Skip to main content

Microbiome Applications for Sustainable Food Systems

  • Chapter
  • First Online:
Biodiversity, Functional Ecosystems and Sustainable Food Production

Abstract

The present chapter, which combines theoretical and experimental knowledge, is divided into two parts. The first part provides critical insights to allow scientists to generate discoveries across microbiome applications for sustainable food systems. It offers a broad view of research of interest to early and experienced scientists, as well as an understanding of the role of microbiomes as vital ecosystems and inter-relations among microbiomes across food chains. In the second part of the chapter, the reuse of spent coffee grounds to increase the resilience of agro-food systems is described as an example of a successful application of a microbiome-related intervention.

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

Access this chapter

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

  • Alves, R. C., Rodrigues, F., Nunes, M. A., Vinha, A. F., & Oliveira, M. P. (2017). State of the art in coffee processing by-products. In C. M. Galanakis (Ed.), Handbook of coffee processing by-products: Sustainable applications (pp. 1–22). Academic Press.

    Google Scholar 

  • Aranda, V., Calero, J., Plaza, I., & Ontiveros-Ortega, A. (2016). Long-term effects of olive mill pomace co-compost on wettability and soil quality in olive groves. Geoderma, 267, 185–195.

    Article  CAS  Google Scholar 

  • Arif, I., Batool, M., & Schenk, P. M. (2020). Plant microbiome engineering: Expected benefits for improved crop growth and resilience. Trends in Biotechnology.

    Google Scholar 

  • Ayres, J. S. (2016). Cooperative microbial tolerance behaviors in host-microbiota mutualism. Cell, 165(6), 1323–1331.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ballesteros, L. F., Teixeira, J. A., & Mussatto, S. I. (2014). Chemical, functional, and structural properties of spent coffee grounds and coffee silver skin. Food and Bioprocess Technology, 7, 3493–3503.

    Article  CAS  Google Scholar 

  • Bang, C., Dagan, T., Deines, P., et al. (2018). Metaorganisms in extreme environments: Do microbes play a role in organismal adaptation? Zoology (Jena, Germany), 127, 1–19.

    Article  PubMed  Google Scholar 

  • Belkaid, Y., & Hand, T. W. (2014). Role of the microbiota in immunity and inflammation. Cell, 157(1), 121–141.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bennett, J. M., Reeves, G., Billman, G. E., & Sturmberg, J. P. (2018). Inflammation-nature’s way to efficiently respond to all types of challenges: Implications for understanding and managing “the epidemic” of chronic diseases. Frontiers in Medicine, 5, 316.

    Article  PubMed  PubMed Central  Google Scholar 

  • Berg, G., Rybakova, D., Grube, M., & Köberl, M. (2016). The plant microbiome explored: Implications for experimental botany. Journal of Experimental Botany, 67(4), 995–1002.

    Article  CAS  PubMed  Google Scholar 

  • Berg, G., Rybakova, D., Fischer, D., et al. (2020). Microbiome definition re-visited: Old concepts and new challenges. Microbiome, 8, 103.

    Article  PubMed  PubMed Central  Google Scholar 

  • Blum, W., Zechmeister-Boltenstern, S., & Keiblinger, K. M. (2019). Does soil contribute to the human gut microbiome? Microorganisms, 7(9), 287.

    Article  PubMed  PubMed Central  Google Scholar 

  • Boon, E., Meehan, C. J., Whidden, C., Wong, D. H., Langille, M. G., & Beiko, R. G. (2014). Interactions in the microbiome: Communities of organisms and communities of genes. FEMS Microbiology Reviews, 38(1), 90–118.

    Article  CAS  PubMed  Google Scholar 

  • Borre, Y. E., O’Keeffe, G. W., Clarke, G., Stanton, C., Dinan, T. G., & Cryan, J. F. (2014). Microbiota and neurodevelopmental windows: Implications for brain disorders. Trends in Molecular Medicine, 20(9), 509–518.

    Article  PubMed  Google Scholar 

  • Brodt, S., Six, J., Feenstra, G., Ingels, C., & Campbell, D. (2011). Sustainable agriculture. Nature Education Knowledge, 3(10), 1.

    Google Scholar 

  • Bronick, C. J., & Lal, R. (2005). Soil structure and management: A review. Geoderma, 124, 3–22.

    Article  CAS  Google Scholar 

  • Busby, P. E., Soman, C., Wagner, M. R., Friesen, M. L., Kremer, J., Bennett, A., Morsy, M., Eisen, J. A., Leach, J. E., & Dangl, J. L. (2017). Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biology, 15(3), e2001793.

    Article  PubMed  PubMed Central  Google Scholar 

  • Calicioglu, O., Flammini, A., Bracco, S., Bellù, L., & Sims, R. (2019). The future challenges of food and agriculture: An integrated analysis of trends and solutions. Sustainability, 11, 222.

    Article  Google Scholar 

  • Caron, P., Ferrero y de Loma-Osorio, G., Nabarro, D., et al. (2018). Food systems for sustainable development: Proposals for a profound four-part transformation. Agronomy for Sustainable Development, 38, 41.

    Article  PubMed  PubMed Central  Google Scholar 

  • Cassán, F. D., & Díaz-Zorita, M. (2016). Azosprillum sp. in current agriculture: From the laboratory to the field. Soil Biology and Biochemistry, 103, 117–130.

    Article  Google Scholar 

  • Cavalier-Smith, T., Brasier, M., & Embley, T. M. (2006). Introduction: How and when did microbes change the world? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 361(1470), 845–850.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cavicchioli, R., Ripple, W. J., Timmis, K. N., et al. (2019). Scientists’ warning to humanity: Microorganisms and climate change. Nature Reviews. Microbiology, 17, 569–586.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cervera-Mata, A., Pastoriza, S., Rufián-Henares, J. A., Martín-García, J. M., & Delgado, G. (2017). Impact of spent coffee grounds as organic amendment on soil fertility and lettuce growth in two Mediterranean agricultural soils. Archives of Agronomy and Soil Science, 64, 790–804.

    Article  Google Scholar 

  • Cervera-Mata, A., Martín-García, J., Delgado, R., Sánchez-Marañón, M., & Delgado, G. (2019a). Short-term effects of spent coffee grounds on the physical properties of two Mediterranean agricultural soils. International Agrophysics, 33, 205–216.

    Article  CAS  Google Scholar 

  • Cervera-Mata, A., Navarro-Alarcón, M., Delgado, G., Pastoriza, S., Montilla-Gómez, J., Llopis, J., Sánchez-González, C., & Rufián-Henares, J. A. (2019b). Spent coffee grounds improve the nutritional value in elements of lettuce (Lactuca sativa L.) and are an ecological alternative to inorganic fertilizers. Food Chemistry, 282, 1–8.

    Article  CAS  PubMed  Google Scholar 

  • Cervera-Mata, A., Aranda, V., Ontiveros-Ortega, A., Comino, F., Martín-García, J., Vela-Cano, M., & Delgado, G. (2020a). Hydrophobicity and surface free energy to assess spent coffee grounds as soil amendment. Relationships with soil quality. Catena. In press.

    Google Scholar 

  • Cervera-Mata, A., Navarro-Alarcón, M., Rufián-Henares, J. Á., Pastoriza, S., Montilla-Gómez, J., & Delgado, G. (2020b). Phytotoxicity and chelating capacity of spent coffee grounds: Two contrasting faces in its use as soil organic amendment. Science of the Total Environment, 717, 137247.

    Article  CAS  PubMed  Google Scholar 

  • Chagas, F. O., Pessotti, R. C., Caraballo-Rodríguez, A. M., & Pupo, M. T. (2018). Chemical signaling involved in plant-microbe interactions. Chemical Society Reviews, 47(5), 1652–1704.

    Article  CAS  PubMed  Google Scholar 

  • Checinska Sielaff, A., Urbaniak, C., Mohan, G. B. M., et al. (2019). Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces. Microbiome, 7, 50.

    Article  PubMed  PubMed Central  Google Scholar 

  • Chrysargyris, A., Antoniou, O., Xylia, P. et al. (2020). The use of spent coffee grounds in growing media for the production of Brassica seedlings in nurseries. Environmental Science and Pollution Research

    Google Scholar 

  • Claus, S. P., Guillou, H., & Ellero-Simatos, S. (2016). The gut microbiota: a major player in the toxicity of environmental pollutants? npj Biofilms Microbiomes, 2.

    Google Scholar 

  • Clemente, J. C., Pehrsson, E. C., Blaser, M. J., Sandhu, K., Gao, Z., Wang, B., Magris, M., Hidalgo, G., Contreras, M., Noya-Alarcón, Ó., Lander, O., McDonald, J., Cox, M., Walter, J., Oh, P. L., Ruiz, J. F., Rodriguez, S., Shen, N., Song, S. J., et al. (2015). The microbiome of uncontacted Amerindians. Science Advances, 1, e1500183.

    Article  PubMed  PubMed Central  Google Scholar 

  • Comino, F., Aranda, V., Domínguez-Vidal, A., & Ayora-Cañada, M. J. (2017). Thermal destruction of organic waste hydrophobicity for agricultural soils application. Journal of Environmental Management, 202, 94–105.

    Article  CAS  PubMed  Google Scholar 

  • Comino, F., Cervera-Mata, A., Aranda, V., Martín-García, J. M., & Delgado, G. (2020). Short-term impact of spent coffee grounds over soil organic matter composition and stability in two contrasted Mediterranean agricultural soils. Journal of Soils Sediments, 20, 1182–1198.

    Article  CAS  Google Scholar 

  • Compant, S., Samad, A., Faist, H., & Sessitsch, A. (2019). A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application. Journal of Advanced Research, 19, 29–37.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cordovez, V., Dini-Andreote, F., Carrión, V. J., & Raaijmakers, J. M. (2019). Ecology and evolution of plant microbiomes. Annual Review of Microbiology, 73, 69–88.

    Article  CAS  PubMed  Google Scholar 

  • Ćosović, B., Vojvodić, V., Bošković, N., Plavšić, M., & Lee, C. (2010). Characterization of natural and synthetic humic substances (melanoidins) by chemical composition and adsorption measurements. Organic Geochemistry, 41, 200–205.

    Article  Google Scholar 

  • Crandall, S. G., Gold, K. M., Jiménez-Gasco, M., Filgueiras, C. C., & Willett, D. S. (2020). A multi-omics approach to solving problems in plant disease ecology. PLoS One, 15(9), e0237975.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cruz, R., Baptista, P., Cunha, S., Pereira, J. A., & Casal, S. (2012). Carotenoids of lettuce (Lactuca sativa L.) grown on soil enriched with spent coffee grounds. Molecules, 17, 1535–1547.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cruz, R., Morais, S., Mendes, E., Pereira, J. A., Baptista, P., & Casal, S. (2014). Improvement of vegetables elemental quality by espresso coffee residues. Food Chemistry, 148, 294–299.

    Article  CAS  PubMed  Google Scholar 

  • Cruz, R., Mendes, E., Torrinha, Á., Morais, S., Alberto Pereira, J., Baptista, P., & Casal, S. (2015a). Revalorization of spent coffee residues by a direct agronomic approach. Food Research International, 73, 190–196.

    Article  CAS  Google Scholar 

  • Cruz, S., Sc, C., & Cordovil, S. (2015b). Espresso coffee residues as a nitrogen amendment for small-scale vegetable. Journal of the Science of Food and Agriculture, 95, 3059–3066.

    Article  CAS  PubMed  Google Scholar 

  • Cui, K., Qi, M., Wang, S., et al. (2019). Dietary energy and protein levels influenced the growth performance, ruminal morphology and fermentation and microbial diversity of lambs. Scientific Reports, 9, 16612.

    Article  PubMed  PubMed Central  Google Scholar 

  • D’Abramo, F., & Neumeyer, S. (2020). A historical and political epistemology of microbes. Centaurus, 62(2), 321–330.

    Article  PubMed  PubMed Central  Google Scholar 

  • de Blas, E., Rodríguez-Alleres, M., & Almendros, G. (2010). Speciation of lipid and humic fractions in soils under pine and eucalyptus forest in northwest Spain and its effect on water repellency. Geoderma, 155, 242–248.

    Article  Google Scholar 

  • de Faria, M. R., Costa, L. S. A. S., Chiaramonte, J. B., et al. (2020). The rhizosphere microbiome: Functions, dynamics, and role in plant protection. Tropical Plant Pathology.

    Google Scholar 

  • De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G., & Lionetti, P. (2010). Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences of the United States of America, 107(33), 14691–14696.

    Article  PubMed  PubMed Central  Google Scholar 

  • de Vries, F. T., Griffiths, R. I., Bailey, M., et al. (2018). Soil bacterial networks are less stable under drought than fungal networks. Nature Communications, 9, 3033.

    Article  PubMed  PubMed Central  Google Scholar 

  • Deines, P., & Bosch, T. C. (2016). Transitioning from microbiome composition to microbial community interactions: The potential of the metaorganism Hydra as an xperimental model. Frontiers in Microbiology, 7, 1610.

    Article  PubMed  PubMed Central  Google Scholar 

  • Deng, S., Wipf, H. M., Pierroz, G., et al. (2019). A plant growth-promoting microbial soil amendment dynamically alters the strawberry root bacterial microbiome. Scientific Reports, 9, 17677.

    Article  PubMed  PubMed Central  Google Scholar 

  • Dexter, A. R. (2004). Soil physical quality part I. theory, effects of soil texture, density, and organic matter, and effects on root growth. Geoderma, 120, 201–214.

    Article  Google Scholar 

  • Dietrich, T., Del Carmen Villaran Velasco, M., Echeverría, P. J., Pop, B., & Rusu, A. (2016). Crop and plant biomass as valuable material for BBB. Alternatives for valorization of green wastes. In Biotransformation of agricultural waste and by-products: The food, feed, fibre, fuel (4F) economy.

    Google Scholar 

  • Doerr, S. H., & Thomas, A. D. (2000). The role of soil moisture in controlling water repellency: New evidence from forest soils in Portugal. Journal of Hydrology, 231-232, 134–147.

    Article  Google Scholar 

  • Dunham Trimmer (LLC). (2017). Biological control global market overview. http://wrir4.ucdavis.edu/events/2017_SLR_Meeting/Presentations/GeneralPresentations/1%20Trimmer%20-%20Global%20Biocontrol%20Market%202017.pdf. Accessed 07 Aug 2020.

  • Environmental Protection Agency (EPA). (2010). Inventory of US U.S. greenhouse gas emissions and sinks: 1998–2008. 15 April 2010. EPA. 430-R-10-006. Washington (DC).

    Google Scholar 

  • European Commission. Communication from the Commission to the European Parliament, the Council, the European Economic and Social Committee and the Committee of the Regions A Farm to Fork Strategy for a fair, healthy and environmentally-friendly food system, COM/2020/381 final. https://eur-lex.europa.eu/legal-content/EN/TXT/?qid=1590404602495&uri=CELEX%3A52020DC0381. Accessed 17 Oct 2020.

  • FAO. (2010). Sustainable diets and biodiversity. Directions and solutions for policy, research and action. In Proceedings of the international scientific symposium: Biodiversity and sustainable diets: United against hunger, 3–5 November 2010. Food and Agriculture Organization of the United Nations (FAO).

    Google Scholar 

  • FAO. (2014). SAFA sustainability assessment of food and agriculture systems. Guideline. Version 3.0. http://www.fao.org/3/a-i3957e.pdf

  • FAO. (2015). Healthy soils are the basis for healthy food production. Food and Agriculture Organization of the United Nations [FAO]. pp. 1–4. http://www.fao.org/documents/card/en/c/645883cd-ba28-4b16-a7b8-34babbb3c505/. Accessed 17 Oct 2020.

  • Federal Ministry of Education and Research (BMBF) and Federal Ministry of Food and Agriculture (BMEL). (2015). Bioeconomy in Germany opportunities for a bio-based and sustainable future. https://www.bmbf.de/upload_filestore/pub/Biooekonomie_in_Deutschland_Eng.pdf

  • Flandroy, L., Poutahidis, T., Berg, G., et al. (2018). The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. Science of the Total Environment, 627, 1018–1038.

    Article  CAS  PubMed  Google Scholar 

  • Foo, J. L., Ling, H., Lee, Y. S., & Chang, M. W. (2017). Microbiome engineering: Current applications and its future. Biotechnology Journal, 12(3). https://doi.org/10.1002/biot.201600099

  • Forstner, S., & Rusu, A. (2015). Development of personalised food for the nutrition of elderly consumers. Know your food: Food ethics and innovation (pp. 24–27). Wageningen Academic Publishers.

    Book  Google Scholar 

  • Frąc, M., Hannula, S. E., Bełka, M., & Jędryczka, M. (2018). Fungal biodiversity and their role in soil health. Frontiers in Microbiology, 9, 707.

    Article  PubMed  PubMed Central  Google Scholar 

  • Frische, T., Egerer, S., Matezki, S., et al. (2018). 5-Point programme for sustainable plant protection. Environmental Sciences Europe, 30, 8.

    Article  PubMed  PubMed Central  Google Scholar 

  • Funabashi, M. (2018). Human augmentation of ecosystems: Objectives for food production and science by 2045. Npj Science of Food, 2, 16.

    Article  PubMed  PubMed Central  Google Scholar 

  • Gan, X., Stegle, O., Behr, J., et al. (2011). Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature, 477, 419–423.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Giacometti, C., Demyanb, M. S., Cavania, L., Marzadoria, C., Ciavatta, C., & Kandelerc, E. (2013). Chemical and microbiological soil quality indicators and their potential to differentiate fertilization regimes in temperate agroecosystems. Applied Soil Ecology, 64, 32–48.

    Article  Google Scholar 

  • Global Forum for Food and Agriculture (GFFA). (2019). Agriculture goes digital – Smart solutions for future farming. https://www.gffa-berlin.de/wp-content/uploads/2019/10/ergebnisbroschuere_2019-EN.pdf

  • Godfray, H. C., & Garnett, T. (2014). Food security and sustainable intensification. Philosophical transactions of the Royal Society of London. Series B, Biological Sciences, 369(1639), 20120273.

    Article  PubMed  PubMed Central  Google Scholar 

  • Goebel, M., Bachmann, J., Woche, S. K., & Fischer, W. R. (2005). Soil wettability, aggregate stability, and the decomposition of soil organic matter. Geoderma, 128, 80–93.

    Article  CAS  Google Scholar 

  • Gross, G., Jaccaud, E., & Hugget, A. C. (1997). Analysis of the content of the diterpenes cafestol and kahweol in coffee brews. Food and Chemical Toxicology, 35, 547–554.

    Article  CAS  PubMed  Google Scholar 

  • Guerrieri, A., Dong, L., & Bouwmeester, H. J. (2019). Role and exploitation of underground chemical signaling in plants. Pest Management Science, 75(9), 2455–2463.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Guth, M., & Smędzik-Ambroży, K. (2020). Economic resources versus the efficiency of different types of agricultural production in regions of the European union. Economic Research-Ekonomska Istraživanja, 33(1), 1036–1051.

    Article  Google Scholar 

  • Hachicha, R., Rekik, O., Hachicha, S., Ferchichi, M., Woodward, S., Moncef, N., Cegarra, J., & Mechichi, T. (2012). Chemosphere co-composting of spent coffee ground with olive mill wastewater sludge and poultry manure and effect of Trametes versicolor inoculation on the compost maturity. Chemosphere, 88, 677–682.

    Article  CAS  PubMed  Google Scholar 

  • Hardgrove, S. J., & Livesley, S. J. (2016). Applying spent coffee grounds directly to urban agriculture soils greatly reduces plant growth. Urban Forestry & Urban Greening, 18, 1–8.

    Article  Google Scholar 

  • Hassani, M. A., Durán, P., & Hacquard, S. (2018). Microbial interactions within the plant holobiont. Microbiome, 6(1), 58.

    Article  PubMed  PubMed Central  Google Scholar 

  • Hatfield, J. L., & Dold, C. (2019). Water-use efficiency: Advances and challenges in a changing climate. Frontiers in Plant Science, 10, 103.

    Article  PubMed  PubMed Central  Google Scholar 

  • Heimler, D., Vignolini, P., Arfaioli, P., Isolani, L., & Romani, A. (2012). Conventional, organic and biodynamic farming: Differences in polyphenol content and antioxidant activity of Batavia lettuce. Journal of the Science of Food and Agriculture, 92, 551–556.

    Article  CAS  PubMed  Google Scholar 

  • Hunter, P. (2016). Plant microbiomes and sustainable agriculture: Deciphering the plant microbiome and its role in nutrient supply and plant immunity has great potential to reduce the use of fertilizers and biocides in agriculture. EMBO Reports, 17(12), 1696–1699.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hutchins, D. A., Jansson, J. K., Remais, J. V., Rich, V. I., Singh, B. K., & Trivedi, P. (2019). Climate change microbiology – problems and perspectives. Nature Reviews. Microbiology, 17, 391–396.

    Article  CAS  PubMed  Google Scholar 

  • ICO. (2020). Historical data on the global coffee trade. International Coffee Organization; [accesed 2020 August 09]. http://www.ico.org/new_historical.asp?section=Statistics

    Google Scholar 

  • Jacoby, R., Peukert, M., Succurro, A., Koprivova, A., & Kopriva, S. (2017). The role of soil microorganisms in plant mineral nutrition-current knowledge and future directions. Frontiers in Plant Science, 8, 1617.

    Article  PubMed  PubMed Central  Google Scholar 

  • Jiménez-Zamora, A., Pastoriza, S., & Rufián-Henares, J. A. (2015). Revalorization of coffee by- products. Prebiotic, antimicrobial and antioxidant properties. LWT – food Sci. Technology, 61, 12–18.

    Google Scholar 

  • Jin, Y., Wu, S., Zeng, Z., & Fu, Z. (2017). Effects of environmental pollutants on gut microbiota. Environmental Pollution, 222, 1–9.

    Article  CAS  PubMed  Google Scholar 

  • Kemp, L., Adam, L., Boehm, C. R., Breitling, R., Casagrande, R., Dando, M., Djikeng, A., Evans, N. G., Hammond, R., Hills, K., Holt, L. A., Kuiken, T., Markotić, A., Millett, P., Napier, J. A., Nelson, C., ÓhÉigeartaigh, S. S., Osbourn, A., Palmer, M., et al. (2020). Bioengineering horizon scan 2020. Elife, 9, e54489.

    Article  PubMed  PubMed Central  Google Scholar 

  • Kim, M. S., Min, H. G., Koo, N., Park, J., Lee, S. H., Bak, G. I., & Kim, J. G. (2014). The effectiveness of spent coffee grounds and its biochar on the amelioration of heavy metals-contaminated water and soil using chemical and biological assessments. Journal of Environmental Management, 146, 124–130.

    Article  CAS  PubMed  Google Scholar 

  • Kudoyarova, G., Arkhipova, T., Korshunova, T., Bakaeva, M., Loginov, O., & Dodd, I. C. (2019). Phytohormone mediation of interactions between plants and non-symbiotic growth promoting bacteria under edaphic stresses. Frontiers in Plant Science, 10, 1368.

    Article  PubMed  PubMed Central  Google Scholar 

  • Kumar, M., Ji, B., Zengler, K., et al. (2019). Modelling approaches for studying the microbiome. Nature Microbiology, 4, 1253–1267.

    Article  CAS  PubMed  Google Scholar 

  • Laforest-Lapointe, I., & Arrieta, M. C. (2018). Microbial eukaryotes: a missing link in gut microbiome studies. mSystems, 3(2), e00201–e00217.

    Article  PubMed  PubMed Central  Google Scholar 

  • Lal, R. (2015). Restoring soil quality to mitigate soil degradation. Sustainability, 7, 5875–5895.

    Article  Google Scholar 

  • Lawson, C. E., Harcombe, W. R., Hatzenpichler, R., Lindemann, S. R., Löffler, F. E., O’Malley, M. A., García Martín, H., Pfleger, B. F., Raskin, L., Venturelli, O. S., Weissbrodt, D. G., Noguera, D. R., & McMahon, K. D. (2019). Common principles and best practices for engineering microbiomes. Nature Reviews. Microbiology, 17(12), 725–741.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lindgren, E., Harris, F., Dangour, A. D., et al. (2018). Sustainable food systems—a health perspective. Sustainability Science, 13, 1505–1517.

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu, Y., & Li, Y. (2017). Revitalize the world’s countryside. Nature, 548, 275–277.

    Article  CAS  PubMed  Google Scholar 

  • Liu, W., Baddeley, J., & Watson, C. (2011). Models of biological nitrogen fixation of legumes. Areview. Agronomy for Sustainable Development, Springer Verlag/EDP Sciences/INRA, 31(1), 155–172.

    Article  Google Scholar 

  • Liu, A., Contador, C. A., Fan, K., & Lam, H. M. (2018). Interaction and regulation of carbon, nitrogen, and phosphorus metabolisms in root nodules of legumes. Frontiers in Plant Science, 9, 1860.

    Article  PubMed  PubMed Central  Google Scholar 

  • Longford, S. R., Campbell, A. H., Nielsen, S., et al. (2019). Interactions within the microbiome alter microbial interactions with host chemical defences and affect disease in a marine holobiont. Scientific Reports, 9, 1363.

    Article  PubMed  PubMed Central  Google Scholar 

  • Lu, T., Ke, M., Lavoie, M., et al. (2018). Rhizosphere microorganisms can influence the timing of plant flowering. Microbiome, 6, 231.

    Article  PubMed  PubMed Central  Google Scholar 

  • Lützow, M. V., Kögel-Knabner, I., Ekschmitt, K., Matzner, E., Guggenberger, G., Marschner, B., & Flessa, H. (2006). Stabilization of organic matter in temperate soils: Mechanisms and their relevance under different soil conditions – a review. European Journal of Soil Science, 57, 426–445.

    Article  Google Scholar 

  • Ma, H., Pineda, A., Hannula, E. S., Kielak, A. M., Setyarinia, S. N., & Bezemer, T. M. (2020). Steering root microbiomes of a commercial horticultural crop with plant-soil feedbacks. Applied Soil Ecology, 150, 103468.

    Article  Google Scholar 

  • Mahmud, K., Makaju, S., Ibrahim, R., & Missaoui, A. (2020). Current progress in nitrogen fixing plants and microbiome research. Plants, 9, 97.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mamuad, L. L., Kim, S. H., Biswas, A. A., et al. (2019). Rumen fermentation and microbial community composition influenced by live Enterococcus faecium supplementation. AMB Express, 9, 123.

    Article  PubMed  PubMed Central  Google Scholar 

  • Mann, A. (2018). Inner workings: Hunting for microbial life throughout the solar system. Proceedings of the National Academy of Sciences of the United States of America, 115(45), 11348–11350.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Massaya, J., Prates Pereira, A., Mills-Lamptey, B., Benjamin, J., & Chuck, C. (2019). Conceptualization of a spent coffee grounds biorefinery: A review of existing valorisation approaches. Food and Bioproducts Processing, 118, 149–166.

    Article  Google Scholar 

  • Matthews, C., Crispie, F., Lewis, E., Reid, M., O’Toole, P. W., & Cotter, P. D. (2019). The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency. Gut Microbes, 10(2), 115–132.

    Article  CAS  PubMed  Google Scholar 

  • McNear, D. H., Jr. (2013). The rhizosphere – roots, soil and everything in between. Nature Education Knowledge, 4(3), 1.

    Google Scholar 

  • Meybeck, A., & Gitz, V. (2017). Sustainable diets within sustainable food systems. The Proceedings of the Nutrition Society, 76, 1–11.

    Article  PubMed  Google Scholar 

  • Mohawesh, O., Mahmoud, M., Janssen, M., & Lennartz, B. (2014). Effect of irrigation with olive mill wastewater on soil hydraulic and solute transport properties. International journal of Environmental Science and Technology, 11, 927–934.

    Article  CAS  Google Scholar 

  • Morgan, J. B., & Connolly, E. L. (2013). Plant-soil interactions: Nutrient uptake. Nature Education Knowledge, 4(8), 2.

    Google Scholar 

  • Morikawa, C. K., & Saigusa, M. (2011). Recycling coffee grounds and tea leaf wastes to improve the yield and mineral content of grains of paddy rice. Journal of the Science of Food and Agriculture, 91, 2108–2111.

    Article  CAS  PubMed  Google Scholar 

  • Moss, E. L., Maghini, D. G., & Bhatt, A. S. (2020). Complete, closed bacterial genomes from microbiomes using nanopore sequencing. Nature Biotechnology, 38, 701–707.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mueller, U. G., & Sachs, J. L. (2015). Engineering Microbiomes to Improve Plant and Animal Health. Trends in Microbiology, 23(10), 606–617.

    Article  CAS  PubMed  Google Scholar 

  • Mulligan, C. M., & Friedman, J. E. (2017). Maternal modifiers of the infant gut microbiota: Metabolic consequences. The Journal of Endocrinology, 235(1), R1–R12.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Murthy, P. S., & Madhava-Naidu, M. (2012). Sustainable management of coffee industry by-products and value addition—A review. Resources, Conservation and Recycling, 66, 45–58.

    Article  Google Scholar 

  • Mus, F., Crook, M. B., Garcia, K., et al. (2016). Symbiotic nitrogen fixation and the challenges to its extension to nonlegumes. Applied and Environmental Microbiology, 82(13), 3698–3710.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mussatto, S. I., Machado, E. M. S., Martins, S., & Teixeira, J. A. (2011). Production, composition, and application of coffee and its industrial residues. Food and Bioprocess Technology, 4, 661–672.

    Article  CAS  Google Scholar 

  • Nanjundappa, A., Bagyaraj, D. J., Saxena, A. K., et al. (2019). Interaction between arbuscular mycorrhizal fungi and Bacillus spp. in soil enhancing growth of crop plants. Fungal Biology and Biotechnology, 6, 2.

    Article  Google Scholar 

  • National Action Plan (NAP) to reduce the use of plant protection products stems from Directive 2009/128/EC of the European Parliament and of the Council of 21October 2009 establishing a framework for Community action to achieve the sustainable use of pesticides, which was transposed into national law by the Law of 19 December 2014 on plant protection products. https://ec.europa.eu/food/sites/food/files/plant/docs/pesticides_sup_nap_lux-rev_en.pdf

  • Nelson, E. B. (2018). The seed microbiome: Origins, interactions, and impacts. Plant and Soil, 422, 7–34.

    Article  CAS  Google Scholar 

  • Noverr, M. C., & Huffnagle, G. B. (2005). The ‘microflora hypothesis’ of allergic diseases. Clinical and Experimental Allergy, 35(12), 1511–1520.

    Article  CAS  PubMed  Google Scholar 

  • O’Banion, B. S., O’Neal, L., Alexandre, G., & Lebeis, S. L. (2020). Bridging the gap between single-strain and community-level plant-microbe chemical interactions. Molecular Plant-Microbe Interactions, 33(2), 124–134.

    Article  PubMed  Google Scholar 

  • Official Journal of the European Union (OJEU). (2008). Directive 2008/98/EC of the European Parliament and of the Council of 19 November 2008 on waste and repealing certain Directives. 22.11.2008. L312/30.

    Google Scholar 

  • Olanrewaju, O. S., Ayangbenro, A. S., Glick, B. R., et al. (2019). Plant health: Feedback effect of root exudates-rhizobiome interactions. Applied Microbiology and Biotechnology, 103, 1155–1166.

    Article  CAS  PubMed  Google Scholar 

  • Oltmanns, J., Licht, O., Bohlen, M.-L., Schwarz, M., Escher, S. E., Silano, V., MacLeod, M., Noteborn, H. P. J. M., Kass, G. E. N., & Merten, C. (2020). Potential emerging chemical risks in the food chain associated with substances registered under REACH. Environmental Science: Processes Impacts, 22, 105–120.

    CAS  PubMed  Google Scholar 

  • Orlova, N., Abakumov, E., Orlova, E., Yakkonen, K., & Shahnazarova, V. (2019). Soil organic matter alteration under biochar amendment: Study in the incubation experiment on the Podzol soils of the Leningrad region (Russia). Journal Soils Sediments, 19, 2708–2716.

    Article  CAS  Google Scholar 

  • Orozco-Mosqueda, M. D. C., Rocha-Granados, M. D. C., Glick, B. R., & Santoyo, G. (2018). Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms. Microbiological Research, 208, 25–31.

    Article  CAS  PubMed  Google Scholar 

  • Ottman, N., Ruokolainen, L., Suomalainen, A., Sinkko, H., Karisola, P., Lehtimäki, J., Lehto, M., Hanski, I., Alenius, H., & Fyhrquist, N. (2019). Soil exposure modifies the gut microbiota and supports immune tolerance in a mouse model. Journal of Allergy Clinical Immunology, 143(3), 1198–1206.e12.

    Article  CAS  PubMed  Google Scholar 

  • Pascale, A., Proietti, S., Pantelides, I. S., & Stringlis, I. A. (2020). Modulation of the root microbiome by plant molecules: The basis for targeted disease suppression and plant growth promotion. Frontiers in Plant Science, 10, 1741.

    Article  PubMed  PubMed Central  Google Scholar 

  • Peoples, M. B., Brockwell, J., Herridge, D. F., et al. (2009). The contributions of nitrogen-fixing crop legumes to the productivity of agricultural systems. Symbiosis, 48, 1–17.

    Article  CAS  Google Scholar 

  • Pérez-Burillo, S., Pastoriza, S., Jiménez-Hernández, N., D’Auria, G., Francino, M. P., & Rufián-Henares, J. A. (2018). Effect of food thermal processing on the composition of the gut microbiota. Journal of Agricultural and Food Chemistry, 66(43), 11500–11509.

    Article  PubMed  Google Scholar 

  • Pérez-Burillo, S., Pastoriza, S., Fernández-Arteaga, A., Luzón, G., Jiménez-Hernández, N., D’Auria, G., Francino, M. P., & Rufián-Henares, J. Á. (2019). Spent coffee grounds extract, rich in mannooligosaccharides, promotes a healthier gut microbial community in a dose-dependent manner. Journal of Agricultural and Food Chemistry, 67(9), 2500–2509.

    Article  PubMed  Google Scholar 

  • Pérez-Jaramillo, J. E., Mendes, R., & Raaijmakers, J. M. (2016). Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Molecular Biology, 90, 635–644.

    Article  PubMed  Google Scholar 

  • Ponter, H., Raichlen, D. A., Wood, B. M., Mabulla, A. Z. P., Racette, S. B., et al. (2012). Hunter-gatherer energetics and human obesity. PLoS One, 7(7), e40503.

    Article  Google Scholar 

  • Popp, J., Pető, K., & Nagy, J. (2013). Pesticide productivity and food security. A review. Agronomy for Sustainable Development, 33, 243–255.

    Article  Google Scholar 

  • Prakash, O., Nimonkar, Y., & Desai, D. A. (2020). Recent overview of microbes and microbiome preservation. Indian Journal of Microbiology, 60, 297–309.

    Article  PubMed  PubMed Central  Google Scholar 

  • Qiu, Z., Egidi, E., Liu, H., Kaur, S., & Singh, B. K. (2019). New frontiers in agriculture productivity: Optimised microbial inoculants and in situ microbiome engineering. Biotechnology Advances, 37(6), 107371.

    Article  CAS  PubMed  Google Scholar 

  • Raynaud, X., & Nunan, N. (2014). Spatial ecology of bacteria at the microscale in soil. PLoS One, 9(1), e87217.

    Article  PubMed  PubMed Central  Google Scholar 

  • Reynolds, W. D., Drury, C. F., Yang, X. M., & Tan, C. S. (2008). Optimal soil physical quality inferred through structural regression and parameter interactions. Geoderma, 146, 466–474.

    Article  Google Scholar 

  • Rivera-Yoshida, N., Arias Del Angel, J. A., & Benítez, M. (2018). Microbial multicellular development: Mechanical forces in action. Current Opinion in Genetics & Development, 51, 37–45.

    Article  CAS  Google Scholar 

  • Rodriguez, P. A., Rothballer, M., Chowdhury, S. P., Nussbaumer, T., Gutjahr, C., & Falter-Braun, P. (2019). Systems biology of plant-microbiome interactions. Molecular Plant, 12(6), 804–821.

    Article  CAS  PubMed  Google Scholar 

  • Rodríguez-Entrena, M., Espinosa-Goded, M., & Barreiro-Hurlé, J. (2014). The role of ancillary benefits on the value of agricultural soils carbon sequestration programmes: Evidence from a latent class approach to Andalusian olive groves. Ecological Economics, 99, 63–73.

    Article  Google Scholar 

  • Rook, G. A., & Brunet, L. R. (2005). Microbes, immunoregulation, and the gut. Gut, 54(3), 317–320.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rusu, A., Alvarez, P., Schwarze, B., Trif, A.-K., & M. (2020a). The impact of Candida spp. on physiological alterations in gut microbiota. Candida elimination diet therapy. In T. Askun & J. S. M. Tondolo (Eds.), Candidiasis. IntechOpen. ISBN: 978-1-83881-112-9.

    Google Scholar 

  • Rusu, A., Randriambelonoro, M., Perrin, C., et al. (2020b). Aspects influencing food intake and approaches towards personalising nutrition in the elderly. Population Ageing, 13, 239–256.

    Article  Google Scholar 

  • Sachidanand, B., Mitra, N. G., Kumar, V., Roy, R., & Mishra, B. B. (2019). Soil as a huge laboratory for microorganisms. Agricultural Research & Technology: Open Access Journal, 22(4), 556205.

    Google Scholar 

  • San Roman, M., & Wagner, A. (2018). An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment. PLoS Computational Biology, 14(7), e1006340.

    Article  PubMed  PubMed Central  Google Scholar 

  • Schaumann, G. E., Braun, B., Kirchner, D., Rotard, W., Szewzyk, U., & Grohmann, E. (2007). Influence of biofilms on the water repellency of urban soil samples. Hydrological Processes, 21, 2276–2284.

    Article  Google Scholar 

  • Schirawski, J., & Perlin, M. H. (2018). Plant-microbe interaction 2017-the good, the bad and the diverse. International Journal of Molecular Sciences, 19(5), 1374.

    Article  PubMed  PubMed Central  Google Scholar 

  • Schloter, M., Nannipieri, P., Sørensen, S. J., et al. (2018). Microbial indicators for soil quality. Biology and Fertility of Soils, 54, 1–10.

    Article  CAS  Google Scholar 

  • Senesi, N., & Plaza, C. (2007). Role of humification processes in recycling organic wastes of various nature and sources as soil amendments. Clean – Soil, Air, Water, 35, 26–41.

    Article  CAS  Google Scholar 

  • Sessitsch, A., Brader, G., Pfaffenbichler, N., Gusenbauer, D., & Mitter, B. (2018). The contribution of plant microbiota to economy growth. Microbial Biotechnology, 11, 801–805.

    Article  PubMed  PubMed Central  Google Scholar 

  • Shankar, V., Gouda, M., Moncivaiz, J., Gordon, A., Reo, N. V., Hussein, L., & Paliy, O. (2017). Differences in gut metabolites and microbial composition and functions between Egyptian and U.S. children are consistent with their diets. mSystems, 2, e00169-16.

    Article  PubMed  PubMed Central  Google Scholar 

  • Simmons, T., Caddell, D. F., Deng, S., & Coleman-Derr, D. (2018). Exploring the root microbiome: Extracting bacterial community data from the soil, rhizosphere, and root endosphere. Journal of Visualized Experiments : JoVE, 135, 57561.

    Google Scholar 

  • Simon, J.-C., Marchesi, J. R., Mougel, C., & Selosse, M. A. (2019). Host-microbiota interactions: From holobiont theory to analysis. Microbiome, 7, 5.

    Article  PubMed  PubMed Central  Google Scholar 

  • Singh, B. K., & Trivedi, P. (2017). Microbiome and the future for food and nutrient security. Microbial Biotechnology, 10(1), 50–53.

    Article  PubMed  PubMed Central  Google Scholar 

  • Singh, N., Gupta, V. K., Kumar, A., & Sharma, B. (2017). Synergistic effects of heavy metals and pesticides in living systems. Frontiers in Chemistry, 5, 70.

    Article  PubMed  PubMed Central  Google Scholar 

  • Sofo, A., Lundegårdh, B., Mårtensson, A., Manfra, M., Pepe, G., Sommella, E., De Nisco, M., Tenore, G. C., Campliglia, P., & Scopa, A. (2016). Different agronomic and fertilization systems affect polyphenolic profile, antioxidant capacity and mineral composition of lettuce. Scientia Horticulturae, 204, 106–115.

    Article  CAS  Google Scholar 

  • Souza, R. d., Ambrosini, A., & Passaglia, L. M. (2015). Plant growth-promoting bacteria as inoculants in agricultural soils. Genetics and Molecular Biology, 38(4), 401–419.

    Article  PubMed  PubMed Central  Google Scholar 

  • Strachan, D. P. (1989). Hay fever, hygiene, and household size. BMJ, 299(6710), 1259–1260.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sundström, J. F., Albihn, A., Boqvist, S., et al. (2014). Future threats to agricultural food production posed by environmental degradation, climate change, and animal and plant diseases – a risk analysis in three economic and climate settings. Food Security, 6, 201–215.

    Article  Google Scholar 

  • Thompson, L. A., & Darwish, W. S. (2019). Environmental chemical contaminants in food: Review of a global problem. Journal of Toxicology, 2345283.

    Google Scholar 

  • Thursby, E., & Juge, N. (2017). Introduction to the human gut microbiota. The Biochemical Journal, 474(11), 1823–1836.

    Article  CAS  PubMed  Google Scholar 

  • Timm, C. M., Loomis, K., Stone, W., et al. (2020). Isolation and characterization of diverse microbial representatives from the human skin microbiome. Microbiome, 8, 58.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trif, M., Vodnar, D. C., Mitrea, L., Rusu, A. V., & Socol, C. T. (2019). Design and development of oleoresins rich in carotenoids coated microbeads. Coatings, 9, 235.

    Article  CAS  Google Scholar 

  • Trinh, P., Zaneveld, J. R., Safranek, S., & Rabinowitz, P. M. (2018). One health relationships between human, animal, and environmental microbiomes: A mini-review. Frontiers in Public Health, 6, 235. https://doi.org/10.3389/fpubh.2018.00235

    Article  PubMed  PubMed Central  Google Scholar 

  • Trivedi, P., Schenk, P. M., Wallenstein, M. D., & Singh, B. K. (2017). Tiny microbes, big yields: Enhancing food crop production with biological solutions. Microbial Biotechnology, 10(5), 999–1003.

    Article  PubMed  PubMed Central  Google Scholar 

  • Turner, T. R., James, E. K., & Poole, P. S. (2013). The plant microbiome. Genome Biology, 14(6), 209.

    Article  PubMed  PubMed Central  Google Scholar 

  • Vallès, Y., & Francino, M. P. (2018). Air pollution, early life microbiome, and development. Current Environmental Health Reports, 5(4), 512–521.

    Article  PubMed  PubMed Central  Google Scholar 

  • van der Heijden, M. G., de Bruin, S., Luckerhoff, L., van Logtestijn, R. S., & Schlaeppi, K. (2016). A widespread plant-fungal-bacterial symbiosis promotes plant biodiversity, plant nutrition and seedling recruitment. The ISME Journal, 10(2), 389–399.

    Article  PubMed  Google Scholar 

  • van Veelen, H. P. J., Falcão Salles, J., Matson, K. D., et al. (2020). Microbial environment shapes immune function and cloacal microbiota dynamics in zebra finches Taeniopygia guttata. Animal Microbiome, 2, 21.

    Article  PubMed  PubMed Central  Google Scholar 

  • Vela-Cano, M., Cervera-Mata, A., Purswani, J., Pozo, C., Delgado, G., & González-López, J. (2019). Bacterial community structure of two Mediterranean agricultural soils amended with spent coffee grounds. Applied Soil Ecology, 137, 12–20.

    Article  Google Scholar 

  • Velásquez, A. C., Castroverde, C., & He, S. Y. (2018). Plant-pathogen warfare under changing climate conditions. Current Biology : CB, 28(10), R619–R634.

    Article  PubMed  Google Scholar 

  • Vítězová, M., Jančiková, S., Dordević, D., Vítěz, T., Elbl, J., Hanišáková, N., Jampílek, J., & Kushkevych, I. (2019). The possibility of using spent coffee grounds to improve wastewater treatment due to respiration activity of microorganisms. Applied Sciences, 9, 3155.

    Article  Google Scholar 

  • Wagner, S. C. (2011). Biological nitrogen fixation. Nature Education Knowledge, 3(10), 15.

    Google Scholar 

  • Wang, M., Sahu, A. K., Rusten, B., & Park, C. (2013). Anaerobic co-digestion of microalgae Chlorella sp. and waste activated sludge. Bioresource Technology, 142, 585–590.

    Article  CAS  PubMed  Google Scholar 

  • Wold, A. E. (1998). The hygiene hypothesis revised: Is the rising frequency of allergy due to changes in the intestinal flora? Allergy, 53(46 Suppl), 20–25.

    Article  CAS  PubMed  Google Scholar 

  • Wolińska, A., Kuźniar, A., Zielenkiewicz, U., et al. (2017). Metagenomic analysis of some potential nitrogen-fixing bacteria in arable soils at different formation processes. Microbial Ecology, 73, 162–176.

    Article  PubMed  Google Scholar 

  • Wu, H. J., & Wu, E. (2012). The role of gut microbiota in immune homeostasis and autoimmunity. Gut Microbes, 3(1), 4–14.

    Article  PubMed  PubMed Central  Google Scholar 

  • Wu, G. D., Compher, C., Chen, E. Z., et al. (2016). Comparative metabolomics in vegans and omnivoresreveal constraints on diet-dependent gut microbiotametabolite production. Gut, 65, 63–72.

    Article  CAS  PubMed  Google Scholar 

  • Wu, L., Ning, D., Zhang, B., Li, Y., Zhang, P., Shan, X., et al. (2019). Global diversity and biogeography of bacterial communities in wastewater treatment plants. Nature Microbiology, 4, 1183–1195.

    Article  CAS  PubMed  Google Scholar 

  • Yamane, K., Kono, M., Fukunaga, T., Iwai, K., & Sekine, R. (2014). Field evaluation of coffee grounds application for crop growth enhancement, weed control, and soil improvement. Plant Production Science, 17, 93–102.

    Article  Google Scholar 

  • Zanella, A., Bolzonella, C., Lowenfels, J., Ponge, J.-F., Bouché, M., Saha, D., Kukal, S. S., Fritz, I., Savory, A., & Blouin, M. (2018). Humusica 2, article 19: Techno humus systems and global change – Conservation agriculture and 4/1000 proposal. Applied Soil Ecology, 122(2), 271–296. https://doi.org/10.1016/j.apsoil.2017.10.036

  • Zdolec, N., Lorenzo, J. M., & Ray, R. C. (2018). Use of microbes for improving food safety and quality. BioMed Research International, 2018, 3902698.

    Article  PubMed  PubMed Central  Google Scholar 

  • Zgadzaj, R., Garrido-Oter, R., Jensen, D. B., Koprivova, A., Schulze-Lefert, P., & Radutoiu, S. (2016). Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities. Proceedings of the National Academy of Sciences of the United States of America, 113(49), E7996–E8005.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang, L., & Sun, X. (2017). Using cow dung and spent coffee grounds to enhance the two-stage co- composting of green waste. Bioresource Technology, 245, 152–161.

    Article  CAS  PubMed  Google Scholar 

  • Zimmerer, K. S., & de Haan, S. (2017). Agrobiodiversity and a sustainable food future. Nature Plants, 3, 17047.

    Article  PubMed  Google Scholar 

Download references

Funding

This work was supported from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 816303 (STANCE4HEALTH), and project AGL2014-53895-R from the Spanish Ministry of Economy and Competitiveness and by the European Regional Development Fund (FEDER).

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Alexandru Vasile Rusu or Jose Ángel Rufián-Henares .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2023 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Trif, M., Rusu, A.V., Francino, M.P., Delgado, G., Rufián-Henares, J.Á. (2023). Microbiome Applications for Sustainable Food Systems. In: Galanakis, C.M. (eds) Biodiversity, Functional Ecosystems and Sustainable Food Production. Springer, Cham. https://doi.org/10.1007/978-3-031-07434-9_8

Download citation

Publish with us

Policies and ethics