Chapter 4.2.3 : Aquatic Biofilms: Development, Cultivation, Analyses, and Applications

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This chapter focuses on microbial biofilms in aquatic environments and attempts to provide a framework for their study based on unifying fundamental concepts of microbial ecology (resilience, resistance, diversity) across micro, community and landscape scales of observation. Biofilm development is briefly considered in terms of classical sequences of events and our current understanding. Growth of microbial communities in natural environments and methods and apparatus for their experimental cultivation at various scales are presented. Critical aspects of biofilm development, the nature and study of exopolymeric substances, predation, grazing, cooperative and trophic interactions, as well as the role of biofilms in the fate of contaminants are reviewed. The essential tools for aquatic biofilm study, from microscale (microscopy), molecular/genomic (FISH/next generation sequencing), to cultivation-based approaches, are laid out for the reader. The effects of environmental stress on aquatic biofilms, as well as their use as bioindicators of ecosystem health and applications in ecotoxicology, risk assessment, and monitoring, are reviewed and discussed.

Citation: Lawrence J, Neu T, Paule A, Korber D, Wolfaardt G. 2016. Aquatic Biofilms: Development, Cultivation, Analyses, and Applications, p 4.2.3-1-4.2.3-33. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.2.3
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Image of FIGURE 1

Selected micrographs illustrating structural, functional, microenvironmental and molecular parameters in microbial biofilms. A1, Natural river biofilm on a stone; A2, Natural river biofilm on a stone; A3, Natural river biofilm on a stone; A4, Natural river biofilm on a stone; B, River water biofilm from bioreactor; C1, Reactor biofilm dual lectin staining + autofluorescence; C2, Zoom on C1 showing microcolony; D, 2 lectin + autofluorescence stained microcolony; E, green lectin + autofluorescence showing cyanobacteria; F, red + green lectin with orange microcolonies; G, red + green lectin with green microcolony shells; H, red lectin microcolony cells surrounded by red capsules and a diffuse red infilling EPS; I1, CTC-stained microcolony showing metabolic activity; I2, Green latex beads on outer shell and blue on the inside of a microcolony; J1, Control biofilm WGA TRITC, SYTO 9, and autofluorescence; J2, Comparison to (J1) 25 mg/liter MeOH-exposed biofilm WGA TRITC, SYTO 9, and autofluorescence; J3, FISH probe image microcolony in J1; J4, FISH probe image microcolony in J2; K1, Snail grazing, left side ungrazed, right side grazed; K2, Xz image of K1 left side (ungrazed); K3, Xz image of K1 right side (grazed); L1, Biofilm pH grayscale gradient dark <pH 5, light = pH 7; L2, Zoom on image L1; M1, Time series of high molecular weight dextran diffusion into microbial biofilm—25 s; M2, high molecular weight dextran diffusion into biofilm—50 s; M3, high molecular weight dextran diffusion into biofilm—80 s; N1, Syto9 green nucleic acid stain of microcolony; N2, FISH probe image of microcolony N1; N3, FISH probe image of coral microcolony N1; O1, STXM image of the biology (protein) in river biofilm; O2, STXM image of the calcium in O1; O3, STXM image of the same area O1, showing Ni, Ca, protein (RGB); O4, STXM image of Ni, protein and lipid (RGB) in O1; P1, Microcolonies exposed to nickel stained with Newport green; P2, X-ray microprobe map of nickel (red dots) in biofilm in P1. doi:10.1128/9781555818821.ch4.2.3.f1

Citation: Lawrence J, Neu T, Paule A, Korber D, Wolfaardt G. 2016. Aquatic Biofilms: Development, Cultivation, Analyses, and Applications, p 4.2.3-1-4.2.3-33. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.2.3
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Image of FIGURE 2

Schematic representation of different parameters integrated for ecotoxicological assessments using attached microbial communities: (i) levels of biological complexity in the experimental methods (field and microcosm); (ii) selected factors modulating the toxicity of the specific chemical or mixture, additional allogenic and autogenic factors influencing biofilm development; and (iii) examples of tools which may be used depending on the suspected exposure and organisms affected. doi:10.1128/9781555818821.ch4.2.3.f2

Citation: Lawrence J, Neu T, Paule A, Korber D, Wolfaardt G. 2016. Aquatic Biofilms: Development, Cultivation, Analyses, and Applications, p 4.2.3-1-4.2.3-33. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.2.3
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Image of FIGURE 3

Results from a transplantation experiment presented as a two-dimensional plot of a nonmetric multidimensional scaling (NMDS) analysis of DGGE banding patterns from gels analyzed for bacterial communities from 3- and 5.5-week biofilms from site L, located in a forested watershed (open circles) and from site A, located in an agricultural watershed (black dots) and from transplanted biofilms (dark squares). Plots issued from the first DGGE gel were rotated (45° counterclockwise—axis represented by dashed lines) to allow superposition of plots from gels 1 and 2. The numbers 1, 2, 3, and 4 indicate replicates from the same experimental condition ( ). doi:10.1128/9781555818821.ch4.2.3.f3

Citation: Lawrence J, Neu T, Paule A, Korber D, Wolfaardt G. 2016. Aquatic Biofilms: Development, Cultivation, Analyses, and Applications, p 4.2.3-1-4.2.3-33. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.2.3
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