The origin of eukaryotic cells, and especially naturally occurring syncytial cells, remains debatable. While a majority of our biomedical research focuses on the eukaryotic result of evolution, our data remain limiting on the prokaryotic precursors of these cells. This is particularly evident when considering extremophile biology, especially in how the genomes of organisms in extreme environments must have evolved and adapted to unique habitats. Might these rapidly diversifying organisms have created new genetic tools eventually used to enhance the evolution of the eukaryotic single nuclear or syncytial cells? Many organisms are capable of surviving, or even thriving, in conditions of extreme temperature, acidity, organic composition, and then rapidly adapt to yet new conditions. This study identified organisms found in extremes of salinity. A lake and a nearby pond in the Ethiopian Rift Valley were interrogated for life by sequencing the DNA of populations of organism collected from the water in these sites. Remarkably, a vast diversity of microbes were identified, and even though the two sites were nearby each other, the populations of organisms were distinctly different. Since these microbes are capable of living in what for humans would be inhospitable conditions, the DNA sequences identified should inform the next step in these investigations; what new gene families, or modifications to common genes, do these organisms employ to survive in these extreme conditions. The relationship between organisms and their environment can be revealed by decoding genomes of organisms living in extreme environments. These genomes disclose new biological mechanisms that enable life outside moderate environmental conditions, new gene functions for application in biotechnology, and may even result in identification of new species. In this study, we have collected samples from two hypersaline sites in the Danakil depression, the shorelines of Lake As'ale and an actively mixing salt pond called Muda'ara (MUP), to identify the microbial community by metagenomics. Shotgun sequencing was applied to high density sampling, and the relative abundance of Operational Taxonomic Units (OTUs) was calculated. Despite the broad taxonomic similarities among the salt-saturated metagenomes analyzed, MUP stood out from Lake As'ale samples. In each sample site, Archaea accounted for 95% of the total OTUs, largely to the class Halobacteria. The remaining 5% of organisms were eubacteria, with an unclassified strain of Salinibacter ruber as the dominant OTU in both the Lake and the Pond. More than 40 different genes coding for stress proteins were identified in the three sample sites of Lake As'ale, and more than 50% of the predicted stress-related genes were associated with oxidative stress response proteins. Chaperone proteins (DnaK, DnaJ, GrpE, and ClpB) were predicted, with percentage of query coverage and similarities ranging between 9.5% and 99.2%. Long reads for ClpB homologous protein from Lake As'ale metagenome datasets were modeled, and compact 3D structures were generated. Considering the extreme environmental conditions of the Danakil depression, this metagenomics dataset can add and complement other studies on unique gene functions on stress response mechanisms of thriving bio-communities that could have contributed to cellular changes leading to single and/or multinucleated eukaryotic cells.
All Science Journal Classification (ASJC) codes
- Developmental Biology
- Cell Biology
Asili ya chembe za eukaryotic, na hasa chembe za syncytial zinazotokea kiasili, bado zinabishaniwa. Ingawa utafiti wetu wa biomedical unazingatia matokeo ya eukaryotic ya mageuzi, data zetu bado zinapunguza kwa viambishi vya prokaryotic vya seli hizi. Hii ni dhahiri hasa wakati wa kuzingatia biolojia ya extremophile, hasa katika jinsi genomes ya viumbe katika mazingira ya kupita kiasi lazima kuwa maendeleo na kukabiliana na makazi ya kipekee. Je, huenda viumbe hao wanaobadilika-badilika haraka waliunda chombo kipya cha urithi ambacho hatimaye kilitumiwa kuendeleza mageuzi ya chembe za kiini-kiini au chembe za kiini-kiini? Viumbe wengi wana uwezo wa kuishi, au hata kusitawi, katika hali ya joto kali, asidi, muundo wa kikaboni, na kisha haraka kukabiliana na hali mpya. Utafiti huo uligundua viumbe walio katika hali ya juu sana ya chumvi. Ziwa la Rift Valley nchini Ethiopia limekuwa likijulikana kwa jina la Ziwa la Rift Valley, na kwa hivyo, DNA ya viumbe vilivyopatikana katika ziwa hilo ilichukuliwa. Kwa kushangaza, aina mbalimbali za vimelea ziligunduliwa, na ingawa maeneo hayo mawili yalikuwa karibu, idadi ya viumbe vilikuwa tofauti sana. Kwa kuwa vimelea hivi vina uwezo wa kuishi katika hali ambazo kwa wanadamu hazingekuwa za kukaribisha, mfululizo wa DNA unaotambuliwa unapaswa kuelezea hatua inayofuata katika uchunguzi huu: ni familia gani mpya za jeni, au marekebisho ya jeni za kawaida, viumbe hawa hutumia kuishi katika hali hizi kali. Uhusiano kati ya viumbe na mazingira yao waweza kufunuliwa kwa kufunua chembe za urithi za viumbe wanaoishi katika mazingira magumu. Genome hizi hufunua utaratibu mpya wa kibiolojia ambao huwezesha maisha nje ya hali za mazingira ya wastani, kazi mpya za jeni kwa matumizi katika teknolojia ya kibiolojia, na inaweza hata kusababisha utambulisho wa spishi mpya. Katika utafiti huu, tulikusanya sampuli kutoka maeneo mawili ya hypersaline katika msongamano wa Danakil, pwani ya Ziwa Asale na dimbwi la chumvi linalochanganyika kwa bidii linaloitwa Muda'ara (MUP), ili kutambua jamii ya vimelea kwa metagenomics. Shotgun mfululizo ilitumiwa kwa sampling high wiani, na kiasi cha jamaa ya Operational Taxonomic Units (OTUs) ilihesabiwa. Licha ya kufanana kwa taxonomic kati ya metagenomes zenye chumvi zilizochunguzwa, MUP ilijitokeza kutoka kwa sampuli za Ziwa Asale. Katika kila eneo la sampuli, Archaea ilifanyiza 95% ya jumla ya OTU, hasa kwa darasa Halobacteria. Vitu vingine 5 vya viumbe vilikuwa eubacteria, na aina isiyojulikana ya Salinobacter ruber kama OTU inayotawala katika Ziwa na Bwawa. Zaidi ya jeni 40 tofauti za kuunda protini za mkazo ziligunduliwa katika maeneo matatu ya sampuli ya Ziwa Asale, na zaidi ya 50% ya jeni zinazohusiana na mkazo zilizotabiriwa zilihusishwa na protini za majibu ya mkazo wa oxidative. Chlorine, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna, Dna. Kwa mfano, mimea ya ClPB ya metagenome ya Ziwa Asale ilichukuliwa na kuundwa kwa muundo wa 3D. Kwa kuzingatia hali mbaya za mazingira ya msongamano wa Danakil, seti hii ya data ya metagenomics inaweza kuongeza na kukamilisha masomo mengine juu ya kazi za kipekee za jeni kwenye utaratibu wa majibu ya mkazo wa jamii za kibiolojia zinazoendelea ambazo zinaweza kuchangia mabadiliko ya seli inayoongoza kwa seli moja na au ya eukaryotic. Nambari zote za Classification ya Jarida la Sayansi (ASJC) - Biolojia ya Maendeleo - Biolojia ya Seli