Nutrient levels and prokaryotes affect viral communities in plateau lakes

Che, Raoqiong; Bai, Meng; Xiao, Wei; Zhang, Shiying; Wang, Yongxia; Cui, Xiaolong

doi:10.1016/j.scitotenv.2022.156033

Cited by 5 publications

(6 citation statements)

References 50 publications

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“…We found that the sludge contained 0.66% human pathogenic viruses, with members of the families Orthoherpesviridae and Poxviridae being the two most common pathogenic viruses. This result was consistent with the findings of other studies on lakes or wastewater [ 11 , 44 ]. Orthoherpesviridae viruses are double-stranded DNA viruses that often infecting amniotes.…”

Section: Discussionsupporting

confidence: 94%

“…After centrifugation at 10,000× g for 30 min, the supernatant was discarded and the pellet was resuspended using SM buffer solution. DNase I (final concentration of 10 U/mL, TaKaRa, Beijing, China) and RNase A (final concentration of 200 μg/mL, TaKaRa, China) were added, and incubated at 37 °C for 2 h. After treatment at 80 °C for 5 min, the mixture was supplemented with proteinase K, EDTA, and SDS, and then incubated at 55 °C for 3 h. Viral DNA was extracted using a phenol-chloroform-isoamyl alcohol method as described by Che in 2022 [ 11 ].…”

Section: Methodsmentioning

confidence: 99%

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A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants

Zhao,

Yang,

Fan

et al. 2024

Viruses

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The concentration of viruses in sewage sludge is significantly higher (10–1000-fold) than that found in natural environments, posing a potential risk for human and animal health. However, the composition of these viruses and their role in the transfer of pathogenic factors, as well as their role in the carbon, nitrogen, and phosphorus cycles remain poorly understood. In this study, we employed a shotgun metagenomic approach to investigate the pathogenic bacteria and viral composition and function in two wastewater treatment plants located on a campus. Our analysis revealed the presence of 1334 amplicon sequence variants (ASVs) across six sludge samples, with 242 ASVs (41.22% of total reads) identified as pathogenic bacteria. Arcobacter was found to be the most dominant pathogen accounting for 6.79% of total reads. The virome analysis identified 613 viral genera with Aorunvirus being the most abundant genus at 41.85%. Approximately 0.66% of these viruses were associated with human and animal diseases. More than 60% of the virome consisted of lytic phages. Host prediction analysis revealed that the phages primarily infected Lactobacillus (37.11%), Streptococcus (21.11%), and Staphylococcus (7.11%). Furthermore, our investigation revealed an abundance of auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and phosphorus cycling within the virome. We also detected a total of 113 antibiotic resistance genes (ARGs), covering major classes of antibiotics across all samples analyzed. Additionally, our findings indicated the presence of virulence factors including the clpP gene accounting for approximately 4.78%, along with toxin genes such as the RecT gene representing approximately 73.48% of all detected virulence factors and toxin genes among all samples analyzed. This study expands our understanding regarding both pathogenic bacteria and viruses present within sewage sludge while providing valuable insights into their ecological functions.

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Section: Discussionsupporting

confidence: 94%

Section: Methodsmentioning

confidence: 99%

A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants

Zhao,

Yang,

Fan

et al. 2024

Viruses

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“…In the datasets, the identi ed viral contigs were classi ed into 31 families of DNA-containing viruses, although the majority of viral contigs could not be taxonomically classi ed. This was consistent with the results of several previous studies, possibly due to the uniqueness of viral populations identi ed in this study [42,43]. The top 5% of viruses in all samples belonged to the families of Microviridae, Siphoviridae, Genomoviridae, Myoviridae, and Podoviridae.…”

Section: Characteristics Of Viral Communities In Bat Cavessupporting

confidence: 93%

Patterns of viral communities and the host–pathogen interactions with ecological factors in bat caves

et al. 2023

Preprint

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Background Bats (Chiroptera) are major sources of epidemics. To understand the dynamics of diseases, it is crucial to study the dynamics of microorganisms in the environment and the relationship between microorganisms and bats. In this study, we investigated the soil virus communities in bat caves using viral metagenomic sequencing technology. We further explored host–pathogen interactions with regard to the effects of the environment by combining analyses of microorganisms (viruses and bacteria) and immune genes (major histocompatibility complex, MHC) of the main resident species (Rhinolophus ferrumequinum) in the bat caves. Results A total of 31 families of viruses were identified. Significant differences were observed in alpha diversity, beta diversity, and the relative abundances of soil virus families, indicating their habitat specificity in bat caves. Zoonotic risk viruses were also found, and the composition of viruses in bat caves was similar to the distribution of virus families of R. ferrumequinum in a previous study. Second, the alpha diversity of both viruses and bacteria was significantly negatively correlated with precipitation of the wettest month. The relative abundances of viral and bacterial families were correlated with MHC allele frequencies. Moreover, a structural equation model further revealed that the precipitation of the coldest quarter significantly negatively affected virus diversity, which in turn significantly negatively affected the MHC allele frequencies in R. ferrumequinum. The MHC allele frequencies were negatively affected by bacterial alpha diversity. Conclusions The results of the present study suggest that the polymorphism of the MHC class I gene of R. ferrumequinum is driven by environmental pathogen selection pressure and that environmental climate affects the host immune genes by regulating the diversity of microorganisms. This study is the first to demonstrate the diversity of virus communities in bat caves, and thus has significance for protecting bat habitats from human disturbance and in preventing zoonotic diseases.

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“…Recent advancements in aquatic ecosystem virus ecology have surged remarkably. Notably, significant strides have been made in marine environments [ 3 , 4 , 5 ], estuaries [ 6 , 7 ], and the epilimnion of lakes [ 8 , 9 , 10 , 11 ]. Microbes in sediment, a crucial component of aquatic ecosystems, exhibit extraordinarily high densities [ 12 ] and significantly influence the biogeochemical cycling of elements, thereby playing a pivotal role in maintaining the Earth’s ecosystem equilibrium [ 13 ].…”

Section: Introductionmentioning

confidence: 99%

“…In addition, environmental microorganisms, including bacteria and archaea, constitute the foundational basis for virus sustenance and multiplication, significantly impacting on virus distribution. Che [ 8 ] has shown that nutrient levels and prokaryotic community structures serve as critical drivers for the diversity in viral community structures within freshwater lake waters. However, explorations into freshwater lake sediments remain scarce.…”

Section: Introductionmentioning

confidence: 99%

Community Structure, Drivers, and Potential Functions of Different Lifestyle Viruses in Chaohu Lake

Zheng,

Gao,

et al. 2024

Viruses

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Viruses, as the most prolific entities on Earth, constitute significant ecological groups within freshwater lakes, exerting pivotal ecological roles. In this study, we selected Chaohu Lake, a representative eutrophic freshwater lake in China, as our research site to explore the community distribution, driving mechanisms, and potential ecological functions of diverse viral communities, the intricate virus–host interaction systems, and the overarching influence of viruses on global biogeochemical cycling.

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Nutrient levels and prokaryotes affect viral communities in plateau lakes

Cited by 5 publications

References 50 publications

A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants

A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants

Patterns of viral communities and the host–pathogen interactions with ecological factors in bat caves

Community Structure, Drivers, and Potential Functions of Different Lifestyle Viruses in Chaohu Lake

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