READING MATTER

Soil Microbiology

Andrews, S., 2010, FastQC: A quality control tool for high throughput sequence data, viewed 01 July 2019, from http://www/bioinformatics.babraham.ac.uk/projects/fastqc.


Bachman, G. & H. Kinzel., 1992, ‘Physiological and ecological aspects of the interactions between plant roots and rhizosphere soil’, Soil Biology and Biochemistry 24(6), 5543–5552. 


Bardgett, R.D., Bowman, W.D., Kaufmann, R. & Schmidt, S.K., 2005, ‘A temporal approach to linking aboveground and belowground ecology’, Trends in Ecology and Evolution 20(11), 634–641. https://doi.org/10.1016/j.tree.2005.08.005.


Berg, G. & Smalla, K., 2009, ‘Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere’, FEMS Microbial Ecology 68(1), 1–13. https:/doi.org/10.1111j.1574-6941.2009.00654.x


Bonkowski, M., Cheng, W., Griffiths, B.S., Alphei, J. & Scheu, S., 2000, ‘Microbial-faunal interactions in the rhizosphere and effects on plant growth’, European Journal of Soil Biology 36(3–4), 135–147. https://doi.org/10.1016/S1164-5563(00)01059-1


Bonkowski, M., Villenave, C. & Griffiths, B., 2009, ‘Rhizosphere fauna: The functional and structural diversity of intimate interactions of soil fauna with plant roots’, Plant Soil 321, 213–233. https://doi.org/10.1007/s11104-009-0013-2

Vermeulen, M., Cason, E.D. & Swart, W.J., 2020, ‘The rhizobiome of herbaceous plants in Clovelly and Sterkspruit soils of the Stevenson–Hamilton supersite’, Koedoe 62(2), a1596. https://doi.org/10.4102/koedoe. v62i2.1596

 

Microbial Inoculants

Adam, M., Heuer, H. and Hallmann, J., 2014. Bacterial antagonists of fungal pathogens also control root-knot nematodes by induced systemic resistance of tomato plants. PloS One, 9(2), p.90402.

 

Adeleke, B.S. and Babalola, O.O., 2020. The endosphere microbial communities, a great promise in agriculture. International Microbiology, 24(1), pp.1-17.

 

Adeleke, B.S. and Babalola, O.O., 2021. Roles of plant endosphere microbes in agriculture-a review. Journal of Plant Growth Regulation, pp.1-18.

 

Berg, G., Grube, M., Schloter, M. and Smalla, K., 2014. The plant microbiome and its importance for plant and human health. Frontiers in Microbiology, 5, p.491.

 

Bernardo-Cravo, A.P., Schmeller, D.S., Chatzinotas, A., Vredenburg, V.T. and Loyau, A., 2020.  Environmental factors and host microbiomes shape host–pathogen dynamics. Trends in Parasitology, 36(7), pp.616-633.

 

Blagodatskaya, E. and Kuzyakov, Y., 2013. Active microorganisms in soil: critical review of estimation criteria and approaches. Soil Biology and Biochemistry, 67, pp.192-211.

 

Bradáčová, K., Florea, A.S., Bar-Tal, A., Minz, D., Yermiyahu, U., Shawahna, R., Kraut-Cohen, J., Zolti, A., Erel, R., Dietel, K. and Weinmann, M., 2019. Microbial consortia versus single-strain inoculants: an advantage in PGPM-assisted tomato production. Agronomy, 9(2), p.105.

 

Brown, M.E., 1974. Seed and root bacterization. Annual Review of Phytopathology, 12(1), pp.181-197.

 

Brunetti, G., Farrag, K., Soler-Rovira, P., Ferrara, M., Nigro, F. and Senesi, N., 2012. The effect of compost and Bacillus licheniformis on the phytoextraction of Cr, Cu, Pb and Zn by three Brassicaceae species from contaminated soils in the Apulia region, Southern Italy. Geoderma, 170, pp.322-330.

 

Digra, S. and Nonzom, S., 2023. An insight into endophytic antimicrobial compounds: an updated analysis. Plant Biotechnology Reports, pp.1-31.

 

Dong, X., 2004. NPR1, all things considered. Current Opinion in Plant Biology, 7(5), pp.547-552.

 

Doornbos, R.F., van Loon, L.C. and Bakker, P.A., 2012. Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. A review. Agronomy for Sustainable Development, 32(1), pp.227-243.

 

Drescher, A., Glaser, R., Richert, C. and Nippes, K.R., 2011. Demand for key nutrients (NPK) in the year 2050. Draft report. University of Freiburg, Department of Geography, p.77.

 

EfficientMicrobes, n.d. Pro-Soil. Available at: https://efficientmicrobes.co.za/product/pro-soil/. Accessed 2023/01/23.

 

Egamberdieva, D., Wirth, S.J., Alqarawi, A.A., Abd_Allah, E.F. and Hashem, A., 2017. Phytohormones and beneficial microbes: essential components for plants to balance stress and fitness. Frontiers in Microbiology, 8, p.2104.

 

Elkoca, E., Turan, M. and Donmez, M.F., 2010. Effects of single, dual and triple inoculations with Bacillus subtilis, Bacillus megaterium and Rhizobium leguminosarum bv. Phaseoli on nodulation, nutrient uptake, yield and yield parameters of common bean (Phaseolus vulgaris l. cv.‘elkoca-05’). Journal of Plant Nutrition, 33(14), pp.2104-2119.

 

Plant Health

Ayangbenro, A.S., Chukwuneme, C.F., Ayilara, M.S., Kutu, F.R., Khantsi, M., Adeleke, B.S., Glick, B.R. and Babalola, O.O., 2022. Harnessing the rhizosphere soil microbiome of organically amended soil for plant productivity. Agronomy, 12(12), p. 3179. https://doi.org/10.3390/agronomy12123179

 

Ayaz, M., Li, C.H., Ali, Q., Zhao, W., Chi, Y.K., Shafiq, M., Ali, F., Yu, X.Y., Yu, Q., Zhao, J.T. and Yu, J.W., 2023. Bacterial and fungal biocontrol agents for plant disease protection: Journey from lab to field, current status, challenges, and global perspectives. Molecules, 28(18), p. 6735. https://doi.org/10.3390/molecules28186735

 

Ayilara, M.S., Adeleke, B.S. and Babalola, O.O., 2023. Bioprospecting and challenges of plant microbiome research for sustainable agriculture, a review on soybean endophytic bacteria. Microbial ecology, 85(3), p. 1113. https://doi.org/10.1007/s00248-022-02136-z

 

Berendsen, R.L., Pieterse, C.M.J. and Bakker, P.A.H.M. (2012).  The rhizosphere microbiome and plant health.  Trends in Plant Science, 17(8), 478–486.

 

Compant, S., Samad, A., Faist, H. and Sessitsch, A. (2019).  A review on the plant microbiome: ecology, functions, and emerging trends in microbial application.  Journal of Advanced Research, 19, 29–37.   https://doi.org/10.1016/j.jare.2019.03.004.

 

Chaparro, J.M., Sheflin, A.M., Manter, D.K. and Vivanco, J.M., 2012. Manipulating the soil microbiome to increase soil health and plant fertility. Biology and fertility of Soils, 48(5), p. 489. https://doi.org/10.1007/s00374-012-0691-4

 

Chitra, P. and Jijeesh, C.M., 2021. Bio-priming of seeds with plant growth promoting bacteria Pseudomonas fluorescens for better germination and seedling vigour of the East Indian sandalwood. New forests, 52(5), p. 829. https://doi.org/10.1007/s11056-020-09823-0

 

Cho, S.J., Kim, M.H. and Lee, Y.O., 2016. Effect of pH on soil bacterial diversity. Journal of ecology and environment, 40(1), p. 1. https://doi.org/10.1186/s41610-016-0004-1

 

Choudhary, D.K., Prakash, A. and Johri, B.N., 2007. Induced systemic resistance (ISR) in plants: mechanism of action. Indian journal of microbiology, 47, p. 289. https://doi.org/10.1007/s12088-007-0054-2

 

Debbink, K., da Silva, C.R., Silva, E.M., Mueller, B.D., Telenko, D.E.P. and Smith, D.L. (2025).  Integrated management of Sclerotinia stem rot of soybean including organically allowed fungicides in the Midwest United States.  PhytoFrontiers, 5(1), 52–59. https://doi.org/10.1094/PHYTOFR-05-24-0053-R.

 

Steffen, W., Richardson, K., Rockström, J. et al. (2015).  Planetary boundaries: guiding human development on a changing planet.  Science, 347(6223), 1259855. https://doi.org/10.1126/science.1259855.

 

Thiele-Bruhn, S., Schloter, M., Wilke, B.-M., Beaudette, L.A., Martin-Laurent, F., Cheviron, N., Mougin, C. and Römbke, J. (2020). Identification of new microbial functional standards for soil quality assessment.  SOIL, 6(1), 17–34. https://doi.org/10.5194/soil-6-17-2020.

 

Timmusk, S., Behers, L., Muthoni, J., Muraya, A. and Aronsson, A.-C. (2017).  Perspectives and challenges of microbial inoculants for sustainable agriculture.  Frontiers in Plant Science, 8, 49. https://doi.org/10.3389/fpls.2017.00049.

 

Fermented Food and Drinks

  1. Allen KJ, Koplin JJ. What can urban/rural differences in food allergy prevalence tell us about the drivers of food allergy? J Allergy Clin Immunol.  2019;143(2):554–556. https://doi.org/10.1016/j.jaci.2018.10.055.
  2. Brick T, Hettinga K, Kirchner B, Pfaffl MW, Ege MJ. The beneficial effect of farm milk consumption on asthma, allergies, and infections: From meta-analysis of evidence to clinical trial. J Allergy Clin Immunol Pract. 2020;8(3):878–889.e3.
  3. Botha M, Basera W, Facey-Thomas HE, et al. Rural and urban food allergy prevalence from the South African Food Allergy (SAFFA) study. J Allergy Clin Immunol. 2019;143(2):662–668.e2.
  4. Genuneit J, Strachan DP, Büchele G, et al. The combined effects of family size and farm exposure on childhood hay  fever and atopy. Pediatr Allergy Immunol. 2013;24(3):293–298. https://doi.org/10.1111/pai.12053.
  5. Melini F, Melini V, Luziatelli F, Ficca AG, Ruzzi M. Health-Promoting Components in Fermented Foods: An Up-to-Date Systematic Review. Nutrients. 2019;11(5):1189. doi:https://doi.org/10.3390/nu11051189
  6. de Waal P, van Niekerk E. FERMENTED FOODS AND ALLERGY PROTECTION: LESSONS FROM RURAL COMMUNITIES. Current Allergy and Clinical Immunology. 2024;37(2):74-80. Accessed October 21, 2024. https://journals.co.za/doi/pdf/10.10520/ejc-caci-v37-n2-a5
  7. Leeuwendaal NK, Stanton C, O’Toole PW, Beresford TP. Fermented Foods, Health and the Gut Microbiome. Nutrients. 2022;14(7):1527. https://pubmed.ncbi.nlm.nih.gov/35406140/
  8. Vercelli D. From Amish farm dust to bacterial lysates: The long and winding road to protection from allergic disease. Semin Immunol. 2023;68:101779.  https://doi.org/10.1016/j.smim.2023.101779 
  9. Levin ME, Botha M, Basera W, et al. Environmental factors associated with allergy in urban and rural children from the South African Food Allergy (SAFFA) cohort. J Allergy Clin Immunol. 2020;145(1):415–426.  https://doi.org/10.1016/j.jaci.2019.07.048.
  10. Dębińska A, Sozańska B. Fermented food in asthma and respiratory allergies – chance or failure? Nutrients. 2022;14(7):1420. Jackson CM, Mahmood MM, Järvinen KM. Farming lifestyle and human milk: Modulation of the infant microbiome and protection against allergy. Acta Paediatr. 2022;111(1):54–58. 

 

Microbes and Human Health

  1. Cho, I. & Blaser, M.J., 2012. The human microbiome: at the interface of health and disease. Nature Reviews Genetics, 13(4), pp.260–270.
    https://doi.org/10.1038/nrg3182

  2. Davenport, E.R., Sanders, J.G., Song, S.J., Amato, K.R., Clark, A.G. & Knight, R., 2017. The human microbiome in evolution. BMC Biology, 15(1), p.127.
    https://doi.org/10.1186/s12915-017-0454-7

  3. Faith, J.J. et al., 2013. The long-term stability of the human gut microbiota. Science, 341(6141), p.1237439.
    https://doi.org/10.1126/science.1237439

  4. Gilbert, J.A., Blaser, M.J., Caporaso, J.G., Jansson, J.K., Lynch, S.V. & Knight, R., 2018. Current understanding of the human microbiome. Nature Medicine, 24(4), pp.392–400.
    https://doi.org/10.1038/nm.4517

  5. Human Microbiome Project Consortium, 2012. Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), pp.207–214.
    https://doi.org/10.1038/nature11234

  6. Integrative HMP (iHMP) Research Network Consortium, 2019. The integrative human microbiome project. Nature, 569(7758), pp.641–648.
    https://doi.org/10.1038/s41586-019-1238-8

  7. Ley, R.E., Turnbaugh, P.J., Klein, S. & Gordon, J.I., 2006. Human gut microbes associated with obesity. Nature, 444(7122), pp.1022–1023.
    https://doi.org/10.1038/4441022a

  8. Lloyd-Price, J., Abu-Ali, G. & Huttenhower, C., 2016. The healthy human microbiome. Genome Medicine, 8(1), p.51.
    https://doi.org/10.1186/s13073-016-0307-y

  9. Lozupone, C.A., Stombaugh, J.I., Gordon, J.I., Jansson, J.K. & Knight, R., 2012. Diversity, stability and resilience of the human gut microbiota. Nature, 489(7415), pp.220–230.
    https://doi.org/10.1038/nature11550

  10. Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K.S. & Manichanh, C., 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464(7285), pp.59–65.
    https://doi.org/10.1038/nature08821

  11. Rinninella, E., Raoul, P., Cintoni, M., Franceschi, F., Miggiano, G.A.D., Gasbarrini, A. & Mele, M.C., 2019. What is the healthy gut microbiota composition? Microorganisms, 7(1), p.14.
    https://doi.org/10.3390/microorganisms7010014

  12. Rooks, M.G. & Garrett, W.S., 2016. Gut microbiota, metabolites and host immunity. Nature Reviews Immunology, 16(6), pp.341–352.
    https://doi.org/10.1038/nri.2016.42

  13. Shreiner, A.B., Kao, J.Y. & Young, V.B., 2015. The gut microbiome in health and in disease. Current Opinion in Gastroenterology, 31(1), pp.69–75.
    https://doi.org/10.1097/MOG.0000000000000139

  14. Sommer, F. & Bäckhed, F., 2013. The gut microbiota—masters of host development and physiology. Nature Reviews Microbiology, 11(4), pp.227–238.
    https://doi.org/10.1038/nrmicro2974

  15. Turnbaugh, P.J. et al., 2009. A core gut microbiome in obese and lean twins. Nature, 457(7228), pp.480–484.
    https://doi.org/10.1038/nature07540

  16. Turnbaugh, P.J., Ley, R.E., Hamady, M., Fraser-Liggett, C.M., Knight, R. & Gordon, J.I., 2007. The human microbiome project. Nature, 449(7164), pp.804–810.
    https://doi.org/10.1038/nature06244

  17. Valdes, A.M., Walter, J., Segal, E. & Spector, T.D., 2018. Role of the gut microbiota in nutrition and health. BMJ, 361, k2179.
    https://doi.org/10.1136/bmj.k2179

  18. Yatsunenko, T. et al., 2012. Human gut microbiome viewed across age and geography. Nature, 486(7402), pp.222–227.
    https://doi.org/10.1038/nature11053

  19. Zheng, D., Liwinski, T. & Elinav, E., 2020. Interaction between microbiota and immunity in health and disease. Cell Research, 30(6), pp.492–506.
    https://doi.org/10.1038/s41422-020-0332-7

  20. Zmora, N., Suez, J. & Elinav, E., 2019. You are what you eat: diet, health and the gut microbiota. Nature Reviews Gastroenterology & Hepatology, 16(1), pp.35–56.
    https://doi.org/10.1038/s41575-018-0061-2