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  1. Article ; Online: Underexplored viral auxiliary metabolic genes in soil: Diversity and eco‐evolutionary significance

    Sun, Mingming / Yuan, Shujian / Xia, Rong / Ye, Mao / Balcázar, José Luis

    Environmental Microbiology. 2023 Apr., v. 25, no. 4 p.800-810

    2023  

    Abstract: 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, ... ...

    Abstract 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.
    Keywords antibiotic resistance ; carbon ; edaphic factors ; horizontal gene transfer ; metabolism ; metagenomics ; phosphorus ; soil ; soil microorganisms ; sulfur
    Language English
    Dates of publication 2023-04
    Size p. 800-810.
    Publishing place John Wiley & Sons, Inc.
    Document type Article ; Online
    Note REVIEW
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/1462-2920.16329
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: Underexplored viral auxiliary metabolic genes in soil: Diversity and eco-evolutionary significance.

    Sun, Mingming / Yuan, Shujian / Xia, Rong / Ye, Mao / Balcázar, José Luis

    Environmental microbiology

    2023  Volume 25, Issue 4, Page(s) 800–810

    Abstract: 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, ... ...

    Abstract 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.
    MeSH term(s) Genes, Viral ; Bacteriophages/genetics ; Biological Evolution ; Bacteria/metabolism ; Microbiota/genetics ; Soil
    Chemical Substances Soil
    Language English
    Publishing date 2023-01-05
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/1462-2920.16329
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  3. Article: Quantitative relationship between earthworms’ sensitivity to organic pollutants and the contaminants’ degradation in soil: A meta-analysis

    Chao, Huizhen / Sun, Mingming / Wu, Yunling / Xia, Rong / Yuan, Shujian / Hu, Feng

    Journal of hazardous materials. 2022 May 05, v. 429

    2022  

    Abstract: Using earthworms to remove soil organic pollutants is a common bioremediation method. However, it remains challenging to evaluate and predict their effect on removing soil organic pollutants based on earthworm toxicology and pollutant degradation rates. ... ...

    Abstract Using earthworms to remove soil organic pollutants is a common bioremediation method. However, it remains challenging to evaluate and predict their effect on removing soil organic pollutants based on earthworm toxicology and pollutant degradation rates. Peer-reviewed journal articles on ecotoxicology and bioremediation from the years 1974–2020 (cutoff date September 2020) were selected for meta-analysis to quantify the effect size of earthworms on organic pollutant degradation. The meta-analysis shows that the average effect size of earthworms on organic pollutant degradation is 128.5% (p < 0.05). Soils with high soil organic matter or clay textures are more conducive to earthworm-mediated removal of organic pollutants. Structural equation modeling reveals that earthworms’ sensitivity to contaminant exposure may be a greater limiting factor on pollutant degradation than environmental factors. In addition, the quantitative relationship existed between LC50 and the pollutants’ degradation that an elevated LC50 threshold resulted in at least 1.5 times increase in the pollutants’ degradation size. This correlation was dually confirmed via meta-analysis and the validation trial. The results of this study contribute to a more profound understanding of the potential to use earthworms to mitigate organic pollution in soils and develop earthworm-based soil remediation techniques on a global scale.
    Keywords bioremediation ; clay ; earthworms ; ecotoxicology ; equations ; lethal concentration 50 ; meta-analysis ; pollutants ; soil ; soil organic matter ; soil remediation
    Language English
    Dates of publication 2022-0505
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 1491302-1
    ISSN 1873-3336 ; 0304-3894
    ISSN (online) 1873-3336
    ISSN 0304-3894
    DOI 10.1016/j.jhazmat.2022.128286
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  4. Article ; Online: Quantitative relationship between earthworms' sensitivity to organic pollutants and the contaminants' degradation in soil: A meta-analysis.

    Chao, Huizhen / Sun, Mingming / Wu, Yunling / Xia, Rong / Yuan, Shujian / Hu, Feng

    Journal of hazardous materials

    2022  Volume 429, Page(s) 128286

    Abstract: Using earthworms to remove soil organic pollutants is a common bioremediation method. However, it remains challenging to evaluate and predict their effect on removing soil organic pollutants based on earthworm toxicology and pollutant degradation rates. ... ...

    Abstract Using earthworms to remove soil organic pollutants is a common bioremediation method. However, it remains challenging to evaluate and predict their effect on removing soil organic pollutants based on earthworm toxicology and pollutant degradation rates. Peer-reviewed journal articles on ecotoxicology and bioremediation from the years 1974-2020 (cutoff date September 2020) were selected for meta-analysis to quantify the effect size of earthworms on organic pollutant degradation. The meta-analysis shows that the average effect size of earthworms on organic pollutant degradation is 128.5% (p < 0.05). Soils with high soil organic matter or clay textures are more conducive to earthworm-mediated removal of organic pollutants. Structural equation modeling reveals that earthworms' sensitivity to contaminant exposure may be a greater limiting factor on pollutant degradation than environmental factors. In addition, the quantitative relationship existed between LC50 and the pollutants' degradation that an elevated LC50 threshold resulted in at least 1.5 times increase in the pollutants' degradation size. This correlation was dually confirmed via meta-analysis and the validation trial. The results of this study contribute to a more profound understanding of the potential to use earthworms to mitigate organic pollution in soils and develop earthworm-based soil remediation techniques on a global scale.
    MeSH term(s) Animals ; Biodegradation, Environmental ; Environmental Pollutants/metabolism ; Oligochaeta/metabolism ; Soil/chemistry ; Soil Pollutants/metabolism
    Chemical Substances Environmental Pollutants ; Soil ; Soil Pollutants
    Language English
    Publishing date 2022-01-22
    Publishing country Netherlands
    Document type Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't
    ZDB-ID 1491302-1
    ISSN 1873-3336 ; 0304-3894
    ISSN (online) 1873-3336
    ISSN 0304-3894
    DOI 10.1016/j.jhazmat.2022.128286
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Viral and Bacterial Communities Collaborate through Complementary Assembly Processes in Soil to Survive Organochlorine Contamination.

    Yuan, Shujian / Friman, Ville-Petri / Balcazar, Jose Luis / Zheng, Xiaoxuan / Ye, Mao / Sun, Mingming / Hu, Feng

    Applied and environmental microbiology

    2023  Volume 89, Issue 3, Page(s) e0181022

    Abstract: The ecological drivers that direct the assembly of viral and host bacterial communities are largely unknown, even though viral-encoded accessory genes help host bacteria survive in polluted environments. To understand the ecological mechanism(s) of ... ...

    Abstract The ecological drivers that direct the assembly of viral and host bacterial communities are largely unknown, even though viral-encoded accessory genes help host bacteria survive in polluted environments. To understand the ecological mechanism(s) of viruses and hosts synergistically surviving under organochlorine pesticide (OCP) stress, we investigated the community assembly processes of viruses and bacteria at the taxon and functional gene levels in clean and OCP-contaminated soils in China using a combination of metagenomics/viromics and bioinformatics approaches. We observed a decreased richness of bacterial taxa and functional genes but an increased richness of viral taxa and auxiliary metabolic genes (AMGs) in OCP-contaminated soils (from 0 to 2,617.6 mg · kg
    MeSH term(s) Soil ; Bacteria ; Microbiota ; Soil Microbiology ; Viruses ; Pesticides/metabolism ; Hydrocarbons, Chlorinated/metabolism
    Chemical Substances Soil ; Pesticides ; Hydrocarbons, Chlorinated
    Language English
    Publishing date 2023-02-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 223011-2
    ISSN 1098-5336 ; 0099-2240
    ISSN (online) 1098-5336
    ISSN 0099-2240
    DOI 10.1128/aem.01810-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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