Microbial Interactions at Nanobiotechnology Interfaces

Navanietha Rathinam is a Research Scientist in the Composite and Nanocomposite Advanced Manufacturing-Biomaterials Center, Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD. His research activities are focused on bio-electrochemical interface technologies, biomaterials, and biofilm engineering. He received the Young Faculty Award for his accomplishments in teaching and research. In 2016, he received the Award for Cutting Edge Research (Fulbright Faculty Award). He has been a PI/Co-I for 4 research grants and served as a panelist for NASA and National Science Foundation. He is currently serving as an Ambassador to the American Society for Microbiology. He also serves as an editor for books on Bioelectrochemical Interface Engineering (WILEY), Biofilm engineering (American Chemical Society), and Biomanufacturing (American Chemical Society). He is an Associate editor for IEEE Access and an editorial board member for a few reputed journals. Rajesh Sani is a Professor in the Departments of Chemical and Biological Engineering and Applied Biological Sciences at South Dakota School of Mines and Technology, South Dakota, USA. His research expertise includes Extremophilic Bioprocessing, Biocatalysis, Rules of Life in Biofilms, Biomaterials, Gas to Liquid Fuels, Genome Editing of Extremophiles and Space Biology. Over the past 14 years, he has been the PI or co-PI on over $44.45 million in funded research. He has one patent, seven invention disclosures, and published over 94 peer-reviewed articles in high impact factor journals and have contributed to over 24 book chapters. In addition, he has edited eight books and one Proceedings for Springer International Publishing AG, Wiley, and ACS publications. Dr Sani has been leading a research consortium funded by the NSF with the aid of 84 scientists and engineers.

Preface xi

List of Contributors xiii

1 Shape- and Size-Dependent Antibacterial Activity of Nanomaterials 1
Senthilguru Kulanthaivel and Prashant Mishra

1.1 Introduction 1

1.2 Synthesis of Nanomaterials 3

1.3 Classification of NMs 4

1.3.1 Classification Based on Dimensions 5

1.3.1.1 Zero-Dimensional NMs 5

1.3.1.2 One-Dimensional NMs 6

1.3.1.3 Two-Dimensional NMs 6

1.3.1.4 Three-Dimensional NMs 6

1.3.2 Classification Based on Chemical Compositions 7

1.3.2.1 Carbon-Based NMs 7

1.3.2.2 Organic-Based NMs 7

1.3.2.3 Inorganic-Based NMs 8

1.3.3 Classification Based on Origin 9

1.4 Application of NMs 9

1.4.1 Advanced Application of NMs as Antimicrobial Agents 9

1.5 Bacterial Resistance to Antibiotics 10

1.5.1 Mechanism of Antibiotic Resistance 10

1.5.1.1 Antibiotics Modification 11

1.5.1.2 Antibiotic Efflux 12

1.5.1.3 Target Modification or Bypass or Protection 12

1.6 Microbial Resistance: Role of NMs 12

1.6.1 Overcoming the Existing Antibiotic Resistance Mechanisms 13

1.6.1.1 Combating Microbes Using Multiple Mechanisms Simultaneously 13

1.6.1.2 Acting as Good Carriers of Antibiotics 13

1.7 Antibacterial Application of NMs 15

1.7.1 Nanometals 16

1.7.2 Metal Oxides 17

1.7.3 Carbonaceous NMs 18

1.7.4 Cationic Polymer NMs 19

1.8 Interaction of NMs with Bacteria 19

1.9 Antibacterial Mechanism of NMs 20

1.10 Factors Affecting the Antibacterial Activity of NMs 22

1.10.1 Size 22

1.10.2 Shape 23

1.10.3 Zeta Potential 24

1.10.4 Roughness 24

1.10.5 Synthesis Methods and Stabilizing Agents 25

1.10.6 Environmental Conditions 26

1.11 Influence of Size on the Antibacterial Activity and Mechanism of Action of Nanomaterials 27

1.12 Influence of Shape on the Antibacterial Activity and Mechanism of Action of Nanomaterials 30

1.13 Effects of Functionalization on the Antimicrobial Property of Nanomaterials 34

1.14 Conclusion and Future Perspectives 35

Questions and Answers 36

References 38

2 Size- and Shape-Selective Synthesis of DNA-Based Nanomaterials and Their Application in Surface-Enhanced Raman Scattering 53
K. Karthick and Subrata Kundu

2.1 Introduction 53

2.2 Mechanism of Surface-Enhanced Raman Scattering (SERS) 55

2.2.1 Significance of Nano-Bio Interfaces and Role of DNA in Enhancing SERS Activity 56

2.3 Size- and Shape-Selective Synthesis of Metal NPs with DNA for SERS Studies 57

2.3.1 Metal NP Assemblies on DNA Using Photochemical Route for SERS Studies 58

2.3.2 Metal NP Assemblies on DNA Using Chemical Reduction Process as Aquasol for SERS Studies 69

2.3.3 Metal NP Assemblies on DNA Using Chemical Reduction as Organosol for SERS Studies 77

2.3.4 Metal NP Assemblies on DNA Prepared Using Microwave Heating for SERS Studies 79

2.3.5 Conclusions and Outcomes of DNA-Based Metal Nanostructures for SERS Studies 83

Take Home Message 85

Questions and Answers 85

References 86

Academic Profile 90

3 Surface Modification Strategies to Control the Nanomaterial–Microbe Interplay 93
T. K. Vasudha, R. Akhil, W. Aadinath, and Vignesh Muthuvijayan

3.1 Introduction 93

3.2 Factors Influencing NM–Microbe Cross talk 96

3.2.1 Surface Features of Microbes 96

3.2.2 Physicochemical Properties of NMs 97

3.3 Surface Functionalization 100

3.3.1 Techniques Used for Surface Functionalization 101

3.3.1.1 Self-Assembled Monolayers 102

3.3.1.2 Layer-by-Layer Technique 102

3.3.2 Surface Functionalization Strategies 103

3.3.2.1 Physicochemical Modifications 103

3.3.2.2 Biofunctionalization 105

3.4 Characterization of NM–Microbe Interactions 106

3.4.1 Microbe Parameters 107

3.4.2 NM Parameters 108

3.5 Toxicity of the Surface-Modified NMs 109

3.6 Challenges and Future Perspectives 110

Questions and Answers 111

Take Home Message 112

References 112

4 Surface Functionalization of Nanoparticles for Stability in Biological Systems 129
Srishti Agarwal and D. Sakthi Kumar

4.1 Introduction 129

4.2 Major Processes Affecting NP Stability in Biological Media 130

4.2.1 Aggregation 130

4.2.2 Nanoparticle Design and Properties 131

4.2.3 Hydrophobicity/Hydrophilicity Effects 133

4.2.4 Effect of Protein Corona 134

4.2.4.1 Effect of Protein Corona on Active Targeting 134

4.2.5 External Factors 135

4.3 Measures to Enhance NP Stability in Biological Systems 135

4.3.1 Stabilization Against Aggregation 135

4.3.2 Ligand Exchange 136

4.3.3 Coating with Additional Layers 136

4.3.3.1 Silica Coating 137

4.3.3.2 PEG Coating 138

4.3.3.3 Lipid Bilayer Coating 141

4.3.3.4 Zwitterionic Coating 141

4.3.3.5 Protein Coating 143

4.3.3.6 Aptamer Coating 144

4.3.4 Subsiding the Nonspecific Protein Interaction 146

4.3.5 Nanoparticle Design 146

4.3.5.1 Particle Functionalization 147

4.3.6 Influence of NM Physicochemical Properties on Microbe–NM Interaction 149

4.4 Conclusion and Future Perspectives 151

4.5 Summary 152

Questions and Answers 152

References 153

5 Molecular Mechanisms Behind Nano-Cancer Therapeutics 167
Surya Prakash Singh and Aravind Kumar Rengan

5.1 Nanotechnology at Nano–Bio Interfaces 167

5.2 Armory of Nanomedicine at Nano–Bio Interfaces 168

5.3 Nanoparticle Edge in Modulating Biological Process 170

5.4 Intracellular Uptake and Trafficking of Nanoparticle 173

5.5 Challenges in Clinical Applications 176

5.6 Conclusion 177

Take Home Message 177

Questions and Answers 178

References 179

6 Protein Nanoparticle Interactions and Factors Influencing These Interactions 187
R. Mala and R. Keerthana

6.1 Introduction 187

6.2 Types and Biomedical Application of Nanoparticles 188

6.3 Methods and Mechanisms of Nanomaterials Synthesis 189

6.4 Routes of Entry of Nanoparticles into Biological System 190

6.5 Rationale for Studying Nanoparticles–Protein Interactions 191

6.6 Formation of Protein Corona 191

6.6.1 Structure and Composition of Corona 191

6.6.2 Kinetics of Formation of Nanoparticles–Corona 193

6.7 Nanoparticles-Induced Structural Changes in Proteins 195

6.7.1 Reversible 195

6.7.2 Irreversible 195

6.8 Factors Influencing Corona Formation 196

6.8.1 Properties of Nanoparticles 196

6.8.1.1 Size 196

6.8.1.2 Shape 198

6.8.1.3 Charge 198

6.8.1.4 Surface Functionalization 198

6.8.1.5 Surface Reactivity 199

6.8.1.6 Solubility 199

6.8.2 Properties of Protein 199

6.8.3 Effect of Surrounding Environment 201

6.8.3.1 Effect of Media Composition on Corona Formation 201

6.8.3.2 Effect of Temperature 201

6.8.3.3 Static In Vitro Model Vs. Dynamic In Vivo System 201

6.9 Interaction of Nanoparticles with Cells and Their Uptake 202

6.10 Pleiotrophic Effect of Nanoparticles 204

6.11 Analytical Methods to Study Nanoparticles–Protein Interaction 204

6.11.1 Spectral Properties 204

6.11.1.1 UV–Vis Spectroscopy 204

6.11.1.2 FTIR 205

6.11.1.3 Raman Spectroscopy 205

6.11.1.4 Fluorescence Spectroscopy 206

6.11.2 Surface Plasmon Resonance 208

6.11.3 Cellular Uptake of Nanoparticles–Protein 208

6.11.3.1 Flow Cytometry 208

6.11.3.2 Confocal Microscopy 208

6.11.4 Binding Affinity 209

6.11.4.1 Differential Scanning Calorimetry and Isothermal Calorimetry 209

6.11.4.2 Isothermal Titration Calorimetry 209

Questions and Answers 209

References 210

7 Interaction Effects of Nanoparticles with Microorganisms Employed in the Remediation of Nitrogen-Rich Wastewater 225
Parmita Chawley and Sheeja Jagadevan

7.1 Introduction 225

7.2 Bacterial Nitrification Process 227

7.2.1 Effect of NPs on Functional Gene Abundance and Transcriptional Response 227

7.2.2 Effect of NPs on Enzyme Activity 229

7.2.3 Effect on Cellular Morphology 230

7.3 Effect of NPs on Denitrifying Bacteria 231

7.3.1 Effect on Functional Gene Abundance and Transcriptional Response 232

7.3.2 Enzymatic Response 234

7.4 Impact of Nanoparticles on Nitrogen Removal 236

7.5 Conclusion 236

Take Home Message 236

Questions and Answers 237

References 238

8 Silver-Based Nanoparticles for Antibacterial Activity: Recent Development and Mechanistic Approaches 245
Arpita Roy, Papia Basuthakur, Shagufta Haque, and Chitta Ranjan Patra

8.1 Introduction 245

8.2 Historical Background of Silver 246

8.3 Synthesis Procedures of Silver Nanoparticles 247

8.3.1 Chemical Synthesis 247

8.3.2 Physical Methods 249

8.3.3 Biological Methods 249

8.4 Biological Application of Silver Nanoparticles 251

8.5 Bacterial Infection and Antibiotic Resistance 251

8.6 Nanosilver for Antibacterial Therapy 254

8.6.1 Metallic Silver Nanoparticles 254

8.6.2 Biosynthesized Silver Nanoparticles 254

8.6.3 Silver Nanocomposites 257

8.6.4 Silver Nanoscaffolds 260

8.7 Influence of Size and Shape of Silver Nanoparticles as Antibacterial Agents 260

8.8 Nanosilver and Its Mechanism of Action for Antibacterial Therapy 261

8.9 Application of Silver Nanoparticle in Commercial Products 266

8.9.1 Silver Nanoparticles in Wound Dressing Materials and Devices 266

8.9.2 Silver Nanoparticles in Soaps and Detergents 268

8.9.3 Silver Nanoparticles in Fabrics 269

8.9.4 Silver Nanoparticles in Cosmetics 271

8.9.5 Silver Nanoparticles in Food Packaging 271

8.9.6 Silver Nanoparticles in Paints 273

8.10 Toxicity of Silver Nanoparticles 273

8.11 Future Prospective and Challenges 275

8.12 Conclusion 276

Take Home Message 276

Questions and Answers 277

Abbreviation 278

References 280

9 Microbial Gold Nanoparticles and Their Biomedical Applications 303
Dindyal Mandal, Rohit Kumar Singh, Uday Suryakant Maharana, Bijayananda Panigrahi, and Sourav Mishra

9.1 Introduction 303

9.2 Microbial Gold Nanoparticles Synthesis 304

9.2.1 Bacteria-Mediated Gold Nanoparticles 306

9.2.2 Algae-Mediated Gold Nanoparticles 308

9.2.3 Fungi-Mediated Gold Nanoparticles 311

9.2.4 Yeast-Mediated Gold Nanoparticles 315

9.2.5 Mechanism Involved in Microbial Nanoparticles Synthesis 315

9.3 Applications of Microbial Gold Nanoparticles 317

9.3.1 Biosensing 317

9.3.2 Antibacterial Activity of Au NPs 318

9.3.3 Anticancer Activity of Microbial Gold Nanoparticles 321

9.4 Conclusion 322

Take Home Message 323

Questions and Answers 323

References 325

10 Nano-Bio Interactions and Their Practical Implications in Agriculture 337
Achintya N. Bezbaruah and Ann-Marie Fortuna

10.1 Introduction 337

10.1.1 Agriculturally Beneficial Soil Microorganisms 339

10.2 Engineered Nanomaterials and Agriculture 340

10.2.1 Pathways for ENM to Soil 340

10.2.2 Fate of ENMs in Soil 340

10.2.3 Chemical Interactions of ENM in Soil 343

10.2.4 Mechanisms Controlling Heteroaggregation 344

10.2.5 Mobility of Colloids and ENMs in Soil 344

10.2.6 Nanoagriculture 345

10.2.7 Nanopesticides 348

10.2.8 ENMs and Agriculturally Beneficial Microorganisms 349

10.3 Summary 352

References 353

11 Biogeochemical Interactions of Bioreduced Uranium Nanoparticles 359
S. Sevinç Şengör and Rajesh K. Sani

11.1 Introduction 359

11.2 Coupled Biogeochemical Mechanisms and Interactions of U in the Subsurface 361

11.3 Biogenic Uraninite Precipitation and Its Nanoparticulate Forms 367

11.4 Re-oxidation and Stability of Bioreduced Uranium 371

11.5 Summary and Conclusions 373

Questions and Answers 374

References 376

12 Characterization and Quantification of Mobile Bioreduced Uranium Phases 383
S. Sevinç Şengör and Rajesh K. Sani

12.1 Introduction 383

12.2 Characterization of Biogenic U(IV) 384

12.3 Quantification of Mobile Bioreduced U(IV) Nanoparticles 386

12.4 Summary and Conclusions 388

Questions and Answers 389

References 391

Index 395