Viral and Bacterial Communities Collaborate through Complementary Assembly Processes in Soil to Survive Organochlorine Contamination.

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-1). In OCP-contaminated soils, the assembly of bacterial taxa and genes was dominated by a deterministic process, of which the relative significance was 93.0% and 88.7%, respectively. In contrast, the assembly of viral taxa and AMGs was driven by a stochastic process, which contributed 83.1% and 69.2%, respectively. The virus-host prediction analysis, which indicated Siphoviridae was linked to 75.0% of bacterial phyla, and the higher migration rate of viral taxa and AMGs in OCP-contaminated soil suggested that viruses show promise for the dissemination of functional genes among bacterial communities. Taken together, the results of this study indicated that the stochastic assembly processes of viral taxa and AMGs facilitated bacterial resistance to OCP stress in soils. Moreover, our findings provide a novel avenue for understanding the synergistic interactions between viruses and bacteria from the perspective of microbial ecology, highlighting the significance of viruses in mediating bioremediation of contaminated soils. IMPORTANCE The interaction between viral communities and microbial hosts has been studied extensively, and the viral community affects host community metabolic function through AMGs. Microbial community assembly is the process by which species colonize and interact to establish and maintain communities. This is the first study that aimed to understand the assembly process of bacterial and viral communities under OCP stress. The findings of this study provide information about microbial community responses to OCP stress and reveal the collaborative interactions between viral and bacterial communities to resist pollutant stress. Thereby, we highlight the importance of viruses in soil bioremediation from the perspective of community assembly.

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

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.

Quantitative relationship between earthworms' sensitivity to organic pollutants and the contaminants' degradation in soil: A meta-analysis.

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.