DSI/NRF SARChI in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
Water-Related Microbiology Laboratory, Water Centre, Pretoria, South Africa.
mSystems. 2023 Feb 23;8(1):e0128222. doi: 10.1128/msystems.01282-22. Epub 2023 Feb 6.
Viruses are the most biologically abundant entities and may be ideal indicators of fecal pollutants in water. Anthropogenic activities have triggered drastic ecosystem changes in rivers, leading to substantial shifts in chemical and biological attributes. Here, we evaluate the viability of using the presence of crAssphage as indicators of fecal contamination in South African rivers. Shotgun analysis revealed diverse crAssphage viruses in these rivers, which are impacted by chemical and biological pollution. Overall, the diversity and relative abundances of these viruses was higher in contaminated sites compared to pristine locations. In contrast to fecal coliform counts, crAssphage sequences were detected in pristine rivers, supporting the assertion that the afore mentioned marker may be a more accurate indicator of fecal contamination. Our data demonstrate the presence of diverse putative hosts which includes members of the phyla , and . Phylogenetic analysis revealed novel subfamilies, suggesting that rivers potentially harbor distinct and uncharacterized clades of crAssphage. These data provide the first insights regarding the diversity, distribution, and functional roles of crAssphage in rivers. Taken together, the results support the potential application of crAssphage as viable markers for water quality monitoring. Rivers support substantial populations and provide important ecosystem services. Despite the application of fecal coliform tests and other markers, we lack rapid and reproducible approaches for determining fecal contamination in rivers. Waterborne viral outbreaks have been reported even after fecal indicator bacteria (FIB) were suggested to be absent or below regulated levels of coliforms. This indicates a need to develop and apply improved indicators of pollutants in aquatic ecosystems. Here, we evaluate the viability of crAssphage as indicators of fecal contamination in two South African rivers. We assess the abundance, distribution, and diversity of these viruses in sites that had been predicted pristine or contaminated by FIB analysis. We show that crAssphage are ideal and sensitive markers for fecal contamination and describe novel clades of crAss-like phages. Known crAss-like subfamilies were unrepresented in our data, suggesting that the diversity of these viruses may reflect geographic locality and dependence.
病毒是生物界中最丰富的实体，可能是水中粪便污染物的理想指标。人为活动引发了河流生态系统的剧烈变化，导致化学和生物属性发生了重大变化。在这里，我们评估了 crAssphage 作为南非河流粪便污染指示物的可行性。 鸟枪法分析显示，这些受化学和生物污染影响的河流中存在多种 crAssphage 病毒。总的来说，与原始地点相比，受污染地点的这些病毒的多样性和相对丰度更高。与粪便大肠菌群计数相反，在原始河流中检测到了 crAssphage 序列，这支持了上述标记物可能是粪便污染更准确指标的说法。我们的数据表明存在多种假定的宿主，包括门和门的成员。系统发育分析揭示了新的亚科，表明河流可能含有独特且未被描述的 crAssphage 进化枝。这些数据首次提供了有关 crAssphage 在河流中的多样性、分布和功能作用的见解。总的来说，这些结果支持将 crAssphage 作为水质监测的可行标志物的应用潜力。河流支持大量的种群，并提供重要的生态系统服务。尽管应用了粪便大肠菌群测试和其他标记物，但我们缺乏快速且可重复的方法来确定河流中的粪便污染。即使在建议不存在或低于大肠菌群规定水平的粪便指示细菌（FIB）时，也报告了水传播病毒爆发。这表明需要开发和应用改进的水生生态系统污染物指标。在这里，我们评估了 crAssphage 作为南非两条河流粪便污染指示物的可行性。我们评估了这些病毒在预测为原始或受 FIB 分析污染的地点的丰度、分布和多样性。我们表明，crAssphage 是粪便污染的理想和敏感标志物，并描述了新型 crAss 样噬菌体进化枝。我们的数据中未出现已知的 crAss 样亚科，这表明这些病毒的多样性可能反映了地理位置和依赖性。
