Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China

Gao, Shao‐Ming; Páez-Espino, David; Li, Jintian; Ai, Hongxia; Liang, Jie-Liang; Luo, Zhen-Hao; Zheng, Jin; Chen, Hao; Shu, Wen‐Sheng; Huang, Li-Nan

doi:10.1038/s41467-022-30049-5

Cited by 48 publications

(32 citation statements)

References 90 publications

(120 reference statements)

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“…In addition, viral groups were found to be closely associated with Fe oxides, including Feo and Fep. Ferric oxides directly govern viral taxonomic and functional abundance in iron-replete sediment …”

Section: Discussionmentioning

confidence: 99%

“…Ferric oxides directly govern viral taxonomic and functional abundance in iron-replete sediment. 51 Similarly, iron-rich paddy soil may provide abundant ironbearing minerals to adsorb viral particles. Furthermore, the tailed phages could incorporate iron ions and have more advantages to infect hosts by competing with siderophorebound iron for uptake receptors.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Bacteria–Virus Interactions Are More Crucial in Soil Organic Carbon Storage than Iron Protection in Biochar-Amended Paddy Soils

Zhou,

Chen,

Zhang

et al. 2023

Environ. Sci. Technol.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Bacteria–Virus Interactions Are More Crucial in Soil Organic Carbon Storage than Iron Protection in Biochar-Amended Paddy Soils

Zhou,

Chen,

Zhang

et al. 2023

Environ. Sci. Technol.

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“…DRAMv v1.2.4 ( Shaffer et al, 2020 ) was used for viral gene annotation. The virus-host linkage analysis was done following the two methods previously reported ( Gao et al, 2022 ). Briefly, viral contigs were compared with the recovered MAGs using BLASTn (E-value ≤ 10–3, bit score ≥ 50, alignment length ≥ 2.5 kb, and identity ≥ 70%).…”

Section: Methodsmentioning

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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“…Viral AMGs associated with organic P mineralization (phnP, phnK, phoD, phoH, phoX), and inorganic P solubilization (gcd and pqqC), biosynthesis (pph) and hydrolysis (ppx and ppx-gppA) have also been detected in soil viromes (Eissler et al, 2020;Gao et al, 2022;Hwang et al, 2021) (Figure 2). Among these P biogeochemical cycling associated AMGs, phoH gene that played a role in the transport of phosphate in conditions of starvation is among the most extensively distributed AMGs in grassland, wetland, desert, and even organic pesticidecontaminated site soils (Hwang et al, 2021;Li et al, 2019;Zheng et al, 2022).…”

Section: Nutrient Transformationmentioning

confidence: 99%

Underexplored viral auxiliary metabolic genes in soil: Diversity and eco‐evolutionary significance

Sun

Yuan

Xia

et al. 2023

Environmental Microbiology

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Bacterial viruses are the most abundant biological entities in soil ecosystems. Owing to the advent of metagenomics and viromics approaches, an ever‐increasing diversity of virus‐encoded auxiliary metabolic genes (AMGs) have been identified in soils, including those involved in the transformation of carbon, phosphorus, and sulfur, degradation of organic pollutants, and antibiotic resistance, among other processes. These viral AMGs can alter soil biogeochemical processes and metabolic activities by interfering with bacterial host metabolism. It is recognized that viral AMGs compensate for host bacterial metabolism outputs by encoding accessory functional genes and are favourable for the hosts' adaptation to stressed soil environments. The eco‐evolutionary mechanisms behind this fascinating diversity of viral AMGs in soil microbiomes have begun to emerge, such as horizontal gene transfer, lytic‐lysogenic conversion, and single‐nucleotide polymorphisms. In this mini‐review, we summarize recent advances in the diversity and function of virus‐encoded AMGs in the soil environment, especially focusing on the evolutionary significance of AMGs involved in virus‐host interactions. This mini‐review also sheds light on the existing gaps and future perspectives that could have major significance for viral AMGs research in soils.

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Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China

Cited by 48 publications

References 90 publications

Bacteria–Virus Interactions Are More Crucial in Soil Organic Carbon Storage than Iron Protection in Biochar-Amended Paddy Soils

Bacteria–Virus Interactions Are More Crucial in Soil Organic Carbon Storage than Iron Protection in Biochar-Amended Paddy Soils

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

Underexplored viral auxiliary metabolic genes in soil: Diversity and eco‐evolutionary significance

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