The Domain-specific Probe EUB338 is Insufficient for the Detection of all Bacteria: Development and Evaluation of a more Comprehensive Probe Set

Daims, Holger; Brühl, A.; Amann, Rudolf; Schleifer, Karl‐Heinz; Wagner, Michael

doi:10.1016/s0723-2020(99)80053-8

Cited by 2,080 publications

(1,102 citation statements)

References 50 publications

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“…Large zones of DAPI stained cells without hybridization to general microbial probes have been observed in anaerobic granules previously and were attributed to substrate limitations at the center and low pH close to the surface of the granules (Batstone et al, 2004). Alternatively, it may reflect incomplete coverage of this microbial community by the Bact0338 probe, as a mixture of probes has been recommended to obtain a more complete bacterial count (Daims et al, 1999).…”

Section: Domain-level Community Structurementioning

confidence: 94%

Effects of the antimicrobial tylosin on the microbial community structure of an anaerobic sequencing batch reactor

Shimada

Zilles

et al. 2010

Biotech & Bioengineering

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Morgenroth, Eberhard; and Raskin, Lutgarde, "Effects of the antimicrobial tylosin on the microbial community structure of an anaerobic sequencing batch reactor" (2010). Civil Engineering Faculty Publications. 37. http://digitalcommons.unl.edu/civilengfacpub/37 AbstractThe effects of the antimicrobial tylosin on a methanogenic microbial community were studied in a glucosefed laboratory-scale anaerobic sequencing batch reactor (ASBR) exposed to stepwise increases of tylosin (0, 1.67, and 167 mg/L). The microbial community structure was determined using quantitative fluorescence in situ hybridization (FISH) and phylogenetic analyses of bacterial 16S ribosomal RNA (rRNA) gene clone libraries of biomass samples. During the periods without tylosin addition and with an influent tylosin concentration of 1.67 mg/L, 16S rRNA gene sequences related to Syntrophobacter were detected and the relative abundance of Methanosaeta species was high. During the highest tylosin dose of 167 mg/L, 16S rRNA gene sequences related to Syntrophobacter species were not detected and the relative abundance of Methanosaeta decreased considerably. Throughout the experimental period, Propionibacteriaceae and high GC Gram-positive bacteria were present, based on 16S rRNA gene sequences and FISH analyses, respectively. The accumulation of propionate and subsequent reactor failure after long-term exposure to tylosin are attributed to the direct inhibition of propionate-oxidizing syntrophic bacteria closely related to Syntrophobacter and the indirect inhibition of Methanosaeta by high propionate concentrations and low pH.

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Section: Domain-level Community Structurementioning

confidence: 94%

Effects of the antimicrobial tylosin on the microbial community structure of an anaerobic sequencing batch reactor

Shimada

Zilles

et al. 2010

Biotech & Bioengineering

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“…Several horseradish peroxidase probes were used to characterize the composition of the bacterial community in the original water samples, using the same procedure as described in Alonso-Sáez and Gasol (2007). The horseradish peroxidase-labeled probes used were as follows: EUB-338, EUB-II and EUB-III (target most Eubacteria; Amann et al, 1990;Daims et al, 1999); GAM42a (targets most Gammaproteobacteria; Manz et al, 1992); ALF968 (targets most Alphaproteobacteria; Neef, 1997); CF319 (targets many groups belonging to the Bacteroidetes group; Manz et al, 1996); ROS537 (targets members of the Roseobacter-SulfitobacterSilicibacter group; Eilers et al, 2001); NOR5-730 (targets members of the NOR5 cluster; Eilers et al, 2001); Alt1413 (targets Alteromonas and Colwellia; Eilers et al, 2000b); and SAR11-441 R (targets the SAR11 cluster; Morris et al, 2002); EUB antisense probe NON338 (Wallner, 1993) was used as a negative control. All probes were purchased from biomers.net (Ulm, Germany).…”

Section: Phytoplankton Cultures and Preparation Of Radiolabeled Exudatesmentioning

confidence: 99%

Bacterioplankton niche partitioning in the use of phytoplankton-derived dissolved organic carbon: quantity is more important than quality

2016

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Some prokaryotes are known to be specialized in the use of phytoplankton-derived dissolved organic carbon (DOCp) originated by exudation or cell lysis; however, direct quantification measurements are extremely rare. Several studies have described bacterial selectivity based on DOCp quality, but very few have focused on the quantity of DOCp, and the relative importance of each of these variables (for example, quantity versus quality) on prokaryote responses. We applied an adapted version of the MAR-FISH (microautoradiography coupled with catalyzed reporter deposition fluorescence in situ hybridization) protocol using radiolabelled exudates from axenic algal cultures to calculate a specialization index (d') for large bacterioplankton phylogenetic groups using DOCp from different phytoplankton species and at different concentrations to elucidate to what extent the bacterial response to DOCp is driven by resource quantity (different DOCp concentrations) or by quality (DOCp from different phytoplankton species). All bacterial phylogenetic groups studied had lower d' at higher DOCp concentration, indicating more generalist behavior at higher resource availabilities. Indeed, at increasing resource concentrations, most bacterial groups incorporated DOCp indiscriminately, regardless of its origin (or quality). At low resource concentrations, only some specialists were able to actively incorporate the various types of organic matter effectively. The variability of bacterial responses to different treatments was systematically higher at varying concentrations than at varying DOCp types, suggesting that, at least for this range of concentrations (10-100 μM), DOCp quantity affects bacterial responses more than quality does. Therefore, resource quantity may be more relevant than resource quality in the bacterial responses to DOCp and affect how bacterioplankton use phytoplankton-derived carbon.

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“…3). First the samples were hybridized with a probe set (EUB338, EUB338-II, EUB338-III) designed to target almost all bacteria [7], then with previously published group specific probes ( Fig. 3; [8,9]).…”

Section: Fluorescence In Situ Hybridization Microscopy and Quantificmentioning

confidence: 99%

Nitrifying and heterotrophic population dynamics in biofilm reactors: effects of hydraulic retention time and the presence of organic carbon

Melo²,

et al. 2002

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Two biofilm reactors operated with hydraulic retention times of 0.8 and 5.0 h were used to study the links between population dynamics and reactor operation performance during a shift in process operation from pure nitrification to combined nitrification and organic carbon removal. The ammonium and the organic carbon loads were identical for both reactors. The composition and dynamics of the microbial consortia were quantified by fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes combined with confocal laser scanning microscopy, and digital image analysis. In contrast to past research, after addition of acetate as organic carbon nitrification performance decreased more drastically in the reactor with longer hydraulic retention time. FISH analysis showed that this effect was caused by the unexpected formation of a heterotrophic microorganism layer on top of the nitrifying biofilm that limited nitrifiers oxygen supply. Our results demonstrate that extension of the hydraulic retention time might be insufficient to improve combined nitrification and organic carbon removal in biofilm reactors. r

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The Domain-specific Probe EUB338 is Insufficient for the Detection of all Bacteria: Development and Evaluation of a more Comprehensive Probe Set

Cited by 2,080 publications

References 50 publications

Effects of the antimicrobial tylosin on the microbial community structure of an anaerobic sequencing batch reactor

Effects of the antimicrobial tylosin on the microbial community structure of an anaerobic sequencing batch reactor

Bacterioplankton niche partitioning in the use of phytoplankton-derived dissolved organic carbon: quantity is more important than quality

Nitrifying and heterotrophic population dynamics in biofilm reactors: effects of hydraulic retention time and the presence of organic carbon

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