Nitrogen-Fixing Archaea and Sustainable Agriculture

  • Chapter
  • First Online:
Nitrogen Fixing Bacteria: Sustainable Growth of Non-legumes

Abstract

Whether free-living or symbiotic, diazotrophic microorganisms are the main and only source of nitrogen fixation and utilization in different biotic systems. The fixed nitrogen is an important component in various anabolic processes of many macromolecules, which are important to the cell in terms of structure and function. The most famous and specialized in nitrogen fixation are the root nodule bacteria, but other types of free-living bacteria and Archaea can fix nitrogen and enrich their environment with this important element. Archaea are a significant division of life forms, abundant in both severe and normal habitats; little attention has been paid to them as an integrated component of various metabolic processes of the plant microbiome. The employment of these microorganisms in agriculture replacing or at least decreasing the input of chemical fertilizers is one of the most important proposals for sustainable agriculture particularly for nonleguminous plants. This chapter is focusing on Archaea as plant growth promoters with special emphasis on their role in nitrogen fixation.

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

Access this chapter

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Alori ET, Emmanuel OC, Glick BR, Babalola OO (2020) Plant–archaea relationships: a potential means to improve crop production in arid and semi-arid regions. World J Microbiol Biotechnol 36(9):1–10

    Article  Google Scholar 

  • Bae H-S, Morrison E, Chanton JP, Ogram A (2018) Methanogens are major contributors to nitrogen fixation in soils of the Florida Everglades. Appl Environ Microbiol 84(7):e02222–e02217

    Article  PubMed  PubMed Central  Google Scholar 

  • Bloom AJ (2015) The increasing importance of distinguishing among plant nitrogen sources. Curr Opin Plant Biol 25:10–16

    Article  CAS  PubMed  Google Scholar 

  • Borrel G, Brugère JF, Gribaldo S, Schmitz RA, Moissl-Eichinger C (2020) The host-associated archaeome. Nat Rev Microbiol 18(11):622–636

    Article  CAS  PubMed  Google Scholar 

  • Boyd E, Anbar A, Miller S, Hamilton T, Lavin M, Peters J (2011) A late methanogen origin for molybdenum-dependent nitrogenase. Geobiology 9(3):221–232

    Article  CAS  PubMed  Google Scholar 

  • Brockwell J, Bottomley PJ (1995) Recent advances in inoculant technology and prospects for the future. Soil Biol Biochem 27(4):683–697

    Article  CAS  Google Scholar 

  • Cabello P, Roldan MD, Moreno-Vivian C (2004) Nitrate reduction and the nitrogen cycle in archaea. Microbiology 150(11):3527–3546

    Article  CAS  PubMed  Google Scholar 

  • Chelius M, Triplett E (2001) The diversity of archaea and bacteria in association with the roots of Zea mays L. Microb Ecol 41(3):252–263

    Article  CAS  PubMed  Google Scholar 

  • Dave BP, Anshuman K, Hajela P (2006) Siderophores of halophilic archaea and their chemical characterization. Int J Exp Biol 44(4):340–344

    CAS  Google Scholar 

  • De Bruijn FJ (2015) Biological nitrogen fixation. In: Lugtenberg B (ed) Principles of plant-microbe interactions. Springer, Cham

    Google Scholar 

  • Dent D, Cocking E (2017) Establishing symbiotic nitrogen fixation in cereals and other non-legume crops: the greener nitrogen revolution. Agric Food Sec 6(1):7

    Article  Google Scholar 

  • Dhakephalkar PK, Prakash O, Lanjekar VB, Tukdeo MP, Ranade DR (2019) Methanogens for human welfare: more boon than bane. In: Satyanarayana T, Das S, Johri B (eds) Microbial diversity in ecosystem sustainability and biotechnological applications. Springer, Singapore, pp 565–591

    Chapter  Google Scholar 

  • Dubey G, Kollah B, Gour VK, Shukla AK, Mohanty SR (2016) Diversity of bacteria and archaea in the rhizosphere of bioenergy crop Jatropha curcas. 3 Biotech 6(2):1–10

    Article  Google Scholar 

  • Fleischman D, Kramer D (1998) Photosynthetic rhizobia. Biochim Biophys Acta Bioenerg 1364(1):17–36

    Article  CAS  Google Scholar 

  • Galloway JN, Townsend AR, Erisman JW, Bekunda M, Cai Z, Freney JR, Martinelli LA, Seitzinger SP, Sutton MA (2008) Transformation of the nitrogen cycle: recent trends, questions, and potential solutions. Science 320(5878):889–892

    Article  CAS  PubMed  Google Scholar 

  • Großkopf R, Stubner S, Liesack W (1998) Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl Environ Microbiol 64(12):4983–4989

    Article  PubMed Central  Google Scholar 

  • Hecht U, Mohr H (1990) Factors controlling nitrate and ammonium accumulation in mustard (Sinapis alba) seedlings. Physiol Plant 78(3):379–387

    Article  CAS  Google Scholar 

  • He Y, Hu W, Ma D, Lan H, Yang Y, Gao Y (2017) Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland. Canadian J Microbiol 63(7):573–582

    Article  CAS  Google Scholar 

  • Hemerly A (2016) Genetic controls of biomass increase in sugarcane by association with beneficial nitrogen-fixing bacteria. In: Plant and animal genome XXIV conference. Plant and animal genome.

    Google Scholar 

  • Herridge DF, Peoples MB, Boddey RM (2008) Global inputs of biological nitrogen fixation in agricultural systems. Plant Soil 311(1–2):1–18

    Article  CAS  Google Scholar 

  • Im YJ, Ji M, Lee A, Killens R, Grunden AM, Boss WF (2009) Expression of Pyrococcus furiosus superoxide reductase in Arabidopsis enhances heat tolerance. Plant Physiol 151(2):893–904

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kaschuk G, Hungria M (2017) Diversity and importance of diazotrophic bacteria to agricultural sustainability in the tropics. In: De Azevedo JL, Quecine MC (eds) Diversity and benefits of microorganisms from the tropics. Springer, Cham, pp 269–292

    Chapter  Google Scholar 

  • Kaur B, Kaur G, Asthir B (2017) Biochemical aspects of nitrogen use efficiency: an overview. J Plant Nutr 40(4):506–523

    Article  CAS  Google Scholar 

  • Knief C, Delmotte N, Chaffron S, Stark M, Innerebner G, Wassmann R, Von Mering C, Vorholt JA (2012) Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J 6(7):1378–1390

    Article  CAS  PubMed  Google Scholar 

  • Leigh JA (2000) Nitrogen fixation in methanogens: the archaeal perspective. Curr Issues Mol Biol 2(4):125–131

    CAS  PubMed  Google Scholar 

  • Liu Y, Li H, Liu QF, Li YH (2015) Archaeal communities associated with roots of the common reed (Phragmites australis) in Bei**g Cuihu wetland. World J Microbiol Biotechnol 31(5):823–832

    Article  PubMed  Google Scholar 

  • Ma M, Du H, Sun T, An S, Yang G, Wang D (2019) Characteristics of archaea and bacteria in rice rhizosphere along a mercury gradient. Sci Total Environ 650:1640–1651

    Article  CAS  PubMed  Google Scholar 

  • MacLeod F, Kindler GS, Wong HL, Chen R, Burns BP (2019) Asgard archaea: diversity, function, and evolutionary implications in a range of microbiomes. AIMS Microbiol 5(1):48

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meena VS, Meena SK, Verma JP, Kumar A, Aeron A, Mishra PK, Bisht JK, Pattanayak A, Naveed M, Dotaniya M (2017) Plant beneficial rhizospheric microorganism (PBRM) strategies to improve nutrients use efficiency: a review. Ecol Eng 107:8–32

    Article  Google Scholar 

  • Mehta MP, Butterfield DA, Baross JA (2003) Phylogenetic diversity of nitrogenase (nifH) genes in deep-sea and hydrothermal vent environments of the Juan de Fuca Ridge. Appl Environ Microbiol 69(2):960–970

    Article  CAS  PubMed  PubMed Central  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 

  • Miller A, Cramer M (2005) Root nitrogen acquisition and assimilation. Plant Soil 274(1):1–36

    Article  CAS  Google Scholar 

  • Mitsui A, Kumazawa S, Takahashi A, Ikemoto H, Cao S, Arai T (1986) Strategy by which nitrogen-fixing unicellular cyanobacteria grow photoautotrophically. Nature 323(6090):720

    Article  CAS  Google Scholar 

  • Moissl-Eichinger C, Pausan M, Taffner J, Berg G, Bang C, Schmitz RA (2018) Archaea are interactive components of complex microbiomes. Trend Microbiol 26(1):70–85

    Article  CAS  Google Scholar 

  • Mowafy MA, Agha MS, Haroun SA, Abbas MA, Elbalkini M (2022) Insights in nodule-inhabiting plant growth promoting bacteria and their ability to stimulate Vicia faba growth. Egypt J Basic Appl Sci 9(1):51–64

    Google Scholar 

  • Müller H, Berg C, Landa BB, Auerbach A, Moissl-Eichinger C, Berg G (2015) Plant genotype-specific archaeal and bacterial endophytes but similar Bacillus antagonists colonize Mediterranean olive trees. Front Microbiol 6:138

    Article  PubMed  PubMed Central  Google Scholar 

  • Naitam MG, Kaushik R (2021) Archaea: an agro-ecological perspective. Curr Microbiol 78(7):2510–2521

    Article  CAS  PubMed  Google Scholar 

  • Oburger E, Schmidt H (2016) New methods to unravel rhizosphere processes. Trends Plant Sci 21(3):243–255

    Article  CAS  PubMed  Google Scholar 

  • Oliveira MN, Santos TM, Vale HM, Delvaux JC, Cordero AP, Ferreira AB, Miguel PS, Tótola MR, Costa MD, Moraes CA (2013) Endophytic microbial diversity in coffee cherries of Coffea arabica from southeastern Brazil. Can J Microbiol 59(4):221–230

    Article  CAS  PubMed  Google Scholar 

  • Pandey A, Nigam P, Soccol CR, Soccol VT, Singh D, Mohan R (2000) Advances in microbial amylases. Biotechnol Appl Biochem 31(2):135–152

    Article  CAS  PubMed  Google Scholar 

  • Patil J, Suryawanshi P, Bajekal S (2016) Siderophores of haloalkaliphilic archaea from Lonar lake, Maharashtra, India. Cur Sci 111(4):621–623

    CAS  Google Scholar 

  • Pires AC, Cleary DF, Almeida A, Cunha Â, Dealtry S, Mendonça-Hagler LC, Smalla K, Gomes NC (2012) Denaturing gradient gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples. Appl Environ Microbiol 78(16):5520–5528

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peoples M, Freney J, Mosier A (1995a) Minimizing gaseous losses of nitrogen. In: Bacon PE (ed) Nitrogen fertilization in the environment. Marcel Dekker, New York, pp 565–602

    Google Scholar 

  • Peoples M, Herridge D, Ladha JK (1995b) Biological nitrogen fixation: an efficient source of nitrogen for sustainable agricultural production? Plant Soil 174(1-2):3–28

    Article  CAS  Google Scholar 

  • Prudence SM, Worsley S, Balis L, Murrell JC, Lehtovirta-Morley L, Hutchings ML (2019) Root-associated archaea: investigating the niche occupied by ammonia oxidising archaea within the wheat root microbiome. Access Microbiol 1(1A):253

    Article  Google Scholar 

  • Pump J, Pratscher J, Conrad R (2015) Colonization of rice roots with methanogenic archaea controls photosynthesis‐derived methane emission. Environ Microbiol 17(7):2254–2260

    Article  CAS  PubMed  Google Scholar 

  • Qi L, Ma Z, Chang SX, Zhou P, Huang R, Wang Y, Wang Z, Gao M (2021) Biochar decreases methanogenic archaea abundance and methane emissions in a flooded paddy soil. Sci Total Environ 752:141958

    Article  CAS  PubMed  Google Scholar 

  • Rosswall T (1983) The nitrogen cycle. In: Bolin B, Cook RB (eds) The major biogeochemical cycles and their interactions. Wiley, New York, pp 21–46–50

    Google Scholar 

  • Simon HM, Jahn CE, Bergerud LT, Sliwinski MK, Weimer PJ, Willis DK, Goodman RM (2005) Cultivation of mesophilic soil crenarchaeotes in enrichment cultures from plant roots. Appl Environ Microbiol 71(8):4751–4760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Song GC, Im H, Jung J, Lee S, Jung MY, Rhee SK, Ryu CM (2019) Plant growth-promoting archaea trigger induced systemic resistance in Arabidopsis thaliana against Pectobacterium carotovorum and Pseudomonas syringae. Environ Microbiol 21(3):940–948

    Article  CAS  PubMed  Google Scholar 

  • Sun W, Shahrajabian MH, Cheng Q (2021) Nitrogen fixation and diazotrophs—a review. Rom Biotechnol Lett 26:2834–2845

    Article  CAS  Google Scholar 

  • Taffner J, Erlacher A, Bragina A, Berg C, Moissl-Eichinger C, Berg G (2018) What is the role of Archaea in plants? New insights from the vegetation of alpine bogs. MSphere 3(3):e00122-00118

    Article  Google Scholar 

  • Taffner J, Cernava T, Erlacher A, Berg G (2019) Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.). J Adv Res 19:39–48

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Turk KA, Rees AP, Zehr JP, Pereira N, Swift P, Shelley R, Lohan M, Woodward EMS, Gilbert J (2011) Nitrogen fixation and nitrogenase (nifH) expression in tropical waters of the eastern North Atlantic. ISME J 5(7):1201

    Article  CAS  PubMed  Google Scholar 

  • Wang S, Zheng Z, Zou H, Li N, Wu M (2019) Characterization of the secondary metabolite biosynthetic gene clusters in archaea. Comput Biol Chem 78:165–169

    Article  CAS  PubMed  Google Scholar 

  • Wassermann B, Cernava T, Müller H, Berg C, Berg G (2019) Seeds of native alpine plants host unique microbial communities embedded in cross-kingdom networks. Microbiome 7(1):1–12

    Article  Google Scholar 

  • Wenli S, Shahrajabian MH, Cheng Q (2021) Archaea, bacteria and termite, nitrogen fixation and sustainable plants production. Not Bot Horti Agrobot Cluj Napoca 49(2):12172–12172

    Article  Google Scholar 

  • White RH (1987) Indole-3-acetic acid and 2-(indol-3-ylmethyl) indol-3-yl acetic acid in the thermophilic archaebacterium Sulfolobus acidocaldarius. J Bacteriol 169(12):5859–5860

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 74(11):5088–5090

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu F, Speth DR, Philosof A, Crémière A, Narayanan A, Barco RA, Connon SA, Amend JP, Antoshechkin IA, Orphan VJ (2022) Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes. Nat Microbiol 7(2):200–212

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yadav AN, Sharma D, Gulati S, Singh S, Dey R, Pal KK, Kaushik R, Saxena AK (2015) Haloarchaea endowed with phosphorus solubilization attribute implicated in phosphorus cycle. Sci Rep 5(1):1–10

    Article  CAS  Google Scholar 

  • Yadav AN, Verma P, Kaushik R, Dhaliwal H, Saxena A (2017) Archaea endowed with plant growth promoting attributes. EC Microbiol 8(6):294–298

    Google Scholar 

  • Yadav AN, Gulati S, Sharma D, Singh RN, Rajawat MVS, Kumar R, Dey R, Pal KK, Kaushik R, Saxena AK (2019) Seasonal variations in culturable archaea and their plant growth promoting attributes to predict their role in establishment of vegetation in Rann of Kutch. Biologia 74(8):1031–1043

    Article  Google Scholar 

Download references

Acknowledgement

Not applicable.

Conflicts of Interest

The author(s) declares(declare) no conflicts of interest.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Amr M. Mowafy .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Mowafy, A.M. et al. (2022). Nitrogen-Fixing Archaea and Sustainable Agriculture. In: Maheshwari, D.K., Dobhal, R., Dheeman, S. (eds) Nitrogen Fixing Bacteria: Sustainable Growth of Non-legumes. Microorganisms for Sustainability, vol 36. Springer, Singapore. https://doi.org/10.1007/978-981-19-4906-7_6

Download citation

Publish with us

Policies and ethics

Navigation