Soliman Hwayda, Ismaeil Mohamed, Soussa Hoda, El-Sayed Wael S
Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt.
Irrigation and Hydraulics Department, Faculty of Engineering, Ain Shams University, Cairo, Egypt.
BMC Microbiol. 2025 Mar 31;25(1):186. doi: 10.1186/s12866-025-03864-1.
Industrial waste, agricultural runoff and untreated sewage contaminate the Nile, leaving a toxic legacy in its sediments. Organohalides-polluted sediment in particular poses serious public health risks and detrimental effects on aquatic life. Sediment microbiomes may harbor bacterial strains that could be utilized in bioremediation of such toxic pollutants.
Two microbiomes from polluted River Nile sediments were analyzed by using 16S rRNA gene amplicon sequencing. In addition, PICRUSt analysis based on 16S rRNA data was used to explore the organohalide respiring bacteria (OHRB) genera and their corresponding organohalide respiration (OHR) activity. Microcosm studies were performed to validate the potential for dechlorination activity of River Nile sediment. Dechlorination of the parent chloroethenes into daughter end product were detected by gas chromatography coupled with flame ionization detection analysis.
Analysis of 16S rRNA gene amplicon sequences using the EZ-biocloud server identified Proteobacteria as the dominant phylum in both microbiomes, with Bacteroidetes and Chloroflexi prevalent in RNS1 sediment and Chlorobi in RNS2 sediment. EZ-biocloud and PCR analyses detected several potential OHRB genera, including Dehalococcoides, Dehalogenimonas, Desulfomonile, Desulfovibrio, and Geobacter, suggesting potential OHR activity. Further evidence for potential OHR activity was provided by PICRUSt functional prediction analysis, which suggested the presence of reductive dehalogenases as functional biomarkers associated with OHR in the sediment samples. Specifically, PICRUSt analysis predicted the presence of potential genes of tetrachloroethene reductive dehalogenase and 3-chloro-4-hydroxyphenylacetate reductive dehalogenase, previously linked to OHR. Microcosm studies confirmed the dechlorination potential of tetrachloroethene to dichloroethene.
This study demonstrates that River Nile sediment in industrialized area harbors distinct microbiomes enclosing various OHRB genera, providing substantial evidence for potential reductive dechlorination activity. It also provides potential functional biomarkers for OHR activity.
工业废料、农业径流和未经处理的污水污染了尼罗河，在其沉积物中留下了有毒残留物。受有机卤化物污染的沉积物尤其对公众健康构成严重风险，并对水生生物产生有害影响。沉积物微生物群落可能含有可用于生物修复此类有毒污染物的细菌菌株。
利用16S rRNA基因扩增子测序分析了尼罗河污染沉积物中的两个微生物群落。此外，基于16S rRNA数据的PICRUSt分析用于探索有机卤化物呼吸细菌（OHRB）属及其相应的有机卤化物呼吸（OHR）活性。进行了微观研究以验证尼罗河沉积物的脱氯活性潜力。通过气相色谱与火焰离子化检测分析检测母体氯乙烯向子体终产物的脱氯情况。
使用EZ-生物云服务器对16S rRNA基因扩增子序列进行分析，确定变形菌门是两个微生物群落中的优势菌门，拟杆菌门和绿弯菌门在RNS1沉积物中普遍存在，而绿菌门在RNS2沉积物中普遍存在。EZ-生物云和PCR分析检测到几种潜在的OHRB属，包括脱卤球菌属、脱卤单胞菌属、脱硫单胞菌属、脱硫弧菌属和地杆菌属，表明存在潜在的OHR活性。PICRUSt功能预测分析为潜在的OHR活性提供了进一步证据，该分析表明沉积物样品中存在与OHR相关的作为功能生物标志物的还原性脱卤酶。具体而言，PICRUSt分析预测存在四氯乙烯还原性脱卤酶和3-氯-4-羟基苯乙酸还原性脱卤酶的潜在基因，这些基因先前与OHR有关。微观研究证实了四氯乙烯向二氯乙烯的脱氯潜力。
本研究表明，工业化地区的尼罗河沉积物含有独特的微生物群落，其中包含各种OHRB属，为潜在的还原性脱氯活性提供了大量证据。它还为OHR活性提供了潜在的功能生物标志物。
