A mixed blessing of viruses in wastewater treatment plants

Shi, Ling-Dong; Dong, Xiyang; Liu, Zongbao; Yang, Yuchun; Lin, Jih‐Gaw; Li, Meng; Gu, Ji‐Dong; Zhu, Lizhong; Zhao, He-Ping

doi:10.1016/j.watres.2022.118237

Cited by 36 publications

(30 citation statements)

References 112 publications

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“…Furthermore, it is possible that bacteria could have evolved phage resistance as observed previously [ 22 , 23 ], which could have decoupled population dynamics, leading to a reduction in phage but not in bacterial abundances due to them being resistant. Together, these findings suggest that R. solanacearum -specific phages exerted relatively stronger top-down regulation in healthy tomato rhizosphere microbiomes, similar to the phage-mediated top-down control of bacteria in aquatic [ 45 , 46 ], plant phyllosphere [ 24 ] and other terrestrial environments [ 25 , 47 ].…”

Section: Discussionmentioning

confidence: 87%

Rhizosphere phage communities drive soil suppressiveness to bacterial wilt disease

et al. 2023

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Background Bacterial viruses, phages, play a key role in nutrient turnover and lysis of bacteria in terrestrial ecosystems. While phages are abundant in soils, their effects on plant pathogens and rhizosphere bacterial communities are poorly understood. Here, we used metagenomics and direct experiments to causally test if differences in rhizosphere phage communities could explain variation in soil suppressiveness and bacterial wilt plant disease outcomes by plant-pathogenic Ralstonia solanacearum bacterium. Specifically, we tested two hypotheses: (1) that healthy plants are associated with stronger top-down pathogen control by R. solanacearum-specific phages (i.e. ‘primary phages’) and (2) that ‘secondary phages’ that target pathogen-inhibiting bacteria play a stronger role in diseased plant rhizosphere microbiomes by indirectly ‘helping’ the pathogen. Results Using a repeated sampling of tomato rhizosphere soil in the field, we show that healthy plants are associated with distinct phage communities that contain relatively higher abundances of R. solanacearum-specific phages that exert strong top-down pathogen density control. Moreover, ‘secondary phages’ that targeted pathogen-inhibiting bacteria were more abundant in the diseased plant microbiomes. The roles of R. solanacearum-specific and ‘secondary phages’ were directly validated in separate greenhouse experiments where we causally show that phages can reduce soil suppressiveness, both directly and indirectly, via top-down control of pathogen densities and by alleviating interference competition between pathogen-inhibiting bacteria and the pathogen. Conclusions Together, our findings demonstrate that soil suppressiveness, which is most often attributed to bacteria, could be driven by rhizosphere phage communities that regulate R. solanacearum densities and strength of interference competition with pathogen-suppressing bacteria. Rhizosphere phage communities are hence likely to be important in determining bacterial wilt disease outcomes and soil suppressiveness in agricultural fields.

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Section: Discussionmentioning

confidence: 87%

Rhizosphere phage communities drive soil suppressiveness to bacterial wilt disease

et al. 2023

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“…In addition, the researchers also pointed out although the specific antibiotics used to treat bacterial infections may be different, the types are often the same, so the rapid rise in drug resistance will eventually affect human beings ( Yang et al, 2022 ). Surprisingly, the potential spread of virus-mediated ARGs is likely to exacerbate AMR, including tetracycline resistance and harm to public health ( Calero-Cáceres et al, 2019 ; Debroas and Siguret, 2019 ; Shi et al, 2022 ), which needs our wider attention. Moreover, viruses might be linked to Enterobacteriaceae or Vibrionaceae and were considered as gene shuttles in ARGs transfer, like plasmids.…”

Section: Discussion and Prospectsmentioning

confidence: 99%

Dissemination and prevalence of plasmid-mediated high-level tigecycline resistance gene tet (X4)

Zhang

Wen²,

Wang³

et al. 2022

Front. Microbiol.

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With the large-scale use of antibiotics, antibiotic resistant bacteria (ARB) continue to rise, and antibiotic resistance genes (ARGs) are regarded as emerging environmental pollutants. The new tetracycline-class antibiotic, tigecycline is the last resort for treating multidrug-resistant (MDR) bacteria. Plasmid-mediated horizontal transfer enables the sharing of genetic information among different bacteria. The tigecycline resistance gene tet(X) threatens the efficacy of tigecycline, and the adjacent ISCR2 or IS26 are often detected upstream and downstream of the tet(X) gene, which may play a crucial driving role in the transmission of the tet(X) gene. Since the first discovery of the plasmid-mediated high-level tigecycline resistance gene tet(X4) in China in 2019, the tet(X) genes, especially tet(X4), have been reported within various reservoirs worldwide, such as ducks, geese, migratory birds, chickens, pigs, cattle, aquatic animals, agricultural field, meat, and humans. Further, our current researches also mentioned viruses as novel environmental reservoirs of antibiotic resistance, which will probably become a focus of studying the transmission of ARGs. Overall, this article mainly aims to discuss the current status of plasmid-mediated transmission of different tet(X) genes, in particular tet(X4), as environmental pollutants, which will risk to public health for the “One Health” concept.

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“…The majority of underexplored viruses have been recovered from wastewater treatment systems ( Shi et al, 2022a ), which could affect functional microbiota in nutrient removal and element cycle ( Chen et al, 2021 ). We obtained 3,360 non-redundant putative viral sequences from the anaerobic activated sludge and found the Siphoviridae , Podoviridae , and Myoviridae were the three main viral families, which was consistent with the previous studies ( Jankowski et al, 2022 ; Lin et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Monthly dynamics of microbial communities and variation of nitrogen-cycling genes in an industrial-scale expanded granular sludge bed reactor

Zhang

Zhang²,

Deng³

et al. 2023

Front. Microbiol.

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IntroductionThe expanded granular sludge bed (EGSB) is a major form of anaerobic digestion system during wastewater treatment. Yet, the dynamics of microbial and viral communities and members functioning in nitrogen cycling along with monthly changing physicochemical properties have not been well elucidated.MethodsHere, by collecting the anaerobic activated sludge samples from a continuously operating industrial-scale EGSB reactor, we conducted 16S rRNA gene amplicon sequencing and metagenome sequencing to reveal the microbial community structure and variation with the ever-changing physicochemical properties along within a year.ResultsWe observed a clear monthly variation of microbial community structures, while COD, the ratio of volatile suspended solids (VSS) to total suspended solids (TSS) (VSS/TSS ratio), and temperature were predominant factors in shaping community dissimilarities examined by generalized boosted regression modeling (GBM) analysis. Meanwhile, a significant correlation was found between the changing physicochemical properties and microbial communities (p <0.05). The alpha diversity (Chao1 and Shannon) was significantly higher (p <0.05) in both winter (December, January, and February) and autumn (September, October, and November) with higher organic loading rate (OLR), higher VSS/TSS ratio, and lower temperature, resulting higher biogas production and nutrition removal efficiency. Further, 18 key genes covering nitrate reduction, denitrification, nitrification, and nitrogen fixation pathways were discovered, the total abundance of which was significantly associated with the changing environmental factors (p <0.05). Among these pathways, the dissimilatory nitrate reduction to ammonia (DNRA) and denitrification had the higher abundance contributed by the top highly abundant genes narGH, nrfABCDH, and hcp. The COD, OLR, and temperature were primary factors in affecting DNRA and denitrification by GBM evaluation. Moreover, by metagenome binning, we found the DNRA populations mainly belonged to Proteobacteria, Planctomycetota, and Nitrospirae, while the denitrifying bacteria with complete denitrification performance were all Proteobacteria. Besides, we detected 3,360 non-redundant viral sequences with great novelty, in which Siphoviridae, Podoviridae, and Myoviridae were dominant viral families. Interestingly, viral communities likewise depicted clear monthly variation and had significant associations with the recovered populations (p <0.05).DiscussionOur work highlights the monthly variation of microbial and viral communities during the continuous operation of EGSB affected by the predominant changing COD, OLR, and temperature, while DNRA and denitrification pathways dominated in this anaerobic system. The results also provide a theoretical basis for the optimization of the engineered system.

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A mixed blessing of viruses in wastewater treatment plants

Cited by 36 publications

References 112 publications

Rhizosphere phage communities drive soil suppressiveness to bacterial wilt disease

Rhizosphere phage communities drive soil suppressiveness to bacterial wilt disease

Dissemination and prevalence of plasmid-mediated high-level tigecycline resistance gene tet (X4)

Monthly dynamics of microbial communities and variation of nitrogen-cycling genes in an industrial-scale expanded granular sludge bed reactor

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