Characterization of depth-related microbial communities in lake sediment by denaturing gradient gel electrophoresis of amplified 16S rRNA fragments

Zhao, Xingqing; Yang, Liuyan; Yu, Zhenyang; Peng, Naiying; Xiao, Lin; Yin, Daqiang; Bo-qiang, Qin

doi:10.1016/s1001-0742(08)60035-2

Cited by 44 publications

(25 citation statements)

References 28 publications

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“…4 B,C). Our results agree with the observation of several studies that BCC in sediment is related to a depth gradient (Hewson and Fuhrman, 2006;Zhao et al, 2008;Liu et al, 2010). The depth gradients in redox potential o n l y diversity and composition of bacterial communities has been reported (Lindström and Bergström, 2005), they o n l y been reported (Lindström and Bergström, 2005), they noted that TP concentration statistically explained the difo n l y noted that TP concentration statistically explained the differences between the microbial community compositions o n l y ferences between the microbial community compositions and oxygen concentration should consistently affect the vertical distribution of bacterial communities (Tšertova et al, 2013).…”

Section: Environmental Factors Regulating the Bacterial Community Comsupporting

confidence: 93%

“…In the present study, no significant correlation (P<0.05) could be observed between the physicochemical parameters and the diversity of the bacterial community (H') at all the observed sites, which was consistent with a previous study in sediment of Lake Taihu by Zhao et al (2008). They speculated that the bacterial community structure in sediment was primarily regulated by integrative conditions rather than a single factor.…”

Section: The Relationship Between the Organic Matter Sources And The supporting

confidence: 91%

“…PCR-DGGE fingerprinting has been widely used in environmental microbiology and has been available to detect the similarities and differences of the dominant populations of microbial communities (Muyzer and Smalla, 1998;Lindstrom, 2000;Dorigo et al, 2005). Although a few studies have focused on assessing microbial distribution in sediments and their function (Macalady et al, 2000;Zhao et al, 2008), data on the relationships between the vertical variation of bacterial community composition (BCC) and OM sources recorded in the sediments are still scarce.…”

Section: Introductionmentioning

confidence: 99%

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Sources of organic matter affect depth-related microbial community composition in sediments of Lake Erhai, Southwest China

et al. 2014

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Sediment cores taken from different areas of the mesotrophic Lake Erhai were analysed to investigate the vertical distribution of bacterial community composition (BCC), as well as physicochemical parameters. PCR-denaturing gradient gel electrophoresis (DGGE), stable carbon isotope (δ 13 C), C/N atomic ratio and canonical correspondence analysis (CCA) were used to explore the relationships between the succession of bacterial communities and environmental variables, emphasising changes in the sources of organic matter (OM). OM sources resulted in a stable higher diversity of bacterial communities and broader enzymatic capabilities to access OM. We conclude that the differences in the diversity of bacterial communities in sediments differing in their sources of OM were related to environmental

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Section: Environmental Factors Regulating the Bacterial Community Comsupporting

confidence: 93%

Section: The Relationship Between the Organic Matter Sources And The supporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

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Sources of organic matter affect depth-related microbial community composition in sediments of Lake Erhai, Southwest China

et al. 2014

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“…DNA isolation was performed according to study of Simmon et al, 2006 andChristensen andBisgaard, 2010. For amplification forward primer 341F (5'-CCTA CGGGAGGCAGCAG-3') and reverse primer 907R (5'-CCGTCAATT CCTTTGAGTTT-3') were used (Zhao, et al, 2008). PCR was performed using commercial kit G2 Hot Start Green Master Mix (ROCHE, Germany).…”

Section: Pcr and Strain Identification By Sequencingmentioning

confidence: 99%

Biogenic amines degradation by microorganisms isolated from cheese

Butor

Pištěková

Purevdorj

et al. 2017

Potr. S. J. F. Sci.

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The aim of this study was the isolation and characterization of microorganisms able to degrade biogenic amines and their identification. Individual microorganisms were obtained by isolation from commercially available foodstuffs and food produced in the technological laboratories of Faculty of Technology, Tomas Bata University in Zlín and subsequently identified by MALDI-TOF MS. The results of MALDI-TOF MS identification were verified by 16S rRNA sequenation. In this work was studied the ability of 5 bacterial strains positive to biogenic amines degradation isolated from dairy products to decrease biogenic amines content in vitro and quantified reduction in the concentration of biogenic amines tryptamine, β-phenylethylamine, putrescine, cadaverine, histamine and tyramine. The level of degradation (decrease of biogenic amines) was determined on the base of the ability to grow in media with biogenic amines as the sole source carbon and nitrogen. The isolated strains with the ability of degradation of one or more biogenic amines were cultured in medium supplemented with relevant biogenic amines, the media derivatized with dansyl chloride and these amines separated by HPLC at a wavelength of 254 nm. From five tested strains identified as Bacillus subtilis, Bacillus pumilus, Enterobacter cloacae, Rhizobium radiobacter and Acinetobacter pitii, isolated from gouda type cheese, the greatest ability of degradation was observed in Bacillus subtilis, which was capable to degrade almost all amount of histamine, cadaverine and putrescine. Other four strains showed a lower rate of degradation than Bacillus subtilis, but the ability to degrade biogenic amines with these microorganisms was still significant.

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“…Their distribution and diversity in marine sediments have been studied for some years (Parkes et al, 1994;D'Hondt et al, 2004;Teske, 2005). Comparable studies in the lacustrine realm, however, are quite scarce and mainly focused on the water column (Humayoun et al, 2003) and/or very shallow sediments (Spring et al, 2000;Zhao et al, 2007). Thus, there is a need to determine the presence of living microbes in older lacustrine sediments, their growth, and metabolic paths, as well as their phylogenies that seem to differ from already known isolates.…”

Section: Introductionmentioning

confidence: 99%

Establishing Sampling Procedures in Lake Cores for Subsurface Biosphere Studies: Assessing In Situ Microbial Activity

Vuillemin

Ariztegui

Vásconcelos

2010

Scientific Drilling

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Sub-recent sediments in modern lakes are ideal to study early diagenetic processes with a combination of physical, chemical, and biological approaches. Current developments in the rapidly evolving ﬁeld of geomicrobiology have allowed determining the role of microbes in these processes. Their distribution and diversity in marine sediments have been studied for some years. Comparable studies in the lacustrine realm, however, are quite scarce and mainly focused on the water column and/or very shallow sedi-ments. Thus, there is a need to determine the presence of living microbes in older lacustrine sediments. During the PASADO (Potrok Aike Maar Lake Sediment Archive Drilling Project) ICDP (International Continental Scientiﬁc Drilling Program) drilling, more than 500 meters of sedimentary cores were retrieved from this crater lake. A 100-m-long core was dedicated to a detailed geomicrobiological study. Here we report a complete in situ sampling procedure that aims to recover aseptic samples as well as determining active in situ biological activit

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Characterization of depth-related microbial communities in lake sediment by denaturing gradient gel electrophoresis of amplified 16S rRNA fragments

Cited by 44 publications

References 28 publications

Sources of organic matter affect depth-related microbial community composition in sediments of Lake Erhai, Southwest China

Sources of organic matter affect depth-related microbial community composition in sediments of Lake Erhai, Southwest China

Biogenic amines degradation by microorganisms isolated from cheese

Establishing Sampling Procedures in Lake Cores for Subsurface Biosphere Studies: Assessing In Situ Microbial Activity

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