Soil “biofilms”: “Bioclusters” would be a much better descriptor


soil microorganisms
soil porosity
spatial analysis


Soil “biofilms”: “Bioclusters” would be a much better descriptor


Aufrecht JA, Fowlkes JD, Bible AN, Morrell-Falvey J, Doktycz MJ, Retterer ST. 2019. Pore-scale hydrodynamics influence the spatial evolution of bacterial biofilms in a microfluidic porous network. PLOS ONE 14(6):e0218316. DOI: 10.1371/journal.pone.0218316.

Baveye PC. 2020. “Soil biofilms”: Misleading description of the spatial distribution of microbial biomass in soils. Soil Ecology Letters 2(1):2-5. DOI: 10.1007/s42832-020-0024-8.

Baveye PC, Darnault C. 2017. Microbial competition and evolution in natural porous environments: Not that simple. Proc Natl Acad Sci. 114:E2802-E2803. DOI: 10.1073/pnas.1700992114.

Baveye PC, Otten W, Kravchenko A, Balseiro Romero M, Beckers É, Chalhoub M, et al. 2018. Emergent properties of microbial activity in heterogeneous soil microenvironments: different research approaches are slowly converging, yet major challenges remain. Front Microbiol. 8:1364. DOI: 10.3389/fmicb.2018.01929.

Baveye P, Valocchi A. 1989. An evaluation of mathematical models of the transport of biologically reacting solutes in saturated soils and aquifers. Water Resour Res. 25:1413-1421. DOI: 10.1029/WR025i006p01413.

Block J-C. 1992. Biofilms in Drinking Water Distribution Systems. In: Melo LF, Bott TR, Fletcher M, Capdeville B, editors. Biofilms — Science and Technology. NATO ASI Series (Series E: Applied Sciences). Volume 223. Dordrecht: Springer.

Block J-C, Haudidier K, Paquin J-L, Miazga J, Levi Y. 1993. Biofilm accumulation in drinking water distribution systems. Biofouling 6:4:333-343. DOI: 10.1080/08927019309386235.

Boltz JP, Smets BF, Rittmann BE, van Loosdrecht MCM, Morgenroth E, Daigger GT. 2017. From biofilm ecology to reactors: a focused review. Water Sci Technol. 75:1753-1760. DOI: 10.2166/wst.2017.061.

Cai P, Sun X, Wu Y, Gao C, Mortimer M, Holden PA, Redmile-Gordon M, Huan, Q. 2019. Soil biofilms: Microbial interactions, challenges, and advanced techniques for ex-situ characterization. Soil Ecology Letters 1(3-4):85-93. DOI: 10.1007/s42832-019-0017-7.

Cai P, Wu Y, Redmile-Gordon M. 2020. Response to Letter to the Editor – “Soil biofilms”: Misleading description of the spatial distribution of microbial biomass in soils. Soil Ecology Letters 2(1):6-7. DOI: 10.1007/s42832-020-0025-7.

Cardinale M. 2014. Scanning a microhabitat: plant-microbe interactions revealed by confocal laser scanning microscopy. Front Microbiol. 5:94. DOI: 10.3389/fmicb.2014.00094.

Carrel M, Morales VL, Beltrán MA, Derlon N, Kaufmann R, Morgentroth E, Holzner M. 2018. Biofilms in 3D porous media: delineating the influence of the pore network geometry, flow and mass transfer on biofilm development. Water Research 134(1):280-291. DOI: 10.1016/j.watres.2018.01.059.

Castorena EVG, Gutiérrez-Castorena MC, Vargas TG, Bontemps LC, Delgadillo Martínez J, Suastegui Méndez E, et al. 2016. Micromapping of microbial hotspots and biofilms from different crops using digital image mosaics of soil thin sections. Geoderma 279:11-21. DOI: 10.1016/j.geoderma.2016.05.017.

Clark FE. 1951. Bacteria in the soil. Experientia 7:78-80. DOI: 10.1007/bf02153840.

Coyte KZ, Tabuteau H, Gaffney EA, Foster KR, Durham WM. 2017. Microbial competition in porous environments can select against rapid biofilm growth. Proc Natl Acad Sci. 114:E161-E170.

Danhorn T, Fuqua C. 2007. Biofilm formation by plant-associated bacteria. Annu Rev Microbiol. 61:401-422. DOI: 10.1146/annurev.micro.61.080706.093316.

Davids L, Flemming HC, Wilderer PA. 2017. Microorganisms and their role in soil. In: Sikdar SK, Irvine RL, editors. Fundamentals and applications of bioremediation. New York: Routledge Press. p. 283-331.

DeLeo PC, Baveye P, Ghiorse WC. 1997. Use of confocal laser scanning microscopy on soil thin-sections for improved characterization of microbial growth in unconsolidated soils and aquifer materials. J Microbiol Methods 30:193-203. DOI: 10.1016/s0167-7012(97)00065-1.

Eickhorst T, Tippkötter R. 2008. Detection of microorganisms in undisturbed soil by combining fluorescence in situ hybridization (FISH) and micropedological methods. Soil Biol Biochem. 40:1284-1293. DOI: 10.1016/j.soilbio.2007.06.019.

Filip Z. 1973. Clay minerals as a factor influencing the biochemical activity of soil microorganisms. Folia Microbiologica 18:56-74.

Filip Z. 1979. Wechselwirkung von Mikroorganismen und Tonmineralen - eine Übersicht. Zeitschrift für Pflanzenernährung und Bodenkunde 142:375-386.

Flemming H-C, Baveye P, Neu TR, Dtoodley P, Szewzyk U, Wingender J, Wuerz S. 2021. Who put the film in biofilm? The migration of a term from wastewater engineering to medicine and beyond. npj Biofilms and Microbiomes 7:10. DOI: 10.1038/s41522-020-00183-3.

Flemming H-C, Wingender J. 2010. The biofilm matrix. Nat Rev Microbiol. 8:623-633.

Flemming H-C, Wuertz S. 2019. Bacteria and archaea on earth and their abundance in biofilms. Nature Reviews Microbiology 17:247-260. DOI: 10.1038/s41579-019-0158-9.

Foster RC. 1988. Microenvironments of soil microorganisms. Biol Fert Soils 6:189-203. DOI: 10.1007/BF00260816.

Jones D, Griffiths E. 1964. The use of thin soil sections for the study of soil microorganisms. Plant Soil 20:232-240. DOI: 10.1007/bf01376452.

Juyal A, Eickhorst T, Falconer R, Baveye PC, Spiers A, Otten W. 2018. Control of pore geometry in soil microcosms and its effect on the growth and spread of Pseudomonas and Bacillus sp. Front. Environ Sci. 6:73. DOI: 10.3389/fenvs.2018.00073.

Juyal A, Otten W, Baveye PC, Eickhorst T. 2020. Influence of soil structure on the spread of Pseudomonas fluorescens in soil at microscale. European Journal of Soil Science 72(1):141-153. DOI: 10.1111/ejss.12975.

Juyal A, Otten W, Falconer R, Hapca S, Schmidt H, Baveye PC, Eickhorst T. 2019. Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales. Geoderma 334:165-174.

Kuzyakov Y, Blagodatskaya E. 2015. Microbial hotspots and hot moments in soil: Concept & review. Soil Biology and Biochemistry 83:184-199. DOI: 10.1016/j.soilbio.2015.01.025.

Lerch TZ, Chenu C, Dignac MF, Barriuso E, Mariotti A. 2017. Biofilm vs. Planktonic Lifestyle: Consequences for Pesticide 2,4-D Metabolism by Cupriavidus necator JMP134. Front Microbiol. 8:904. DOI: 10.3389/fmicb.2017.00904.

Li Y, Dick WA, Tuovinen OH. 2003. Evaluation of fluorochromes for imaging bacteria in soil. Soil Biol Biochem. 35:737-744. DOI: 10.1016/s0038-0717(02)00196-7.

Li Y, Dick WA, Tuovinen OH. 2004. Fluorescence microscopy for visualization of soil microorganisms – A review. Biol Fertil Soils 39:301-311. DOI: 10.1007/s00374-004-0722-x.

Marshall KC. 1980. Adsorption of microorganisms to soils and sediments. In: Bitton G, Marshall KC, editors. Adsorption of microorganisms to surfaces. New York: John Wiley. p. 317-329.

Molz FJ, Widdowson MA, Benefield LD. 1986. Simulation of microbial growth dynamics coupled to nutrient and oxygen transport in porous media. Water Resour Res. 22(8):207-1216.

Moshynets OV, Spiers AJ. 2016. Viewing biofilms within the larger context of bacterial aggregations. In: Dhanasekaran D, Tajuddin N, editors. Microbial Biofilms: Importance and Applications. Rijeka, Croatia: InTech. p. 3-22.

Nunan N, Ritz K, Crabb D, Harris K, Wu K, Crawford JW, et al. 2001. Quantification of the in situ distribution of soil bacteria by large scale imaging of thin sections of undisturbed soil. FEMS Micro Ecol. 37:67-77. DOI: 10.1111/j.1574-6941.2001.tb00854.x.

Pachepsky Y, Devin B, Polyanskay L, Shelton D, Shein E, Guber A. 2006. Limited entrapment model to simulate the breakthrough of Arthrobacter and Aquaspirillum in soil columns. International Agrophysics 20(3):207-218.

Raynaud X, Nunan N. 2014. Spatial ecology of bacteria at the microscale in soil. PLoS One 9:287217. DOI: 10.1371/journal.pone.0087217.

Redmile-Gordon MA, Brookes PC, Evershed RP, Goulding KWT, Hirsch PR. 2014. Measuring the soil-microbial interface: Extraction of extracellular polymeric substances (EPS) from soil biofilms. Soil Biology and Biochemistry 72:163-171. DOI: 10.1016/j.soilbio.2014.01.025.

Schmidt H, Nunan N, Höck A, Eickhorst T, Kaiser C, Woebken D, Raynaud X. 2018. Recognizing patterns: Spatial analysis of observed microbial colonization on root surfaces. Front Environ Sci. 6:61. DOI: 10.3389/fenvs.2018.00061.

Stotsky G. 1985. Mechanisms of adhesion to clays, with reference to soil systems. In: Savage DC, Fletcher MM, editors. Bacterial adhesion. New York: Plenum Press. p. 195-253.

Vandevivere P, Baveye P. 1992a. Saturated hydraulic conductivity reduction caused by aerobic bacteria in sand columns. Soil Sci Soc Am J. 56:1-13.

Vandevivere P, Baveye P. 1992b. Improved preservation of bacterial exopolymers for scanning electron microscopy. J Microsc Oxford 167:323-330. DOI: 10.1111/j.1365-2818.1992.tb03242.x.

Vandevivere P, Baveye P. 1992c. Sampling method for the observation of microorganisms in unconsolidated porous media via scanning electron microscopy. Soil Sci. 153:482-485. DOI: 10.1097/00010694-199206000-00007.

Van Veen JA, Kuikman PJ, Van Elsas JD. 1994. Modelling microbial interactions in soil” Preliminary considerations and approaches. In: Bazin MJ, Lynch JM, editors. Environmental gene release: Models, experiments and risk assessment. London, United Kingdom: Chapman and Hall. p. 29-46.

Volk E, Iden SC, Furman A, Durner W, Rosenzweig R. 2016. Biofilm effect on soil hydraulic properties: Experimental investigation using soil-grown real biofilm. Water Resour Res. 52:5813-5828, DOI:10.1002/2016WR018866.

Vos M, Wolf AB, Jennings S J, Kowalchuk GA. 2013. Micro-scale determinants of bacterial diversity in soil. FEMS Microbiol Rev. 37:936-954. DOI: 10.1111/1574-6976.12023.

Watteau F, Villemin G. 2018. Soil microstructures examined through transmission electron microscopy reveal soil-microorganisms interactions. Front Environ Sci. 6:106. DOI: 10.3389/fenvs.2018.00106.

White D, FitzPatrick EA, Kilham K. 1994. Use of stained bacterial inocula to assess spatial distribution after introduction into soil. Geoderma 63:245-254. DOI: 10.1016/0016-7061(94)90066-3.

Wilpiszeski RL, Aufrecht JA, Retterer ST, Sullivan MB, Graham DE. 2019. Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales. Appl Environ Microbiol. 85(14):e00324-19. DOI:10.1128/AEM.00324-19.

Wu Y, Cai P, Jing X, Niu X, Ji D, Ashry NM, Gao C, Huang Q. 2019. Soil biofilm formation enhances microbial community diversity and metabolic activity. Environment International 132:105116. DOI: 10.1016/j.envint.2019.105116.