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De novo metagenomic assembly of microbial communities from the lower convective layer of the Red Sea Atlantis II brine environment.
The lower convective layer of the Red Sea Atlantis II brine pool (ATII-LCL) is an unexplored environment that is characterized by harsh conditions of high temperature (68ºC), high salinity (26%), high concentration of heavy metals and very low oxygen content. Microbial communities inhabiting this ex...
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2013
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| _version_ | 1867613416357625856 |
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| access_status_str | Open Access |
| author | Ali, Osama Said |
| author_browse | Ali, Osama Said |
| author_facet | Ali, Osama Said |
| author_sort | Ali, Osama Said |
| collection | Thesis |
| dc_rights_str_mv | The author retains all rights with regard to copyright. The author certifies that written permission from the owner(s) of third-party copyrighted matter included in the thesis, dissertation, paper, or record of study has been obtained. The author further certifies that IRB approval has been obtained for this thesis, or that IRB approval is not necessary for this thesis. Insofar as this thesis, dissertation, paper, or record of study is an educational record as defined in the Family Educational Rights and Privacy Act (FERPA) (20 USC 1232g), the author has granted consent to disclosure of it to anyone who requests a copy. |
| description | The lower convective layer of the Red Sea Atlantis II brine pool (ATII-LCL) is an unexplored environment that is characterized by harsh conditions of high temperature (68ºC), high salinity (26%), high concentration of heavy metals and very low oxygen content. Microbial communities inhabiting this extreme environment are expected to have unique structural and functional adaptations to survive such harsh conditions. These adaptations can be expressed by novel genes or new metabolic pathways. The recent advances in the next generation sequencing technologies have increased the size of the generated reads (500 bps in 454 pyrosequencing) and lowered the sequencing cost per gigabase. As a result, research efforts became more feasible to reveal the mystery of such an interesting environment and to discover novel proteins that might have a useful biotechnological application. This study is the first attempt to establish a metagenomic assembled dataset of the environmental sample taken from the ATII-LCL. Three successive runs of 454 random shotgun sequencing were performed producing a large size dataset of 1.5 Gbs and 4.4 million reads. This approach has been used to increase the sequence coverage of metagenomic datasets in order to overcome the high diversity of some microbial communities. De novo assembly of the pooled reads from all sequencing runs resulted in a 40,693 contigs with maximum contig size of 350 kb. The comparison of different assembly versions of individual runs showed that we have not yet reached a complete coverage of the genomes contained in the metagenomic sample. Also, this metagenomic dataset has shown a high complexity concerning the community structure due to the absence of a dominant taxonomic classification. The taxonomic classification of the assembled dataset has been distributed between three major bacterial orders, Burkholderiales, Rhizobiales and Pseudomonadales and one Archaeal class Euryarchaeota. The newly established dataset has been used to annotate an operon for mercury resistance genes. The annotated Mercuric reductase gene (MerA) has been synthesized and expressed in the lab showing a high enzyme activity compared to its terrestrial peers. |
| format | Thesis |
| id | oai:fount.aucegypt.edu:etds-2177 |
| institution | American University in Cairo (Egypt) |
| last_indexed | 2026-06-10T12:35:47.730Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from AUC Knowledge Fountain — bepress |
| publishDate | 2013 |
| publishDateRange | 2013 |
| publishDateSort | 2013 |
| publisher | AUC Knowledge Fountain |
| publisherStr | AUC Knowledge Fountain |
| record_format | dspace |
| source_str | AUC Knowledge Fountain — bepress |
| spelling | oai:fount.aucegypt.edu:etds-2177 De novo metagenomic assembly of microbial communities from the lower convective layer of the Red Sea Atlantis II brine environment. Ali, Osama Said The lower convective layer of the Red Sea Atlantis II brine pool (ATII-LCL) is an unexplored environment that is characterized by harsh conditions of high temperature (68ºC), high salinity (26%), high concentration of heavy metals and very low oxygen content. Microbial communities inhabiting this extreme environment are expected to have unique structural and functional adaptations to survive such harsh conditions. These adaptations can be expressed by novel genes or new metabolic pathways. The recent advances in the next generation sequencing technologies have increased the size of the generated reads (500 bps in 454 pyrosequencing) and lowered the sequencing cost per gigabase. As a result, research efforts became more feasible to reveal the mystery of such an interesting environment and to discover novel proteins that might have a useful biotechnological application. This study is the first attempt to establish a metagenomic assembled dataset of the environmental sample taken from the ATII-LCL. Three successive runs of 454 random shotgun sequencing were performed producing a large size dataset of 1.5 Gbs and 4.4 million reads. This approach has been used to increase the sequence coverage of metagenomic datasets in order to overcome the high diversity of some microbial communities. De novo assembly of the pooled reads from all sequencing runs resulted in a 40,693 contigs with maximum contig size of 350 kb. The comparison of different assembly versions of individual runs showed that we have not yet reached a complete coverage of the genomes contained in the metagenomic sample. Also, this metagenomic dataset has shown a high complexity concerning the community structure due to the absence of a dominant taxonomic classification. The taxonomic classification of the assembled dataset has been distributed between three major bacterial orders, Burkholderiales, Rhizobiales and Pseudomonadales and one Archaeal class Euryarchaeota. The newly established dataset has been used to annotate an operon for mercury resistance genes. The annotated Mercuric reductase gene (MerA) has been synthesized and expressed in the lab showing a high enzyme activity compared to its terrestrial peers. 2013-02-01T08:00:00Z thesis application/pdf https://fount.aucegypt.edu/etds/1178 https://fount.aucegypt.edu/context/etds/article/2177/viewcontent/Thesis_Final_Corrected.pdf The author retains all rights with regard to copyright. The author certifies that written permission from the owner(s) of third-party copyrighted matter included in the thesis, dissertation, paper, or record of study has been obtained. The author further certifies that IRB approval has been obtained for this thesis, or that IRB approval is not necessary for this thesis. Insofar as this thesis, dissertation, paper, or record of study is an educational record as defined in the Family Educational Rights and Privacy Act (FERPA) (20 USC 1232g), the author has granted consent to disclosure of it to anyone who requests a copy. Theses and Dissertations AUC Knowledge Fountain Red Sea Egypt |
| spellingShingle | Red Sea Egypt Ali, Osama Said De novo metagenomic assembly of microbial communities from the lower convective layer of the Red Sea Atlantis II brine environment. |
| title | De novo metagenomic assembly of microbial communities from the lower convective layer of the Red Sea Atlantis II brine environment. |
| title_full | De novo metagenomic assembly of microbial communities from the lower convective layer of the Red Sea Atlantis II brine environment. |
| title_fullStr | De novo metagenomic assembly of microbial communities from the lower convective layer of the Red Sea Atlantis II brine environment. |
| title_full_unstemmed | De novo metagenomic assembly of microbial communities from the lower convective layer of the Red Sea Atlantis II brine environment. |
| title_short | De novo metagenomic assembly of microbial communities from the lower convective layer of the Red Sea Atlantis II brine environment. |
| title_sort | de novo metagenomic assembly of microbial communities from the lower convective layer of the red sea atlantis ii brine environment |
| topic | Red Sea Egypt |
| url | https://fount.aucegypt.edu/etds/1178 https://fount.aucegypt.edu/context/etds/article/2177/viewcontent/Thesis_Final_Corrected.pdf |
| work_keys_str_mv | AT aliosamasaid denovometagenomicassemblyofmicrobialcommunitiesfromthelowerconvectivelayeroftheredseaatlantisiibrineenvironment |