Abuzahrah Samah S, Baeshen Mohammed N, Alkaladi Ali, Bataweel Noor M, Alhejen Ahmed M, Abdelkader Hayam
Department of Biological Sciences, College of Science, University of Jeddah, Saudi Arabia.
king Fahd medical research center, king Abdul-Aziz university P.O.BOX 80203 Jeddah 21589, Saudi Arabia.
Saudi J Biol Sci. 2022 Aug;29(8):103342. doi: 10.1016/j.sjbs.2022.103342. Epub 2022 Jun 26.
Diverse marine habitats along Jeddah's Red Sea coast support rich biodiversity. Few studies have been done on its diverse communities, especially its microbial counterparts. Metagenomic analysis of marine benthic micro-eukaryotic communities was performed for the first time on the Red Sea coast of Jeddah. This research looks into their community structure and metabolic potential.
Next-generation sequencing was used to examine the micro-eukaryotic communities of seven sedimentary soil samples from four Jeddah coast locations. After isolating DNA from seven benthic sedimentary soil samples, the 18S rDNA V4 regions were amplified and sequenced on the Illumina MiSeq. It was also verified using an Agilent Technologies 2100 Bioanalyzer with a DNA 1000 chip (Agilent Technologies, Fisher Scientific). A standard curve of fluorescence readings generated by qPCR quantification using the Illumina library was achieved using the GS FLX library. Metagenomic data analysis was used to evaluate the microbial communities' biochemical and enzymatic allocations in studied samples.
Blast analysis showed that the top ten phyla were Annelida, Eukaryota, Diatomea, Porifera, Phragmoplastophyta, Arthropoda, Dinoflagellata, Xenacoelomorpha Nematoda, and uncultured. Annelida was also found in the highest percentage (93%), in the sample M followed by Porifera (64%), the most abundant in the control sample then Eukaryotes (61%), Phragmatoplastophyta (55%), Arthropoda, and Diatomea (the least common) (32%). community diversity analysis: using Shannon and inverse Simpson indices showed sediment composition to be effective. Also, PICRUST2 indicated that the most abundant pathways were pyruvate fermentation to isobutanol, pyrimidine deoxyribonucleotide phosphorylation, adenosine ribonucleotide de novo biosynthesis, guanosine ribonucleotide de novo biosynthesis, NAD salvage pathway I, the super pathway of glyoxylate bypass and aerobic respiration I (cytochrome ).
Results showed that high throughput metagenomics could reveal species diversity and estimate gene profiles. Environmental factors appear to be more important than geographic variation in determining the structure of these microbial communities. This study provides the first report of marine benthic micro-eukaryotic communities found on the Red Sea coast of Jeddah and will serve as a good platform for future research.
吉达红海沿岸多样的海洋栖息地孕育了丰富的生物多样性。针对其多样的群落，尤其是微生物群落的研究较少。首次对吉达红海沿岸的海洋底栖微型真核生物群落进行了宏基因组分析。本研究探究了它们的群落结构和代谢潜力。
采用下一代测序技术检测来自吉达海岸四个地点的七个沉积土壤样本中的微型真核生物群落。从七个底栖沉积土壤样本中分离出DNA后，对18S rDNA V4区域进行扩增，并在Illumina MiSeq上进行测序。还用安捷伦科技2100生物分析仪和DNA 1000芯片（安捷伦科技，赛默飞世尔科技）进行了验证。使用Illumina文库通过qPCR定量生成荧光读数的标准曲线，该文库是使用GS FLX文库获得的。宏基因组数据分析用于评估研究样本中微生物群落的生化和酶分配情况。
Blast分析表明，排名前十的门为环节动物门、真核生物界、硅藻纲、多孔动物门、有胚植物门、节肢动物门、甲藻纲、异涡虫纲、线虫纲和未培养类群。在样本M中还发现环节动物门的占比最高（93%），其次是多孔动物门（64%），在对照样本中最为丰富，然后是真核生物（61%）、有胚植物门（55%）、节肢动物门和硅藻纲（最不常见）（32%）。群落多样性分析：使用香农指数和反辛普森指数表明沉积物组成是有效的。此外，PICRUST2表明最丰富的途径是丙酮酸发酵生成异丁醇、嘧啶脱氧核糖核苷酸磷酸化、腺苷核糖核苷酸从头生物合成、鸟苷核糖核苷酸从头生物合成、NAD补救途径I、乙醛酸旁路的超级途径和有氧呼吸I（细胞色素）。
结果表明，高通量宏基因组学可以揭示物种多样性并估计基因图谱。在决定这些微生物群落的结构方面，环境因素似乎比地理变异更重要。本研究首次报告了在吉达红海沿岸发现的海洋底栖微型真核生物群落，将为未来的研究提供一个良好的平台。
