from Mikhail A. Ilyushchenko,, Vladimir Y. Panichkin, Paul Randall, and Rustam I. Kamberov writing in Bioremediation of Mercury: Current Research and Industrial Applications:

In 1975, a mercury cell chlor-alkali facility in Pavlodar, Kazakhstan began operations. This facility is located at the Pavlodar Chemical Plant (PCP) and began operations when mercury cell technology was at its peak in the former USSR. For a number of reasons, this plant had the highest rate of mercury use among similar designs (estimated at 1500 g of mercury per ton of caustic soda produced). After the collapse of the USSR in 1992, the facility was shut down. Despite a poor economy, scientists, PCP administrators, local environmental NGOs, regional authorities, and local politicians of Kazakhstan persisted to reduce mercury contamination that was inherited from the former USSR military-industrial establishment. Due to financial support from the European Union (EU) and the United States (i.e. U.S. Environmental Protection Agency) as well as contributions from Ukrainian scientists, field research was conducted. This research consisted of comprehensive monitoring of the atmosphere, soils, surface water and groundwater to determine the environmental risks posed by localized mercury 'hotspots' that occurred from mercury cell production losses of about 1310 tons of metallic mercury.

Further reading: Bioremediation of Mercury: Current Research and Industrial Applications

"This book edited by Diana Marco highlights the current state of the art of metagenomics and introduces the reader to recent advances in this field. More than twenty international experts have contributed chapters covering a very broad range of topics. The topics addressed extend from theoretical questions (such as the concepts of metagenomics, its integration with other approaches in life sciences or sequence data management) to metagenomic studies of various habitats (e.g. the human microbiome, plant-microbe interactions) and chapters with a strongly applied focus (e.g. bioremediation, biotechnology) to philosophical questions raised through the results of metagenome research. Generally, the mixture of theory/background and practice/applications is well balanced. Lucid descriptions of methodical approaches and technical details are given. Accounts of specific limitations and problems related to metagenomics in a certain area are simultaneously provided with a wealth of references for further reading ... the book can be highly recommended to advanced students or anyone starting research in this field. " from Kathleen Schleinitz (Helmholtz Centre for Environmental Research, Leipzig, Germany) writing in Biotechnol. J. (2011) 6: 124-125. read more ...

Metagenomics: Theory, Methods and Applications Edited by: Diana Marco ISBN: 978-1-904455-54-7 Publisher: Caister Academic Press Publication Date: January 2010 Cover: hardback "highly recommended" (Biotechnol. J.)

from Irene Wagner-Döbler writing in Bioremediation of Mercury: Current Research and Industrial Applications:

This review covers approximately the last ten years of research. It is based on appr. 150 publications on mercury remediation in Medline, including 83 citations of our papers from 1999 and 2000 (von Canstein et al., 1999; Wagner-Döbler et al., 2000a). After eliminating citations which were not directly related to the topic, roughly 120 references remained. Completeness is not claimed by this review, and I apologize for work that may have been over-looked or not been thoroughly appreciated. Many reviews on metal or mercury bioremediation have been published during this period and provide additional information (Nascimento and Chartone-Souza, 2003; Doty, 2008; Eapen and D'Souza, 2005; Kramer, 2005; LeDuc and Terry, 2005; Meagher and Heaton, 2005; Miretzky and Cirelli, 2009; Ruiz and Daniell, 2009; Wagner-Dobler, 2003; Nascimento and Chartone-Souza, 2003; Lloyd and Lovley, 2001; Lloyd et al., 2003; Lovley, 2003; Means and Hinchee, 1994; Pan-Hou, 2010).

Further reading: Bioremediation of Mercury: Current Research and Industrial Applications

from L.D. Lacerda and W.R. Bastos writing in Bioremediation of Mercury: Current Research and Industrial Applications:

Mercury is an ubiquitously presence in large areas of the Amazon, resultant form the gold rush which occurred in the region during the past century and from emissions of colonial mining operations, which used Hg amalgamation as major mining procedure. High Hg environmental levels are also favored by the capacity of most Amazon soils to accumulate and immobilize atmospheric Hg deposition over millennia. The immobilization of Hg, however, depends on the integrity of the ecosystems functioning, directly influenced by the recent development of the region. The effect of land use change on Hg mobilization from Amazon soils and sediments to the atmosphere and waterways is discussed, based on decadal data on Hg distribution in soil profiles under different land use categories; primary tropical forest, slashed forest prior to burning, silviculture and pastures. Degassing rates from these soils were monitored under different sampling periods, as well as air Hg concentrations over them. Comparisons of the Hg distribution in water, suspended solids and bottom sediments along a 1,600 km stretch of the Madeira River obtained in 5-years interval cruises are also discussed in view of large scale changes in the basin. All the results suggest strong mobilization of deposited Hg, both to the atmosphere and waterways. This process is suggested as responsible for the maintenance of elevated Hg concentrations in top carnivorous fish and riverside human populations reported recently, even after a decade of the cessation of Hg emission from gold mining in the region.

Further reading: Bioremediation of Mercury: Current Research and Industrial Applications

from Johannes Leonhäuser, Harald von Canstein , Wolf-Dieter Deckwer and Irene Wagner-Döbler writing in Bioremediation of Mercury: Current Research and Industrial Applications:

A plant for BIOlogical MERcury Remediation (BIOMER) based on mercury resistant bacteria was operated for three years at a chlor-alkali factory in technical scale. Here we report on the performance of the plant and on the technical problems that had to be solved until a stable and continuous operation could be guaranteed. One basic improvement was the installation of a pre-treatment unit. Basic process characteristics were determined during long-term operation. The BIOMER plant could treat wastewater with up to 10 mg/L of mercury. The optimal operation temperature was between 25-35°C. A salt concentration of up to 40 g/L of chloride could be tolerated by the microbes, but the fluctuations should be as small as possible. The bioreactor has to be operated at a pH of 7.0 ± 1.0. A space velocity of up to 4 h^-1 could be obtained. The wastewater flow rate should be constant to avoid export of fine particles. Finally a space time yield of 1 kg mercury per day and m³ bed volume corresponding to 100 m³ wastewater per day is possible.

Further reading: Bioremediation of Mercury: Current Research and Industrial Applications

from Pawel Gluszcz, Katarzyna Fürch and Stanislaw Ledakowicz writing in Bioremediation of Mercury: Current Research and Industrial Applications:

This report is based on all publicly available information sources, technical reports and analyses of international consortia. Its task is to provide up to date data on chlor-alkali plants, in particular those using the mercury cell process, in the most comprehensive way. Except the global analyses of chlor-alkali industry some fundamental knowledge about the mercury (amalgam process) cell technology is provided.

Further reading: Bioremediation of Mercury: Current Research and Industrial Applications

from Irene Wagner-Döbler writing in Bioremediation of Mercury: Current Research and Industrial Applications:

Mercury toxicity, industrial uses, and current status of bioremediation technologies are highlighted. The various book chapters are then put into a conceptual framework ranging from laboratory research to full scale industrial application.

Further reading: Bioremediation of Mercury: Current Research and Industrial Applications

from Johannes Leonhäuser, Wolf-Dieter Deckwer and Irene Wagner-Döbler writing in Bioremediation of Mercury: Current Research and Industrial Applications:

A microbiological treatment system comprising three consecutive stages of packed bed bioreactors inoculated with mercury reducing bacteria was operated in laboratory scale. The efficiency of this system for removal of mercury from the following types of industrial wastewater were determined: (1) chlor-alkali electrolysis; (2) gas scrubber solutions from the waste incineration plant TAMARA; (3) gas scrubber solutions from incineration of various types of waste from a chemical factory. The data show that all three types of wastewater could be efficiently cleaned. Factory wastewater with mercury concentrations of up to 460 mg/L had to be diluted to obtain a mercury concentration < 10 mg/L. Treatment efficiency was reduced by chloride concentrations above 39 g/L or toxic compounds, which were present in one of the wastewater batches from the chemical factory. The sandfilter buffered transient changes in the bioreactor efficiency. The activated carbon filter functioned as a polishing step so that effluent concentrations below 50 µg/L could always be maintained. The best and most stable bioreactor performance was obtained for electrolysis wastewater, which has a relatively predictable composition.

Further reading: Bioremediation of Mercury: Current Research and Industrial Applications

"This book collects the work of renowned researchers to provide chapters outlining the mechanisms Archaea, Bacteria and Eukarya use to survive extremes of temperature, pH, pressure and ionizing radiation. It focuses strongly on commercial applications ... recommended for senior undergraduates' independent reading or the reference of workers in the field alike" from Arwyn Edwards, Aberystwyth University, UK writing in Microbiology Today (2012) read more ...

Extremophiles: Microbiology and Biotechnology Edited by: Roberto Paul Anitori ISBN: 978-1-904455-98-1 Publisher: Caister Academic Press Publication Date: January 2012 Cover: hardback "recommended" Micro. Today

"the book comprises 11 papers addressing different applications of biofilm research ... each paper provides a useful update/review of a given area - I particularly like the interactions described in the quorum sensing paper." from Joanna Verran, Manchester Metropolitan University, UK writing in Microbiology Today (2012) read more ...

Microbial Biofilms: Current Research and Applications Edited by: Gavin Lear and Gillian D. Lewis ISBN: 978-1-904455-96-7 Publisher: Caister Academic Press Publication Date: February 2012 Cover: hardback "a useful update" Micro. Today

from Pranvera Lazo and Jaroslav Reif writing in Bioremediation of Mercury: Current Research and Industrial Applications:

North of Vlora in Albania is the site of a former chemical manufacturing complex consisting of a chlor-alkali factory and plants for the production of vinyl chloride monomer (VCM) and polyvinylchloride (PVC). The factory closed in 1992 and was completely destroyed during a civil uprising in 1997. It covers an area of approximately 1 km² located directly at the coast of the Adriatic Sea. The major environmental problems are the destroyed mercury cells of the chlor-alkali electrolysis plant, the waste-water which has been discharged into the Bay of Vlora without treatment in the past, and the sludge from the former production processes which was dumped in the area between the plant and the Bay. Hydrological, geochemical and geophysical investigations showed that mercury concentrations in ambient air exceeded the emission limit of 50 ng m^-3 in about 40% of measurements; the maximum was reached with 50 µg m^-3. The soils were found to be contaminated only within the unsaturated zone. Here the maximum mercury concentration was greater than 20,000 mg kg^-1. The mercury distribution in marine deposits of the Adriatic Sea did not indicate any influence of the discharged waste water. A significant contamination hot spot was the electrolysis building. Here, mercury concentration was higher than 60,000 mg kg^-1. Most of the mercury was present in elemental form. Therefore the impact of mercury pollution in the Bay of Vlora on humans and indicator organisms was small.

Further reading: Bioremediation of Mercury: Current Research and Industrial Applications

"a solid and critical review of the impact that extremophiles have in biotechnology. It discusses the adaptation of thermophilic, psychrophilic, acidophilic, and radiation-resistant microorganisms in their respective habitats ... the book offers newcomers to the biotechnology industry a good overview and a simple introduction to the subject, above all on future trends and web sources. " from Sonja Albers (Marburg) writing in BIOspektrum (2012) 18: 224. read more ...

Extremophiles: Microbiology and Biotechnology Edited by: Roberto Paul Anitori ISBN: 978-1-904455-98-1 Publisher: Caister Academic Press Publication Date: January 2012 Cover: hardback "a good overview" (Biospektrum)

from Mark Paul Taylor, Lonnie Van Zyl, Marla Tuffin and Don Cowan writing in Extremophiles: Microbiology and Biotechnology:

In principle, extremophiles have much to offer the biotechnology industry, from robust, process hardy enzymes to metabolically and physiologically diverse whole cell biocatalysts. However, the penetration of extremophilic organisms and their products into biotechnology markets has been modest at best, with preference given to engineered, cost effective enzyme variants and organisms for which established genetic tools are widely available. Interest in 'xtreme' products has often been dissuaded due to the unattractive need for the sometimes costly and complicated cultivation equipment and the complexities of culture maintenance. The lack of suitable genetic tools by which to improve, adapt or engineer a process involving an extremophilic host further complicates the issue. Legislative controls over national biological resources and allegations of biopiracy have also retarded commercialisation and industry-academia collaborations. However, commercial success stories have been described and form part of this review. Future prospects are optimistic, as several new biotechnology companies involved in the production of biomolecules from renewable resources have based their platform technology on extremophiles.

Further reading: Extremophiles: Microbiology and Biotechnology

from Hans Kristian Kotlar writing in Extremophiles: Microbiology and Biotechnology:

In the deep biosphere, extraordinary new types of microorganisms, sedimented or buried 200 - 500 million years ago, can be found. These organisms can be identified and characterized. The information obtained can be developed into novel tools for searching for new oil in sensitive regions like the Arctic, Antarctica and jungle areas. Relatively few enzymes are used in large-scale industrial applications. Enzymes isolated from these extremophile/ thermophile organisms might provide “game changing” new possibilities. They may furnish new incentives for the development of entirely new technical processes. These microbes provide opportunities for new technologies in second generation biofuel production. Several companies are working on alternative routes for the production of fuels using biomass as the raw source material. Traditional heavy oil extraction methods have major difficulties in justifying their high energy usage, CO₂ emissions and soil and environment pollution. The first company implementing a large-scale process based on biotechnology principles in enhanced oil recovery will gain huge strategic and economic benefits. The knowledge of this huge subsurface population of diverse microorganisms provides excellent opportunities for bioprospecting. There should be a multitude of spin-offs outside the oil industry. The world is desperately in need of new enzymes, new antibiotics, new immunosuppressant, new anticancer agents, etc. This chapter reviews just some of the areas we have been working on at Statoil. Hopefully some of these investigations could one day solve some of the problems we will face in the future. One day these extremophiles could be on the payroll of many different companies.

Further reading: Extremophiles: Microbiology and Biotechnology

from Anna M. Romaní, Joan Artigas and Irene Ylla writing in Microbial Biofilms: Current Research and Applications:

Biofilms in aquatic ecosystems colonize various compartments (sand, rocks, leaves) and play a key role in the uptake of inorganic and organic nutrients. Due to their extracellular enzyme capabilities, biofilm microorganisms are able to use organic matter from the surrounding water and increasing activities are related to the availability of biodegradable organic carbon. The most common extracellular enzymes analysed are those involved in the decomposition of polysaccharides, peptides and organic phosphorus compounds, and changes in enzyme expression have been related to the use of different sources of organic matter available in the ecosystem (i.e., during drought-storm and/or pollution episodes). Enzymes important for microbial acquisition of nitrogen and phosphorus also respond to nutrient content and/or imbalances in the flowing water. Additionally, biofilm extracellular enzyme activities are modified by the internal recycling of organic matter and microbial interactions (competition/synergism) within the biofilm, such as algal-bacterial and fungal-bacterial interactions. Although an extensive knowledge of the biofilm structure is required for the interpretation of extracellular enzyme activities in aquatic biofilms, they give a very useful, integrative measure of the biofilm community function in relation to organic matter use and cycling.

Further reading: Microbial Biofilms: Current Research and Applications

"Highly recommended is the chapter on interactions between plants and biofilms" from Hans-Curt Flemming (Duisburg, Germany) writing in Biospektrum (2012) 18: 109. read more ...

Microbial Biofilms: Current Research and Applications Edited by: Gavin Lear and Gillian D. Lewis ISBN: 978-1-904455-96-7 Publisher: Caister Academic Press Publication Date: February 2012 Cover: hardback "Highly recommended" (Biospektrum)

from Helena Nevalainen, Ron Bradner, Sania Wadud, Suja Mohammed, Christopher McRae and Junior Te'o writing in Extremophiles: Microbiology and Biotechnology:

Fungi are eukaryotic organisms and considered to be less adaptable to extreme environments when compared to bacteria. While there are no thermophilic microfungi in a strict sense, some fungi have adapted to life in the cold. Cold-active microfungi have been isolated from the Antarctic and their enzyme activities explored with a view to finding new candidates for industrial use. On another front, environmental pollution by petroleum products in the Antarctic has led to a search for, and the subsequent discovery of, fungal isolates capable of degrading hydrocarbons. The work has paved the way to developing a bioremedial approach to containing this type of contamination in cold climates. Here we discuss our efforts to map the capability of Antarctic microfungi to degrade oil and also introduce a novel cold-active fungal lipase enzyme.

Further reading: Extremophiles: Microbiology and Biotechnology

from Michel Sylvestre and Jean-Patrick Toussaint writing in Microbial Bioremediation of Non-metals: Current Research:

The fate of PCBs in soil and sediments is driven by a combination of interacting processes including several known biological processes. Under anaerobic conditions some bacteria use organohalides (including PCBs) as terminal acceptors. This process is responsible for the depletion of highly chlorinated congeners. Under aerobic conditions, PCBs are oxidized and mineralized by fungi through various pathways involving ligninolytic enzymes and monooxygenases and by bacteria through an initial dioxygenation reaction. Furthermore, several investigations have brought evidence that the rhizosphere provides a remarkable ecological niche to enhance the PCB degradation process by rhizobacteria. In this review, we will briefly summarize our current knowledge regarding the four above-mentioned biological processes involved in PCB degradation. Currently, the biochemistry of the anaerobic PCB-degrading process is still poorly understood. In the case of fungal enzymes, it is not yet clear which of the ligninolytic or monooxygenase systems prevails in PCB degradation. However, the bacterial oxidative enzymes have been investigated extensively. Furthermore, recent studies suggest that designing processes based on plant-microbe association are very promising avenues to remediate PCB-contaminated sites. In this review emphasis will be placed on the current state of knowledge regarding the strategies that are proposed to engineer PCB-degrading bacterial oxidative enzymes and PCB-degrading plant-microbe systems to degrade PCBs.

Further reading: Microbial Bioremediation of Non-metals: Current Research

from Koichi Nishio, Atsushi Kouzuma, Souichiro Kato and Kazuya Watanabe writing in Microbial Biofilms: Current Research and Applications:

Microbial fuel cells (MFCs) are devices that exploit microbial catabolic activities to generate electricity from a variety of starting materials, including complex organic waste and renewable biomass. The use of these energy sources provides MFCs with a great advantage over chemical fuel cells that utilize only purified reactive fuels (e.g., hydrogen). In an MFC bioreactor, microbes that respire using an anode with organics as electron donors grow preferentially, resulting in accelerated and increased current generation with time. The placement of an anode in either soil or sediment represents a simplified MFC system, known as a sediment MFC, which generates current as soil microbes utilize the anode as an electron acceptor. In addition, the irradiation of an MFC system results in the proliferation of photosynthetic microbes together with anode-respiring microbes, resulting in the syntrophic conversion of light energy into electricity. These examples demonstrate that the MFC system is based on a variety of fundamental and sustainable bioenergy processes, and we suggest that a deeper understanding of how microbes transfer electrons to anodes is essential for further developments of MFC systems.

Further reading: Microbial Biofilms: Current Research and Applications

from Steve Flint and Gideon Wolfaardt writing in Microbial Biofilms: Current Research and Applications:

Biofilms can directly or indirectly be attributed to deterioration of the underlying substratum. Corrosion may result, particularly if the surface comprises metal or metal alloy. This phenomenon, referred to as microbially influenced corrosion (MIC) affects many industries from food manufacture to medicine. The economic impact of corrosion is significant due to the need for replacing corroded equipment, repairs and attempts to prevent corrosion. MIC is believed to be responsible for one third of all metallic corrosion. Although there have been many studies into the mechanisms of MIC, the process is relatively poorly understood. Most information relates to pure cultures, however biofilms are rarely composed of single species thus most models are a simplification of the real process. It is likely the MIC depends on the composition of the biofilm and the environment surrounding the biofilm. Prevention and control methods rely on mechanical cleaning of fouling and chemical removal and killing of biofilms. Future control measures are likely to focus on preventing biofilm formation.

Further reading: Microbial Biofilms: Current Research and Applications

from T.A. Vishnivetskaya, B. Raman, T.J. Phelps, M. Podar and J.G. Elkins writing in Extremophiles: Microbiology and Biotechnology:

Conversion of lignocellulosic biomass to liquid fuels using biological processes offers a potential solution to partially offset the world's dependence on fossil fuels for energy. In nature, decomposition of organic plant biomass is brought about by the combined action of several interacting microorganisms existing in complex communities. Bioprospecting in natural environments with high cellulolytic activity (for example, thermal springs) may yield novel cellulolytic microorganisms and enzymes with elevated rates of biomass hydrolysis for use in industrial biofuel production. In this chapter, various cellulose-degrading microorganisms (in particular, thermophilic anaerobic bacteria), their hydrolytic enzymes, and recent developments in the application of biomass fermentations for production of sustainable bioenergy are reviewed. In this context, results from ongoing research at the Oak Ridge National Laboratory in the isolation and subsequent phylogenetic and metabolic characterization of thermophilic, anaerobic, cellulolytic bacteria from the hot springs of Yellowstone National Park are presented.

Further reading: Extremophiles: Microbiology and Biotechnology

from Rainer Gross, Andreas Schmid and Katja Buehler writing in Microbial Biofilms: Current Research and Applications:

Biofilms are mainly known for causing problems in medical and industrial settings due to their persistence towards treatment with bactericides, including antibiotics. However, in the area of bioremediation they are widely recognized for their ability to degrade hazardous or organic compounds to CO₂ and biomass. Biofilms represent a highly interesting biological concept since they unite important characteristics such as the ability of self-immobilization and increased robustness to various physical, chemical and biological stressors, which make them exceedingly attractive for productive catalysis. The following review provides a detailed survey of biofilm applications for productive biocatalysis on lab-, pilot-, and industrial scales, regarding fermentation as well as biotransformation reactions. It discusses technological as well as biological challenges of biofilm driven catalysis, presenting developments in the field of biofilm reactor technology and the latest findings in understanding biofilm dynamics. Biocatalysis related issues like genetic stability, evolution, uncontrolled growth as well as detachment, contamination risks, monitoring of biomass, EPS, chemical and biological heterogeneity are considered.

Further reading: Microbial Biofilms: Current Research and Applications

from Gabriele Pastorella, Giulio Gazzola, Seratna Guadarrama and Enrico Marsili writing in Microbial Biofilms: Current Research and Applications:

Bioremediation uses microorganisms to remove, detoxify, or immobilize pollutants, and does not require addition of harmful chemicals. Bioremediation is particularly suitable for large areas where contaminant concentrations are relatively low and the hydrology of the soil does not support an aggressive chemical remediation strategy. In the last few years, researchers have described the mechanisms of bioremediation for numerous priority pollutants, including chlorinated hydrocarbons, polyaromatic hydrocarbons, and heavy metals. However, most studies published to date have dealt with planktonic cultures grown under controlled laboratory conditions. Microorganisms in the environment occur mostly as biofilms, whose development is encouraged by the presence of solid surfaces and the limited amounts of organic carbon. Therefore, optimization of bioremediation processes in the field requires a thorough knowledge of biofilm structure, dynamic, and interaction with pollutants and other environmental factors. In this chapter, we describe the recent advances in bioremediation, with particular regard to the role of microbial biofilms. We discuss emerging technologies, such as bioelectroremediation and microbially produced surfactants. We also show how genetic engineering technologies may be employed to improve bioremediation effectiveness, both in laboratory and in field applications.

Further reading: Microbial Biofilms: Current Research and Applications

from G.A. Clark Ehlers and Susan J. Turner writing in Microbial Biofilms: Current Research and Applications:

Biofilms occur frequently inside various engineered systems for wastewater treatment. These include traditional trickling filter systems, modified lagoons, and specialized supplementary systems for nutrient removal or treatment of specialized wastes. The major advantages of biofilm systems over suspension treatment is the high microbial density that can be achieved, leading to smaller treatment system footprints, and the inherent development of aerobic, anoxic and anaerobic zones which enable simultaneous biological nutrient removal. The intrinsic resistance of biofilm communities to changing environmental conditions creates the added advantage that biofilm-based treatment systems are more resilient to influent variation in toxicity and nutrient concentrations. In contrast to biofilms of environmental or biomedical relevance comparatively little is known about development and stability in waste treatment systems. The advent of tools that enable the study of biofilms in reactor systems on a molecular level has enabled greater insight into the physiologically and biochemically relevant pathways that may facilitate optimized processes. In this chapter, the current literature on biofilms in wastewater treatment systems is reviewed and opportunities for further development in this field are identified.

Further reading: Microbial Biofilms: Current Research and Applications

from Gavin Lear, Andrew Dopheide, Pierre-Yves Ancion, Kelly Roberts, Vidya Washington, Jo Smith and Gillian D. Lewis writing in Microbial Biofilms: Current Research and Applications:

This chapter reviews our current understanding of the roles biofilm-associated microbial communities play in both maintaining and improving the ecological health of freshwater rivers and streams. Biofilms are where most of the bacteria present in freshwater systems are found, and have been identified as major sites for primary production, carbon and nutrient cycling. Advances in various scientific methodologies have recently been used to characterise the enormous diversity of biofilms, in terms of their structural, chemical and biological traits. The microbial life present within most natural biofilms, as well as associated exudates and lysates have been identified as a valuable, nutrient rich food source for a variety of benthic consumers. Furthermore, the diverse metabolic potential of these complex communities, in combination with various protective traits offered by the biofilm 'mode-of-life', provide biofilms with an excellent ability to degrade, or otherwise transform a vast array of freshwater pollutants. Despite this apparent resilience, we highlight the sensitivity of these poorly studied freshwater biofilm communities to various human activities, and consider their potential as a reliable and sensitive biological indicator of freshwater ecological health.

Further reading: Microbial Biofilms: Current Research and Applications

from James D. Bryers writing in Microbial Biofilms: Current Research and Applications:

Clinically related research on biofilms has expanded exponentially in the past ten years due to the pandemic of nosocomial (hospital-related) infections. Biofilms are thought to cause a significant amount of all human microbial infections, according to the Centers for Disease Control and Prevention. Nosocomial infections are the fifth leading cause of death in the U.S. with more than two million cases annually (or approximately 10% of American hospital patients). The difficulty of eradicating biofilm bacteria with classic systemic antibiotic treatments is a prime concern of medicine. Biofilm bacteria can be up to a thousand times less susceptible to antimicrobial stress than their freely suspended counterparts. This chapter discusses the pathogenesis of a number of biofilm-mediated infections, including: oral infections, biomedical device based infections, osteomyelitis, otitis media, and others. Emerging research in biofilm control and prevention is also reviewed.

Further reading: Microbial Biofilms: Current Research and Applications

from Mette Burmølle, Annelise Kjøller and Søren J. Sørensen writing in Microbial Biofilms: Current Research and Applications:

Biofilms in soil are composed of multiple species microbial consortia attached to soil particles and biotic surfaces including roots, fungal hyphae and decomposing organic material. The bacteria present in these biofilms gain several advantages including protection from predation, desiccation and exposure to antibacterial substances, and optimized acquisition of nutrients released in the mycosphere. Studies of soil biofilms are complicated by the composite structure of the soil environment; therefore, various simplified model systems have been applied to study succession and bacterial interactions in soil biofilms. Model system observations indicate an increased efficiency to degrade and decompose organic material and xenobiotic compounds by these multispecies bacterial communities. Consequently, soil biofilms may be valuable tools for bioremediation and biocontrol. However, soil biofilms may also provide survival sites for opportunistic pathogenic bacteria, providing enhanced protection and increasing their potential to survive and evolve in the soil environment. In this review, we provide evidence that biofilms are of major importance for the fitness of individual bacteria and the wider soil ecology, due to the accumulated selective advantage provided to bacteria by the biofilm mode-of-life.

Further reading: Microbial Biofilms: Current Research and Applications

from Anna-Irini Koukkou and Elpiniki Vandera writing in Microbial Bioremediation of Non-metals: Current Research:

Hydrocarbons are the major representatives of non-metal pollutants found in many contaminated soils by natural or industrial and social activities. Their removal from polluted environmental niches depends to a great extent on microbial degradation, which can also be applied on several technological applications. The extended microbial diversity in soil has served as a rich source for the isolation of efficient PAH-degrading strains. Bacterial isolates with the ability to use PAHs as an alternative source of carbon and energy facilitate their mineralisation to harmless products. Culture-based approaches have resulted in the isolation of a range of soil hydrocarbon-degrading bacteria, which primarily are members of different subdivisions of Proteobacteria as well as of the high G+C Gram-positive bacteria. Generally, in polluted-soils Gram-negative bacteria such as Pseudomonas, Burkholderia and Sphingomonas seem to degrade preferentially lower molecular weight PAHs such as naphthalene and phenanthrene, while Gram-positive isolates are more specialized in the degradation of high molecular weight PAHs such as pyrene.

Further reading: Microbial Bioremediation of Non-metals: Current Research

from Kazem Kashefi writing in Extremophiles: Microbiology and Biotechnology:

The isolation and characterization of novel hyperthermophilic, microorganisms from modern hot environments have greatly increased our understanding of how microbes can live and thrive in such inhospitable environments. The finding that microorganisms have the ability to grow at these high temperature has implications for delimiting when and where life might have evolved on a hot, early Earth; the depth to which life exists in the Earth's subsurface; and the potential for life in hot, extraterrestrial environments. The study of hyperthermophilic microorganisms provides valuable insights into microbial respiration in a diversity of modern and ancient hydrothermal systems. In addition, it provides information about the fate of metals such as iron, uranium, technetium, and even gold. Reduction of these metals by hyperthermophiles provides, for example, a likely explanation for a number of geologically, environmentally and economically important ore deposits. This allows us to identify geological signatures for biological processes, something that may prove instrumental in our search for life on other planets. Finally, enzymes capable of functioning at high temperatures have a number of important applications in biomass conversion, in biotechnology, and in the pharmaceutical, food and cosmetic industries.

Further reading: Extremophiles: Microbiology and Biotechnology

from Kelley R. Gwin and John R. Battista writing in Extremophiles: Microbiology and Biotechnology:

Of all the phenotypes associated with microorganisms, ionizing radiation resistance - the ability to survive exposure to high dose gamma radiation - is perhaps the most difficult to rationalize in terms of the natural world. There is no obvious selective advantage to being ionizing radiation resistant on Earth, as average yearly exposures to ionizing radiation from cosmic rays and radioactive decay are extremely low. Yet a significant number of genera exhibit this characteristic, displaying a remarkable capacity to tolerate levels of damage to cellular macromolecules that eradicates other forms of life. We argue that ionizing radiation resistance is an incidental characteristic, an inadvertent consequence of an evolutionary path that permitted these species to survive a selective pressure capable of damaging the cell in a manner similar to that of ionizing radiation. The phylogenetic distribution of ionizing radiation resistant species argues that these events occurred multiple times during the evolution of the Bacteria and Archaea, suggesting that different mechanisms may mediate ionizing radiation resistance.

Further reading: Extremophiles: Microbiology and Biotechnology

from Elizaveta Bonch-Osmolovskaya writing in Extremophiles: Microbiology and Biotechnology:

Thermophilic microorganisms, though known since the beginning of the 20th century, were intensively studied in its last three decades. Natural terrestrial and submarine thermal environments were found to be populated by moderate, extreme and hyperthermophilic microorganisms representing diverse metabolic groups. However, during the past few years this knowledge has been extended, and new metabolic groups of thermophilic prokaryotes described. Among these are ammonia-oxidizing archaea, thermoacidophilic methanotrophs of the phylum Verrucomicrobia, microorganisms gaining energy for growth from the disproportionation of sulfur species, and archaea and bacteria metabolizing one carbon (C1) compounds. Other novel metabolic groups, such as thermophilic anammox bacteria, nitrite-oxidizing thermophiles, and microorganisms performing anaerobic methane oxidation in thermal ecosystems, have been detected using molecular or geochemical approaches. These data will, certainly, stimulate further cultivation and isolation efforts.

Further reading: Extremophiles: Microbiology and Biotechnology

from Nazia Mojib, Jack T. Trevors and Asim K. Bej writing in Microbial Bioremediation of Non-metals: Current Research:

Bioremediation is an attractive, generally low cost, innovative technology that is a fundamental and sustainable approach to clean up non-metal or organic compounds from contaminated environments. These pollutants include hydrocarbons- principal components of petroleum and fossil fuels, polychlorinated biphenyls (PCBs) - broad family of man-made organic chemicals also known as chlorinated hydrocarbons, polyaromatic hydrocarbons (PAHs)- industrial pollutants that are significant byproducts of coal, chemical, petroleum processing and refining and toxic pesticides used in agricultural lands. The principle of bioremediation lies in the diverse metabolism of microorganisms to degrade or transform organic compounds to assimilate energy with the help of enzymes encoded by diverse biodegradative genes. This can lead to the efficient removal of a wide range of pollutants and wastes from the environment. This chapter elucidates the structure, diversity and function of the biodegradative genes and enzymes involved in the biodegradation pathways of different contaminants. Also, the use of modern genetic methodologies and genome-based global techniques to better understand the function of these biodegradative genes are briefly discussed. Since, many degradation pathways, along with the enzymes and their respective genes are known and reactions are well understood, a bioinformatics approach in predicting enzymes and reactions involved in biodegradation of new compounds is also examined.

Further reading: Microbial Bioremediation of Non-metals: Current Research

from Chiaki Kato writing in Extremophiles: Microbiology and Biotechnology:

Piezophilic microorganisms, which are defined as "pressure-loving" microorganisms, are isolated and characterized from high pressure environments. They grow better at high-hydrostatic pressures than at atmospheric pressures, and only exist at deeper water column environments, particularly in the deep-sea bottoms. Therefore, piezophilic microorganisms are typical deep-sea microorganisms that are well adapted to deep-sea pressure and temperature conditions. These microorganisms have special strategies for surviving in such extreme environments, where gene expression and enzyme activities could be controlled by pressure. Studies on adaptations to high pressure environments have recently been studied in detail, and the mechanisms involved are being elucidated. In this chapter, the distribution, taxonomy, cultivation and molecular characters of piezophiles are described.

Further reading: Extremophiles: Microbiology and Biotechnology

from Yuki Kasai writing in Microbial Bioremediation of Non-metals: Current Research:

Bioremediation is a cost-effective technique for treatment of polluted environments and it involves usage of microorganisms for pollutant degradation. It can be defined as natural attenuation (intrinsic bioremediation), biostimulation (introduction of nutrients and chemicals to stimulate indigenous microorganisms), and bioaugmentation (inoculation with exogenous microorganisms). When carrying out bioremediation, special attention should be paid to its effects on the indigenous microbiota and dispersal and outbreaks of the inoculated organisms. Recent advances in microbial ecology have provided molecular technologies, such as community fingerprinting, molecular detection of degradative genes, and metagenomics, which facilitate the analysis and monitoring of indigenous and inoculated microorganisms in contaminated sites. This chapter outlines these technologies and discusses how they can contribute to bioremediation.

Further reading: Microbial Bioremediation of Non-metals: Current Research

from Mark Dopson writing in Extremophiles: Microbiology and Biotechnology:

Acidophilic microorganisms are capable of growth at low pH and are defined as having an optimum below pH 5, with some extreme acidophiles capable of growth at pH 0. Acidophiles have an important role in ecology by catalyzing the generation of acidic, metal-containing solutions that can inhibit plant and animal growth, and in biotechnology via their propensity to solubilize metals from sulfide minerals. This review summarizes the most important aspects of acidophile physiology, including growth substrates (e.g. inorganic and organic carbon) and energy sources; temperature optima (from cold environments to high temperature thermal pools); and adaptations to metals in solution and low growth pH. The exploitation of acidophiles in biotechnology (e.g. in biomining) and potential future trends in research are also discussed. Due to a lack of general genetic systems in acidophiles, much of the latest research has been generated by systems biology approaches and these data have been focused upon.

Further reading: Extremophiles: Microbiology and Biotechnology

from Corien Bakermans writing in Extremophiles: Microbiology and Biotechnology:

Psychrophilic, or cold-loving, organisms actively live at low temperatures. Psychrophily is not an uncommon trait; cold-adapted organisms are found throughout the three domains of life and successfully inhabit a wide variety of low temperature environments. The ongoing investigation of these environments continues to broaden our view of what is possible for life on Earth. Cold-adapted microorganisms have evolved mechanisms to deal with the thermodynamic constraints of low temperatures. To combat the stability and decreased flexibility of macromolecules, psychrophiles generally increase the disorder within macromolecules to maintain fluidity or flexibility and hence function at low temperatures. To contend with reduced water activity and the presence of ice crystals, cryoprotectants are produced. To counteract decreased reaction and diffusion rates, psychrophiles practice efficient growth. Currently, the functional low-temperature limits of psychrophiles are minus 12 degrees celsius for reproduction and minus 20 degrees celsius for metabolism. The availability of liquid water appears to be the major growth-limiting factor at subzero temperatures. Examination of molecular and physiological adaptations to low temperatures is increasing our comprehension and appreciation of the capabilities of psychrophiles and their contribution to nutrient cycling in low temperature environments.

Further reading: Extremophiles: Microbiology and Biotechnology

from Robert J. Goldstone, Roman Popat, Matthew P. Fletcher, Shanika A. Crusz and Stephen P. Diggle writing in Microbial Biofilms: Current Research and Applications:

It is now well recognised that populations of bacteria from many Gram-positive and Gram-negative species cooperate and communicate to perform diverse social behaviours including swarming, toxin production and biofilm formation. Communication between bacterial cells involves the production and detection of diffusible signal molecules and has become commonly known as quorum sensing (QS). In addition, an evolutionary perspective on QS illuminates important phenomena which help in understanding the prevalence and diversity of QS phenotypes and strategies under various conditions. The research fields of QS and biofilm formation often overlap with a number of studies demonstrating that QS is an important regulatory mechanism of biofilm formation in a variety of bacterial species. However in contrast, there are conflicting reports, demonstrating that QS appears to play a minimal role in the development of biofilms. Our aim in this review is to highlight the key findings with respect to QS and the subsequent impact on biofilm formation. We also discuss QS and cooperation in the context of social evolution and how this may impact on the development and maintenance of microbial biofilms.

Further reading: Microbial Biofilms: Current Research and Applications

from Christine Moissl-Eichinger, Ruth Henneberger and Robert Huber writing in Extremophiles: Microbiology and Biotechnology:

The SM1 euryarchaeon represents an extraordinary microorganism: in the surface waters of cold, sulfidic springs, it lives together with filamentous bacteria, forming the so called string-of-pearls community. In the subsurface however, it can grow partner-independently as a "monospecies" biofilm. Even though the SM1 euryarchaeon is still uncultivated in the laboratory, it is accessible via an in situ cultivation technique using its own biotope as a natural chemostat. This approach allowed the study of its biology, and enabled the discovery of unique cell surface appendices with unexpected and unusually high complexity. Each of the archaeal cells is surrounded by approximately 100 protein filaments that are up to 3 micrometres long and show a high resemblance to barbwire with a tripartite grappling hook at their tip. Based on this structure the appendices were called "hami" (lat. hamus = (grappling) hook). These hami represent perfectly evolved, natural mechanical nano-tools that could find applications in the growing field of nanobiotechnology.

Further reading: Extremophiles: Microbiology and Biotechnology

from Venkatachalam Lakshmanan, Amutha Sampath Kumar and Harsh P. Bais writing in Microbial Biofilms: Current Research and Applications:

Microorganisms have historically been studied as planktonic or free-swimming cells, but most exist as sessile communities attached to surfaces, in multicellular assemblies known as biofilms. In the process of coping with both the pathogenic and beneficial interactions, the rhizosphere of plant roots encourages formation of sessile communities that begins with the attachment of free-floating microorganisms to a surface. Certain bacteria such as plant growth promoting rhizobacteria not only induce plant growth but also protect plants from soil-borne pathogens in a process known as biocontrol. Contrastingly, other rhizobacteria in a biofilm matrix may cause pathogenesis in plants. Although research suggests that biofilm formation on plants is associated with biological control and pathogenic response, little is known about how plants regulate this association. The scope of this chapter is restricted to biofilm-forming bacteria and their interactions with terrestrial plants, specifically emphasizing recent work. After an overview of documented interactions between bacteria and plant tissues, we examine some of the more prominent mechanisms of biofilm formation on and around plant surfaces.

Further reading: Microbial Biofilms: Current Research and Applications

from Amalia S. Afendra, Maria Parapouli and Constantin Drainas writing in Microbial Bioremediation of Non-metals: Current Research:

During the last century, xenobiotic pollutants harmful to environment and health were dramatically increased as a consequence of human activities, such as petroleum industries, agro-industries, household or commercial use. In the polluted areas a large diversity of bacteria with the ability to use these compounds as carbon and/or nitrogen source were developed and proved to be useful for bioremediation applications. Their biodegradation properties are due to genes, which were modified, recombined and improved accordingly over the years helping bacteria to adapt in the new harsh xenobiotic environment. Over time, catabolic genes were evolutionary grouped in clusters, established through genetic rearrangements in transmissible regions of mobile genetic elements, and spread by horizontal gene transfer among bacteria of different genera or taxa coexisting in polluted areas. This chapter focuses on plasmids and other mobile genetic elements which carry genes or gene clusters coding for catabolic enzymes involved in the degradation of a number of industrially important xenobiotic pollutants. These include chlorinated and polychlorinated compounds, phthalates, sulfur compounds and some major groups of pesticides. The origin and evolution of these catabolic pathways to different genera is also reviewed.

Further reading: Microbial Bioremediation of Non-metals: Current Research

from Maria Pouli and Spiros N. Agathos writing in Microbial Bioremediation of Non-metals: Current Research:

Polycyclic aromatic hydrocarbons (PAHs) are widespread pollutants found in industrial sites linked with petroleum, gas production or other activities involving incomplete combustion of organic matter. These compounds constitute a priority for treatment of contaminated soils and sediments due to their toxicity and carcinogenicity. Microbial degradation represents an important mechanism of PAH removal and can be used for the treatment of contaminated sites by in situ or ex situ bioremediation. This technology is taking advantage of a few established peripheral catabolic pathways converting different PAHs into a limited number of central intermediates. Peripheral pathways are typically initiated by dioxygenases, oxidizing PAHs into dihydroxylated intermediates, which, in turn, are catabolized further and degraded via central pathways into TCA cycle metabolites. However, both the hydrophobic characteristics of most PAHs as well as the physicochemical properties of soils diminish the bioavailability of these pollutants and thus limit the degradation capacity of naturally occurring microorganisms for bioremediation of contaminated sites. The success of biotreatment interventions can be enhanced by measures promoting bioavailability (e.g. addition of surfactants or solvents) and/or boosting microbial activity (e.g. by biostimulation or bioaugmentation). The same strategies can be further optimized by implementing appropriately designed bioreactors for faster and more complete removal of recalcitrant PAHs from contaminated soils and sediments.

Further reading: Microbial Bioremediation of Non-metals: Current Research

from Philippe Cuny, Cristiana Cravo-Laureau, Vincent Grossi, Franck Gilbert and Cécile Militon writing in Microbial Bioremediation of Non-metals: Current Research:

Sediments can serve as sinks for hydrocarbon contaminants in marine ecosystems. Once settled, hydrocarbons fate will be dominated by several abiotic and biotic processes that will result in either their partial or total degradation or in a selective preservation when buried within the sediment. Biodegradation of hydrocarbons in marine sediments is mainly due to the existence of prokaryotes harboring specific catabolic genes enabling the degradation of these compounds under oxic, suboxic and anoxic conditions. The interplay of the various factors that govern hydrocarbons biodegradation in marine sediments is highly complex as illustrated by bioturbation processes carried out by macrofaunal organisms. For instance, the redox oscillation regimes generated by macrofaunal organisms, and the efficiency of metabolic coupling between functional groups associated to these specific redox regimes, are probably determinant factors controlling the biodegradation rates of hydrocarbons in marine sediments. From the understanding of how these natural occurring factors may modulate the rates of hydrocarbons biodegradation, innovative bioremediation strategies may emerge.

Further reading: Microbial Bioremediation of Non-metals: Current Research

from J.L. García , Iria Uhía, Esther García and Beatriz Galán writing in Microbial Bioremediation of Non-metals: Current Research:

Cholesterol is a steroid highly abundant in the environment that plays a major role in the global carbon cycle. Many synthetic steroidic compounds like some sexual hormones frequently appear in municipal and industrial wastewaters, acting as environmental pollutants with strong metabolic activities negatively affecting the ecosystems. Since these compounds are common carbon sources for many different microorganisms their aerobic and anaerobic mineralization has been extensively studied. The interest of these studies lies on the biotechnological applications of sterol transforming enzymes for the industrial synthesis of sexual hormones and corticoids. Very recently the catabolism of cholesterol has acquired a high relevance because it is involved in the infectivity of Mycobacterium tuberculosis. This review describes the current knowledge on the catabolism of cholesterol and related steroids in bacteria both at biochemical and genetic levels.

Further reading: Microbial Bioremediation of Non-metals: Current Research

from Katsumasa Abe, Shouji Takahashi and Yoshio Kera writing in Microbial Bioremediation of Non-metals: Current Research:

Organophosphorus compounds are widely used as pesticides, flame retardants and plasticizers. Due to their large-scale use, they have been detected in various environments, including surface and ground water, soil and air in the world. Since many of these compounds are toxic for many organisms including human, their widespread contamination has become a serious problem for various organisms in the environment. Microbial degradation of organophosphorus compounds has received attention, because it is thought to be more environmentally friendly way than chemical methods. Therefore, many microorganisms capable of degrading organophosphorus compounds have been isolated and characterized. In this chapter, we describe organophosphorus compounds-degrading bacteria and enzymes, and also their application for bioremediation purpose.

Further reading: Microbial Bioremediation of Non-metals: Current Research

from Federico Aulenta, Mauro Majone, Marco Petrangeli Papini, Simona Rossetti and Valter Tandoi writing in Microbial Bioremediation of Non-metals: Current Research:

In situ technologies are cost-effective, expanding technologies for the clean-up of soil and groundwater in contaminated sites. On the other hand, these technologies are knowledge-intensive and their application requires thoroughly understanding of the microbiology, ecology, hydrogeology, and geochemistry of contaminated soils and aquifers, under both natural and enhanced conditions. In this chapter, we summarize current knowledge and future perspectives in the area of microbial anaerobic dechlorination of chlorinated solvents, particularly chloroethenes. Main attention is paid at discussing environmental factors and conditions that influence microbial activity under field conditions. Approaches to stimulate and manipulate the activity of native dechlorinating populations in order to meet target remediation goals are examined. Finally, appropriate characterization procedures for optimal evaluation and design of the in situ remediation strategies are examined with main reference to three tools: a) microbial tools, b) modelling, c) microcosms vs field studies.

Further reading: Microbial Bioremediation of Non-metals: Current Research

from Yves Jouanneau, Florence Martin, Serge Krivobok and John C. Willison writing in Microbial Bioremediation of Non-metals: Current Research:

The first step in the biodegradation of PAHs by aerobic bacteria is catalyzed by metalloenzymes known as ring-hydroxylating dioxygenases (RHDs). Because of the hydrophobic nature and chemical resistance of PAHs, their initial attack by RHDs is a difficult reaction, which is critical to the whole degradation process. This chapter gives an overview of the current knowledge on the genetics, structure, catalytic mechanism and diversity of RHDs involved in PAH degradation. In the past decade, the crystal structures of 10 RHDs have been determined, giving insights into the mechanism of substrate recognition and regioselectivity of dioxygenation. The reaction catalyzed by the archetypal naphthalene dioxygenase has been investigated in detail, thus providing a better understanding of the RHD catalytic mechanism. Studies on the catabolic genes responsible for PAH degradation in several bacterial taxa have highlighted the great phylogenetic diversity of RHDs. The implementation of culture-independent methods has afforded means to further explore the environmental diversity of PAH-degrading bacteria and RHDs. Recent advances in this field now allow the in situ identification of bacteria responsible for pollutant removal. Further biotechnological developments based on microarrays and functional metagenomics should lead to the conception of molecular tools useful for the bioremediation of PAH-contaminated ecosystems.

Further reading: Microbial Bioremediation of Non-metals: Current Research

from Nicolas Kalogerakis writing in Microbial Bioremediation of Non-metals: Current Research:

Although in-situ bioremediation technologies for the treatment of contaminated soils are economically attractive, ex-situ approaches are more often used for surface contaminated soils (typical depths less than 5 m) since they allow a much tighter control of the bioremediation process and provide better estimates of the residual contamination at the end of the treatment period. Ex-situ bioremediation is the method of choice for hot spot treatment if they are reasonably accessible. In this chapter, the classical ex-situ technologies (Landfarming, Composting, Biopiling and Slurry-phase bioremediation) are presented with a few examples of innovative modifications that enhance their productivity and/or effectiveness. Ex-situ bioremediation typically refers to the methods applied for the remediation of excavated contaminated soils. Besides slurry-phase bioremediation where the soil is mixed with water and other nutrients in mechanically agitated bioreactors, ex-situ bioremediation includes solid phase bioremediation that covers the techniques of landfarming and the various forms of composting, namely windrows, biopiles and in-vessel composting. In the following sections, the above methods are presented focusing on design principles and on experience gathered from their application.

Further reading: Microbial Bioremediation of Non-metals: Current Research