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Soil ecology is the study of the interactions among soil organisms, and between biotic and abiotic aspects of the soil environment. It is particularly concerned with the cycling of nutrients, formation and stabilization of the pore structure, the spread and vitality of pathogens, and the biodiversity of this rich biological community.

Microfauna.

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Recent advances are emerging from studying sub-organism level responses using environmental DNA [1] and various omics approaches, such as metagenomics, metatranscriptomics, proteomics and proteogenomics, are rapidly advancing, at least for the microbial world.[2] Metaphenomics has been proposed recently as a better way to encompass the omics and the environmental constraints.[3]

Soil Microbes.

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Soil harbors an immense amount of microbes comprising of bacteria, fungi, and viruses.[4] A majority of these microbes have not been cultured and remain relatively unknown. However, the development of next generation sequencing tools offer an avenue to investigate their diversity.[5] One feature of the distribution of microbes in the soil is spatial separation.[6] Spatial distribution of microbes influences their interactions and in consequence ecosystem functioning.[7] A vast volume of this heterogenous habitat is punctured with microorganisms concentrated in specific sites, referred to as 'hot spots' where there is an abundance of resources.[8] An example of such spaces are the rhizosphere and areas with accumulated organic matter such as the detritusphere, biopores and aggregate surfaces.[9] Active microbes in these hotspots are significantly higher than in the bulk soil and are characterized by higher process rates (such as respiration, microbial growth, enzyme activity and mineralization potential) and intense microbial interactions[9]. Spatial separation of soil microbes, may be influenced by temperature and moisture content in addition to other factors such as the availability of labile organic carbon.[10] Other abiotic factors like pH and mineral nutrient composition may also influence the distribution of microorganisms in soil.[11] The variability of these factors make the soil a dynamic system[12]. Interactions between members of the soil microhabitat is mediated by chemical signaling examples are soluble metabolites and volatile organic compound, in addition to extracellular polysaccharides.[13] Chemical signals enable communication among microbes, for example bacterial peptidoglycans stimulate growth of Candida albicans.[14] Reciprocally, C. albicans production of the metabolite farnesol, influences bacterial quorum sensing by modulating the expression of virulence genes. [15] Trophic interactions among microbes in the same environment driven by molecular communication .[16] Microbes may exchange metabolites to support each other's growth e.g. the release of extracellular enzymes by ectomycorrhiza decomposes organic matter and releases nutrients which then benefits other members of the population, in exchange organic acids from bacteria stimulate fungal growth. [17] These examples of trophic interactions, especially metabolite dependencies, drive species interactions and are important in the assembly of microbial communities.[18]

Bacteria.

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Almost 99% of the bacteria in the soil remain

  1. ^ Thomsen, Philip Francis; Willerslev, Eske (2015). "Environmental DNA – an emerging tool in conservation for monitoring past and present biodiversity". Biological Conservation. 183: 4–18. doi:10.1016/j.biocon.2014.11.019. S2CID 27384537.
  2. ^ Nannipieri, Paolo (2014). "Soil as a Biological System and Omics Approaches". EQA - International Journal of Environmental Quality. 13: 61–66. doi:10.6092/issn.2281-4485/4541.
  3. ^ Jansson, Janet K.; Hofmockel, Kirsten S. (2018). "The soil microbiome — from metagenomics to metaphenomics". Current Opinion in Microbiology. 43: 162–168. doi:10.1016/j.mib.2018.01.013. PMID 29454931. S2CID 3377418.
  4. ^ Nannipieri, Paolo (2014-12-01). "Soil as a Biological System and Omics Approaches". EQA - International Journal of Environmental Quality. 13: 61–66. doi:10.6092/issn.2281-4485/4541. ISSN 2281-4485.
  5. ^ Chaudhary, Dhiraj Kumar; Khulan, Altankhuu; Kim, Jaisoo (2019-04-30). "Development of a novel cultivation technique for uncultured soil bacteria". Scientific Reports. 9 (1): 6666. doi:10.1038/s41598-019-43182-x. ISSN 2045-2322.
  6. ^ Bardgett, Richard D.; van der Putten, Wim H. (2014-11). "Belowground biodiversity and ecosystem functioning". Nature. 515 (7528): 505–511. doi:10.1038/nature13855. ISSN 1476-4687. {{cite journal}}: Check date values in: |date= (help)
  7. ^ Cao, Tingting; Kong, Xiangshi; He, Weihua; Chen, Yunru; Fang, You; Li, Qiang; Chen, Qi; Luo, Yunchao; Tian, Xingjun (2022-09-01). "Spatiotemporal characteristics of enzymatic hotspots in subtropical forests: In situ evidence from 2D zymography images". CATENA. 216: 106365. doi:10.1016/j.catena.2022.106365. ISSN 0341-8162.
  8. ^ Kuzyakov, Yakov; Blagodatskaya, Evgenia (2015-04-01). "Microbial hotspots and hot moments in soil: Concept & review". Soil Biology and Biochemistry. 83: 184–199. doi:10.1016/j.soilbio.2015.01.025. ISSN 0038-0717.
  9. ^ a b Kuzyakov, Yakov; Blagodatskaya, Evgenia (2015-04-01). "Microbial hotspots and hot moments in soil: Concept & review". Soil Biology and Biochemistry. 83: 184–199. doi:10.1016/j.soilbio.2015.01.025. ISSN 0038-0717.
  10. ^ Tiedje, J. M.; Cho, J. C.; Murray, A.; Treves, D.; Xia, B.; Zhou, J. (2001-01), Rees, R. M.; Ball, B. C.; Campbell, C. D.; Watson, C. A. (eds.), "Soil teeming with life: new frontiers for soil science.", Sustainable management of soil organic matter (1 ed.), UK: CABI Publishing, pp. 393–425, doi:10.1079/9780851994659.0393, ISBN 978-0-85199-465-9, retrieved 2024-10-07 {{citation}}: Check date values in: |date= (help)
  11. ^ Zhalnina, Kateryna; Dias, Raquel; de Quadros, Patricia Dörr; Davis-Richardson, Austin; Camargo, Flavio A. O.; Clark, Ian M.; McGrath, Steve P.; Hirsch, Penny R.; Triplett, Eric W. (2015-02-01). "Soil pH Determines Microbial Diversity and Composition in the Park Grass Experiment". Microbial Ecology. 69 (2): 395–406. doi:10.1007/s00248-014-0530-2. ISSN 1432-184X.
  12. ^ Nannipieri, P.; Ascher, J.; Ceccherini, M. T.; Landi, L.; Pietramellara, G.; Renella, G. (2003-12). "Microbial diversity and soil functions". European Journal of Soil Science. 54 (4): 655–670. doi:10.1046/j.1351-0754.2003.0556.x. ISSN 1351-0754. {{cite journal}}: Check date values in: |date= (help)
  13. ^ Cao, Tingting; Luo, Yunchao; Shi, Man; Tian, Xingjun; Kuzyakov, Yakov (2024-01-01). "Microbial interactions for nutrient acquisition in soil: Miners, scavengers, and carriers". Soil Biology and Biochemistry. 188: 109215. doi:10.1016/j.soilbio.2023.109215. ISSN 0038-0717.
  14. ^ Cugini, Carla; Calfee, M. Worth; Farrow, John M.; Morales, Diana K.; Pesci, Everett C.; Hogan, Deborah A. (2007-08). "Farnesol, a common sesquiterpene, inhibits PQS production in Pseudomonas aeruginosa". Molecular Microbiology. 65 (4): 896–906. doi:10.1111/j.1365-2958.2007.05840.x. ISSN 0950-382X. {{cite journal}}: Check date values in: |date= (help)
  15. ^ Cugini, Carla; Morales, Diana K.; Hogan, Deborah A. (2010). "Candida albicans-produced farnesol stimulates Pseudomonas quinolone signal production in LasR-defective Pseudomonas aeruginosa strains". Microbiology. 156 (10): 3096–3107. doi:10.1099/mic.0.037911-0. ISSN 1465-2080. PMC 3068698. PMID 20656785.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  16. ^ Zelezniak, Aleksej; Andrejev, Sergej; Ponomarova, Olga; Mende, Daniel R.; Bork, Peer; Patil, Kiran Raosaheb (2015-05-19). "Metabolic dependencies drive species co-occurrence in diverse microbial communities". Proceedings of the National Academy of Sciences. 112 (20): 6449–6454. doi:10.1073/pnas.1421834112. ISSN 0027-8424. PMC 4443341. PMID 25941371.{{cite journal}}: CS1 maint: PMC format (link)
  17. ^ Olsson, PÃ¥l Axel; Wallander, HÃ¥kan (1998-10). "Interactions between ectomycorrhizal fungi and the bacterial community in soils amended with various primary minerals". FEMS Microbiology Ecology. 27 (2): 195–205. doi:10.1111/j.1574-6941.1998.tb00537.x. ISSN 0168-6496. {{cite journal}}: Check date values in: |date= (help)
  18. ^ Zelezniak, Aleksej; Andrejev, Sergej; Ponomarova, Olga; Mende, Daniel R.; Bork, Peer; Patil, Kiran Raosaheb (2015-05-19). "Metabolic dependencies drive species co-occurrence in diverse microbial communities". Proceedings of the National Academy of Sciences. 112 (20): 6449–6454. doi:10.1073/pnas.1421834112. ISSN 0027-8424. PMC 4443341. PMID 25941371.{{cite journal}}: CS1 maint: PMC format (link)
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