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Detection of Changes in Soil Microbial Community Physiological Profiles in Relation to Forest Types and Presence of Antibiotics Using BIOLOG EcoPlate

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Abstract

Soil is home to microbiota with diverse metabolic activities. These microorganisms play vital roles in many ecological processes. Thus, the assessment of microbial functional diversity is an important quality indicator of soil ecosystems. In this study, we collected soil samples from three distinct forest habitats, i.e., an agroforest, a primary forest (PF), and a secondary forest, within the Angat Watershed Reservation in Bulacan, Northern Philippines. Community-level physiological profiling (CLPP) was done with the BIOLOG EcoPlate™ to analyze the responses of the soil microbial communities from the three forest habitats in the absence or presence of antibiotics. The BIOLOG EcoPlate represents 31 utilizable carbon sources. Based on the CLPP analysis, soil samples from the PF showed significantly higher utilization of most carbon sources than the other forest types (p < 0.05). Thus, less disturbed forest types constitute more functionally diverse microbial communities. The presence of antibiotics significantly decreased the carbon utilization patterns of the soil microbial communities (p < 0.05), indicating the possible use of CLPP in monitoring contamination in soil.

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References

  1. Doran JW, Zeiss MR (2000) Soil health and sustainability: managing the biotic component of soil quality. Appl Soil Ecol 15:3–11. https://doi.org/10.1016/S0929-1393(00)00067-6

    Article  Google Scholar 

  2. Grzadziel J, Furtak K, Galazka A (2018) Community-level physiological profiles of microorganisms from different types of soil that are characteristic to poland-a long-term microplot experiment. Sustainability. https://doi.org/10.3390/su11010056

    Article  Google Scholar 

  3. Raynaud X, Nunan N (2014) Spatial ecology of bacteria at the microscale in soil. PLoS ONE. https://doi.org/10.1371/journal.pone.0087217

    Article  PubMed  PubMed Central  Google Scholar 

  4. Gałązka A, Furtak K (2019) Functional microbial diversity in context to agriculture. In: Das S, Dash HR (eds) Microbial diversity in the genomic era. Academic Press, New York, pp 347–358

    Chapter  Google Scholar 

  5. Kirk JL, Beaudette LA, Hart M, Moutoglis P, Klironomos JN, Lee H, Trevors JT (2004) Methods of studying soil microbial diversity. J Microbiol Method 58:169–188. https://doi.org/10.1016/j.mimet.2004.04.006

    Article  CAS  Google Scholar 

  6. Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M (2002) Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions. Appl Environ Microbiol 68:2391–2396. https://doi.org/10.1128/AEM.68.5.2391-2396.2002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Chaudhary DK, Khulan A, Kim J (2019) Development of a novel cultivation technique for uncultured soil bacteria. Sci Rep 9:1–11. https://doi.org/10.1038/s41598-019-43182-x

    Article  CAS  Google Scholar 

  8. Banaay CGB, Cruz CMV, Cuevas VC (2013) Effect of organic matter amendment on the rhizosphere microbial community and root-infecting pathogens of aerobic rice variety Apo. Philipp Sci Lett 6:107–118

    Google Scholar 

  9. Chodak M, Pietrzykowski M, Sroka K (2015) Physiological profiles of microbial communities in mine soils afforested with different tree species. Ecol Eng 81:462–470. https://doi.org/10.1016/j.ecoleng.2015.04.077

    Article  Google Scholar 

  10. Siles JA, Cajthaml T, Filipová A, Minerbi S, Margesin R (2017) Altitudinal, seasonal and interannual shifts in microbial communities and chemical composition of soil organic matter in Alpine forest soils. Soil Biol Biochem 112:1–13. https://doi.org/10.1016/j.soilbio.2017.04.014

    Article  CAS  Google Scholar 

  11. Maillard F, Leduc V, Bach C, Reichard A, Fauchery L, Saint-André L, Zeller B, Buée M (2019) Soil microbial functions are affected by organic matter removal in temperate deciduous forest. Soil Biol Biochem 133:28–36. https://doi.org/10.1016/j.soilbio.2019.02.015

    Article  CAS  Google Scholar 

  12. Feigl V, Ujaczki É, Vaszita E, Molnár M (2017) Influence of red mud on soil microbial communities: application and comprehensive evaluation of the BIOLOG EcoPlate approach as a tool in soil microbiological studies. Sci Total Environ 595:903–911. https://doi.org/10.1016/j.scitotenv.2017.03.266

    Article  CAS  PubMed  Google Scholar 

  13. Siles JA, Öhlinger B, Cajthaml T, Kistler E, Margesin R (2018) Characterization of soil bacterial, archaeal, and fungal communities inhabiting archaeological human-impacted layers at Monte Iato settlement (Sicily, Italy). Sci Rep 8:1–14. https://doi.org/10.1038/s41598-018-20347-8

    Article  CAS  Google Scholar 

  14. Barreiro A, Fontúrbel MT, Lombao A, Martín A, Vega JA, Fernández C, Carballas T, Díaz-Raviña M (2015) Using phospholipid fatty acid and community level physiological profiling techniques to characterize soil microbial communities following an experimental fire and different stabilization treatments. CATENA 135:419–429. https://doi.org/10.1016/j.catena.2014.07.011

    Article  CAS  Google Scholar 

  15. Xu W, Ge Z, Poudel DR (2015) Application and optimization of BIOLOG EcoPlates in functional diversity studies of soil microbial communities. MATEC Web Conf 22:1–6. https://doi.org/10.1051/matecconf/20152204015

    Article  Google Scholar 

  16. Pinna VM, Castaldi P, Deiana P, Pusino A, Garau G (2012) Sorption behavior of sulfamethazine on unamended and manure-amended soils and short-term impact on soil microbial community. Ecotoxicol Environ Saf 84:234–242. https://doi.org/10.1016/j.ecoenv.2012.07.006

    Article  CAS  PubMed  Google Scholar 

  17. Liu B, Li Y, Zhang X, Wang J, Gao M (2015) Effects of chlortetracycline on soil microbial communities: comparisons of enzyme activities to the functional diversity via BIOLOG EcoPlates™. Eur J Soil Biol 68:69–76. https://doi.org/10.1016/j.ejsobi.2015.01.002

    Article  CAS  Google Scholar 

  18. Ma T, Pan X, Chen L, Liu W, Christie P, Luo Y, Wu L (2016) Effects of different concentrations and application frequencies of oxytetracycline on soil enzyme activities and microbial community diversity. Eur J Soil Biol 76:53–60. https://doi.org/10.1016/j.ejsobi.2016.07.004

    Article  CAS  Google Scholar 

  19. Preston-Mafham J, Boddy L, Randerson PF (2002) Analysis of microbial community functional diversity using sole-carbon-source utilization profiles—a critique. FEMS Microbiol Ecol 42:1–14

    CAS  PubMed  Google Scholar 

  20. Mann A, Nehra K, Rana JS, Dahiya T (2021) Antibiotic resistance in agriculture: perspectives on upcoming strategies to overcome upsurge in resistance. Curr Res Microb Sci 2:100030. https://doi.org/10.1016/j.crmicr.2021.100030

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. da Silva FL, de Lima BR, da Silva BA, Volcão LM, da Silva Júnior FMR, Ramos DF (2023) Assessment of the impact of ceftriaxone on the functional profile of soil microbiota using BIOLOG EcoPlate™. Soil Syst 7:55. https://doi.org/10.3390/soilsystems7020055

    Article  CAS  Google Scholar 

  22. Garland JL (1997) Analysis and interpretation of community-level physiological profiles in microbial ecology. FEMS Microbiol Ecol 24:289–300

    Article  CAS  Google Scholar 

  23. Xu Y, Yu W, Ma Q, Wang J, Zhou H, Jiang C (2016) The combined effect of sulfadiazine and copper on soil microbial activity and community structure. Ecotoxicol Environ Saf 134:43–52. https://doi.org/10.1016/j.ecoenv.2016.06.041

    Article  CAS  Google Scholar 

  24. Sang X, Li K, Zhu Y, Ma X, Hao H, Bi J, Zhang G, Hou H (2020) The impact of microbial diversity on biogenic amines formation in grasshopper sub shrimp paste during fermentation. Front Microbiol 11:782. https://doi.org/10.3389/fmicb.2020.00782

    Article  PubMed  PubMed Central  Google Scholar 

  25. Beaumont M, Roura E, Lambert W, Turni C, Michiels J, Chalvon-Demersay T (2022) Selective nourishing of gut microbiota with amino acids: a novel prebiotic approach? Front Nutr. https://doi.org/10.3389/fnut.2022.1066898

    Article  PubMed  PubMed Central  Google Scholar 

  26. Shrestha K, Stevens S, Shrestha P, Adetutu EM, Walsh KB, Ball AS, Midmore DJ (2015) Characterization of the soil microbial community of cultivated and uncultivated vertisol in Australia under several management regimes. Agric Ecosyst Environ 199:418–427. https://doi.org/10.1016/j.agee.2014.10.002

    Article  CAS  Google Scholar 

  27. Ravindra PS, Bhardwaj A (2023) β-glucans: a potential source for maintaining gut microbiota and the immune system. Front Nutr 10:1143682. https://doi.org/10.3389/fnut.2023.1143682

    Article  CAS  Google Scholar 

  28. Groisillier A, Labourel A, Michel G, Tonon T (2015) The mannitol utilization system of the marine bacterium Zobellia galactanivorans. Appl Environ Microbiol 81:1799–1812. https://doi.org/10.1128/aem.02808-14

    Article  PubMed  PubMed Central  Google Scholar 

  29. Sun J, Li S, Fan C, Cui K, Tan H, Liao Q, Lu L (2022) N-Acetylglucosamine promotes tomato plant growth by sha** the community structure and metabolism of the rhizosphere microbiome. Microbiol Spectr. https://doi.org/10.1128/spectrum.00358-22

    Article  PubMed  PubMed Central  Google Scholar 

  30. Ucar RA, Pérez-Díaz IM, Dean LL (2020) Gentiobiose and cellobiose content in fresh and fermenting cucumbers and utilization of such disaccharides by lactic acid bacteria in fermented cucumber juice medium. Food Sci Nutr 8:5798–5810. https://doi.org/10.1002/fsn3.1830

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Klimek B, Chodak M, Jaźwa M, Solak A, Tarasek A, Niklińska M (2016) The relationship between soil bacteria substrate utilisation patterns and the vegetation structure in temperate forests. Eur J For Res 135:179–189. https://doi.org/10.1007/s10342-015-0929-4

    Article  Google Scholar 

  32. Adeleke R, Nwangburuka C, Oboirien B (2017) Origins, roles, and fate of organic acids in soils: a review. S Afr J Bot 108:393–406. https://doi.org/10.1016/j.sajb.2016.09.002

    Article  CAS  Google Scholar 

  33. Zhu T, Zhang B, Feng Y, Li Z, Tang X, Ban X, Kong H, Li C (2022) Beneficial effects of three dietary cyclodextrins on preventing fat accumulation and remodeling gut microbiota in mice fed a high-fat diet. Foods 11:1118. https://doi.org/10.3390/foods11081118

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Reitermayer D, Kafka TA, Lenz CA, Vogel RF (2018) Interrelation between Tween and the membrane properties and high-pressure tolerance of Lactobacillus plantarum. BMC Microbiol 18:72. https://doi.org/10.1186/s12866-018-1203-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Banning NC, Lalor BM, Cookson WR, Grigg AH, Murphy DV (2012) Analysis of soil microbial community level physiological profiles in native and post-mining rehabilitation forest: which substrates discriminate? Appl Soil Ecol 56:27–34. https://doi.org/10.1016/j.apsoil.2012.01.009

    Article  Google Scholar 

  36. Klimek B, Chodak M, Jaźwa M, Niklińska M (2016) Functional diversity of soil microbial communities in boreal and temperate scots pine forests. Eur J For Res 135:731–742. https://doi.org/10.1007/s10342-016-0968-5

    Article  CAS  Google Scholar 

  37. Sofo A, Ricciuti P (2019) A standardized method for estimating the functional diversity of soil bacterial community by BIOLOG EcoPlates™ assay—The case study of a sustainable olive orchard. Appl Sci 9:4035. https://doi.org/10.3390/app9194035

    Article  CAS  Google Scholar 

  38. Gajda AM, Czyż EA, Furtak K, Jończyk K (2019) Effects of crop production practices on soil characteristics and metabolic diversity of microbial communities under winter wheat. Soil Res 57:124–131. https://doi.org/10.1071/SR18113

    Article  Google Scholar 

  39. Chinthalapudi DPM, Pokhrel S, Kingery WL, Shankle MW, Ganapathi Shanmugam S (2023) Exploring the synergistic impacts of cover crops and fertilization on soil microbial metabolic diversity in dryland soybean production systems using BIOLOG EcoPlates. Appl Biosci 2:328–346. https://doi.org/10.3390/applbiosci2030022

    Article  Google Scholar 

  40. Zhang B-H, Hong J-P, Zhang Q, ** D-S, Gao C-H (2020) Contrast in soil microbial metabolic functional diversity to fertilization and crop rotation under rhizosphere and non-rhizosphere in the coal gangue landfill reclamation area of Loess Hills. PLoS ONE 15:e0229341. https://doi.org/10.1371/journal.pone.0229341

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Muñiz S, Lacarta J, Pata MP, Jimenez JJ, Navarro E (2014) Analysis of the diversity of substrate utilisation of soil bacteria exposed to Cd and earthworm activity using generalised additive models. PLoS ONE 9:e85057. https://doi.org/10.1371/journal.pone.0085057

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Borgulat J, Łukasik W, Borgulat A, Nadgórska-Socha A, Kandziora-Ciupa M (2021) Influence of lead on the activity of soil microorganisms in two Beskidy landscape parks. Environ Monit Assess 193:839. https://doi.org/10.1007/s10661-021-09503-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors would like to thank the National Power Corporation—Angat Watershed Area for providing the necessary permit and assistance during the soil sample collection.

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Authors and Affiliations

  1. The Graduate School, University of Santo Tomas, Espana Blvd., 1015, Manila, Philippines

    Benjamin C. Decena Jr.

  2. Department of Biological Sciences, College of Science, University of Santo Tomas, Espana Blvd., 1015, Manila, Philippines

    Thomas Edison E. dela Cruz

  3. Fungal Biodiversity, Ecogenomics and Systematics-Metabolomics (FBeS) Group, Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., 1015, Manila, Philippines

    Benjamin C. Decena Jr.

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Correspondence to Thomas Edison E. dela Cruz.

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Decena, B.C., dela Cruz, T.E.E. Detection of Changes in Soil Microbial Community Physiological Profiles in Relation to Forest Types and Presence of Antibiotics Using BIOLOG EcoPlate. Indian J Microbiol 64, 773–779 (2024). https://doi.org/10.1007/s12088-024-01294-7

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