Microbial Biodegradation: From Omics to Function and Application
"a valuable companion to both early and established researchers" (Micro. Today)
"review(s) the most important current research" (Biotechnol. Agron. Soc. Environ.)
Caister Academic Press
Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Łódź, Poland
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Pollution is a major challenge for mankind responsible for millions of premature deaths globally. Current research aims to harness and enhance the natural ability of microbes to degrade or metabolise a huge range of compounds including hydrocarbons, radionuclides and metals. In recent years the application of omics technologies to biodegradation research has generated a plethora of new data providing a greater understanding of the key pathways and new insights into the adaptability of organisms to changing environmental conditions.
In this timely book, expert authors critically review the most important current research in this exciting field. Topics include the genomics, metagenomics and metatranscriptomics of biodegradation, molecular markers in biodegradation, metabolomics and crucial enzymes, proteomics in metabolic pathways inspection, lipidomics in microbial adaptation to toxic compounds, degradation of endocrine disrupting compounds, dyes decolourisation and degradation, polycyclic aromatic hydrocarbon biodegradation, biosurfactants enhancement factors, degradation of volatile compounds, heavy metals removal, and examples of the applications of recent research.
Essential reading for scientists working in the field of microbial degradation and bioremediation and recommended reading for everyone interested in environmental microbiology, biotechnology and molecular biology.
"This book is a timely and well-written contribution to this subject area. It presents in a clear framework ... the latest advances ... Undergraduate students will find the introductory chapters easy to follow and provide a good starting point on the current state-of-the-art research in the field of omics related to microbial biodegradation. Postgraduate and more seasoned researchers will benefit from the thorough reviews ... The quality of the content of this book is very high; it will be a valuable companion to both early and established researchers." from Microbiology Today
"expert authors critically review the most important current research" from Biotechnol. Agron. Soc. Environ.
Table of contents
1. Organic Pollutants Degradation by Microorganisms: Genomics, Metagenomics and Metatranstriptomics Backgrounds
Sylwia Róźalska and Roksana Iwanicka-Nowicka
Environment pollution by organic compounds of anthropogenic origin is a major global problem. Microorganisms persistent in the environment play a crucial role in removal of pollutants, but until recently it was difficult to determine their exact functions in the elimination of contaminants. Here, the next-generation sequencing (NGS) techniques, which have had a remarkable impact on microbial studies and provided new insights into microbial communities, their biodiversity, and function, are discussed. This review also describes recent achievements in genomics, metagenomics, and metatranscriptomics, which have been implemented in studies on the microbial composition of environments contaminated with organic compounds. The importance of the new approaches for determination of the genes responsible for degradation of toxic compounds and metabolic genes are also discussed.
2. Heavy Metals Resistance, Metabolism and Transformation: Genomic, Metagenomic and Metatranscriptomic Studies
Lukasz Dziewit and Lukasz Drewniak
Heavy metal-contaminated regions are common across the planet. The treatment of such regions (especially those co-contaminated with other toxic substances), remains one of the most costly environmental challenges currently faced by many countries. It appears that the employment of microorganisms in biotransformation of heavy metals is a good solution to this problem, however a key step in the waste management technologies is the understanding of the mechanism of heavy metals resistance, metabolism and transformation. Recent advances in genomics, metagenomics and metatranscriptomics increased their role in identifying traits that may maximize the benefits of heavy metals bioremediation technologies.
3. Molecular Markers in Biodegradation Processes
Biological decomposition of various substrates is performed by a large number of microorganisms. Microbial performance in biodegradation processes has been observed and analysed for years only for microbiological cultivation methods. For the last 30 years, molecular biology tools that are useful for describing the microbial world have been discovered, improved and introduced for routine microbial studies. These molecular methods are performed on a wide variety of molecular markers-housekeeping genes that are always present in the microbial genome as well as functional genes that are responsible for the production of a particular enzyme. Biodegradation processes are performed in the environment by microbial communities; thus, it is important to study the microbiological part of these biodegradation processes utilizing a combination of molecular tools and markers. This chapter provides brief characteristics of the housekeeping genes used in microbial identification together with a description of the functional genes that are commonly used as molecular markers in the biodegradation of cellulose, hemicellulose, lignin, chlorinated compounds, plastics and polycyclic aromatic hydrocarbons.
4. Metabolomics and Crucial Enzymes in Microbial Degradation of Contaminants
Rafał Szewczyk and Konrad Kowalski
Metabolic pathways in living organisms are series of chemical reactions and typically consist of the enzymatic activities of intra- or extracellular enzymes. This chapter focuses on the metabolomic workflow characterization, which may be briefly characterised as the initial discovery, profiling, and final quantitation of the compound or a class of compounds of interest. This approach incorporates different instrumentation techniques and bioinformatics tools described in the chapter. The metabolomics of biodegradation processes is presented here as a direct result of enzymatic activity of the microbes, plants, and higher organisms towards xenobiotics, and includes examples of the typical degradation pathways catalysed by enzymes involved in certain steps of toxic substance removal. In the last section, the examples of targeted and untargeted biodegradation process characterisations at the cellular metabolism level are described.
5. Proteomics as a Tool for Metabolic Pathways Inspection in Microbial Cells
Rafał Szewczyk and Konrad Kowalski
Proteomics has become an important part of the characterization of biological systems or single organisms. In this chapter, background relating to proteomics studies including definitions, instrumentation, and basic as well as more complex workflows for protein extraction and identification with different instrumental techniques and bioinformatics tools are described. The application of proteomics in biodegradation is described in terms of selected research studies covering typical approaches: gel-free and gel-based as well as qualitative and quantitative comparative proteomics workflows and metaproteomics.
6. Lipidomics in Studies on Adaptation Mechanisms of Microorganisms to the Toxic Effects of Hazardous Compounds
Anomalies in environmental conditions activate a series of processes in microbial cells that allow them to minimise the negative impact of the environmental stress. These environmental factors, such as temperature, nutrient shortage, or dangerous pollutants, may result in changes in the cytoplasmic membrane. Since membranes constitute the main target for the action of toxic compounds, most adaptive mechanisms are concerned with maintenance of the membrane fluidity and lipid-phase stability. These processes can be modulated by altering the lipid composition of the membrane. In order to understand the contribution of membrane lipid composition to the functionality of membranes, comprehensive structural and quantitative information on the organellar lipidomics is essential. Improved lipidomic technologies, which are described in this review, have greatly enhanced our knowledge about the lipid biology of microorganisms at the level of individual species.
7. Microbial Elimination of Endocrine Disrupting Compounds
Endocrine disrupting compounds (EDCs) are chemicals that interfere with the proper functioning of the endocrine system in humans and animals, modulating it in a way that favors the activity of female sex hormones (estrogens). As well as being slowly degraded by microorganisms, EDCs are insufficiently eliminated in waste water treatment plants. Some of the compounds are discharged into aquatic environments in quantities of a few to tens of ngl-1
where they can accumulate in the bodies of different organisms (including humans) and subsequently stimulate numerous deleterious changes including fertility disorders and cancer processes.
In this chapter special attention is focused on the mechanisms of microbial detoxification and elimination of EDCs and the accomplishments of recent lipidomic, proteomic and metabolomic studies in these topics . This review also provides the results of the latest research on the parallel elimination of EDCs and heavy metals in saline environments, which has practical significance for the development of effective strategies for the removal of complex pollutants from contaminated areas.
8. Dyes Decolourisation and Degradation by Microorganisms
Anna Jasińska, Aleksandra Góralczyk and Jerzy Długoński
Owing to their industrial applications, many synthetic dyes are commonly present in wastewater and cause serious pollution of the aquatic environment. Most synthetic dyes are toxic, mutagenic, and carcinogenic. No universal method is available for the treatment of dye-contaminated wastewater because of the complex and varied chemical structures of these dyes. Of the current methods used for treating wastewater, microbial methods offer considerable advantages such as high efficiency, are environment friendly, and involve low operation costs. This review presents the latest research on microbial decolourisation of synthetic dye. Mechanisms involved in the bioremoval of dyes, pathways underlying the biodegradation of most important dye classes, and physicochemical parameters affecting dye decolourisation have been summarised in this review. In addition, this review discusses genetic manipulation of microorganisms and enzymes used for dye decolourisation.
9. Novel Insights into Polycyclic Aromatic Hydrocarbon Biodegradation Pathways Using Systems Biology and Bioinformatics
Ohgew Kweon, Seong-Jae Kim, John B. Sutherland and Carl E. Cerniglia
Biodegradation of polycyclic aromatic hydrocarbons (PAHs entails a complex and diverse set of biological reactions. Although there has been a massive effort over the years, understanding of the mechanism of PAH biodegradation has been limited when using the traditional approaches of genetics and biochemistry. The application of systems biology approaches, with advanced high-throughput analytical technologies, provides new global insights into not only the direct molecular mechanisms but also the genome-wide cellular ecophysiological responses involved in PAH degradation. This review describes research accomplishments from earlier traditional genetic and biochemical studies as well as the recent achievements of a combination of genomic, proteomic, and bioinformatics approaches to elucidate pathways for the degradation of high-molecular-weight (HMW) PAHs.
10. Biosurfactant Enhancement Factors in Microbial Degradation Processes
The efficiency of remediation processes is often limited by a strong hydrophobicity of contaminant compounds. This characteristic facilitates the pollutant sorption to solid particles causing an additional decrease in the contaminant concentration in the aqueous phase. Consequently, hydrophobic compounds are characterized by poor bioavailability for organisms with potent biodegradation activity. Due to their amphiphilic structure, molecules of surface active agents (surfactants) accumulate at interfaces between immiscible phases and cause a reduction in the interfacial tension. Surfactants also exhibit emulsifying, foaming, and dispersing properties; act as detergents facilitating desorption processes; and increase the apparent water solubility and mobility of hydrophobic compounds. Moreover, surfactants can modify microbial cell properties/activity and have the same influence on contaminant bioavailability and the kinetics of microbial biodegradation processes. Biosurfactants (surfactants of biological origin, mainly produced by microorganisms) exhibit not only multidirectional activity but are also eco-friendly. The full potential of biosurfactants in remediation technologies is not utilized mostly due to the limited understanding of interactions between these compounds and the environment (organisms, contaminants, and environmental abiotic elements), as well as their high production cost.
11. Microorganisms Application for Volatile Compounds Degradation
Christian Kennes, Haris N. Abubackar, Jianmeng Chen and María C. Veiga
The emission of volatile pollutants to the atmosphere and air pollution have become a major concern. Volatile pollutants are emitted from either stationary sources or mobiles sources. Common air pollutants are particulate matter as well as volatile organic and inorganic compounds. Different technologies can be used for their removal, including bioprocesses in case of volatile compounds. Both bacteria and fungi are able to degrade a rather wide range of natural as well as anthropogenic substrates. Although less research has been done on fungi, the latter have recently proven to be efficient biocatalysts for the removal of some of those pollutants, tolerating acidic conditions and environments with limited moisture content. Rather than simply mineralizing pollutants into harmless compounds, recent approaches have also considered the possibility to convert them into end metabolites with added value and commercial interest, e.g. fuels or platform chemicals. The biodegradation or bioconversion of volatile pollutants is performed in bioreactors. The most common bioreactors used in full-scale installations include the biofilter, the biotrickling filter, the bioscrubber and systems based on gas diffusion through suspended-growth bioreactors. Some other bioreactor configurations have been tested at laboratory scale as well. In most cases, such bioprocesses allow for a complete and efficient removal of volatile organic and inorganic compounds.
12. Heavy Metals Removal by Microbial Cells
Mirosława Słaba, Katarzyna Hrynkiewicz and Geoffrey M. Gadd
Environmental pollution with heavy metals poses a real ecological and human-health threat due to their high toxicity to living organisms. Metals cannot be degraded. Hence, microbial removal by binding to biomass, leaching, enzymatic transformations, and changes in metal solubility and, as a consequence, in toxicity are major strategies for the remediation of metal-contaminated environments. For this reason, more knowledge on the mechanisms responsible for microbial tolerance and transformations of toxic metals are important for possible applications in environmental biotechnology. This chapter includes the results of studies on passive metal removal through biosorption and metal uptake and accumulation involving the metabolic activity of microbial cells. Selected aspects of metal-microbe interactions have been presented. Proteomic studies that were carried out to identify microbial responses to heavy metal toxicity are also described. In the second part of the review, the potential of different groups of microorganisms for remediation and enhanced phytoremediation of metal-polluted soils is discussed. Attention has also been focused on the role of microorganisms in plant protection against metal stress as well as the mechanisms related to plant-microbe associations under unfavourable soil conditions.
13. Application of Recent Omics Achievements in Bioremediation Processes Illustrated by Progress in Microbial Surfactants Commercialization
Katarzyna Paraszkiewicz, Jerzy Długoński and Dariusz Trzmielak
This section comprises a critical analysis of microbial surfactant commercialization. Petroleum-derived active surface agents (synthetic surfactants) are applicable in various industrial sectors but pose significant environmental risks. In comparison with synthetic equivalents, microbial surfactants are environmentally friendly, biodegradable, and less toxic, as well as exhibit higher surface activity and selectivity; however, they are still too expensive to compete on the market. However, available reports forecast an increased share of biosurfactants as market products. Progress in biosurfactants commercialization (coupled with a better understanding of the roles of these compounds in microbial physiology and in biodegradation processes) results from advances in cell and molecular biology (e.g., genomics, proteomics, metabolomics and lipidomics).
How to buy this book
(EAN: 9781910190456 9781910190463 Subjects: [bacteriology] [environmental microbiology] [microbiology] [molecular microbiology] )