Metagenomics Assessment of Soil Fertilization on the Chemotaxis and Disease Suppressive Genes Abundance in the Maize Rhizosphere

Green Waste Compost Impacts Microbial Functions Related to Carbohydrate Use and Active Dispersal in Plant Pathogen-Infested Soil

The effects of compost on physical and chemical characteristics of soil are well-studied but impacts on soil microbiomes are poorly understood. This research tested effects of green waste compost on bacterial communities in soil infested with the plant pathogen Fusarium oxysporum. Compost was added to pathogen-infested soil and maintained in mesocosms in a greenhouse experiment and replicated growth chamber experiments. Bacteria and F. oxysporum abundance were quantified using quantitative PCR. Taxonomic and functional characteristics of bacterial communities were measured using shotgun metagenome sequencing. Compost significantly increased bacterial abundance 8 weeks after amendment in one experiment. Compost increased concentrations of chemical characteristics of soil, including phosphorus, potassium, organic matter, and pH. In all experiments, compost significantly reduced abundance of F. oxysporum and altered the taxonomic composition of soil bacterial communities. Sixteen bacterial genera were significantly increased from compost in every experiment, potentially playing a role in pathogen suppression. In all experiments, there was a consistent negative effect of compost on functions related to carbohydrate use and a positive effect on bacteria with flagella. Results from this work demonstrate that compost can reduce the abundance of soilborne plant pathogens and raise questions about the role of microbes in plant pathogen suppression.

Effects of vermicompost leachate on nitrogen, phosphorus, and microbiome in a food waste bioponic system

Food waste is rich in nutrients, such as nitrogen and phosphorus, and can be integrated with bioponics, a closed-loop agricultural system that combines hydroponics with biological nutrient recovery. Vermicompost leachate (VCL) supplementation has been shown to improve the co-composting of organic waste (i.e., compost quality) and the biodegradation of organic compounds. Thus, VCL has high potential for enhancing nutrient availability in bioponics from food waste. However, the understanding of nitrogen and phosphorus availability in food waste-based bioponics is limited, both with and without VCL. In this study, food waste derived from cafeteria vegetable waste was used as the substrate (500 g dry wt./system) in bioponics to grow lettuce (Lactuca sativa L.) for two consecutive cycles (35 days/cycle) without substrate replacement. VCL was applied weekly (1-5% v/v) and compared to the control without VCL. The results showed that the food waste in bioponics provided nitrogen and phosphorus for plant growth (15.5-65.8 g/lettuce head). Organic-degrading and nutrient-transforming bacteria (Hydrogenispora, Clostridium_sensu_stricto_1, Ruminiclostridium_1, Cellvibrio, Thauera, Hydrogenophaga, and Bacillus) were predominantly found in plant roots and residual food waste. VCL addition significantly increased nitrate, phosphate, and chemical oxygen demand levels in bioponics, owing to the nutrients in VCL and the enhancement of keystone microorganisms responsible for organic degradation and nutrient cycling (e.g., Ellin6067, Actinomyces, and Pirellula). These findings suggest that nitrogen, phosphorus, and organic carbon concentrations in an ecosystem of nutrient-transforming and organic-degrading microbes are key in managing nutrient recovery from food waste in bioponics.

Shotgun metagenomics evaluation of soil fertilization effect on the rhizosphere viral community of maize plants

The need for sustainability in food supply has led to progressive increase in soil nutrient enrichment. Fertilizer application effects both biological and abiotic processes in the soil, of which the bacterial community that support viral multiplication are equally influenced. Nevertheless, little is known on the effect of soil fertilization on the Soil viral community composition and dynamics. In this study, we evaluated the influence of soil fertilization on the maize rhizosphere viral community growing in Luvisolic soil. The highest abundance of bacteriophages were detected in soil treated with 8 tons/ha compost manure (Cp8), 60 kg/ha inorganic fertilizer (N1), 4 tons/ha compost manure (Cp4) and the unfertilized control (Cn0). Our result showed higher relative abundance of Myoviridae, Podoviridae and Siphoviridae in 8 tons/ha organic manure (Cp8) fertilized compared to others. While Inoviridae and Microviridae were the most relative abundant phage families in 4 tons/ha organic manure (Cp4) fertilized soil. This demonstrate that soil fertilization with organic manure increases the abundance and diversity of viruses in the soil due to its soil conditioning effects.

Metagenomic Analyses of Plant Growth-Promoting and Carbon-Cycling Genes in Maize Rhizosphere Soils with Distinct Land-Use and Management Histories

Many studies have shown that the maize rhizosphere comprises several plant growth-promoting microbes, but there is little or no study on the effects of land-use and management histories on microbial functional gene diversity in the maize rhizosphere soils in Africa. Analyzing microbial genes in the rhizosphere of plants, especially those associated with plant growth promotion and carbon cycling, is important for improving soil fertility and crop productivity. Here, we provide a comparative analysis of microbial genes present in the rhizosphere samples of two maize fields with different agricultural histories using shotgun metagenomics. Genes involved in the nutrient mobilization, including nifA, fixJ, norB, pstA, kefA and B, and ktrB were significantly more abundant (α = 0.05) in former grassland (F1) rhizosphere soils. Among the carbon-cycling genes, the abundance of 12 genes, including all those involved in the degradation of methane were more significant (α = 0.05) in the F1 soils, whereas only five genes were significantly more abundant in the F2 soils. α-diversity indices were different across the samples and significant differences were observed in the β diversity of plant growth-promoting and carbon-cycling genes between the fields (ANOSIM, p = 0.01 and R = 0.52). Nitrate-nitrogen (N-NO₃) was the most influential physicochemical parameter (p = 0.05 and contribution = 31.3%) that affected the distribution of the functional genes across the samples. The results indicate that land-use and management histories impact the composition and diversity of plant growth-promoting and carbon-cycling genes in the plant rhizosphere. The study widens our understanding of the effects of anthropogenic activities on plant health and major biogeochemical processes in soils.