Composition of soil viral and bacterial communities after long-term tillage, fertilization, and cover cropping management

Highlights

• Management and substrate availability influence bacterial community structure.

• Cover crops, soil water, and bacterial abundance affect soil viral communities.

• Bacterial abundance positively influenced viral abundance.

• There is positive feedback between viral abundance and substrate availability.

Abstract

Soil bacterial communities are critical for stability and function of terrestrial ecosystems. Viruses are ubiquitous in soils and have significant impacts on the structure and functions of bacterial host communities. However, little is known concerning the impact of various land use management practices on bacterial and viral communities. This study aimed to estimate variations of composition and structure of bacterial and viral communities under long term management practices including inorganic N fertilization, cover cropping, and tillage treatments in a long-term conservation management experimental site in western Tennessee USA. We evaluated bacterial and DNA viral diversity using 16s rRNA sequencing and RAPD-PCR, respectively, and enumerated viral and bacterial abundance via epifluorescence microscopy. Structural equation modeling was applied on the dataset to reveal relationships among viruses, bacteria and soil properties. No significant differences in bacterial alpha-diversity were identified among inorganic N fertilization (ammonia nitrate), cover cropping, and tillage treatments. However, community structure (beta-diversity) differed significantly. Higher soil pH and water content favored greater bacterial abundances. Cover cropping, soil water content, and bacterial abundances were the main factors explaining the variation of viral abundances and community structure in soil. Structural equation modeling suggested that bacterial abundances positively influenced viral abundances, and in turn virus abundances and bacterial alpha diversity affected the level of extractable dissolved organic C, which exerted a feedback effect on the structure of bacterial communities. This feedback loop suggests that bacterial lysates resulting from viral infection might significantly contribute to the reshaping of bacterial community structure while indirectly influencing bacterial alpha diversity. This supports the theory of the “viral shunt” in soil ecosystems. This study suggests that the structure of soil bacteria and viruses can be reshaped by long-term management practices. Viruses may indirectly involve in C cycling through positively influencing microbial dissolved organic C under long-term conservation management practices.

Introduction

In agroecosystems, management practices such as conventional tillage, fertilization, and cover cropping can greatly influence soil properties, including soil physical structure, organic matter accumulation, water and nutrient retention, and the distribution of microbes in the soil profile. Conventional tillage practices, for example, increase soil disturbance, destabilize soil aggregate structures, and increase soil erosion, and decrease soil organic matter and water holding capacity (Kladivko and Research, 2001; Lienhard et al., 2013). Therefore, conventional tillage management practices can change the bacterial community composition. Previous studies reported that increasing of Proteobaceria and Planctomycetes may be found under conventional tillage than no tillage in a sandy soil and that tillage can significantly impact the abundances of nitrifiers and denitrifies (Zhang et al., 2022). Fertilizer nitrogen (N) provides direct nutrient resources for plant and microbial growth, which potentially decreases soil pH, increases soil organic matter inputs and carbon sequestration leading to the shifts in the structure of bacterial communities. For example, the bacterial alpha-diversity may be lower due to the decreasing of soil pH after a long-term N fertilization (Zhou et al., 2015; Zhou et al., 2017b). The relative abundance of Proteobacteria, Verrucomicrobia, and Actinobacteria increased in N-fertilized treatments, but Acidobacteria and Nitrospirae decreased compared to unfertilized soil in northeast China (Zhou et al., 2015). Cover cropping provides alternative organic residues to the main crop, affecting the quantity and chemical quality of the bioavailable pool of soil organic matter. For example, nitrogen (N)-fixing cover crops (e.g., hairy vetch) have a low C:N ratio and a greater proportion of labile vs. recalcitrant C compared to non-N fixing crops such as winter wheat (NRCS, 1977; Lowry and Brainard, 2016; Ruark and Franzen, 2020). The quality of plant litters can shape microbial communities by selecting microbes with ability to use ambient resources (Fanin et al., 2016; Vukicevich et al., 2016). Both fertilization and cover cropping have been observed to change the input of crop residues, root exudates, and dynamics of soil habitat properties (e.g. moisture and temperature), which in turn can influence soil microbial biomass, activity and functional composition and structure (Geisseler and Scow, 2014; Mbuthia, 2014; Vukicevich et al., 2016; Finney et al., 2017; Zhou et al., 2017a). Actinobacteria and Firmicutes were enriched in the soil with wheat materials (Chávez-Romero et al., 2016) and the relative abundance of plant-beneficial bacterial taxa including Mycobacterium and Pseudomonas were greater under fertilization with vetch cover crops than control, and the combination of two practices can optimize bacterial community structure (Xiang et al., 2021).

Soil is a complex ecological system which contains up to 10¹⁰ bacteria cells representing thousands of different microbial species in each gram of soil (Raynaud and Nunan, 2014). Viruses are an understudied component of the soil biosphere that are rapidly gaining the attention of researchers (Kimura et al., 2008; Emerson et al., 2018; Trubl et al., 2018b; Ter Horst et al., 2021). Evidence for viral-mediated top-down regulation of the structure and functions of microbial communities has been reported in soil ecosystems (Ashelford et al., 2003; Williamson et al., 2007; Chow et al., 2014; Emerson et al., 2018; Trubl et al., 2018a). During the top-down regulation, the microbial cell lysate (i.e., necromass) due to viral infection can release labile substrates of microbial origin into the soil. This bioavailable dissolved organic matter (DOM) can be readily taken up by other surviving microbes for their metabolism and growth. This cycle is often referred to as the “viral shunt”, first put forth in 1999 in marine ecosystems, it has been revealed as an important role of viruses on C-cycling (Wilhelm and Suttle, 1999; Jover et al., 2014; Kuzyakov and Mason-Jones, 2018). The ecological interactions between soil viruses and microbes maybe crucial indicators for functional processes in soil ecosystems. However, the impact of the “viral shunt” on soil microbial food web and nutrient cycling remains unknown.

In this study, the impacts of long-term conservation management practices on microbial and viral community structure were investigated. We hypothesized that (1) long-term (40 years) tillage, fertilization, and cover cropping would significantly change the strucutre of bacterial and viral communities, compared to conventionally (i.e., intensively) managed soils; (2) viral community compostion would be structured in patterns similar to bacterial communities; and (3) viruses may be related to the supply of readily degradable organic C variation and drive the differences in bacterial community structure. To test these hypotheses, high-throughput amplicon sequencing and RAPD-PCR were used to estimate the long-term effect of the management practices on bacterial and viral community structure, respectively. Structural equation modeling and multivariate analysis were performed to analyze the interrelationships among bacteria, virus, and environmental factors.