Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: molecular and cultivation studies

Spring, Stefan; Schulze, Renate; Overmann, Jörg; Schleifer, Karl‐Heinz

doi:10.1111/j.1574-6976.2000.tb00559.x

Cited by 183 publications

(98 citation statements)

References 108 publications

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“…Our sequence analysis further identified phylotypes which affiliate with the novel Holophaga/Acidobacterium and the Nitrospira phylum, from which only 3 and 2 isolates are known, respectively (Watson et al 1986, Ehrlich et al 1995, Spring et al 2000. Bacteria of the Holophaga/Acidobacterium group have recently been found in sediments of Lake Baikal and Lake Constance (Spring et al 2000).…”

Section: Discussionmentioning

confidence: 74%

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Seasonal patterns of the bacterioplankton community composition in a large mesotrophic lake

Zwisler¹,

Selje²,

Simon³

2003

Aquat. Microb. Ecol.

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The composition of the bacterioplankton community in mesotrophic Lake Constance was studied from April 1996 to December 1997 by fluorescence in situ hybridization (FISH) with group specific oligonucleotide probes and denaturing gradient gel electrophoresis (DGGE). Between 10 and 59% of the DAPI-stained cells were detected as Bacteria with means of 38 ± 12, 27 ± 10 and 23 ± 6% at 3, 20, and 50 m depth, respectively. In the euphotic zone at 3 m depth, β-Proteobacteria always constituted highest proportions of the bacterial community detected by FISH and constituted 6 to 23% of the DAPIstained cells with a mean of 12%. Proportions of bacteria belonging to the Cytophaga/Flavobacteria (CF) cluster and the α-Proteobacteria at this depth were 5.4 ± 2.5 and 4.1 ± 3.5%, respectively. Proportions of β-Proteobacteria decreased at 20 and 50 m, whereas that of α-Proteobacteria remained constant and that of the CF-cluster increased to 7.4%, such that they comprised similar proportions as β-Proteobacteria at 50 m depth. γ-Proteobacteria were always of minor importance and constituted only 2.2 ± 1.3% of the DAPI cell counts. Cumulative proportions of all detected bacterial groups constituted 75% of the Bacteria counts at 3 m, 84% at 20 m and 99% at 50 m. The DGGE analysis of the bacterioplankton community showed seasonal and vertical variations of the banding patterns even though several bands occurred throughout the study period and at all depths. A cluster analysis revealed distinct bacterial clusters of the phytoplankton spring bloom and the later period and of epilimnetic and hypolimnetic waters. The sequence analysis of the excised bands indicated that all groups which were detected by FISH were represented in the patterns. Sequence similarities of the retrieved sequences to known isolates were < 90 to 96.1%, and to other phylotypes as close as 99%. Phylotypes of β-Proteobacteria and Actinobacteria of the typical banding patterns affiliated closely with recently described clusters of typical freshwater bacteria. In addition, we identified phylotypes of the Holophaga/Acidobacterium and Nitrospira phylum during the stratified period in samples from 50 m and during mixing from all 3 depths. KEY WORDS: Bacteria · DGGE · Fluorescence in situ hybridization · Lake Constance · Actinobacteria · Nitrospira · Holophaga Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 31: [211][212][213][214][215][216][217][218][219][220][221][222][223][224][225] 2003

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Section: Discussionmentioning

confidence: 74%

“…Bacteria of the Holophaga/Acidobacterium group have recently been found in sediments of Lake Baikal and Lake Constance (Spring et al 2000). Obviously, bacteria of this novel phylum are also present in the hypolimnion.…”

Section: Discussionmentioning

confidence: 99%

Seasonal patterns of the bacterioplankton community composition in a large mesotrophic lake

Zwisler¹,

Selje²,

Simon³

2003

Aquat. Microb. Ecol.

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“…Phospholipids were saponified and methylated to fatty acid methyl esters (FAMEs) under N 2 at 37°C and then dissolved in hexane containing a 19:0 (methyl nonadecanoate fatty acid) FAME standard. The resulting FAMEs were analyzed with a gas chromatograph mass spectrometer ( (Sundh et al 1997;Spring et al 2000;ZechmeisterBoltenstern et al 2011); 18:1ω9c, 18:2ω6c, and 18:2ω9t for fungi (Frostegard and Bååth 1996;ZechmeisterBoltenstern et al 2011); and 10Me18:0 for Actinobacteria (Sundh et al 1997;Spring et al 2000). The PLFAs 16:1ω7c,18:1ω7t,19:1ω9t,18:1ω8t,18:1ω9t, and 18:1ω9c represent monounsaturated fatty acids, while 15:0, 16:0, 17:0, 18:0, i15:0, a13:0, a15:0, a17:0, cyc17:0, and 10Me18:0 represent saturated fatty acids.…”

Section: Soil Sampling and Analysismentioning

confidence: 99%

Crop residue management and fertilization effects on soil organic matter and associated biological properties

Zhao

Zhang

et al. 2016

Environ Sci Pollut Res

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Xiying, "Crop residue management and fertilization effects on soil organic matter and associated biological properties" (2016 Abstract Returning crop residue may result in nutrient reduction in soil in the first few years. A two-year field experiment was conducted to assess whether this negative effect is alleviated by improved crop residue management (CRM). Nine treatments (3 CRM and 3 N fertilizer rates) were used. The CRM treatments were (1) R0: 100 % of the N using mineral fertilizer with no crop residues return; (2) R: crop residue plus mineral fertilizer as for the R0; and (3) Rc: crop residue plus 83 % of the N using mineral and 17 % manure fertilizer. Each CRM received N fertilizer rates at 270, 360, and 450 kg N ha −1 year −1 . At the end of the experiment, soil NO 3 -N was reduced by 33 % from the R relative to the R0 treatment, while the Rc treatment resulted in a 21 to 44 % increase in occluded particulate organic C and N, and 80°C extracted dissolved organic N, 19 to 32 % increase in microbial biomass C and protease activity, and higher monounsaturated phospholipid fatty acid (PLFA):saturated PLFA ratio from stimulating growth of indigenous bacteria when compared with the R treatment. Principal component analysis showed that the Biolog and PLFA profiles in the three CRM treatments were different from each other. Overall, these properties were not influenced by the used N fertilizer rates. Our results indicated that application of 17 % of the total N using manure in a field with crop residues return was effective for improving potential plant N availability and labile soil organic matter, primarily due to a shift in the dominant microorganisms.

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“…33 MALDI-TOF MS has also been applied to obtain abundant, accurate mass ion signals of the phospholipids in bacteria. [34][35][36][37][38][39] Therefore, the characterization of lipids in bacteria and other microorganisms plays a crucial role for taxonomic identification, differentiation of pathogenic species, and understanding of metabolic processes under normal or stressed growth conditions.…”

Section: Introductionmentioning

confidence: 99%

Lipid fingerprinting of Bacillus spp. using online MALDI-TOF mass spectrometry

et al. 2012

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Rapid identification of Bacillus spores has attracted great interest in the medical and forensic communities due to the highly pathogenic nature of certain Bacillus species and its potential application in bioweapons. In this study, we evaluated the feasibility of rapid and reliable identification of several Bacillus spp. (B. subtilis, B. cereus, B. megaterium, B. pumilus, and B. sphaericus) using online MALDI-TOF mass spectrometry combined with lipid profiling. The bacterial cultures in liquid medium were extracted with methanol and chloroform, and the extracts were aerosolized into droplets and immediately analyzed with an online MALDI-TOF mass spectrometer. Results showed that phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and diglycosyldiacylglycerol (DGDG) were present in the mass spectra, as alkali metal adducts. The unique lipid profiles obtained from these Bacillus spp. allowed us to differentiate between them. The reliability and reproducibility of the rapid identification method for Bacillus were tested under different experimental conditions. An alternative online chemotaxonomic method for bacterial identification is demonstrated.

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Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: molecular and cultivation studies

Cited by 183 publications

References 108 publications

Seasonal patterns of the bacterioplankton community composition in a large mesotrophic lake

Seasonal patterns of the bacterioplankton community composition in a large mesotrophic lake

Crop residue management and fertilization effects on soil organic matter and associated biological properties

Lipid fingerprinting of Bacillus spp. using online MALDI-TOF mass spectrometry

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