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Elvy L Ginting - One of the best experts on this subject based on the ideXlab platform.
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identifikasi mikroba yang koeksis dengan ascidia lissoclinum patella menggunakan sekuens gen 16s rrna identification of the co exist microbial with ascidian lissoclinum patella by using 16s rrna gene sequences
2015Co-Authors: Patricia Untu, Inneke F M Rumengan, Elvy L GintingAbstract:*This study was conducted to determine the types of co-existed microbes in ascidians Lissoclinum patella with using 16S rRNA gene sequences. The samples that used in this study were taken from tissues of L. patella in Malalayang sea water, Manado, North Sulawesi. The samples were inoculated in Hirata medium for ± 1 week. The DNA were isolated from microbial samples, amplification by using the PCR (Polymerase Chain Reaction), electrophoresis agarose gel and data analyze using BLAST (Basic Local Alignment Search Tool) in NCBI (National Center for Biotechnology Information). The results show, that there are 15 species of microbes in the Gene Bank that have a high degree of similarity with the 16S rRNA gene sequences of microbial sample, namely cyanobacterium enrichment culture CAWBG121 and CAWBG120 clones, uncultured Symploca sp. DRTO clone-55, Leptolyngbya sp. PCC7376 complete genome, Leptolyngbya sp. PCC7376, uncultured bacterium clone PINFEBB02, uncultured bacterium clone 5M47, Synechococcus elongatus CCMP1630, uncultured bacterium clone H09 reef, Synechococcus sp. PCC7002 complete genome, Synechococcus sp. 16S rRNA gene strain PCC7002, Synechococcus sp. DNA for 16 ribosomal RNA, Synechoccous sp. L21-BG-1, Oscillatoria rosea IAM M-220 and Synechococcus sp. PCC 8807. The level similarity of microbes in the NCBI and the microbial samples ranged between 98-99%.
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identifikasi mikroba yang koeksis dengan ascidia lissoclinum patella menggunakan sekuens gen 16s rrna
JURNAL PESISIR DAN LAUT TROPIS, 2014Co-Authors: Patricia Untu, Inneke F M Rumengan, Elvy L GintingAbstract:Penelitian ini dilakukan dengan tujuan untuk menentukan jenis mikroba koeksis denganascidia Lissoclinum patella menggunakan sekuens gen 16S rRNA. Sampel yang digunakandalam penelitian ini diambil dari jaringan tissue pada ascidia L. patella yang diambil dariperairan Malalayang, Sulawesi Utara. Sampel mikroba diinokulasi dalam media Hirata dandikultur selama ± 1 minggu. Sampel mikroba tersebut diisolasi DNA, amplifikasi melalui PCR(Polymerase Chain Reaction), elektroforesis gel agarose dan dianalisis data DNAnyamenggunakan BLAST pada NCBI (National Center for Biotechnology Information). Identifikasiyang dilakukan menggunakan BLAST diperoleh hasil 15 mikroba yang memiliki tingkatkemiripan yang tinggi dengan sekuens gen 16S rRNA sampel mikroba yaitu cyanobacteriumenrichment culture CAWBG121 dan CAWBG120 clone, uncultured Symploca sp. clone DRTO-55, Leptolyngbya sp. PCC7376 complete genome, Leptolyngbya sp. PCC7376, unculturedbacterium clone PINFEBB02, uncultured bacterium clone 5M47, Synechococcus elongatusCCMP1630, uncultured bacterium clone reef H09, Synechococcus sp. PCC7002 completegenome, Synechococcus sp. 16S rRNA gene strain PCC7002, Synechococcus sp. DNA untuk16 ribosomal RNA, Synechoccous sp. L21-BG-1, Oscillatoria rosea IAM M-220 danSynechococcus sp. PCC 8807. Tingkat kemiripan mikroba dalam NCBI dengan sampel H1berkisar antara 98-99 %.
Wilmotte Annick - One of the best experts on this subject based on the ideXlab platform.
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Past cyanobacteria biodiversity in herbarium collections: a time travel to a lost world?
2020Co-Authors: Wilmotte Annick, Durieu Benoit, Pessi, Igor Stelmach, Velazquez David, Laughinghouse Iv HaywoodAbstract:A pilot study of the cyanobacterial diversity in ten herbarium samples from the Smithsonian Institution (Washington DC, USA) was carried out. The samples had been collected between 1897 and 1964 in Antarctica, Alaska, Yellowstone Park and Austrian and American glaciers. The V3-V4 portion of the 16S rRNA gene was sequenced by multiplex 454 pyrosequencing and data was analyzed using the bioinformatic pipeline of Pessi et al. (2016). We obtained 131 OTUs (threshold of 97.5% 16S rRNA similarity), of which 74 were very closely related to existing sequences in public databases. Moreover, the diversity patterns were different between samples, ruling out an homogenization due to contaminations during the handling of herbarium samples since their collection and in our laboratory. The older specimen (1898) came from a pool at 46°C in Yellowstone Park with dominant sequences of Stigonema and Leptolyngbya, that are known from these biotopes. For the Antarctic samples taken in 1948-9 from Ross Island, in 1940 from Deception Island and in 1964 from Victoria Land, the DNA could be amplified in all cases and 55 OTUs were detected. Sequences of Nostoc sp., Microcoleus sp., Phormidesmis priestleyi, Leptolyngbya sp., and Timaviella sp. were retrieved. An Alaskan river specimen from 1949 yielded mostly Nostoc sequences, as could be expected from the herbarium label. This study gives access to the cyanobacterial community composition in a period where anthropogenic and climatic pressures were still low in the remote polar regions. We will assess if it is possible to detect changes in biogeographic patterns or shifts of genotypes towards more generalist ones
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Past cyanobacterial biodiversity in polar regions
2020Co-Authors: Wilmotte Annick, Pessi, Igor Stelmach, Velazquez David, Laughinghouse Iv HaywoodAbstract:Looking to the past, the FNRS project HERBA aims to study the past diversity and biogeography of cyanobacteria in polar regions by investigating herbaria specimens from the Smithsonian Institution (Washington, DC, USA). First results, obtained with 454 pyrosequencing of the 16S rRNA gene V3-V4 segment, showed that it was possible to retrieve the sequences of Antarctic samples taken in 1948-9 from Ross Island, in 1940 from Deception Island and in 1964 from Victoria Land. DNA could be amplified in all cases and 55 OTUs (97.5% similarity) were detected. Sequences of Nostoc sp., Microcoleus sp., Phormidesmis priestleyi, Leptolyngbya sp., and Timaviella sp. were retrieved and compared with present-day sequences. This study gives access to the cyanobacterial community composition in a period where anthropogenic and climatic pressures were still low in the remote polar regions and will allow to detect possible changes in biogeographic patterns or shifts of genotypes towards more generalist ones
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Polyphasic characterization of 10 selected ecologically relevant filamentous cyanobacterial strains from the South Shetland Islands, Maritime Antarctica
2016Co-Authors: Jancusova Miroslava, Kovacik Lubomir, Pereira, Antonio Batista, Dusinsky Roman, Wilmotte AnnickAbstract:The evolutionary relationships of 10 Antarctic cyanobacterial strains of the order Oscillatoriales isolated from King George and Deception Islands, South Shetland Islands were studied by a polyphasic approach (morphology, 16S rRNA and internal transcribed spacer sequences). The studied taxa are characteristic of coastal Antarctic biotopes, where they form distinct populations and ecologically delimited communities. They were isolated from terrestrial habitats: microbial mats in seepages; crusts on soil, rocks, bones and mosses; mud, sometimes close to bird colonies; and from guano. Based on major phenotypic features, the strains were divided into four distinct morphotypes: Leptolyngbya borchgrevinkii (A), Leptolyngbya frigida (B), Microcoleus sp. (C) and Wilmottia murrayi (D). This morphological identification was in agreement with the phylogenetic relationships. For the first time, the 16S rRNA gene sequence of a strain corresponding to the L. borchgrevinkii morphotype was determined. Morphotype B is most related to sequences assigned to L. frigida isolated from microbial mats of coastal lakes in East Antarctica. Morphotype C belongs to a cluster including strains with morphotypes corresponding to Microcoleus attenuatus, Microcoleus favosus and Microcoleus sp., which are from Antarctica and other continents. Morphotype D is grouped with sequences assigned to W. murrayi mostly isolated from Antarctica.Peer reviewe
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Elucidating diversity of thin filamentous mat-forming Antarctic cyanobacteria
2016Co-Authors: Lara Yannick, Durieu Benoit, Deblander Victor, Defise Antoine, Laughinghouse, Haywood D., Wilmotte AnnickAbstract:Freshwater ecosystems range from glacial cryoecosystems, ice shelf meltwater ponds to perennially ice-covered lakes where conspicuous benthic microbial mat communities constitute most of the biomass. In these mats, cyanobacteria form matrices that shelter other organisms, and carry out the primary production. Narrow filamentous cyanobacteria belonging to the genera Leptolyngbya and Phormidium are especially abundant in Antarctic microbial mats and are essential for the formation of matrix. However, the lack of morphological criteria and the small cell size of cyanobacteria belonging to these two genera make their identification problematic. Indeed, they are known as polyphyletic taxa according to botanical and bacteriological criteria. The characterization of strains is the first step for an assessment of the real diversity and for understanding their role in the environment. We designed a polyphasic approach that combines molecular analyses, environmental physiology experiments and microscopic observations. Briefly, we amplified and sequenced three loci (16S rRNA, ITS, and rpoC1) for 31 strains of Leptolyngbya and Phormidium. We performed whole genome sequencing for five strains. Cultures at different stage were observed by light and epifluorescence microscopy. Finally, selected strains were grown in nitrogen-limited. The Leptolyngbya and Phormidium strains were distributed into four lineages. Phylogenetic trees supported the distribution of P. priestleyi strains into at least two potentially new lineages, and L. antarctica strains were separated into one endemic and one cosmopolitan lineage. This was supported by the microscopic observations of 1-year old cultures. Genome analyses revealed the presence of sequences related to the production of secondary metabolites in strains from two of the studied lineages. Secondary metabolites are often known for their antimicrobial activities. Such properties would partly explain how cyanobacterial mats survive to predation and degradation by other bacteria. This work provides the first building block to the understanding of survival strategies developed by mat-forming cyanobacteria and how they succeeded as the most abundant phototrophs on the Antarctic continent. This work was realized in the frame of the BelSPo project CCAMBIO
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Polyphasic characterization of 10 selected ecologically relevant filamentous cyanobacterial strains from the South Shetland Islands, Maritime Antarctica
'Oxford University Press (OUP)', 2016Co-Authors: Jancusova Miroslava, Kovacik Lubomir, Pereira, Antonio Batista, Dusinsky Roman, Wilmotte AnnickAbstract:The evolutionary relationships of 10 Antarctic cyanobacterial strains of the order Oscillatoriales isolated from King George and Deception Islands, South Shetland Islands were studied by a polyphasic approach (morphology, 16S rRNA and internal transcribed spacer sequences). The studied taxa are characteristic of coastal Antarctic biotopes, where they form distinct populations and ecologically delimited communities. They were isolated from terrestrial habitats: microbial mats in seepages; crusts on soil, rocks, bones and mosses; mud, sometimes close to bird colonies; and from guano. Based on major phenotypic features, the strains were divided into four distinct morphotypes: Leptolyngbya borchgrevinkii (A), Leptolyngbya frigida (B), Microcoleus sp. (C) and Wilmottia murrayi (D). This morphological identification was in agreement with the phylogenetic relationships. For the first time, the 16S rRNA gene sequence of a strain corresponding to the L. borchgrevinkii morphotype was determined. Morphotype B is most related to sequences assigned to L. frigida isolated from microbial mats of coastal lakes in East Antarctica. Morphotype C belongs to a cluster including strains with morphotypes corresponding to Microcoleus attenuatus, Microcoleus favosus and Microcoleus sp., which are from Antarctica and other continents. Morphotype D is grouped with sequences assigned to W. murrayi mostly isolated from Antarctica.Biodiversity of Antarctic cyanobacteri
Patricia Untu - One of the best experts on this subject based on the ideXlab platform.
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identifikasi mikroba yang koeksis dengan ascidia lissoclinum patella menggunakan sekuens gen 16s rrna identification of the co exist microbial with ascidian lissoclinum patella by using 16s rrna gene sequences
2015Co-Authors: Patricia Untu, Inneke F M Rumengan, Elvy L GintingAbstract:*This study was conducted to determine the types of co-existed microbes in ascidians Lissoclinum patella with using 16S rRNA gene sequences. The samples that used in this study were taken from tissues of L. patella in Malalayang sea water, Manado, North Sulawesi. The samples were inoculated in Hirata medium for ± 1 week. The DNA were isolated from microbial samples, amplification by using the PCR (Polymerase Chain Reaction), electrophoresis agarose gel and data analyze using BLAST (Basic Local Alignment Search Tool) in NCBI (National Center for Biotechnology Information). The results show, that there are 15 species of microbes in the Gene Bank that have a high degree of similarity with the 16S rRNA gene sequences of microbial sample, namely cyanobacterium enrichment culture CAWBG121 and CAWBG120 clones, uncultured Symploca sp. DRTO clone-55, Leptolyngbya sp. PCC7376 complete genome, Leptolyngbya sp. PCC7376, uncultured bacterium clone PINFEBB02, uncultured bacterium clone 5M47, Synechococcus elongatus CCMP1630, uncultured bacterium clone H09 reef, Synechococcus sp. PCC7002 complete genome, Synechococcus sp. 16S rRNA gene strain PCC7002, Synechococcus sp. DNA for 16 ribosomal RNA, Synechoccous sp. L21-BG-1, Oscillatoria rosea IAM M-220 and Synechococcus sp. PCC 8807. The level similarity of microbes in the NCBI and the microbial samples ranged between 98-99%.
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identifikasi mikroba yang koeksis dengan ascidia lissoclinum patella menggunakan sekuens gen 16s rrna
JURNAL PESISIR DAN LAUT TROPIS, 2014Co-Authors: Patricia Untu, Inneke F M Rumengan, Elvy L GintingAbstract:Penelitian ini dilakukan dengan tujuan untuk menentukan jenis mikroba koeksis denganascidia Lissoclinum patella menggunakan sekuens gen 16S rRNA. Sampel yang digunakandalam penelitian ini diambil dari jaringan tissue pada ascidia L. patella yang diambil dariperairan Malalayang, Sulawesi Utara. Sampel mikroba diinokulasi dalam media Hirata dandikultur selama ± 1 minggu. Sampel mikroba tersebut diisolasi DNA, amplifikasi melalui PCR(Polymerase Chain Reaction), elektroforesis gel agarose dan dianalisis data DNAnyamenggunakan BLAST pada NCBI (National Center for Biotechnology Information). Identifikasiyang dilakukan menggunakan BLAST diperoleh hasil 15 mikroba yang memiliki tingkatkemiripan yang tinggi dengan sekuens gen 16S rRNA sampel mikroba yaitu cyanobacteriumenrichment culture CAWBG121 dan CAWBG120 clone, uncultured Symploca sp. clone DRTO-55, Leptolyngbya sp. PCC7376 complete genome, Leptolyngbya sp. PCC7376, unculturedbacterium clone PINFEBB02, uncultured bacterium clone 5M47, Synechococcus elongatusCCMP1630, uncultured bacterium clone reef H09, Synechococcus sp. PCC7002 completegenome, Synechococcus sp. 16S rRNA gene strain PCC7002, Synechococcus sp. DNA untuk16 ribosomal RNA, Synechoccous sp. L21-BG-1, Oscillatoria rosea IAM M-220 danSynechococcus sp. PCC 8807. Tingkat kemiripan mikroba dalam NCBI dengan sampel H1berkisar antara 98-99 %.
Alexander K Goroncy - One of the best experts on this subject based on the ideXlab platform.
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microbial mat communities along an oxygen gradient in a perennially ice covered antarctic lake
Applied and Environmental Microbiology, 2016Co-Authors: Anne D. Jungblut, Ian Hawes, Tyler J. Mackey, Megan L Krusor, Peter T Doran, D Y Sumner, Jonathan A Eisen, Colin Hillman, Alexander K GoroncyAbstract:Lake Fryxell is a perennially ice-covered lake in the McMurdo Dry Valleys, Antarctica, with a sharp oxycline in a water column that is density stabilized by a gradient in salt concentration. Dissolved oxygen falls from 20 mg liter(-1) to undetectable over one vertical meter from 8.9- to 9.9-m depth. We provide the first description of the benthic mat community that falls within this oxygen gradient on the sloping floor of the lake, using a combination of micro- and macroscopic morphological descriptions, pigment analysis, and 16S rRNA gene bacterial community analysis. Our work focused on three macroscopic mat morphologies that were associated with different parts of the oxygen gradient: (i) "cuspate pinnacles" in the upper hyperoxic zone, which displayed complex topography and were dominated by phycoerythrin-rich cyanobacteria attributable to the genus Leptolyngbya and a diverse but sparse assemblage of pennate diatoms; (ii) a less topographically complex "ridge-pit" mat located immediately above the oxic-anoxic transition containing Leptolyngbya and an increasing abundance of diatoms; and (iii) flat prostrate mats in the upper anoxic zone, dominated by a green cyanobacterium phylogenetically identified as Phormidium pseudopriestleyi and a single diatom, Diadesmis contenta. Zonation of bacteria was by lake depth and by depth into individual mats. Deeper mats had higher abundances of bacteriochlorophylls and anoxygenic phototrophs, including Chlorobi and Chloroflexi. This suggests that microbial communities form assemblages specific to niche-like locations. Mat morphologies, underpinned by cyanobacterial and diatom composition, are the result of local habitat conditions likely defined by irradiance and oxygen and sulfide concentrations.
Wonbo Shim - One of the best experts on this subject based on the ideXlab platform.
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isolation and characterization of Leptolyngbya sp kiost 1 a basophilic and euryhaline filamentous cyanobacterium from an open paddle wheel raceway arthrospira culture pond in korea
Journal of Applied Microbiology, 2015Co-Authors: Ji Hyung Kim, Woo Seok Choi, Seonmi Jeon, Taeho Kim, Areumi Park, Junseong Kim, Soojin Heo, Wonbo ShimAbstract:Aims Cyanobacteria have been used as sustainable bioresource producers for foods, feeds and other valuable natural products. However, selection of a new species (other than Arthrospira), with advantageous properties for alimentary purposes, continues to be a challenge due to potential toxicity and low biomass productivity. In this study, we report a valuable filamentous cyanobacterium isolated from Korea. Methods and Results Morphological and phylogenetic analyses demonstrated that the isolate belongs to the genus Leptolyngbya, and consequently designated Leptolyngbya sp. KIOST-1. Interestingly, Leptolyngbya sp. KIOST-1 possessed numerous advantageous characteristics for biomass production, similar to Arthrospira. The isolate readily propagated in SOT medium with efficient biomass productivity, and its optimum growth was observed at 30°C under alkaline and saline conditions. Moreover, more than half of the cellular components in Leptolyngbya sp. KIOST-1 were composed of protein, with approx. 40% of essential amino acids. Most importantly, no significant cytotoxicity was detected in the isolate. Conclusions Leptolyngbya sp. KIOST-1 has a number of advantageous characteristics for alimentary purposes due to its efficient productivity, high protein content and lack of potential cytotoxicity. Significance and Impact of the Study Leptolyngbya sp. KIOST-1 may be considered a potential candidate for industrial biomass production, similar to Arthrospira.