3D-Fluorescence In Situ Hybridization of Intact, Anaerobic Biofilm

Brileya, Kristen A.; Camilleri, Laura B.

doi:10.1007/978-1-4939-0554-6_13

Cited by 14 publications

(11 citation statements)

References 11 publications

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“…A modified CARD-FISH analysis (21,22) was used to probe Archaea-dominated acidic hot spring environmental samples. Fixed samples were placed in the wells of glass slides (PL-2026 Precision Lab Products) and air dried for 10 min at 46°C.…”

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confidence: 99%

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs

Munson-McGee

Field

Bateson

et al. 2015

Appl Environ Microbiol

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e Nanoarchaeota are obligate symbionts with reduced genomes first described from marine thermal vent environments. Here, both community metagenomics and single-cell analysis revealed the presence of Nanoarchaeota in high-temperature (ϳ90°C), acidic (pH Ϸ 2.5 to 3.0) hot springs in Yellowstone National Park (YNP) (United States). Single-cell genome analysis of two cells resulted in two nearly identical genomes, with an estimated full length of 650 kbp. Genome comparison showed that these two cells are more closely related to the recently proposed Nanobsidianus stetteri from a more neutral YNP hot spring than to the marine Nanoarchaeum equitans. Single-cell and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) analysis of environmental hot spring samples identified the host of the YNP Nanoarchaeota as a Sulfolobales species known to inhabit the hot springs. Furthermore, we demonstrate that Nanoarchaeota are widespread in acidic to near neutral hot springs in YNP. An integrated viral sequence was also found within one Nanoarchaeota single-cell genome and further analysis of the purified viral fraction from environmental samples indicates that this is likely a virus replicating within the YNP Nanoarchaeota.

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confidence: 99%

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs

Munson-McGee

Field

Bateson

et al. 2015

Appl Environ Microbiol

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“…3D-FISH ( Daims et al, 2006 ) was used to determine colocalization patterns on intact, unscraped biofilm. For 3D-FISH, whole fixed biofilm on the glass coupons was embedded in polyacrylamide prior to dehydration ( Daims et al, 2006 ; Brileya et al, 2014 ).…”

Section: Methodsmentioning

confidence: 99%

Biofilm growth mode promotes maximum carrying capacity and community stability during product inhibition syntrophy

et al. 2014

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Sulfate-reducing bacteria (SRB) can interact syntrophically with other community members in the absence of sulfate, and interactions with hydrogen-consuming methanogens are beneficial when these archaea consume potentially inhibitory H2 produced by the SRB. A dual continuous culture approach was used to characterize population structure within a syntrophic biofilm formed by the SRB Desulfovibrio vulgaris Hildenborough and the methanogenic archaeum Methanococcus maripaludis. Under the tested conditions, monocultures of D. vulgaris formed thin, stable biofilms, but monoculture M. maripaludis did not. Microscopy of intact syntrophic biofilm confirmed that D. vulgaris formed a scaffold for the biofilm, while intermediate and steady-state images revealed that M. maripaludis joined the biofilm later, likely in response to H2 produced by the SRB. Close interactions in structured biofilm allowed efficient transfer of H2 to M. maripaludis, and H2 was only detected in cocultures with a mutant SRB that was deficient in biofilm formation (ΔpilA). M. maripaludis produced more carbohydrate (uronic acid, hexose, and pentose) as a monoculture compared to total coculture biofilm, and this suggested an altered carbon flux during syntrophy. The syntrophic biofilm was structured into ridges (∼300 × 50 μm) and models predicted lactate limitation at ∼50 μm biofilm depth. The biofilm had structure that likely facilitated mass transfer of H2 and lactate, yet maximized biomass with a more even population composition (number of each organism) when compared to the bulk-phase community. Total biomass protein was equivalent in lactate-limited and lactate-excess conditions when a biofilm was present, but in the absence of biofilm, total biomass protein was significantly reduced. The results suggest that multispecies biofilms create an environment conducive to resource sharing, resulting in increased biomass retention, or carrying capacity, for cooperative populations.

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“…FISH has been used on a variety of biofilm samples. For example, FISH was used to determine spatial distribution of ammonia-oxidizing and nitrite-oxidizing bacteria in nitrifying aggregates or biofilms (78, 234) and the methanogen and sulfate-reducer components of anaerobic biofilms (75). Traditional and modified FISH have also been used to detect localized abundance of specific mRNAs in biofilm or termite gut microflora (235, 236).…”

Section: Biofilm Imagingmentioning

confidence: 99%

New Technologies for Studying Biofilms

et al. 2015

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Bacteria have traditionally been studied as single-cell organisms. In laboratory settings, aerobic bacteria are usually cultured in aerated flasks, where the cells are considered essentially homogenous. However, in many natural environments, bacteria and other microorganisms grow in mixed communities, often associated with surfaces. Biofilms are comprised of surface-associated microorganisms, their extracellular matrix material, and environmental chemicals that have adsorbed to the bacteria or their matrix material. While this definition of a biofilm is fairly simple, biofilms are complex and dynamic. Our understanding of the activities of individual biofilm cells and whole biofilm systems has developed rapidly, due in part to advances in molecular, analytical, and imaging tools and the miniaturization of tools designed to characterize biofilms at the enzyme level, cellular level, and systems level.

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3D-Fluorescence In Situ Hybridization of Intact, Anaerobic Biofilm

Cited by 14 publications

References 11 publications

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs

Biofilm growth mode promotes maximum carrying capacity and community stability during product inhibition syntrophy

New Technologies for Studying Biofilms

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