“Soil biofilms”: Misleading description of the spatial distribution of microbial biomass in soils

Philippe C. Baveye

PDF(92 KB)
PDF(92 KB)
Soil Ecology Letters ›› 2020, Vol. 2 ›› Issue (1) : 2-5. DOI: 10.1007/s42832-020-0024-8
LETTER TO THE EDITOR
LETTER TO THE EDITOR

“Soil biofilms”: Misleading description of the spatial distribution of microbial biomass in soils

Author information +
History +

Cite this article

Download citation ▾
Philippe C. Baveye. “Soil biofilms”: Misleading description of the spatial distribution of microbial biomass in soils. Soil Ecology Letters, 2020, 2(1): 2‒5 https://doi.org/10.1007/s42832-020-0024-8

References

[1]
Aufrecht, J.A., Fowlkes, J.D., Bible, A.N., Morrell-Falvey, J., Doktycz, M.J., Retterer, S.T., 2019. Pore-scale hydrodynamics influence the spatial evolution of bacterial biofilms in a microfluidic porous network. PLoS One 14(6): e0218316.
CrossRef Google scholar
[2]
Baveye, P.C., Otten, W., Kravchenko, A., Balseiro Romero, M., Beckers, É, Chalhoub, M., Christophe, D.,  Thilo, E., Patricia, G.,   Simona, H., Serkan, K., Olivier, M.,   Carsten, W.M.,   Naoise, N., Valérie, P., Steffen, S., Hannes, S., Hans-Jörg, Vogel., 2018. Emergent properties of microbial activity in heterogeneous soil microenvironments: different research approaches are slowly converging, yet major challenges remain. Frontiers in Microbiology  8, 1364.
CrossRef Google scholar
[3]
Baveye, P., Valocchi, A., 1989. An evaluation of mathematical models of the transport of biologically reacting solutes in saturated soils and aquifers.  Water Resources Research 25, 1413–1421.
CrossRef Google scholar
[4]
Block, J.C., 1992. Biofilms in Drinking Water Distribution Systems. In: Melo, L.F., Bott, T.R., Fletcher, M., Capdeville, B. (eds.) Biofilms — Science and Technology. NATO ASI Series (Series E: Applied Sciences), vol 223. Springer, Dordrecht
[5]
Block, J.C., Haudidier, K., Paquin, J.L., Miazga, J., Levi, Y.,  1993,  Biofilm accumulation in drinking water distribution systems, Biofouling 6,  333-343, 
CrossRef Google scholar
[6]
Boltz, J.P., Smets, B.F., Rittmann, B.E., van Loosdrecht, M.C.M., Morgenroth, E., Daigger, G.T., 2017. From biofilm ecology to reactors: a focused review. Water Science and Technology 75,1753–1760.
CrossRef Google scholar
[7]
Cai, P., Sun, X., Wu, Y., Gao, C., Mortimer, M., Holden, P.A., Redmile-Gordon, M., Huang, Q., 2019. Soil biofilms: microbial interactions, challenges, and advanced techniques for ex-situ characterization. Soil Ecology Letters 1(3-4), 85–93.
CrossRef Google scholar
[8]
Cardinale, M., 2014. Scanning a microhabitat: plant-microbe interactions revealed by confocal laser scanning microscopy. Frontiers in Microbiology 5, 94.
CrossRef Google scholar
[9]
Castorena, E.V.G., Gutierrez-Castorena, M.C., Vargas, T.G., Bontemps, L.C., Delgadillo Martinez, J., Suastegui Mendez, E., Solorio, C.A.O. 2016. Micromapping of microbial hotspots and biofilms from different crops using digital image mosaics of soil thin sections.  Geoderma  279, 11–21.
CrossRef Google scholar
[10]
Clark, F.E., 1951. Bacteria in the soil.  Experientia  7, 78–80.
CrossRef Google scholar
[11]
Coyte, K.Z., Tabuteau, H., Gaffney, E.A., Foster, K.R., Durham, W.M., 2017. Biofilm competition in porous environments. Proceedings of the National Academy of Sciences  114,   E161–E170; 
CrossRef Google scholar
[12]
Danhorn, T., Fuqua, C., 2007. Biofilm formation by plant-associated bacteria. Annual Review of Microbiology 61, 401–422.
CrossRef Google scholar
[13]
DeLeo, P.C., Baveye, P., Ghiorse, W.C., 1997. Use of confocal laser scanning microscopy on soil thin-sections for improved characterization of microbial growth in unconsolidated soils and aquifer materials.  Journal of Microbiological Methods  30, 193–203.
CrossRef Google scholar
[14]
Eickhorst, T., Tippkötte, R., 2008. Detection of microorganisms in undisturbed soil by combining fluorescence in situ hybridization (FISH) and micropedological methods.  Soil Biology Biochemistry  40, 1284–1293.
CrossRef Google scholar
[15]
Flemming, H.C., Wuertz, S., 2019. Bacteria and archaea on earth and their abundance in biofilms. Nature Reviews Microbiology 17, 247–260.
CrossRef Google scholar
[16]
Foster, R.C., 1988. Microenvironments of soil microorganisms.  Biology and Fertility of Soils   6, 189–203.
CrossRef Google scholar
[17]
Foster, R.C., Rovira, A.D., Cock, T.W., 1983.  Ultrastructure of the Root-Soil Interface.  St Paul, MN: American Phytophathological Society.
[18]
Grundmann, G.L., 2004. Spatial scales of soil bacterial diversity – The size of a clone.  FEMS Microbiology Ecology 48, 119–127.
CrossRef Google scholar
[19]
Jones, D., Griffiths, E., 1964. The use of thin soil sections for the study of soil microorganisms.  Plant Soil  20, 232–240.
CrossRef Google scholar
[20]
Juyal A., Otten W., Falconer R., Hapca S., Schmidt H., Baveye P.C., Eickhorst T., 2019. Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales.  Geoderma 334, 165–174.
[21]
Kravchenko, A.N., Otten, W., Garnier, P., Pot, V. and Baveye, P.C., 2019. Soil aggregates as biogeochemical reactors: Not a way forward in the research on soil-atmosphere exchange of greenhouse gases. Global Change Biology 25, 2205–2208.
CrossRef Google scholar
[22]
Kuzyakov, Y., Blagodatskaya, E., 2015. Microbial hotspots and hot moments in soil: concept and review.  Soil Biology Biochemistry 83, 184–199.
CrossRef Google scholar
[23]
Lerch, T.Z., Chenu, C., Dignac M.F., Barriuso, E., Mariotti, A., 2017. Biofilm vs. planktonic lifestyle: consequences for pesticide 2,4-D metabolism by Cupriavidus necator JMP134.  Frontiers in Microbiology 8, 904.
CrossRef Google scholar
[24]
Li, Y., Dick, W.A., Tuovinen, O.H., 2003. Evaluation of fluorochromes for imaging bacteria in soil.  Soil Biology Biochemistry  35, 737–744.
CrossRef Google scholar
[25]
Li, Y., Dick, W.A., Tuovinen, O.H., 2004. Fluorescence microscopy for visualization of soil microorganisms – A review.  Biology and Fertility of Soils   39, 301–311.
CrossRef Google scholar
[26]
Molz, F.J., Widdowson, M.A., Benefield, L.D., 1986. Simulation of microbial growth dynamics coupled to nutrient and oxygen transport in porous media, Water Resources Research 22, 1207–1216.
[27]
Nunan, N., 2017. The microbial habitat in soil: scale, heterogeneity and functional consequences. Journal of Plant Nutrition and Soil Science 180, 425–429.
[28]
Nunan, N., Ritz, K., Crabb, D., Harris, K., Wu, K., Crawford, J.W., Young, I.M., 2001. Quantification of the in situ distribution of soil bacteria by large scale imaging of thin sections of undisturbed soil. FEMS Microbiology Ecology 37, 67–77.
CrossRef Google scholar
[29]
O’Donnell, A.G., Young, I.M., Rushton, S.P., Shirley, M.D., Crawford, J.W., 2007. Visualization, modelling and prediction in soil microbiology.  Nature Reviews Microbiology  5, 689–699.
CrossRef Google scholar
[30]
Or, D., Smets, B.F., Wraith, J.M., Dechesne, A., Friedman, S.P., 2007. Physical constraints affecting bacterial habitats and activity in unsaturated porous media – a review, Advances in Water Resources 30, 1505–1527.
[31]
Pennell, K.D. (2016). “Specific surface area,” in Elias, S.A. (ed.) Reference Module in Earth Systems and Environmental Sciences, Oxford: Elsevier, 1–8.
[32]
Postma, J., van Veen, J.A., 1990. Habitable pore space and survival of Rhizobium leguminosarum biovartrifolii introduced into soil.  Microbial Ecology 19, 149–161.
CrossRef Google scholar
[33]
Redmile-Gordon, M.A., Brookes, P.C., Evershed, R.P., Goulding, K.W.T., Hirsch, P.R., 2014. Measuring the soil-microbial interface: Extraction of extracellular polymeric substances (EPS) from soil biofilms, Soil Biology and Biochemistry 72, 163–171.
CrossRef Google scholar
[34]
Raynaud, X., Nunan, N., 2014. Spatial ecology of bacteria at the microscale in soil.  PLoS One  9, 287217.
CrossRef Google scholar
[35]
Thullner, M., Baveye, P., 2008. Computational pore network modeling of the influence of biofilm permeability on bioclogging in porous media.  Biotechnology & Bioengineering  99, 1337–1351.
CrossRef Google scholar
[36]
Vandevivere P., Baveye P., 1992a.  Saturated hydraulic conductivity reduction caused by aerobic bacteria in sand columns.  Soil Science Society of America Journal   56,1–13
[37]
Vandevivere, P., Baveye, P., 1992b. Improved preservation of bacterial exoplolymers for scanning elecrton microscopy.  Journal of Microscopy-Oxford 167, 323–330.
CrossRef Google scholar
[38]
Vandevivere, P., Baveye, P., 1992c. Sampling method for the observation of microorganisms in unconsolidated porous media via scanning electron microscopy.  Soil Science  153, 482–485.
CrossRef Google scholar
[39]
Vandevivere, P., Baveye, P., de Lozada, D.S., DeLeo, P., 1995. Microbial clogging of saturated soils and aquifer materials: Evaluation of mathematical models. Water Resources Research 31, 2173–2180.
[40]
Volk, E., Iden, S.C., Furman, A., Durner, W., Rosenzweig, R., 2016. Biofilm effect on soil hydraulic properties: Experimental investigation using soil-grown real biofilm, Water Resources Research 52, 5813–5828.
CrossRef Google scholar
[41]
Vos, M., Wolf, A.B., Jennings, S.J., Kowalchuk, G.A., 2013. Micro-scale determinants of bacterial diversity in soil.  FEMS Microbiology Reviews  37, 936–954.
CrossRef Google scholar
[42]
Watteau, F., Villemin, G., 2018. Soil microstructures examined through transmission Electron microscopy reveal soil-microorganisms interactions.  Frontiers in Environmental Science  6, 106.
CrossRef Google scholar
[43]
White, D., FitzPatrick, E.A., Kilham, K., 1994. Use of stained bacterial inocula to assess spatial distribution after introduction into soil.  Geoderma 63, 245–254.
CrossRef Google scholar
[44]
Wilpiszeski, R.L., Aufrecht,  J.A., Retterer, S.T., Sullivan, M.B., Graham, D.E., Pierce,  M., Zablocki, E., Palumbo, A.V., Elias, D.A., 2019. Soil aggregate microbial communities: towards understanding microbiome interactions at biologically relevant scales. Applied and Environmental Microbiology 85,  e00324–19. 
CrossRef Google scholar
[45]
Young, I.M., Crawford, J.W., 2004. Interactions and self-organization in the soil-microbe complex.  Science  304, 1634–1637.
CrossRef Google scholar

RIGHTS & PERMISSIONS

2020 Higher Education Press
AI Summary AI Mindmap
PDF(92 KB)

Accesses

Citations

Detail

Sections
Recommended

/