Contents

Cover

Preface

Part 1: Soil Microenvironment and Biotransformation Mechanisms

Chapter 1: Applications of Microorganisms in Agriculture for Nutrients Availability
1. 1.1 Introduction
2. 1.2 Biofertilizers
3. 1.3 Rhizosphere
4. 1.4 Plant Growth Promoting Bacteria
5. 1.5 Microbial Mechanisms of Phosphate Solubilization
6. 1.6 Bacterial and Fungi Coinoculation
7. 1.7 Conclusion
8. References
Chapter 2: Native Soil Bacteria: Potential Agent for Bioremediation
1. 2.1 Introduction
2. 2.2 Current Soil Pollution Scenario
3. 2.3 Effects of Soil Pollution
4. 2.4 Diversity of Soil Microbes from Contaminated Sites
5. 2.5 Bioremediation of Toxic Pollutants
6. 2.6 Bioremediation Mechanisms
7. 2.7 Factors Affecting Bioremediation/Biosorption Process
8. 2.8 Microbial Bioremediation Approaches
9. 2.9 Conclusion and Future Prospective
10. Acknowledgements
11. References
Chapter 3: Bacterial Mediated Remediation: A Strategy to Combat Pesticide Residues in Agricultural Soil
1. 3.1 Introduction
2. 3.2 Effects of Pesticides
3. 3.3 Pesticide Degradation
4. 3.4 Bacterial Mediated Biodegradation of Various Pesticides
5. 3.5 Conclusion
6. References
Chapter 4: Study of Plant Microbial Interaction in Formation of Cheese Production: A Vegan’s Delight
1. 4.1 Introduction
2. 4.2 Cheese Concern—Vegan’s Delight
3. 4.3 Microorganism Interaction Pattern
4. 4.4 Types of Microorganism Involved in Cheese Production
5. 4.5 Lactic Acid Role in Fermentation
6. 4.6 Microorganism Involved in Lactic Acid Fermentation
7. 4.7 Streptococcus
8. 4.8 Propionibacterium
9. 4.9 Leuconostoc
10. 4.10 Microorganisms in Flavor Development
11. 4.11 Flavor Production
12. 4.12 Enzyme Interaction During Ripening of Cheese
13. 4.13 Pathways Involved in Cheese Ripening
14. 4.14 Microbes of Interest in Flavor Formation
15. 4.15 Structure of Flavored Compound in Cheese
16. 4.16 Plant-Based Cheese Analogs
17. 4.17 Plant-Based Proteins
18. 4.18 Aspartic Protease
19. 4.19 Cysteine Protease
20. 4.20 Plant-Based Milk Alternatives
21. 4.21 Types of Vegan Cheese
22. 4.22 Future Scope and Conclusion
23. Acknowledgment
24. References
Chapter 5: Microbial Remediation of Pesticide Polluted Soils
1. 5.1 Introduction
2. 5.2 Types of Pesticides
3. 5.3 Fate of Pesticides in the Environment
4. 5.4 Screening for Pesticide Degrading Microorganisms
5. 5.5 Designing Pesticide Degrading Consortia
6. 5.6 Challenges to be Addressed and Future Perspectives
7. References
Chapter 6: Eco-Friendly and Economical Method for Detoxification of Pesticides by Microbes
1. 6.1 Introduction
2. 6.2 Classification of Pesticides
3. 6.3 Fate of Pesticide in Soil
4. 6.4 Microbial and Phytoremediation of Pesticides
5. 6.5 Effect on Humans and the Environment
6. 6.6 Advancement in Pesticide Bioremediation
7. 6.7 Limitations of Bioremediation
8. 6.8 Future Perspectives
9. Acknowledgment
10. References

Part 2: Synergistic Effects Between Substrates and Microbes

Chapter 7: Bioleaching: A Bioremediation Process to Treat Hazardous Wastes
1. 7.1 Introduction
2. 7.2 Microbes in Bioleaching
3. 7.3 Acidophilic Bioleaching
4. 7.4 Metal Removal Pathways
5. 7.5 Fungal Bioleaching
6. 7.6 Various Hazardous Wastes
7. 7.7 Applications of Bioleaching Approach to Various Hazardous Wastes
8. 7.8 Conclusion
9. Acknowledgements
10. References
Chapter 8: Microbial Bioremediation of Azo Dyes in Textile Industry Effluent: A Review on Bioreactor-Based Studies
1. 8.1 Introduction
2. 8.2 Microorganisms Involved in Dye Bioremediation
3. 8.3 Mechanism of Dye Biodegradation
4. 8.4 Reactor Design for Dye Bioremediation
5. 8.5 Limitations and Future Prospects
6. 8.6 Conclusions
7. References
Chapter 9: Antibiofilm Property of Biosurfactant Produced by Nesterenkonia sp. MCCB 225 Against Shrimp Pathogen, Vibrio harveyi
1. 9.1 Introduction
2. 9.2 Materials and Methods
3. 9.3 Results and Discussion
4. 9.4 Conclusion
5. Acknowledgements
6. References
Chapter 10: Role of Cr(VI) Resistant Bacillus megaterium in Phytoremediation
1. 10.1 Introduction
2. 10.2 Materials and Methods
3. 10.3 Results
4. 10.4 Discussion
5. 10.5 Conclusion
6. Acknowledgment
7. References
Chapter 11: Conjugate Magnetic Nanoparticles and Microbial Remediation, a Genuine Technology to Remediate Radioactive Waste
1. 11.1 Introduction
2. 11.2 Use of Magnetic Nanoparticles Conjugates
3. 11.3 Microbial Communities
4. 11.4 Conclusion
5. References

Part 3: Polyhydroxyalakanoates: Resources, Demands and Sustainability

Chapter 12: Microbial Degradation of Plastics: New Plastic Degraders, Mixed Cultures and Engineering Strategies
1. 12.1 Introduction
2. 12.2 Plastics
3. 12.3 Plastic Disposal, Reuse and Recycling
4. 12.4 Plastic Biodegradation
5. 12.5 Analytical Techniques to Study Plastic Degradation
6. 12.6 Future Perspectives
7. References
Chapter 13: Fatty Acids as Novel Building-Blocks for Biomaterial Synthesis
1. 13.1 Introduction
2. 13.2 Polyurethane (PUs)
3. 13.3 Polyhydroxyalkanoates (PHAs)
4. 13.4 Other Functional Attributes of Fatty Acids
5. 13.5 Future Perspectives
6. References
Chapter 14: Polyhydroxyalkanoates: Resources, Demands and Sustainability
1. 14.1 Introduction
2. 14.2 Polyhydroxyalkanoates
3. 14.3 Applications of PHA
4. 14.4 Future Prospects
5. References
Chapter 15: Polyhydroxyalkanoates Synthesis by Bacillus aryabhattai C48 Isolated from Cassava Dumpsites in Southwestern, Nigeria
1. 15.1 Introduction
2. 15.2 Materials and Methods
3. 15.3 Results and Discussion
4. 15.4 Conclusion
5. Acknowledgements
6. References

Part 4: Cellulose Based Biomaterials: Benefits and Challenges

Chapter 16: Cellulose Nanocrystals-Based Composites
1. 16.1 Introduction
2. 16.2 Classification of Polymers
3. 16.3 Preparation of Cellulose Nanocrystals Composites
4. 16.4 Cellulose Nanocrystals Reinforced Biopolymers
5. 16.5 Hybrids
6. 16.6 Conclusion and Future Trends
7. Acknowledgements
8. References
Chapter 17: Progress on Production of Cellulose from Bacteria
1. 17.1 Introduction
2. 17.2 Production of Microbial Cellulose (MC)
3. 17.3 Applications of Microbial Cellulose (MC)
4. Future Perspective
5. References
Chapter 18: Recent Developments of Cellulose-Based Biomaterials
1. 18.1 Introduction
2. 18.2 Extraction of Cellulose Fibers
3. 18.3 Nanocellulose
4. 18.4 Surface Modification
5. 18.5 Cellulose-Based Biomaterials
6. 18.6 Summary and Future Prospect of Cellulose-Based Biomaterials
7. Reference
Chapter 19: Insights of Bacterial Cellulose: Bio and Nano-Polymer Composites Toward Industrial Application
1. 19.1 Introduction
2. 19.2 Bacterial Cellulose
3. 19.3 Nanocomposites
4. 19.4 Methods of Synthesis of Bacterial Cellulose Composites
5. 19.5 Combination of Bacterial Cellulose With Other Materials
6. 19.6 Industrial Applications of Bacterial Cellulose Composites
7. 19.7 Future Scope and Conclusion
8. Acknowledgment
9. References
Chapter 20: Biodegradable Polymers Reinforced with Lignin and Lignocellulosic Materials
1. 20.1 Introduction
2. 20.2 Biodegradable Polymers
3. 20.3 Biodegradable Fillers
4. 20.4 Properties of Different Biopolymers Reinforced with Lignin
5. 20.5 Applications of Bio-Nanocomposites
6. Concluding Remarks
7. Acknowledgements
8. References
Chapter 21: Structure and Properties of Lignin-Based Biopolymers in Polymer Production
1. 21.1 Introduction
2. 21.2 An Insight to the Biopolymers
3. 21.3 Extraction and Post-Treatment of Lignin Biomaterial
4. 21.4 Characterization Methods and Validation of Lignin-Biopolymers
5. 21.5 Indispensability of LBB on the Chemical Release Control in the Environment
6. 21.6 Conclusion and Future Remarks
7. References

Index

End User License Agreement

List of Illustrations

Chapter 1

Figure 1.1 Various acid production by phosphate solubilising microbes.

Chapter 2

Figure 2.1 The metabolism-dependent (active) and metabolism-independent (passive) mechanisms…

Chapter 4

Figure 4.1 Various enzymes involved in formation of volatile compounds that contributes…
Figure 4.2 General pathways for the catabolism of free fatty acids in cheese ([37] and [59]).
Figure 4.3 General pathways for the catabolism of FAA
Figure 4.4 Cheese analogs.

Chapter 5

Figure 5.1 Chemical structure of some pyrethrins and pyrethroids.
Figure 5.2 World map of the pesticide contamination risk in surface waters. Modelled based…
Figure 5.3 Chemical structures of typical organochlorinated and organophosphorus pesticides…
Figure 5.4 Suggested pathways involved in the bioconversion of endosulfan.
Figure 5.5 Main factors affecting the fate of the pesticide.
Figure 5.6 Different processes affecting mobility and persistence of pesticides.
Figure 5.7 Antagonism assay on malathion (a), dimethoate (b) and dicamba (c).

Chapter 6

Figure 6.1 Transport of pesticides in the environment.
Figure 6.2 Various biochemical pathways followed by microbes in pesticide bioremediation…

Chapter 7

Figure 7.1 The contact and non-contact bioleaching mechanisms (EPS: extracellular polymeric…
Figure 7.2 Schematic presentation of thiosulphate and polysulphide pathways…

Chapter 8

Figure 8.1 Diagrammatic representation of the different mechanisms of aerobic azo dye…
Figure 8.2 Flowchart showing different types of reactors used for treatment of dyes in…

Chapter 9

Figure 9.1 Plate assay (zone of clearance) showing haemolytic activity.
Figure 9.2 Plate assay (zone of clearance) showing lipolytic activity.
Figure 9.3 Phylogenetic tree showing taxonomic position of MCCB 225.
Figure 9.4 Biofilm disruption a, b and d disruption and c control.

Chapter 10

Figure 10.1 Estimation of chromium reduction potential of isolates.
Figure 10.2 Phylogenetic tree of Strain rCrI Bacillus megaterium (represented in block)…
Figure 10.3 Growth curve studies of bacterial isolate rCrI (I=without Cr stress, I(Cr)=with…

Chapter 11

Figure 11.1 Flowchart showing separation of radionuclide from conjugate particles.
Figure 11.2 Process of magnetic nanoparticles conjugates activity.
Figure 11.3 Diagrammatic representation of processes and microbes involved in enzymatic and…

Chapter 12

Figure 12.1 Structure of polyethylene terephthalate (PET).
Figure 12.2 Repeating unit of polyethylene (PE) and scheme of the branched polymeric…
Figure 12.3 Hydrolysis of polybutylene succinate (PBS) into succinic acid and 1,4-butanediol…
Figure 12.4 Hydrolysis of polyethylene terephthalate (PET) into mono(2-hydroxyethyl)…

Chapter 13

Figure 13.1 Bioconversion of oils into polyols (DOD and TOD) for polyurethane synthesis…

Chapter 14

Figure 14.1 Structure of PHA.
Figure 14.2 Different classes of polymers which are bio based and biodegradable.
Figure 14.3 Development of PHA science and technology through the twentieth century [26].
Figure 14.4 Mechanism of thermal degradation of PHB.
Figure 14.5 A model showing the structure of in vivo inclusions with its association…
Figure 14.6 Biosynthetic pathway of Polyhydroxyalkanoates.
Figure 14.7 Selection of vegetable-oil-degrading isolates that are accumulating PHAs in the…

Chapter 15

Figure 15.1 Phylogenetic tree of B. aryabhattai C48. The tree was constructed using…
Figure 15.2 Time profile of B. aryabhattai C48 in four carbon sources. GLU - Glucose;…
Figure 15.3 PHA extracted from B. aryabhattai C48.
Figure 15.4 Phylogenetic tree of the predicted PhaC protein of B. aryabhattai C48.…
Figure 15.5 FTIR Spectra of PHA produced by B. aryabhattai C48 using four carbon…

Chapter 16

Figure 16.1 Classification of polymer fibers.
Figure 16.2 Schematic of electrospinning and experimental configuration.
Figure 16.3 Rheological properties of DM-OA-CNC ink and 3D-printed pattern. (a) Apparent…

Chapter 17

Figure 17.1 The structure of bacterial cellulose showing inter- and intra hydrogen bonding…

Chapter 18

Figure 18.1 Structure of cellulose [5].
Figure 18.2 AFM image of CNF (a) and CNC (b) [10].
Figure 18.3 SEM image of untreated (a) and Borassus fine fibers treated with alkaline for…
Figure 18.4 Schematic diagram of the silanization process of natural fibers [37].
Figure 18.5 Bacterial cellulose applied on wounded torso and face [47]. This study was…

Chapter 19

Figure 19.1 Schematic image of high pressure homogenizer converting celluloic fiber to…
Figure 19.2 Diagrammatic representation of bacterial cellulose cultivation with the presence…
Figure 19.3 (a) Schematic representaion of synthesis of bacterial cellulose composites…
Figure 19.4 Schematic representation of synthesis of bacterial cellulose composites from…

Chapter 20

Figure 20.1 A detailed description of the structure of a typical plant fiber (37).
Figure 20.2 Basic chemical structure of cellulose [41].
Figure 20.3 SEM micrographs of composites (a and c) 50% PBS/lignin composites (low and high…
Figure 20.4 Values for tensile strength (σ) (a), Young’s modulus (E…
Figure 20.5 Residual mass curves and derivative curves vs temperature (Tmax zoom in the insert)…

Chapter 21

Figure 21.1 The three main monolignols of lignin biopolymer [16],
Figure 21.2 Schematic presentation to synthesize production of new active sites.

List of Tables

Chapter 1

Table 1.1 Most common bacteria studied for nitrogen fixation.

Chapter 2

Table 2.1 A compilation of the microbial diversity reported from contaminated soils.

Chapter 3

Table 3.1 Different effects of pesticides exposure on abiotic and biotic factors.
Table 3.2 Bacterial mediated bioremediation in various region of agricultural soil.

Chapter 4

Table 4.1 Various types of lactic acid bacteria used in milk fermentation [43].
Table 4.2 Representing the important flavor-producing compounds and their respective…

Chapter 5

Table 5.1 Examples of losses in the food production, with and without pesticides. Extracte…
Table 5.2 Shows the persistence of pesticides/xenobiotics. Adapted from [20].
Table 5.3 Persistence of pesticides/xenobiotics. Adapted from [20].
Table 5.4 GUS values to estimate the potential reach groundwaters. GUS=log₁₀…
Table 5.5 Soil half-life, water solubility, and sorption coefficient of different pesticides,…

Chapter 6

Table 6.1 Classification of pesticides.
Table 6.2 Soil bacteria involved in degradation of the most persistent pesticides [101].
Table 6.3 Health effects of common pesticides [84].

Chapter 8

Table 8.1 Bacterial decolorization of azo dyes.
Table 8.2 Dye degradation potential of various fungi.
Table 8.3 Dye decolorization by algae.
Table 8.4 Different anaerobic and aerobic reactors for the treatment of dye containing…
Table 8.5 Different sequential/combined reactors for the treatment of dye containing…

Chapter 10

Table 10.1 Growth parameters of Triticum aestivum seedlings inoculated with bacterial…
Table 10.2 Biochemical parameters of Triticum aestivum seedlings inoculated with…

Chapter 11

Table 11.1 Activities and health effects of different radionuclides.
Table 11.2 List of important chelators and detachment processes induced through magnetic…

Chapter 12

Table 12.1 Example of plastic-degrading microorganisms and respective enzymes…
Table 12.2 Tested mutations to PETase and relative activity in relation to the wildtype…
Table 12.3 Main analytical techniques used to characterize plastic polymers and its…
Table 12.4 Main analytical techniques used to characterize plastic degradation products.
Table 12.5 Main analytical techniques used to estimate plastic degradation through microbial…

Chapter 13

Table 13.1 Bioconversion of oily substrates to polyhydroxyalkanoates.
Table 13.2 Hydroxy fatty acids properties and use.

Chapter 14

Table 14.1 Common properties of PHAs.
Table 14.2 Production of PHA by various bacteria.

Chapter 15

Table 15.1 Extracted polyhydroxyalkanoates and dry cell weight in four carbon sources.

Chapter 16

Table 16.1 Selected studies of CNCs nanocomposites.

Chapter 18

Table 18.1 Treatment of biomass by hybrid methods.
Table 18.2 Extraction of nanocellulose by different methods.

Chapter 20

Table 20.1 Mechanical properties of common food plastics (55).

Chapter 21

Table 21.1 Properties of technical lignins extracted by various industrial methods [2, 19,…

Soil Microenvironment for Bioremediation and Polymer Production

Edited by

Nazia Jamil,

Prasun Kumar

and

Rida Batool

This edition first published 2020 by John Wiley & Sons, Inc., Ill River Street, Hoboken, NJ 07030, USA and Scrivener Publishing LLC, 100 Cummings Center, Suite 541J, Beverly, MA 01915, USA
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Library of Congress Cataloging-in-Publication Data
Name: Jamil, Nazia, editor.
Title: Soil microenvironment for bioremediation and polymer production / edited by Nazia Jamil, Prasun Kumar and Rida Batool.
Description: First edition. | Hoboken, NJ : Wiley-Scrivener, 2020. | Includes bibliographical references and index.
Identifiers: LCCN 2019040532 (print) | LCCN 2019040533 (ebook) | ISBN 9781119592051 (hardback) | ISBN 9781119592150 (adobe pdf) | ISBN 9781119592174 (epub)
Subjects: LCSH: Soil microbiology. | Soil remediation. | Bioremediation.
Classification: LCC QR111 .S6735 2020 (print) | LCC QR111 (ebook) | DDC 579/.1757–dc23
LC record available at https://lccn.loc.gov/2019040532
LC ebook record available at https://lccn.loc.gov/2019040533

Preface

Microenvironmental conditions in soil provide a natural niche for ultra structures, microbes and microenvironments. These microenvironments surrounding microbial substrates are very crucial for synergistic exchanges. The natural biodiversity of these microenvironments is being disturbed by industrialization and the proliferation of urban centers; and synthetic contaminants found in these micro-places are causing stress and instability in the biochemical systems of microbes. The development of new metabolic pathways from intrinsic metabolic cycles facilitates microbial degradation of diverse resistant synthetic compounds present in soil. These are a vital, competent and cost-effective substitute to conventional treatments. At the moment, highly developed techniques for bioremediation of these synthetic compounds are on the rise. These techniques facilitate the development of a safe environment using renewable biomaterial for removal of toxic heavy metals and xenobiotics.

The current book presents research data and reviews under the title of Soil Microenvironment for Bioremediation and Polymer Production. Included in the chapters are classical bioremediation approaches and advances in the use of nanoparticles for removal of radioactive waste. The chapters included in Parts 3 and 4 discuss the production of applied emerging biopolymers using diverse microorganisms. All chapters are supplemented with comprehensive illustrative diagrams and comparative tables. This book will be beneficial for both beginners and experts in the field of applied microbial bioremediation and renewable biomaterials. It is our hope that by reading this book researchers and conservationists will be inspired to apply microbial bioremediation and renewable biomaterial. Finally, we wish to thank all the authors with expertise in this field of research for their valuable contributions in making this a successful venture.

Nazia Jamil

Prasun Kumar

Rida Batool
October 2019