Skip to main content
SpringerLink
Log in

Sensing Soil Microbes and Interactions: How Can Nanomaterials Help?

  • Chapter
  • First Online:
Book cover Microbial Nanobionics

Part of the book series: Nanotechnology in the Life Sciences ((NALIS))

Abstract

Detecting microbial life in the soil environment is a goal of space exploration because of its influence not only on the plant growth but also on the human health. In order to identify the soil microbes contributing to the nutrient cycling and sustainable agriculture, various studies have been attempted to capture the microbial activity in vivo and to understand their role individually. However, these attempts have not been successful owing to the presence of nonculturable microbes in abundance. Advances in metagenomics study and sensor-based technology have contributed to a great extent to identify such microbes. Conventional soil microbial detection involving culture-dependent methods have failed to deliver in real time. Nanomaterial incorporation into biosensors can enhance the performance of biosensors due to their unique physicochemical properties. This field has initiated the understanding of the complex interplay between nanomaterials and microbes and the resulting biological consequences. This chapter provides brief insights into the importance of the soil microbiome and biosensors with nanomaterial interventions for bacterial detection. A range of nanomaterials have been investigated for their role in biorecognition. Additionally, the mechanistic aspects of nanomaterial-microbe interaction with implications for microbial detection are touched upon.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abbasian F, Ghafar-Zadeh E, Magierowski S (2018) Microbiology sensing technology: a review. Bioengineering 5(1):20

    Article  PubMed Central  CAS  Google Scholar 

  • Abd-Elsalam K, Mohamed AA, Prasad R (2019) Magnetic nanostructures: environmental and agricultural applications. Springer International Publishing. https://www.springer.com/gp/book/9783030164386. isbn:978-3-030-16438-6

  • Ahemad M, Kibret M (2014) Mechanisms and applications of plant growth promoting rhizobacteria: current perspective. J King Saud Univ Sci 26(1):1–20

    Article  Google Scholar 

  • Algar WR, Tavares AJ, Krull UJ (2010) Beyond labels: a review of the application of quantum dots as integrated components of assays, bioprobes, and biosensors utilizing optical transduction. Anal Chim Acta 673(1):1–25

    Article  CAS  PubMed  Google Scholar 

  • Arakha M, Jha S (2018) Interfacial phenomena on biological membranes. Springer. https://doi.org/10.1007/978-3-319-73326-5

    Book  Google Scholar 

  • Aruguete DM, Hochella MF (2010) Bacteria–nanoparticle interactions and their environmental implications. Environ Chem 7(1):3–9

    Article  CAS  Google Scholar 

  • Barve A, Wagner A (2013) A latent capacity for evolutionary innovation through exaptation in metabolic systems. Nature 500(7461):203

    Article  CAS  PubMed  Google Scholar 

  • Beattie GA (2007) Plant-associated bacteria: survey, molecular phylogeny, genomics and recent advances. In: Plant-associated bacteria. Springer, Dordrecht pp 1–56

    Google Scholar 

  • Berendsen RL, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17(8):478–486

    Article  CAS  PubMed  Google Scholar 

  • Berg G, Rybakova D, Grube M, Köberl M (2015) The plant microbiome explored: implications for experimental botany. J Exp Bot 67(4):995–1002

    Article  PubMed  CAS  Google Scholar 

  • Bhattacharyya PN, Jha DK (2012) Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture. World J Microbiol Biotechnol 28(4):1327–1350

    Article  CAS  PubMed  Google Scholar 

  • Biju V, Itoh T, Ishikawa M (2010) Delivering quantum dots to cells: bioconjugated quantum dots for targeted and nonspecific extracellular and intracellular imaging. Chem Soc Rev 39(8):3031–3056

    Article  CAS  PubMed  Google Scholar 

  • Bonfante P, Anca IA (2009) Plants, mycorrhizal fungi, and bacteria: a network of interactions. Annu Rev Microbiol 63:363–383

    Article  CAS  PubMed  Google Scholar 

  • Borneman J (1999) Culture-independent identification of microorganisms that respond to specified stimuli. Appl Environ Microbiol 65(8):3398–3400

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bose S, Hochella MF Jr, Gorby YA, Kennedy DW, McCready DE, Madden AS, Lower BH (2009) Bioreduction of hematite nanoparticles by the dissimilatory iron reducing bacterium Shewanella oneidensis MR-1. Geochim Cosmochim Acta 73(4):962–976

    Article  CAS  Google Scholar 

  • Braud A, Jézéquel K, Bazot S, Lebeau T (2009) Enhanced phytoextraction of an agricultural Cr-and Pb-contaminated soil by bioaugmentation with siderophore-producing bacteria. Chemosphere 74(2):280–286

    Article  PubMed  CAS  Google Scholar 

  • Bu D, Zhuang H, Yang G, Ping X (2014) An immunosensor designed for polybrominated biphenyl detection based on fluorescence resonance energy transfer (FRET) between carbon dots and gold nanoparticles. Sens Actuators B Chem 195:540–548

    Article  CAS  Google Scholar 

  • Cao C, Kim JH, Yoon D, Hwang E-S, Kim Y-J, Baik S (2008) Optical detection of DNA hybridization using absorption spectra of single-walled carbon nanotubes. Mater Chem Phys 112(3):738–741

    Article  CAS  Google Scholar 

  • Chalmeau J, Dagkessamanskaia A, Le Grimellec C, Francois J-M, Sternick J, Vieu C (2009) Contribution to the elucidation of the structure of the bacterial flagellum nano-motor through AFM imaging of the M-Ring. Ultramicroscopy 109(8):845–853

    Article  CAS  PubMed  Google Scholar 

  • Chandler D, Davidson G, Grant W, Greaves J, Tatchell G (2008) Microbial biopesticides for integrated crop management: an assessment of environmental and regulatory sustainability. Trends Food Sci Technol 19(5):275–283

    Article  CAS  Google Scholar 

  • Chen J, Andler SM, Goddard JM, Nugen SR, Rotello VM (2017) Integrating recognition elements with nanomaterials for bacteria sensing. Chem Soc Rev 46(5):1272–1283

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Creasey RC, Shingaya Y, Nakayama T (2015) Improved electrical conductance through self-assembly of bioinspired peptides into nanoscale fibers. Mater Chem Phys 158:52–59

    Article  CAS  Google Scholar 

  • Creus CM, Graziano M, Casanovas EM, Pereyra MA, Simontacchi M, Puntarulo S, Barassi CA, Lamattina L (2005) Nitric oxide is involved in the Azospirillum brasilense-induced lateral root formation in tomato. Planta 221(2):297–303

    Article  CAS  PubMed  Google Scholar 

  • Dary M, Chamber-Pérez M, Palomares A, Pajuelo E (2010) “In situ” phytostabilisation of heavy metal polluted soils using Lupinus luteus inoculated with metal resistant plant-growth promoting rhizobacteria. J Hazard Mater 177(1–3):323–330

    Article  CAS  PubMed  Google Scholar 

  • del Carmen Orozco-Mosqueda M, del Carmen Rocha-Granados M, Glick BR, Santoyo G (2018) Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms. Microbiol Res 208:25–31

    Article  CAS  Google Scholar 

  • Dessaux Y, Hinsinger P, Lemanceau P (2009) Rhizosphere: so many achievements and even more challenges. Springer 321(1):1–3

    CAS  Google Scholar 

  • Dickert FL, Haunschild A (1993) Sensor materials for solvent vapor detection—donor–acceptor and host–guest interactions. Adv Mater 5(12):887–895

    Article  CAS  Google Scholar 

  • El-Ansary A, Faddah LM (2010) Nanoparticles as biochemical sensors. Nanotechnol Sci Appl 3:65

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Edgar R, McKinstry M, Hwang J, Oppenheim AB, Fekete RA, Giulian G, Merril C, Nagashima K, Adhya S (2006) High-sensitivity bacterial detection using biotin-tagged phage and quantum-dot nanocomplexes. Proc Natl Acad Sci U S A 103(13): 4841–4845

    Article  CAS  Google Scholar 

  • Fierer N (2017) Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol 15(10):579

    Article  CAS  PubMed  Google Scholar 

  • Frankowski J, Lorito M, Scala F, Schmid R, Berg G, Bahl H (2001) Purification and properties of two chitinolytic enzymes of Serratia plymuthica HRO-C48. Arch Microbiol 176(6):421–426

    Article  CAS  PubMed  Google Scholar 

  • Gajjar P, Pettee B, Britt DW, Huang W, Johnson WP, Anderson AJ (2009) Antimicrobial activities of commercial nanoparticles against an environmental soil microbe, pseudomonas putida KT2440. J Biol Eng 3(1):9

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gallie J, Libby E, Bertels F, Remigi P, Jendresen CB, Ferguson GC, Desprat N, Buffing MF, Sauer U, Beaumont HJ (2015) Bistability in a metabolic network underpins the de novo evolution of colony switching in Pseudomonas fluorescens. PLoS Biol 13(3):e1002109

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Giraldo JP, Landry MP, Faltermeier SM, McNicholas TP, Iverson NM, Boghossian AA, Reuel NF, Hilmer AJ, Sen F, Brew JA (2014) Plant nanobionics approach to augment photosynthesis and biochemical sensing. Nat Mater 13(4):400

    Article  CAS  PubMed  Google Scholar 

  • Giri B, Giang PH, Kumari R, Prasad R, Sachdev M, Garg AP, Oelmuller R, Varma A (2005) Mycorrhizosphere: Strategies and Functions. In: Microorganisms in Soils: Roles in Genesis and Functions. (eds. Buscot F and Varma A), Springer-Verlag, Berlin, Heidelberg, 3:213–252

    Google Scholar 

  • Haney CH, Samuel BS, Bush J, Ausubel FM (2015) Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nat Plants 1(6):15051

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hidalgo G, Burns A, Herz E, Hay AG, Houston PL, Wiesner U, Lion LW (2009) Functional tomographic fluorescence imaging of pH microenvironments in microbial biofilms by use of silica nanoparticle sensors. Appl Environ Microbiol 75(23):7426–7435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Himaja A, Karthik P, Singh SP (2015) Carbon dots: the newest member of the carbon nanomaterials family. Chem Rec 15(3):595–615

    Article  CAS  PubMed  Google Scholar 

  • Hobson N, Tothill I, Turner A (1996) Microbial detection. Biosens Bioelectron 11(5):455–477

    Article  CAS  PubMed  Google Scholar 

  • Indiragandhi P, Anandham R, Madhaiyan M, Sa T (2008) Characterization of plant growth–promoting traits of bacteria isolated from larval guts of diamondback moth Plutella xylostella (Lepidoptera: Plutellidae). Curr Microbiol 56(4):327–333

    Article  CAS  PubMed  Google Scholar 

  • Jha P, Kumar A (2007) Endophytic colonization of Typha australis by a plant growth-promoting bacterium Klebsiella oxytoca strain GR-3. J Appl Microbiol 103(4):1311–1320

    Article  CAS  PubMed  Google Scholar 

  • Jiang C-Y, Sheng X-F, Qian M, Wang Q-Y (2008) Isolation and characterization of a heavy metal-resistant Burkholderia sp. from heavy metal-contaminated paddy field soil and its potential in promoting plant growth and heavy metal accumulation in metal-polluted soil. Chemosphere 72(2):157–164

    Article  CAS  PubMed  Google Scholar 

  • Johnsen K, Jacobsen CS, Torsvik V, Sørensen J (2001) Pesticide effects on bacterial diversity in agricultural soils–a review. Biol Fertil Soils 33(6):443–453

    Article  CAS  Google Scholar 

  • Kaittanis C, Naser SA, Perez JM (2007) One-step, nanoparticle-mediated bacterial detection with magnetic relaxation. Nano Lett 7(2):380–383

    Article  CAS  PubMed  Google Scholar 

  • Kaittanis C, Santra S, Perez JM (2010) Emerging nanotechnology-based strategies for the identification of microbial pathogenesis. Adv Drug Delivery Rev 62(4–5):408–423

    Article  CAS  Google Scholar 

  • Kamal S, Prasad R, Varma A (2010) Soil microbial diversity in relation to heavy metals. In: Soil Heavy Metals (eds. Sherameti I and Varma A) Springer-Verlag, Berlin, Heidelberg, 19:31–64

    Google Scholar 

  • Kim YC, Jung H, Kim KY, Park SK (2008) An effective biocontrol bioformulation against Phytophthora blight of pepper using growth mixtures of combined chitinolytic bacteria under different field conditions. Eur J Plant Pathol 120(4):373–382

    Article  Google Scholar 

  • Kim JY, Voznyy O, Zhitomirsky D, Sargent EH (2013) 25th anniversary article: colloidal quantum dot materials and devices: a quarter-century of advances. Adv Mater 25(36):4986–5010

    Article  CAS  PubMed  Google Scholar 

  • Kivirand K, Kagan M, Rinken T (2015) Biosensors for the detection of antibiotic residues in milk. InBiosensors-micro and nanoscale applications 2015. InTech. https://doi.org/10.5772/60464

    Google Scholar 

  • Kloepper JW (1978) Plant growth-promoting rhizobacteria on radishes. In: Proceedings of the 4th international conference on plant pathogenic bacteria, Station de Pathologie Vegetale et Phytobacteriologie, INRA, Angers, France, pp 879–882

    Google Scholar 

  • Kloepper JW (1994) Plant growth-promoting rhizobacteria (other systems). Azospirillum/Plant Assoc 187:137–166

    Google Scholar 

  • Kulp T, Hoeft S, Asao M, Madigan M, Hollibaugh J, Fisher J, Stolz J, Culbertson C, Miller L, Oremland R (2008) Arsenic (III) fuels anoxygenic photosynthesis in hot spring biofilms from Mono Lake, California. Science 321(5891):967–970

    Article  CAS  PubMed  Google Scholar 

  • Kumar KV, Singh N, Behl H, Srivastava S (2008) Influence of plant growth promoting bacteria and its mutant on heavy metal toxicity in Brassica juncea grown in fly ash amended soil. Chemosphere 72(4):678–683

    Article  CAS  PubMed  Google Scholar 

  • Kurt H, Yüce M, Hussain B, Budak H (2016) Dual-excitation upconverting nanoparticle and quantum dot aptasensor for multiplexed food pathogen detection. Biosens Bioelectron 81:280–286

    Article  CAS  PubMed  Google Scholar 

  • Kwak S-Y, Wong MH, Lew TTS, Bisker G, Lee MA, Kaplan A, Dong J, Liu AT, Koman VB, Sinclair R (2017) Nanosensor technology applied to living plant systems. Annu Rev Anal Chem 10:113–140

    Article  Google Scholar 

  • Li Y, Li H (2014) Type IV pili of Acidithiobacillus ferrooxidans can transfer electrons from extracellular electron donors. J Basic Microbiol 54(3):226–231

    Article  CAS  PubMed  Google Scholar 

  • Liesack W, Weyland H, Stackebrandt E (1991) Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. Microb Ecol 21(1):191–198

    Article  CAS  PubMed  Google Scholar 

  • Lim JW, Ha D, Lee J, Lee SK, Kim T (2015) Review of micro/nanotechnologies for microbial biosensors. Front Bioeng Biotechnol 3:61

    Article  PubMed  PubMed Central  Google Scholar 

  • Lovley DR (2017) Happy together: microbial communities that hook up to swap electrons. ISME J 11(2):327

    Article  CAS  PubMed  Google Scholar 

  • Ma Y, Jiao K, Yang T, Sun D (2008) Sensitive PAT gene sequence detection by nano-SiO2/p-aminothiophenol self-assembled films DNA electrochemical biosensor based on impedance measurement. Sens Actuators B Chem 131(2):565–571

    Article  CAS  Google Scholar 

  • Ma Y, Rajkumar M, Vicente J, Freitas H (2010) Inoculation of Ni-resistant plant growth promoting bacterium Psychrobacter sp. strain SRS8 for the improvement of nickel phytoextraction by energy crops. Int J Phytoremediation 13(2):126–139

    Article  CAS  Google Scholar 

  • Ma Y, Rajkumar M, Luo Y, Freitas H (2011) Inoculation of endophytic bacteria on host and non-host plants—effects on plant growth and Ni uptake. J Hazard Mater 195:230–237

    Article  CAS  PubMed  Google Scholar 

  • Mahmoudi M, Serpooshan V (2012) Silver-coated engineered magnetic nanoparticles are promising for the success in the fight against antibacterial resistance threat. ACS Nano 6(3):2656–2664

    Article  CAS  PubMed  Google Scholar 

  • Maki WC, Mishra NN, Cameron EG, Filanoski B, Rastogi SK, Maki GK (2008) Nanowire-transistor based ultra-sensitive DNA methylation detection. Biosens Bioelectron 23(6):780–787

    Article  CAS  PubMed  Google Scholar 

  • Mao X, Yang L, Su X-L, Li Y (2006) A nanoparticle amplification based quartz crystal microbalance DNA sensor for detection of Escherichia coli O157: H7. Biosens Bioelectron 21(7):1178–1185

    Article  CAS  PubMed  Google Scholar 

  • Martínez-Viveros O, Jorquera M, Crowley D, Gajardo G, Mora M (2010) Mechanisms and practical considerations involved in plant growth promotion by rhizobacteria. J Soil Sci Plant Nutr 10(3):293–319

    Article  Google Scholar 

  • Mauchline TH, Malone JG (2017) Life in earth–the root microbiome to the rescue? Curr Opin Microbiol 37:23–28

    Article  PubMed  Google Scholar 

  • Mauchline T, Chedom-Fotso D, Chandra G, Samuels T, Greenaway N, Backhaus A, McMillan V, Canning G, Powers S, Hammond-Kosack K (2015) An analysis of P seudomonas genomic diversity in take-all infected wheat fields reveals the lasting impact of wheat cultivars on the soil microbiota. Environ Microbiol 17(11):4764–4778

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mayak S, Tirosh T, Glick B (1999) Effect of wild-type and mutant plant growth-promoting rhizobacteria on the rooting of mung bean cuttings. J Plant Growth Regul 18(2):49–53

    Article  CAS  PubMed  Google Scholar 

  • Maye MM, Gang O, Cotlet M (2010) Photoluminescence enhancement in CdSe/ZnS–DNA linked–Au nanoparticle heterodimers probed by single molecule spectroscopy. Chem Commun 46(33):6111–6113

    Article  CAS  Google Scholar 

  • McKenzie F, Faulds K, Graham D (2007) Sequence-specific DNA detection using high-affinity LNA-functionalized gold nanoparticles. Small 3(11):1866–1868

    Article  CAS  PubMed  Google Scholar 

  • Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37(5):634–663

    Article  CAS  PubMed  Google Scholar 

  • Moyano DF, Rotello VM (2011) Nano meets biology: structure and function at the nanoparticle interface. Langmuir 27(17):10376–10385

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mueller UG, Sachs JL (2015) Engineering microbiomes to improve plant and animal health. Trends Microbiol 23(10):606–617

    Article  CAS  PubMed  Google Scholar 

  • Nannipieri P, Ascher J, Ceccherini M, Landi L, Pietramellara G, Renella G (2003) Microbial diversity and soil functions. Eur J Soil Sci 54(4):655–670

    Article  Google Scholar 

  • Nel AE, Mädler L, Velegol D, Xia T, Hoek EM, Somasundaran P, Klaessig F, Castranova V, Thompson M (2009) Understanding biophysicochemical interactions at the nano–bio interface. Nat Mater 8(7):543

    Article  CAS  PubMed  Google Scholar 

  • Noel TC, Sheng C, Yost C, Pharis R, Hynes M (1996) Rhizobium leguminosarum as a plant growth-promoting rhizobacterium: direct growth promotion of canola and lettuce. Can J Microbiol 42(3):279–283

    Article  CAS  PubMed  Google Scholar 

  • Pal S, Tak YK, Song JM (2007) Does the antibacterial activity of silver nanoparticles depend on the shape of the nanoparticle? A study of the gram-negative bacterium Escherichia coli. Appl Environ Microbiol 73(6):1712–1720

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parejko JA, Mavrodi DV, Mavrodi OV, Weller DM, Thomashow LS (2012) Population structure and diversity of phenazine-1-carboxylic acid producing fluorescent Pseudomonas spp. from dryland cereal fields of Central Washington State (USA). Microb Ecol 64(1):226–241

    Article  PubMed  Google Scholar 

  • Park S, Worobo RW, Durst RA (1999) Escherichia coli O157: H7 as an emerging foodborne pathogen: a literature review. Crit Rev Food Sci Nutr 39(6):481–502

    Article  CAS  PubMed  Google Scholar 

  • Petrov A, Audette GF (2012) Peptide and protein-based nanotubes for nanobiotechnology. Wiley Interdiscip Rev Nanomed Nanobiotechnol 4(5):575–585

    Article  CAS  PubMed  Google Scholar 

  • Phi Q-T, Park Y-M, Seul K-J, Ryu C-M, Park S-H, Kim J-G, Ghim S-Y (2010) Assessment of root-associated Paenibacillus polymyxa groups on growth promotion and induced systemic resistance in pepper. J Microbiol Biotechnol 20(12):1605–1613

    CAS  PubMed  Google Scholar 

  • Picard C, Ponsonnet C, Paget E, Nesme X, Simonet P (1992) Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl Environ Microbiol 58(9):2717–2722

    CAS  PubMed  PubMed Central  Google Scholar 

  • Prasad R (2014) Synthesis of silver nanoparticles in photosynthetic plants. J Nanopart:963961. https://doi.org/10.1155/2014/963961

    Article  CAS  Google Scholar 

  • Prasad R, Kumar V, Prasad KS (2014) Nanotechnology in sustainable agriculture: present concerns and future aspects. Afr J Biotechnol 13(6):705–713

    Article  CAS  Google Scholar 

  • Prasad R, Kumar M, Varma A (2015) Role of PGPR in soil fertility and plant health. In: Egamberdieva D, Shrivastava S, Varma A (eds) Plant growth-promoting rhizobacteria (PGPR) and medicinal plants. Springer, Switzerland, pp 247–260

    Google Scholar 

  • Prasad R, Pandey R, Barman I (2016) Engineering tailored nanoparticles with microbes: quo vadis. Wiley Interdiscip Rev Nanomed Nanobiotechnol 8:316–330. https://doi.org/10.1002/wnan.1363

    PubMed  Google Scholar 

  • Prasad R, Bhattacharyya A, Nguyen QD (2017a) Nanotechnology in sustainable agriculture: recent developments, challenges, and perspectives. Front Microbiol 8:1014. https://doi.org/10.3389/fmicb.2017.01014

  • Prasad R, Kumar M, Kumar V (2017b) Nanotechnology: an agriculture paradigm. Springer Nature, Singapore. isbn:978-981-10-4678-0

    Google Scholar 

  • Prasad R, Jha A, Prasad K (2018) Exploring the realms of nature for nanosynthesis. Springer International Publishing. https://www.springer.com/978-3-319-99570-0. isbn:978-3-319-99570-0

  • Raaijmakers JM, Paulitz TC, Steinberg C, Alabouvette C, Moënne-Loccoz Y (2009) The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil 321(1–2):341–361

    Article  CAS  Google Scholar 

  • Rabbi SMF, Daniel H, Lockwood PV, Macdonald C, Pereg L, Tighe M, Wilson BR, Young IM (2016) Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity. Sci Rep 6:33012

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rai M, Ingle A (2012) Role of nanotechnology in agriculture with special reference to management of insect pests. Appl Microbiol Biotechnol 94(2):287–293

    Article  CAS  PubMed  Google Scholar 

  • Rai V, Acharya S, Dey N (2012) Implications of nanobiosensors in agriculture. J Biomater Nanobiotechnol 3(2A):315

    Article  CAS  Google Scholar 

  • Rajkumar M, Freitas H (2008) Effects of inoculation of plant-growth promoting bacteria on Ni uptake by Indian mustard. Bioresour Technol 99(9):3491–3498

    Article  CAS  PubMed  Google Scholar 

  • Ravindranath SP, Mauer LJ, Deb-Roy C, Irudayaraj J (2009) Biofunctionalized magnetic nanoparticle integrated mid-infrared pathogen sensor for food matrixes. Anal Chem 81(8):2840–2846

    Article  CAS  PubMed  Google Scholar 

  • Reches M, Gazit E (2003) Casting metal nanowires within discrete self-assembled peptide nanotubes. Science 300(5619):625–627

    Article  CAS  PubMed  Google Scholar 

  • Reguera G, McCarthy KD, Mehta T, Nicoll JS, Tuominen MT, Lovley DR (2005) Extracellular electron transfer via microbial nanowires. Nature 435(7045):1098

    Article  CAS  PubMed  Google Scholar 

  • Rodrigues EP, Rodrigues LS, de Oliveira ALM, Baldani VLD, dos Santos Teixeira KR, Urquiaga S, Reis VM (2008) Azospirillum amazonense inoculation: effects on growth, yield and N 2 fixation of rice (Oryza sativa L.). Plant Soil 302(1–2):249–261

    Article  CAS  Google Scholar 

  • Rokhbakhsh-Zamin F, Sachdev D, Kazemi-Pour N, Engineer A, Pardesi KR, Zinjarde S, Dhakephalkar PK, Chopade BA (2011) Characterization of plant-growth-promoting traits of Acinetobacter species isolated from rhizosphere of Pennisetum glaucum. J Microbiol Biotechnol 21(6):556–566

    PubMed  Google Scholar 

  • Rosenman G, Beker P, Koren I, Yevnin M, Bank-Srour B, Mishina E, Semin S (2011) Bioinspired peptide nanotubes: deposition technology, basic physics and nanotechnology applications. J Pept Sci 17(2):75–87

    Article  CAS  PubMed  Google Scholar 

  • Ruamps LS, Nunan N, Pouteau V, Leloup J, Raynaud X, Roy V, Chenu C (2013) Regulation of soil organic C mineralisation at the pore scale. FEMS Microbiol Ecol 86(1):26–35

    Article  CAS  PubMed  Google Scholar 

  • Saha K, Agasti SS, Kim C, Li X, Rotello VM (2012) Gold nanoparticles in chemical and biological sensing. Chem Rev 112(5):2739–2779

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sangeetha J, Thangadurai D, Hospet R, Harish ER, Purushotham P, Mujeeb MA, Shrinivas J, David M, Mundaragi AC, Thimmappa AC, Arakera SB, Prasad R (2017) Nanoagrotechnology for soil quality, crop performance and environmental management. In: Prasad R, Kumar M, Kumar V (eds) Nanotechnology. Springer Nature Singapore Pte Ltd, pp 73–97

    Google Scholar 

  • Saravanakumar D, Vijayakumar C, Kumar N, Samiyappan R (2007) PGPR-induced defense responses in the tea plant against blister blight disease. Crop Prot 26(4):556–565

    Article  Google Scholar 

  • Saravanan V, Madhaiyan M, Thangaraju M (2007) Solubilization of zinc compounds by the diazotrophic, plant growth promoting bacterium Gluconacetobacter diazotrophicus. Chemosphere 66(9):1794–1798

    Article  CAS  PubMed  Google Scholar 

  • Scanlon S, Aggeli A (2008) Self-assembling peptide nanotubes. Nano Today 3(3–4):22–30

    Article  CAS  Google Scholar 

  • Schmidt H, Eickhorst T (2014) Detection and quantification of native microbial populations on soil-grown rice roots by catalyzed reporter deposition-fluorescence in situ hybridization. FEMS Microbiol Ecol 87(2):390–402

    Article  CAS  PubMed  Google Scholar 

  • Sebastianelli A, Sen T, Bruce IJ (2008) Extraction of DNA from soil using nanoparticles by magnetic bioseparation. Lett Appl Microbiol 46(4):488–491

    Article  CAS  PubMed  Google Scholar 

  • Selvakumar G, Mohan M, Kundu S, Gupta A, Joshi P, Nazim S, Gupta H (2008) Cold tolerance and plant growth promotion potential of Serratia marcescens strain SRM (MTCC 8708) isolated from flowers of summer squash (Cucurbita pepo). Lett Appl Microbiol 46(2):171–175

    Article  CAS  PubMed  Google Scholar 

  • Sheng X-F, Xia J-J (2006) Improvement of rape (Brassica napus) plant growth and cadmium uptake by cadmium-resistant bacteria. Chemosphere 64(6):1036–1042

    Article  CAS  PubMed  Google Scholar 

  • Shrivastava S, Prasad R, Varma A (2014) Anatomy of root from eyes of a microbiologist. In: Morte A, Varma A (eds) Root engineering, vol 40. Springer, Berlin\Heidelberg, pp 3–22

    Chapter  Google Scholar 

  • Singh PP, Shin YC, Park CS, Chung YR (1999) Biological control of Fusarium wilt of cucumber by chitinolytic bacteria. Phytopathology 89(1):92–99

    Article  CAS  PubMed  Google Scholar 

  • Singh AK, Senapati D, Wang S, Griffin J, Neely A, Naylor KM, Varisli B, Kalluri JR, Ray PC (2009) Gold nanorod based selective identification of Escherichia coli bacteria using two-photon Rayleigh scattering spectroscopy. ACS Nano 3(7):1906–1912

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singh S, Singh M, Agrawal VV, Kumar A (2010) An attempt to develop surface plasmon resonance based immunosensor for Karnal bunt (Tilletia indica) diagnosis based on the experience of nano-gold based lateral flow immuno-dipstick test. Thin Solid Films 519(3):1156–1159

    Article  CAS  Google Scholar 

  • Singh D, Raina TK, Kumar A, Singh J, Prasad R (2019) Plant microbiome: A reservoir of novel genes and metabolites. Plant Gene. https://doi.org/10.1016/j.plgene.2019.100177

    Article  CAS  Google Scholar 

  • Slomberg DL, Lu Y, Broadnax AD, Hunter RA, Carpenter AW, Schoenfisch MH (2013) Role of size and shape on biofilm eradication for nitric oxide-releasing silica nanoparticles. ACS Appl Mater Interfaces 5(19):9322–9329

    Article  CAS  PubMed  Google Scholar 

  • Sure S, Ackland ML, Gaur A, Gupta P, Adholeya A, Kochar M (2016a) Probing synechocystis-arsenic interactions through extracellular nanowires. Front Microbiol 7:1134

    Article  PubMed  PubMed Central  Google Scholar 

  • Sure S, Ackland ML, Torriero AAJ, Adholeya A, Kochar M (2016b) Microbial nanowires: an electrifying tale. Microbiology 162:2017–2028

    Article  CAS  PubMed  Google Scholar 

  • Sutarlie L, Ow SY, Su X (2017) Nanomaterials-based biosensors for detection of microorganisms and microbial toxins. Biotechnol J 12(4): 1500459.

    Google Scholar 

  • Tank N, Saraf M (2009) Enhancement of plant growth and decontamination of nickel-spiked soil using PGPR. J Basic Microbiol 49(2):195–204

    Article  CAS  PubMed  Google Scholar 

  • Taton TA, Mirkin CA, Letsinger RL (2000) Scanometric DNA array detection with nanoparticle probes. Science 289(5485):1757–1760

    Article  CAS  PubMed  Google Scholar 

  • Taton TA, Lu G, Mirkin CA (2001) Two-color labeling of oligonucleotide arrays via size-selective scattering of nanoparticle probes. J Am Chem Soc 123(21):5164–5165

    Article  CAS  PubMed  Google Scholar 

  • Tiedje J, Cho J, Murray A, Treves D, Xia B, Zhou J (2001) Soil teeming with life: new frontiers for soil science. In: Sustainable management of soil organic matter. CABI Int’l, Wallingford, pp 393–412

    Chapter  Google Scholar 

  • Torsvik V (1994) Use of DNA analysis to determine the diversity of microbial communities. In: Beyond the biomass: compositional and functional analysis of soil microbial communities, Wiley-VCH, pp 39–48

    Google Scholar 

  • Torsvik V, Sørheim R, Goksøyr J (1996) Total bacterial diversity in soil and sediment communities—a review. J Ind Microbiol 17(3–4):170–178

    CAS  Google Scholar 

  • Tsavkelova E, Cherdyntseva T, Netrusov A (2005) Auxin production by bacteria associated with orchid roots. Microbiology 74(1):46–53

    Article  CAS  Google Scholar 

  • Uslu B, Ozkan SA (2007) Electroanalytical application of carbon based electrodes to the pharmaceuticals. Anal Lett 40(5):817–853

    Article  CAS  Google Scholar 

  • Verma A, Stellacci F (2010) Effect of surface properties on nanoparticle–cell interactions. Small 6(1):12–21

    Article  CAS  PubMed  Google Scholar 

  • Verma A, Kukreja K, Pathak D, Suneja S, Narula N (2001) In vitro production of plant growth regulators (PGRs) by. Indian J Microbiol 41:305–307

    Google Scholar 

  • Verma MS, Chen PZ, Jones L, Gu FX (2014) “Chemical nose” for the visual identification of emerging ocular pathogens using gold nanostars. Biosens Bioelectron 61:386–390

    Article  CAS  PubMed  Google Scholar 

  • Verma MS, Wei S-C, Rogowski JL, Tsuji JM, Chen PZ, Lin C-W, Jones L, Gu FX (2016) Interactions between bacterial surface and nanoparticles govern the performance of “chemical nose” biosensors. Biosens Bioelectron 83:115–125

    Article  CAS  PubMed  Google Scholar 

  • Vessey JK (2003) Plant growth promoting rhizobacteria as biofertilizers. Plant Soil 255(2):571–586

    Article  CAS  Google Scholar 

  • Vivas A, Biro B, Ruiz-Lozano J, Barea J, Azcon R (2006) Two bacterial strains isolated from a Zn-polluted soil enhance plant growth and mycorrhizal efficiency under Zn-toxicity. Chemosphere 62(9):1523–1533

    Article  CAS  PubMed  Google Scholar 

  • Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev Microbiol 10(12):828

    Article  CAS  PubMed  Google Scholar 

  • Walker TS, Bais HP, Grotewold E, Vivanco JM (2003) Root exudation and rhizosphere biology. Plant Physiol 132(1):44–51

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wani P, Khan M, Zaidi A (2007) Co-inoculation of nitrogen-fixing and phosphate-solubilizing bacteria to promote growth, yield and nutrient uptake in chickpea. Acta Agron Hung 55(3):315–323

    Article  CAS  Google Scholar 

  • Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, Barnstead M, Beeson KY, Bibbs L, Bolanos R, Keller M (2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci 100(22):12984–12988

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu CH, Wood TK, Mulchandani A, Chen W (2006) Engineering plant-microbe symbiosis for rhizoremediation of heavy metals. Appl Environ Microbiol 72(2):1129–1134

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu S, Duan N, Shi Z, Fang C, Wang Z (2014) Simultaneous aptasensor for multiplex pathogenic bacteria detection based on multicolor upconversion nanoparticles labels. Anal Chem 86(6):3100–3107

    Article  CAS  PubMed  Google Scholar 

  • Zahir Z, Shah MK, Naveed M, Akhter MJ (2010) Substrate-dependent auxin production by Rhizobium phaseoli improves the growth and yield of Vigna radiata L. under salt stress conditions. J Microbiol Biotechnol 20(9):1288–1294

    Article  CAS  PubMed  Google Scholar 

  • Zhang W, Yang T, Huang D, Jiao K, Li G (2008a) Synergistic effects of nano-ZnO/multi-walled carbon nanotubes/chitosan nanocomposite membrane for the sensitive detection of sequence-specific of PAT gene and PCR amplification of NOS gene. J Membr Sci 325(1):245–251

    Article  CAS  Google Scholar 

  • Zhang W, Yang T, Huang DM, Jiao K (2008b) Electrochemical sensing of DNA immobilization and hybridization based on carbon nanotubes/nano zinc oxide/chitosan composite film. Chin Chem Lett 19(5):589–591

    Article  CAS  Google Scholar 

  • Zhu N, Chang Z, He P, Fang Y (2005) Electrochemical DNA biosensors based on platinum nanoparticles combined carbon nanotubes. Anal Chim Acta 545(1):21–26

    Article  CAS  Google Scholar 

  • Ziegler C, Göpel W (1998) Biosensor development. Curr Opin Chem Biol 2(5):585–591

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, TERI Gram, Gwal Pahari, Gurugram Faridabad Road, Gurugram, Haryana, India

    Poonam Sashidhar, Mukul Kumar Dubey & Mandira Kochar

Authors
  1. Poonam Sashidhar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mukul Kumar Dubey
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mandira Kochar
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mandira Kochar .

Editor information

Editors and Affiliations

  1. Amity Institute of Microbial Technology, Amity University, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China, Noida, Uttar Pradesh, India

    Ram Prasad

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Sashidhar, P., Dubey, M.K., Kochar, M. (2019). Sensing Soil Microbes and Interactions: How Can Nanomaterials Help?. In: Prasad, R. (eds) Microbial Nanobionics. Nanotechnology in the Life Sciences. Springer, Cham. https://doi.org/10.1007/978-3-030-16534-5_11

Download citation

Publish with us

Policies and ethics

Search

Navigation