Chapter 4.2.1 : The Microbial Ecology of Benthic Environments

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Within the benthic realm life carpets the sedimentary surface of all aquatic ecosystems including the oceans, lakes, rivers and streams. Microorganisms of all types, bacteria, archaea and eukaryotes, inhabit these environments and through their metabolic activities contribute to the biogeochemical cycles that sustain life on earth. In this chapter we address the question "Why live on or in sediments, or in some cases, attached to rocks or other hard surfaces?" and then explore major questions in the ecology of benthic microbial life in freshwater and shallow marine systems and current methodological approaches used in addressing these questions. Our first focus is on the abiotic and biotic factors that strongly influence the distribution and abundance of benthic microorganisms. Elemental cycles and the possibility of bacterial biogeography within the benthic realm are also addresses. Obtaining high quality samples and methods for determining microbial activity, biomass and community structure are discussed with classical/direct observation, biochemical and molecular approaches highlighted. Characterization of dissolved organic matter, methods for foodweb analysis and identification of the active component of microbial communities are specifically addressed. We conclude with a brief examination of several current questions within the general field of benthic microbial ecology.

Citation: Findlay R, Battin T. 2016. The Microbial Ecology of Benthic Environments, p 4.2.1-1-4.2.1-20. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.2.1
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Image of FIGURE 1.

Typical benthic ecosystems ranging from (a) headwater streams (b) to coastal waters. Copious microbial communities also including significant amounts of algae that can carpet gravel streams (c), whereas microbial communities in the sandy habitats of coastal waters often have lower microbial biomass (d). doi:10.1128/9781555818821.ch4.2.1.f1

Citation: Findlay R, Battin T. 2016. The Microbial Ecology of Benthic Environments, p 4.2.1-1-4.2.1-20. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.2.1
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Image of FIGURE 2.

Photographs of benthic microbial communities. (a) An initial state of a benthic community showing the various forms of microbial organisms. (b) A filamentous streamer with a pronounced head and a long tail; streamers tend to develop in turbulent flow. (c) Long streamers (extending up to 10 cm and more) can harbor various microorganisms and algae. All photographs from epifluorescence microscopy using SYTOX (green) and autofluorescence (red) of algae. Courtesy of Iris Hödl. doi:10.1128/9781555818821.ch4.2.1.f2

Citation: Findlay R, Battin T. 2016. The Microbial Ecology of Benthic Environments, p 4.2.1-1-4.2.1-20. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.2.1
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Image of FIGURE 3.

The supply of carbon and oxygen to sediment strongly influences the distribution of bacterial and archaeal metabolic types. (a) Experimentally determined relationship between carbon flux to the benthos and the supply of O influenced by water velocity. The curved line represents maximum O flux rate for 15°C seawater at O saturation—for any site with a flow velocity × carbon flux rate that falls below or to the right of the curve, oxygen supply will exceed demand, and for those sites that fall above or to the left of the curve oxygen demand will exceed supply. In these cases, aerobic decomposition will be limited (redrawn from ). (b) Effect on water velocity on benthic boundary layer. Curves represent O concentration of water and sediment as determined by microelectrode with the embedded numbers representing water velocity (cm s). Horizontal lines represent variation among multiple measurements. The vertical portion of each line indicates the well-mixed portion of the water column and the thickness of the benthic boundary layer can be determined as the distance between the sediment–water interface and the bottom of the well-mixed layer (redrawn from 110, with permission). (c) The effect of benthic photosynthetic activity on sediment O concentration. Open bar represent photosynthetic rate and circles O concentration during early afternoon and sundown. Note the subsurface O maximum (redrawn from ). (d) Idealized distribution of bacterial and archaeal metabolic types within sediment. Light crosshatching indicates the suboxic zone and dark crosshatching anaerobic zone (redrawn from 80, with permission). (e) Drawing from a photomicrograph of a mix microcolony in a depression on the surface of sand grain (from 188, with permission). (f) Scanning electron micrograph of a syntrophic coculture of G20 and . Fermentation of butyrate to acetate and H is energetically inhibited at standard temperatures and concentrations. G20 cannot oxidize butyrate alone (although some sulfate-reducing bacteria can), however, via a tightly coupled mutualistic interaction G20 and successful oxidize butyrate. In general, syntrophy is currently thought to proceed through hydrogen or formate production and can also involve methanogenic archaea ( ). doi:10.1128/9781555818821.ch4.2.1.f3

Citation: Findlay R, Battin T. 2016. The Microbial Ecology of Benthic Environments, p 4.2.1-1-4.2.1-20. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.2.1
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Image of FIGURE 4.

Meso- and microcosms typically used to study benthic microbial communities. (a) A header tank ensures constant pressure and computerized valves regulate the water flow in 32 3-m-long flumes. (b) Large (40 m long) streamside flumes are typically used to study the effect of the flow environment on benthic microbial life and the effect of benthic microorganisms on ecosystem processes. (c) Bioreactors serve study how benthic microorganisms transform dissolved organic or how bioturbation affect sedimentary microbial communities. Courtesy of Mia Bengtsson and Iris Hödl. doi:10.1128/9781555818821.ch4.2.1.f4

Citation: Findlay R, Battin T. 2016. The Microbial Ecology of Benthic Environments, p 4.2.1-1-4.2.1-20. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.2.1
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Standard-state free energy change of some bacterial metabolisms

Citation: Findlay R, Battin T. 2016. The Microbial Ecology of Benthic Environments, p 4.2.1-1-4.2.1-20. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.2.1

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