth E Falconer, Wilfred Otten, Nia A White
The role of fungi in shaping ecosystems is well evidenced and there is growing recognition of their importance among scientists and the general public. Establishing and separating the role of key local (soil chemical, biological, and physical properties) and global (climate, dispersal limitation) drivers in fungal community structure and functioning is currently a source of frustration to mycologists. The quest to determine niche processes and environmental characteristics shaping fungal community structure, known to be important for plant and animal communities, is proving difficult, resulting in the acknowledgment that niche neutral processes (climate, dispersal limitations) may dominate...
2015: Advances in Applied Microbiology
Kristina Heinrich, David J Leslie, Kristina Jonas
The cell cycle is one of the most fundamental processes in biology, underlying the proliferation and growth of all living organisms. In bacteria, the cell cycle has been extensively studied since the 1950s. Most of this research has focused on cell cycle regulation in a few model bacteria, cultured under standard growth conditions. However in nature, bacteria are exposed to drastic environmental changes. Recent work shows that by modulating their own growth and proliferation bacteria can increase their survival under stressful conditions, including antibiotic treatment...
2015: Advances in Applied Microbiology
William Kricka, James Fitzpatrick, Ursula Bond
Lignocellulose biomass, one of the most abundant renewable resources on the planet, is an alternative sustainable energy source for the production of second-generation biofuels. Energy in the form of simple or complex carbohydrates can be extracted from lignocellulose biomass and fermented by microorganisms to produce bioethanol. Despite 40 years of active and cutting-edge research invested into the development of technologies to produce bioethanol from lignocellulosic biomass, the process remains commercially unviable...
2015: Advances in Applied Microbiology
Daniela De Biase, Peter A Lund
Escherichia coli has a remarkable ability to survive low pH and possesses a number of different genetic systems that enable it to do this. These may be expressed constitutively, typically in stationary phase, or induced by growth under a variety of conditions. The activities of these systems have been implicated in the ability of E. coli to pass the acidic barrier of the stomach and to become established in the gastrointestinal tract, something causing serious infections. However, much of the work characterizing these systems has been done on standard laboratory strains of E...
2015: Advances in Applied Microbiology
Ali H Hussein, Beata K Lisowska, David J Leak
The genus Geobacillus comprises a group of Gram-positive thermophilic bacteria, including obligate aerobes, denitrifiers, and facultative anaerobes that can grow over a range of 45-75°C. Originally classified as group five Bacillus spp., strains of Bacillus stearothermophilus came to prominence as contaminants of canned food and soon became the organism of choice for comparative studies of metabolism and enzymology between mesophiles and thermophiles. More recently, their catabolic versatility, particularly in the degradation of hemicellulose and starch, and rapid growth rates have raised their profile as organisms with potential for second-generation (lignocellulosic) biorefineries for biofuel or chemical production...
2015: Advances in Applied Microbiology
Jana K Hiltner, Iain S Hunter, Paul A Hoskisson
Streptomycetes are prolific producers of a plethora of medically useful metabolites. These compounds are made by complex secondary (specialized) metabolic pathways, which utilize primary metabolic intermediates as building blocks. In this review we discuss the evolution of specialized metabolites and how expansion of gene families in primary metabolism has lead to the evolution of diversity in these specialized metabolic pathways and how developing a better understanding of expanded primary metabolic pathways can help enhance synthetic biology approaches to industrial pathway engineering...
2015: Advances in Applied Microbiology
Melanie Polke, Bernhard Hube, Ilse D Jacobsen
Only few Candida species, e.g., Candida albicans, Candida glabrata, Candida dubliniensis, and Candida parapsilosis, are successful colonizers of a human host. Under certain circumstances these species can cause infections ranging from superficial to life-threatening disseminated candidiasis. The success of C. albicans, the most prevalent and best studied Candida species, as both commensal and human pathogen depends on its genetic, biochemical, and morphological flexibility which facilitates adaptation to a wide range of host niches...
2015: Advances in Applied Microbiology
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