Urban areas play an increasingly important role in human society with more than half of the global population living in urban areas and increasing to 68% by 2050. Urban soils are considered highly disturbed, anthropogenic in origin, and often contaminated and significantly altered by human activity. However, they are of increasing interest as a resource for food production, for mitigating heat island impacts, and for population health. Soil microbial diversity is the functional foundation of terrestrial ecosystems. This project compared soil microbial diversity of urban soil, a commercial farm, and a high intensity, small acreage regenerative farm. Also investigated was microbial diversity generated by organic composting as a means of developing a high microbial resource for regenerating soils. Methods included assessing soil and compost samples for environmental parameters, fungal and bacterial diversity using agar smear plates, PCR amplification, and DNA genomic sequencing. Loss-On-Ignition identified patterns in organic matter content and soil moisture with the regenerative farm soil highest in each. Visual analysis of agar plate colonies revealed similarities and stark differences in microbial abundance and diversity. These patterns are supported by the 16S rRNA gene analysis results which identified the diversity and abundance of bacteria highest in the compost and regenerative soils. The compost has exponentially more microbial diversity when compared to soil from commercial and urban lots. An unexpected result was the degree of impoverishment of the commercial farm soil. Soil microbial composition from a variety of settings provides critical information for regenerating soils and potential urban food production.
References
[1]
United Nations (2022) 68% of the World Population Projected to Live in Urban Areas by 2050, Say UN. UN Department of Economic and Social Affairs News. https://www.un.org/development/desa/en/news/population/2018-revision-of-world-urbanization-prospects.html
[2]
Ghadiri, M., Krawchenko, T. and Newell, R. (2024) Applying a Climate-Biodiversity-Health Framework to Support Integrated Food Systems Planning and Policy. JournalofEnvironmentalManagement, 358, Article 120769. https://doi.org/10.1016/j.jenvman.2024.120769
[3]
Salomon, M.J., Watts-Williams, S.J., McLaughlin, M.J. and Cavagnaro, T.R. (2020) Urban Soil Health: A City-Wide Survey of Chemical and Biological Properties of Urban Agriculture Soils. JournalofCleanerProduction, 275, Article 122900. https://doi.org/10.1016/j.jclepro.2020.122900
[4]
Meulemans, G. (2020) Urban Pedogeneses: The Making of City Soils from Hard Surfacing to the Urban Soil Sciences. EnvironmentalHumanities, 12, 250-266. https://doi.org/10.1215/22011919-8142330
[5]
(2023) USDA Web Soil Survey. https://websoilsurvey.nrcs.usda.gov/app/
[6]
Ajmone-Marsan, F., Certini, G. and Scalenghe, R. (2016) Describing Urban Soils through a Faceted System Ensures More Informed Decision-Making. LandUsePolicy, 51, 109-119. https://doi.org/10.1016/j.landusepol.2015.10.025
[7]
EPA (2019) Anatomy of Brownfields Redevelopment. EPA 560-F-19-012. https://www.epa.gov/system/files/documents/2024-06/anat_bf_redev_101106.pdf
[8]
Aelion, C.M., Davis, H.T., Lawson, A.B., Cai, B. and McDermott, S. (2013) Associations between Soil Lead Concentrations and Populations by Race/Ethnicity and Income-to-Poverty Ratio in Urban and Rural Areas. EnvironmentalGeochemistryandHealth, 35, 1-12. https://doi.org/10.1007/s10653-012-9472-0
[9]
Pr？v？lie, R. (2021) Exploring the Multiple Land Degradation Pathways across the Planet. Earth-ScienceReviews, 220, Article 103689. https://doi.org/10.1016/j.earscirev.2021.103689
[10]
Fierer, N., Wood, S.A. and Bueno de Mesquita, C.P. (2021) How Microbes Can, and Cannot, Be Used to Assess Soil Health. SoilBiologyandBiochemistry, 153, Article 108111. https://doi.org/10.1016/j.soilbio.2020.108111
[11]
Aislabie, J. and Deslippe, J.R. (2013) Soil Microbes and Their Contribution to Soil Services. In: Dymond, J.R. Ed., Ecosystem Services in New ZealandConditions and Trends. Manaaki Whenua Press, 143-161.
[12]
Peddle, S.D., Hodgson, R.J., Borrett, R.J., Brachmann, S., Davies, T.C., Erickson, T.E., et al. (2024) Practical Applications of Soil Microbiota to Improve Ecosystem Restoration: Current Knowledge and Future Directions. BiologicalReviews, 100, 1-18. https://doi.org/10.1111/brv.13124
[13]
Karlen, D.L., Mausbach, M.J., Doran, J.W., Cline, R.G., Harris, R.F. and Schuman, G.E. (1997) Soil Quality: A Concept, Definition, and Framework for Evaluation (A Guest Editorial). SoilScienceSocietyofAmericaJournal, 61, 4-10. https://doi.org/10.2136/sssaj1997.03615995006100010001x
[14]
Gupta, A., Singh, U.B., Sahu, P.K., Paul, S., Kumar, A., Malviya, D., et al. (2022) Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review. InternationalJournalofEnvironmentalResearchandPublicHealth, 19, Article 3141. https://doi.org/10.3390/ijerph19053141
[15]
LaCanne, C.E. and Lundgren, J.G. (2018) Regenerative Agriculture: Merging Farming and Natural Resource Conservation Profitably. PeerJ, 6, e4428. https://doi.org/10.7717/peerj.4428
[16]
Hermans, S.M., Lear, G., Case, B.S. and Buckley, H.L. (2023) The Soil Microbiome: An Essential, but Neglected, Component of Regenerative Agroecosystems. iScience, 26, Article 106028. https://doi.org/10.1016/j.isci.2023.106028
[17]
Abdul Rahman, N.S.N., Abdul Hamid, N.W. and Nadarajah, K. (2021) Effects of Abiotic Stress on Soil Microbiome. InternationalJournalofMolecularSciences, 22, Article 9036. https://doi.org/10.3390/ijms22169036
[18]
Sahu, N., Vasu, D., Sahu, A., Lal, N. and Singh, S.K. (2017) Strength of Microbes in Nutrient Cycling: A Key to Soil Health. In: Meena, V., Mishra, P., Bisht, J., and Pattanayak, A., Eds., AgriculturallyImportantMicrobesforSustainableAgriculture, Springer, 69-86. https://doi.org/10.1007/978-981-10-5589-8_4
[19]
Costa, O.Y.A., Raaijmakers, J.M. and Kuramae, E.E. (2018) Microbial Extracellular Polymeric Substances: Ecological Function and Impact on Soil Aggregation. FrontiersinMicrobiology, 9, Article ID: 1636. https://doi.org/10.3389/fmicb.2018.01636
[20]
Op De Beeck, M., Persson, P. and Tunlid, A. (2021) Fungal Extracellular Polymeric Substance Matrices-Highly Specialized Microenvironments That Allow Fungi to Control Soil Organic Matter Decomposition Reactions. SoilBiologyandBiochemistry, 159, Article 108304. https://doi.org/10.1016/j.soilbio.2021.108304
[21]
Gonzalez-Qui？ones, V., Stockdale, E.A., Banning, N.C., Hoyle, F.C., Sawada, Y., Wherrett, A.D., et al. (2011) Soil Microbial Biomass—Interpretation and Consideration for Soil Monitoring. SoilResearch, 49, 287-304. https://doi.org/10.1071/sr10203
[22]
Zhang, Y., Chen, M., Guo, J., Liu, N., Yi, W., Yuan, Z., et al. (2022) Study on Dynamic Changes of Microbial Community and Lignocellulose Transformation Mechanism during Green Waste Composting. EngineeringinLifeSciences, 22, 376-390. https://doi.org/10.1002/elsc.202100102
[23]
Miao, Y., Li, J., Li, Y., Niu, Y., He, T., Liu, D., et al. (2022) Long-Term Compost Amendment Spurs Cellulose Decomposition by Driving Shifts in Fungal Community Composition and Promoting Fungal Diversity and Phylogenetic Relatedness. mBio, 13, e00323-22. https://doi.org/10.1128/mbio.00323-22
[24]
Johnson, D.C. and Johnson, H.S. (2025) Adoption of a Biologically-Enhanced Agricultural Management (BEAM) Approach in Agroecosystems for Regenerating Soil Fertility, Improving Farm Profitability and Achieving Productive Utilization of Atmospheric CO2. PeerJ, 13, e19167. https://doi.org/10.7717/peerj.19167
[25]
Troeh, F.R. and Thompson, L.M. (2005) Soils and Soil Fertility. 6th Edition, Wiley-Blackwell, 489.
[26]
T？umer, K., Stoffregen, H. and Wessolek, G. (2005) Determination of Repellency Distribution Using Soil Organic Matter and Water Content. Geoderma, 125, 107-115. https://doi.org/10.1016/j.geoderma.2004.07.004
[27]
Libohova, Z., Seybold, C., Wysocki, D., Wills, S., Schoeneberger, P., Williams, C., et al. (2018) Reevaluating the Effects of Soil Organic Matter and Other Properties on Available Water-Holding Capacity Using the National Cooperative Soil Survey Characterization Database. JournalofSoilandWaterConservation, 73, 411-421. https://doi.org/10.2489/jswc.73.4.411
[28]
Nelson, D.W. and Sommers, L.E. (1982) Total Carbon, Organic Carbon, and Organic Matter. In: Page, A.L., et al., Eds., Methods of Soil Analysis, Part 2. Chemical and Microbiological Properties, 2nd Edition, Agronomy Monograph No. 9, Madison, 539-579.
[29]
Yeates, C., Gillings, M.R., Davison, A.D., Altavilla, N. and Veal, D.A. (1998) Methods for Microbial DNA Extraction from Soil for PCR Amplification. BiologicalProceduresOnline, 1, 40-47. https://doi.org/10.1251/bpo6
[30]
Soriano-Lerma, A., Pérez-Carrasco, V., Sánchez-Mara？ón, M., Ortiz-González, M., Sánchez-Martín, V., Gijón, J., et al. (2020) Influence of 16S rRNA Target Region on the Outcome of Microbiome Studies in Soil and Saliva Samples. ScientificReports, 10, Article No. 13637. https://doi.org/10.1038/s41598-020-70141-8
[31]
Bose, N. and Moore, S.D. (2023) Variable Region Sequences Influence 16S rRNA Performance. MicrobiologySpectrum, 11, Article No. 3. https://doi.org/10.1128/spectrum.01252-23
[32]
Bradshaw, M.J., Aime, M.C., Rokas, A., Maust, A., Moparthi, S., Jellings, K., et al. (2023) Extensive Intragenomic Variation in the Internal Transcribed Spacer Region of Fungi. iScience, 26, Article 107317. https://doi.org/10.1016/j.isci.2023.107317
[33]
Sayers, E.W., Beck, J., Bolton, E.E., Brister, J.R., Chan, J., Connor, R., et al. (2024) Database Resources of the National Center for Biotechnology Information in 2025. NucleicAcidsResearch, 53, D20-D29. https://doi.org/10.1093/nar/gkae979
[34]
Ogodo, A.C., Agwaranze, D.I., Daji, M. and Aso, R.E. (2022) Microbial Techniques and Methods: Basic Techniques and Microscopy. In: Egbuna, C., Patrick-Iwuanyanwu, K.C., Shah, MA., Ifemeje, J.C. and Rasul, A., Eds., AnalyticalTechniquesinBiosciences, Elsevier, 201-220. https://doi.org/10.1016/b978-0-12-822654-4.00003-8
[35]
Shannon, C.E. and Weaver, W. (1949) The Mathematical Theory of Communication. The University of Illinois Press, 1-117.
[36]
Bhattacharyya, S.S., Ros, G.H., Furtak, K., Iqbal, H.M.N. and Parra-Saldívar, R. (2022) Soil Carbon Sequestration—An Interplay between Soil Microbial Community and Soil Organic Matter Dynamics. ScienceofTheTotalEnvironment, 815, Article 152928. https://doi.org/10.1016/j.scitotenv.2022.152928
[37]
Philippot, L., Chenu, C., Kappler, A., Rillig, M.C. and Fierer, N. (2024) The Interplay between Microbial Communities and Soil Properties. NatureReviewsMicrobiology, 22, 226-239. https://doi.org/10.1038/s41579-023-00980-5
[38]
Wagg, C., Bender, S.F., Widmer, F. and van der Heijden, M.G.A. (2014) Soil Biodiversity and Soil Community Composition Determine Ecosystem Multifunctionality. ProceedingsoftheNationalAcademyofSciences, 111, 5266-5270. https://doi.org/10.1073/pnas.1320054111
[39]
Jiao, S., Peng, Z., Qi, J., Gao, J. and Wei, G. (2021) Linking Bacterial-Fungal Relationships to Microbial Diversity and Soil Nutrient Cycling. mSystems, 6, e01052-20. https://doi.org/10.1128/msystems.01052-20
[40]
Wang, M., Chen, S., Chen, L. and Wang, D. (2020) Microbial Mechanisms Responsible for the Variation of Soil Cd Availability under Different pe + pH Environments. EcotoxicologyandEnvironmentalSafety, 206, Article 111057. https://doi.org/10.1016/j.ecoenv.2020.111057
[41]
Yang, Y., Cui, K., Huang, Y., Yu, K., Li, C. and Chen, Y. (2025) Differential Insights into the Distribution Characteristics of Bacterial Communities and Their Response to Typical Pollutants in the Sediment and Soil of Large Drinking Water Reservoir. JournalofEnvironmentalManagement, 373, Article 123947. https://doi.org/10.1016/j.jenvman.2024.123947
[42]
Long, H., Xiong, S.Y., Mo, Y.M., Zeng, B.B., Shan, B.X., Xiao, T., Gao, Y. and Cui, C. (2024) Assembly and Co-Occurrence Pattern of Microbial Communities in Bulk and Rhizosphere Soils of Pinus Elliottii Plantations on Sandy Lands in China. PlantandSoil, 511, 309-322. https://doi.org/10.1007/s11104-024-06988-x
[43]
Berg, G., K？berl, M., Rybakova, D., Müller, H., Grosch, R. and Smalla, K. (2017) Plant Microbial Diversity Is Suggested as the Key to Future Biocontrol and Health Trends. FEMSMicrobiologyEcology, 93, fix050. https://doi.org/10.1093/femsec/fix050
[44]
Coban, O., De Deyn, G.B. and van der Ploeg, M. (2022) Soil Microbiota as Game-Changers in Restoration of Degraded Lands. Science, 375, abe0725. https://doi.org/10.1126/science.abe0725
[45]
Dinakarkumar, Y., Ramakrishnan, G., Gujjula, K.R., Vasu, V., Balamurugan, P. and Murali, G. (2024) Fungal Bioremediation: An Overview of the Mechanisms, Applications and Future Perspectives. EnvironmentalChemistryandEcotoxicology, 6, 293-302. https://doi.org/10.1016/j.enceco.2024.07.002
[46]
Baek, K.H., Yoon, B.D., Kim, B.H., Cho, D.H., Lee, I.S., Oh, H.M. and Kim, H.S. (2007) Monitoring of Microbial Diversity and Activity during Bioremediation of Crude Oil-Contaminated Soil with Different Treatments. Journal of Microbiology and Biotechnology, 17, 67-73.
