Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metagenomic data of free cyanide and thiocyanate degrading bacterial communities.

ABSTRACT: The data presented in this article contains the bacterial community structure of the free cyanide (CN-) and thiocyanate (SCN-) degrading organisms that were isolated from electroplating wastewater and synthetic SCN- containing wastewater. PCR amplification of the 16S rRNA V1-V3 regions was undertaken using the 27F and 518R oligonucleotide primers following the metacommunity DNA extraction procedure. The PCR amplicons were processed using the illumina® reaction kits as per manufacturer?s instruction and sequenced using the illumina® MiSeq-2000, using the MiSeq V3 kit. The data was processed using bioinformatics tools such as QIIME and the raw sequence files are available via NCBI?s Sequence Read Archive (SRA) database.

SUBMITTER: Mekuto L

PROVIDER: S-EPMC5512189 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Metagenomic data of free cyanide and thiocyanate degrading bacterial communities.

Mekuto Lukhanyo L Ntwampe Seteno K O SKO Mudumbi John B N JBN Akinpelu Enoch A EA Mewa-Ngongang Maxwell M

Data in brief 20170704

The data presented in this article contains the bacterial community structure of the free cyanide (CN-) and thiocyanate (SCN-) degrading organisms that were isolated from electroplating wastewater and synthetic SCN- containing wastewater. PCR amplification of the 16S rRNA V1-V3 regions was undertaken using the 27F and 518R oligonucleotide primers following the metacommunity DNA extraction procedure. The PCR amplicons were processed using the illumina® reaction ki ...[more]

PMID: 28748209

Similar Datasets

Microbial communities associated with the co-metabolism of free cyanide and thiocyanate under alkaline conditions.

Project description:This study focused on the identification of free cyanide (CDO) and thiocyanate (TDO) degrading microbial communities using a culture-dependent and independent approach. Culturable microbial species were isolated from the CDOs (n = 13) and TDOs (n = 18). The CDOs were largely dominated by Bacillus sp. while the TDOs were dominated by Bacillus sp., Klebsiella oxytoca, Providencia sp. and Pseudomonas sp. However, 16S rRNA amplicon gene-sequencing revealed the complexity and diversity of the microbial communities in contrast to the organisms that were detected using culture-dependent technique. Overall, the organisms were mainly dominated by Myroides odoratimimus and Proteus sp. at 37.82 and 30.5% for CDOs, and 35.26 and 17.58% for TDOs, respectively. The co-culturing of the CDOs and TDOs resulted in biochemical changes of key metabolic enzymes, and this resulted in the complete degradation of CN- and SCN- simultaneously; a phenomenon which has not been witnessed, especially under alkaline conditions. Current ongoing studies are focused on the application of these organisms for the biodegradation of CN- and SCN- in a continuous system, under changing operational parameters, to assess their effectiveness in the biodegradation of CN- and SCN-.

| S-EPMC5796949 | biostudies-literature

Co-metabolism of thiocyanate and free cyanide by Exiguobacterium acetylicum and Bacillus marisflavi under alkaline conditions.

Project description:The continuous discharge of cyanide-containing effluents to the environment has necessitated for the development of environmentally benign treatment processes that would result in complete detoxification of the cyanide-containing wastewaters, without producing additional environmental toxicants. Since biological detoxification of hazardous chemical compounds has been renowned for its robustness and environmental-friendliness, the ability of the Exiguobacterium acetylicum (GenBank accession number KT282229) and Bacillus marisflavi (GenBank accession number KR016603) to co-metabolise thiocyanate (SCN-) and free cyanide (CN-) under alkaline conditions was evaluated. E. acetylicum had an SCN- degradation efficiency of 99.9 % from an initial SCN- concentration of 150 mg SCN-/L, but the organism was unable to degrade CN-. Consequently, B. marisflavi had a CN- degradation efficiency of 99 % from an initial concentration of 200 mg CN-/L. Similarly, the organism was unable to degrade SCN-; hence, this resulted in the evaluation of co-metabolism of SCN- and CN- by the two microbial species. Optimisation of operational conditions was evaluated using response surface methodology (RSM). A numeric optimisation technique was used to evaluate the optimisation of the input variables i.e. pH, temperature, SCN- and CN- concentrations. The optimum conditions were found to be as follows: pH 9.0, temperature 34 °C, 140 mg SCN-/L and 205 mg CN-/L under which complete SCN- and CN- degradation would be achieved over a 168-h period. Using the optimised data, co-metabolism of SCN- and CN- by both E. acetylicum and B. marisflavi was evaluated, achieving a combined degradation efficiency of ?99.9 %. The high degradative capacity of these organisms has resulted in their supplementation on an active continuous biological degradation system that is treating both SCN- and CN-.

| S-EPMC4990519 | biostudies-literature

Isoprene-Degrading Bacterial Communities

Project description:Analysis of Isoprene-degrading Bacteria

| PRJEB42641 | ENA

Lignocellulosic degrading bacterial communities

Project description:Lignocellulosic degrading bacterial communities Raw sequence reads

| PRJNA865006 | ENA

Free cyanide and thiocyanate biodegradation by Pseudomonas aeruginosa STK 03 capable of heterotrophic nitrification under alkaline conditions.

Project description:An alkali-tolerant bacterium, Pseudomonas aeruginosa STK 03 (accession number KR011154), isolated from an oil spill site, was evaluated for the biodegradation of free cyanide and thiocyanate under alkaline conditions. The organism had a free cyanide degradation efficiency of 80 and 32 % from an initial concentration of 250 and 450 mg CN-/L, respectively. Additionally, the organism was able to degrade thiocyanate, achieving a degradation efficiency of 78 and 98 % from non- and free cyanide spiked cultures, respectively. The organism was capable of heterotrophic nitrification but was unable to denitrify aerobically. The organism was unable to degrade free cyanide in the absence of a carbon source, but it was able to degrade thiocyanate heterotrophically, achieving a degradation efficiency of 79 % from an initial concentration of 250 mg SCN-/L. Further increases in thiocyanate degradation efficiency were only observed when the cultures were spiked with free cyanide (50 mg CN-/L), achieving a degradation efficiency of 98 % from an initial concentration of 250 mg SCN-/L. This is the first study to report free cyanide and thiocyanate degradation by Pseudomonas aeruginosa. The higher free cyanide and thiocyanate tolerance of the isolate STK 03, which surpasses the stipulated tolerance threshold of 200 mg CN-/L for most organisms, could be valuable in microbial consortia for the degradation of cyanides in an industrial setting.

| S-EPMC4697911 | biostudies-literature

Metagenomic insights into zooplankton-associated bacterial communities.

Project description:Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene, we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton-associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton-associated bacterial community is able to colonize the zooplankton's internal and external surfaces using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton-associated microbiome suggests that this zooplankton-associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters.

| S-EPMC5836950 | biostudies-literature

Data on metagenomic profiles of bacterial endophyte communities associated with Dicoma anomala.

Project description:Plants harbor varied communities of bacterial endophytes which play a crucial role in plant health and growth. Dicoma anomala is a medicinal plant that is known for its excellent ethnomedicinal uses which include treatment of coughs, fever, ulcers, and dysentery. This data in Brief article provides information on the diversity of bacterial endophytes associated with a medicinal plant, Dicoma anomala targeting the 16S rRNA gene using Illumina sequencing technology during three different seasons. Plant samples were collected in Eisleben, Limpopo province, South Africa, in the months of April, June, August and October 2018. The dataset revealed that the leaf samples collected in August had the highest species diversity as indicated by the Shannon index (4.25), Chao1 (1456.01), abundance-based coverage estimator (ACE) (1492.07) and the Simpson indices of diversity (0.05) irrespective of the species. The order of the bacterial endophyte's richness in D. anomala was April> October> June> August, from lowest to highest. The taxonomic composition analysis showed that most endophytic bacteria were composed of Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Chloroflexi. Some endophytic bacteria were found to be tissue specific. Sequences of Cutibacterium, Acinetobacter and Methylobacterium were prevalent in the leaves, whereas Amycolatopsis and Bradyrhizobium were the dominant genera in the root samples.

| S-EPMC9006632 | biostudies-literature

Insertion Loci in Synthetic and Thiocyanate Degrading Microbial Communities

Project description:Insertion Loci Sequencing in Synthetic and Thiocyanate Degrading Microbial Communities

| PRJNA649017 | ENA

Metagenomic analysis reveals specific BTEX degrading microorganisms of a bacterial consortium.

Project description:Petroleum hydrocarbon contamination is of environmental and public health concerns due to its toxic components. Bioremediation utilizes microbial organisms to metabolism and remove these contaminants. The aim of this study was to enrich a microbial community and examine its potential to degrade petroleum hydrocarbon. Through successive enrichment, we obtained a bacterial consortium using crude oil as sole carbon source. The 16 S rRNA gene analysis illustrated the structural characteristics of this community. Metagenomic analysis revealed the specific microbial organisms involved in the degradation of cyclohexane and all the six BTEX components, with a demonstration of the versatile metabolic pathways involved in these reactions. Results showed that our consortium contained the full range of CDSs that could potentially degrade cyclohexane, benzene, toluene, and (o-, m-, p-) xylene completely. Interestingly, a single taxon that possessed all the genes involved in either the activation or the central intermediates degrading pathway was not detected, except for the Novosphingobium which contained all the genes involved in the upper degradation pathway of benzene, indicating the synergistic interactions between different bacterial genera during the hydrocarbon degradation.

| S-EPMC10192505 | biostudies-literature

Metagenomic data on Anadara granosa associated bacterial communities using culture dependent approaches and 16S rRNA sequencing.

Project description:This article contains data on the bacterial communities and its diversity associated with Anadara granosa. The A. granosa samples were obtained from two major estuaries in Penang, Malaysia using a culture dependent and 16S rRNA Illumina sequencing approaches. A. granosa, a commercial blood cockles and popular seafoods, is fragile to the surrounding environments. Thus, our research focused to better understand the bacterial communities and it diversity in the A. granosa, as well as on the generation of a metagenomic library from A. granosa to further understanding on it diversity. The bacteria Vibrionaceae (34.1%) was predominant in the A. granosa from both environments followed by Enterobacteriaceae (33.3%) and Bacillaceae (16.75%). Vibrio sp., Klebsiella sp., and Bacillus subtilis were the most abundant species present. The data generated in this research is the first metagenomic examination of A. granosa and will provide as a baseline to understand the bacterial communities associated with A. granosa and its surrounding natural environments.

| S-EPMC5997914 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data