Microbial Diversity in Water and Sediment of Lake Chaka, an Athalassohaline Lake in Northwestern China

Jiang, Hongchen; Hc,; Dong, Shen; Hl,; Zhang, Bo; Gx,; A, Yu; Bs,; Chapman, Mary; Lr,; Mw,

doi:10.1128/aem.02230-06

Cited by 23 publications

(21 citation statements)

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“…Salinibacter has been found to the most abundant bacterium in solar salterns of Mallorca and Alicante (Spain) (Anton et al, 1999(Anton et al, , 2000, contributing between 5% and 25% of the total prokaryotic community. Salinibacter is also well represented in the bacterial community of other saline habitats such as Tuz Lake (Mutlu et al, 2008), the thalassohaline Lake Chaka (Jiang et al, 2006), as well as in the athalassohaline lakes from Los Andes (Demergasso et al, 2004). On the other hand, P. halophila has been defined as an extremely halophilic bacterium, although its phylogenetic affiliation is not clear and studies have to be undertaken to clarify its taxonomic position (Sorokin & Tindall, 2006).…”

Section: Discussionmentioning

confidence: 99%

Characterization of Salicola sp. âIC10, a lipase- and protease-producing extreme halophile

Moreno

Garcı́a²,

Ventosa

et al. 2009

FEMS Microbiology Ecology

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In order to explore the diversity of extreme halophiles able to produce different hydrolytic enzymes (amylase, protease, lipase and DNAse) in hypersaline habitats of South Spain, a screening program was performed. A total of 43 extreme halophiles showing hydrolytic activities have been isolated and characterized. The isolated strains were able to grow optimally in media with 15-20% (w/v) total salts and in most cases, growth was detected up to 30% (w/v) total salts. Most hydrolase producers were assigned to the family Halobacteriaceae, belonging to the genera Halorubrum (22 strains), Haloarcula (nine strains) and Halobacterium (nine strains), and three isolates were characterized as extremely halophilic bacteria (genera Salicola, Salinibacter and Pseudomonas). An extremely halophilic isolate, strain IC10, showing lipase and protease activities and identified as a Salicola strain of potential biotechnological interest, was further studied. The optimum growth conditions for this strain were 15-20% (w/v) NaCl, pH 8.0, and 37 degrees C. Zymographic analysis of strain IC10 detected the lipolytic activity in the intracellular fraction, showing the highest activity against p-nitrophenyl-butyrate as a substrate in a colorimetric assay, whereas the proteolytic activity was detected in the extracellular fraction. This protease degraded casein, gelatin, bovine serum albumin and egg albumin.

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Section: Discussionmentioning

confidence: 99%

Characterization of Salicola sp. âIC10, a lipase- and protease-producing extreme halophile

Moreno

Garcı́a²,

Ventosa

et al. 2009

FEMS Microbiology Ecology

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“…Bacterial DNA was purified using DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) and used as a PCR template. PCR amplification of 16S rRNA genes was conducted using the 16S Barcoding Kit (SQK-RAB204; Oxford Nanopore Technologies, Oxford, UK) containing the 27F/1492R primer set [19,20] and LongAmp TM Taq 29 Master Mix (New England Biolabs, Ipswich, MA, USA). Amplification was performed using an Applied Biosystems Veriti TM Thermal Cycler (Thermo Fischer Scientific, Waltham, MA, USA) with the following PCR conditions: initial denaturation at 95°C for 3 min, 25 cycles of 95°C for 20 s, 55°C for 30 s, and 65°C for 2 min, followed by a final extension at 65°C for 5 min.…”

Section: Direct Pcr Amplification Of 16s Rrna Genesmentioning

confidence: 99%

“…We used a commercially available kit (16S Barcoding Kit; Oxford Nanopore Technologies) with primers optimized for 16S rRNA amplicon sequencing on the MinION TM platform. The primers were designed to amplify the near-full-length 16S rRNA gene for bacterial identification [19,20]. Each indexing primer has a unique barcode for multiplexing and contains a tag sequence at the 5ʹ-end for attachment of sequencing adapters.…”

Section: Direct Pcr Approach For Amplifying 16s Rrna Genes From Crudementioning

confidence: 99%

Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION™ nanopore sequencer

et al. 2019

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Rapid identification of bacterial pathogens is crucial for appropriate and adequate antibiotic treatment, which significantly improves patient outcomes. 16S ribosomal RNA (rRNA) gene amplicon sequencing has proven to be a powerful strategy for diagnosing bacterial infections. We have recently established a sequencing method and bioinformatics pipeline for 16S rRNA gene analysis utilizing the Oxford Nanopore Technologies MinION™ sequencer. In combination with our taxonomy annotation analysis pipeline, the system enabled the molecular detection of bacterial DNA in a reasonable time frame for diagnostic purposes. However, purification of bacterial DNA from specimens remains a rate‐limiting step in the workflow. To further accelerate the process of sample preparation, we adopted a direct PCR strategy that amplifies 16S rRNA genes from bacterial cell suspensions without DNA purification. Our results indicate that differences in cell wall morphology significantly affect direct PCR efficiency and sequencing data. Notably, mechanical cell disruption preceding direct PCR was indispensable for obtaining an accurate representation of the specimen bacterial composition. Furthermore, 16S rRNA gene analysis of mock polymicrobial samples indicated that primer sequence optimization is required to avoid preferential detection of particular taxa and to cover a broad range of bacterial species. This study establishes a relatively simple workflow for rapid bacterial identification via MinION™ sequencing, which reduces the turnaround time from sample to result, and provides a reliable method that may be applicable to clinical settings.

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“…On the other side, and despite their ecological interest, the underlying sediments of these ponds have been studied only very sparsely. The intriguing biogeochemistry of the salt-saturated sediments and the importance of microbial mats as model systems of the early Earth (Dundas, 1998;Hoehler et al, 2001) have induced numerous studies focused on the benthic microbial assemblages of a variety of other saline and hypersaline habitats, such as inland lakes, lagoons and deep-sea basins (van der Wielen et al, 2005;Jiang et al, 2006;Ley et al, 2006;Sahl et al, 2008). The first molecular diversity survey on anoxic sediments of crystallizer ponds reported a surprisingly high level of prokaryotic diversity and community structures strongly influenced by salinity (Mouné et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

Extremely halophilic microbial communities in anaerobic sediments from a solar saltern

López‐López

Yarza

Richter

et al. 2010

Environ Microbiol Rep

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The prokaryotic communities inhabiting hypersaline sediments underlying a crystallizer pond of a Mediterranean solar saltern have been studied in a polyphasic approach including 16S rRNA and dsrAB gene libraries analysis [the last encoding for dissimilatory (bi)sulfite reductase], most probable number of cultivable counts, and metabolic measurements of sulfate reduction. The samples studied here represent one of the most hypersaline anoxic environments sampled worldwide that harbour a highly diverse microbial community different from those previously reported in other hypersaline sediments. Both bacterial and archaeal types are present but, contrarily to the overlying brine system, the former dominates. Molecular analyses indicated that the bacterial fraction is highly diverse and mostly composed by groups related to sulfate-reducing bacteria (SRB). In good agreement with this, sulfate-reducing activity was detected in the sediment, as well as the metabolic diversity within SRB (as indicated by the use of different electron donors in enrichments). On the other hand, the archaeal fraction was phylogenetically homogeneous and, surprisingly, strongly affiliated with the MBSl-1 candidate division, an euryarchaeotal group only reported in deep-sea hypersaline anoxic basins of the Western Mediterranean, for which a methanogenic metabolism was hypothesized. The hypersaline studied samples constitute a valuable source of new prokaryotic types with metabolisms adapted to the prevalent in situ extreme conditions.

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Microbial Diversity in Water and Sediment of Lake Chaka, an Athalassohaline Lake in Northwestern China

Cited by 23 publications

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Characterization of Salicola sp. âIC10, a lipase- and protease-producing extreme halophile

Characterization of Salicola sp. âIC10, a lipase- and protease-producing extreme halophile

Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION™ nanopore sequencer

Extremely halophilic microbial communities in anaerobic sediments from a solar saltern

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Microbial Diversity in Water and Sediment of Lake Chaka, an Athalassohaline Lake in Northwestern China

Cited by 23 publications

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Characterization of Salicola sp. âIC10, a lipase- and protease-producing extreme halophile

Characterization of Salicola sp. âIC10, a lipase- and protease-producing extreme halophile

Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION™ nanopore sequencer

Extremely halophilic microbial communities in anaerobic sediments from a solar saltern

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Characterization of Salicola sp. âIC10, a lipase- and protease-producing extreme halophile

Characterization of Salicola sp. âIC10, a lipase- and protease-producing extreme halophile