Deborah Pagliaccia

Biochar and bokashi liquid digestate (Bok-L) valorize agricultural waste. Their incorporation supports soil ecosystem services, facilitating a circular, low-input approach nursery management. In this study, we evaluated the use of almond-shell biochar (10 % v/v) and citrus-waste Bok-L (0.5 % v/v) in two separate 21-week greenhouse experiments using Carrizo and C-35 rootstocks. The treatment with both biochar and Bok-L (T7) and the primed-microbiome version (T8) significantly enhanced both soil and root microbiomes, nearly doubling aerobic heterotrophic bacteria and increasing fungal diversity by approximately 28% compared to the control. Furthermore, the abundance of nutrient‑cycling Actinomycetales, was highly correlated to total organic carbon (ρ = 0.68, p < 0.01) and seedling biomass (ρ = 0.65, p < 0.01) in the T7 and T8 treatments. Companion carbon‑dynamics analyses demonstrated that T7 and T8 treatments resulted in an additional 46% in soil organic carbon compared to the control and reduced water-extractable N loss by 32%. Germination for Carrizo rootstock was 17% higher, and shoot dry weight was 20% greater in the T7 treatment; however, the primed-microbiome treatment sometimes resulted in lower germination rates, indicating the need for consideration of application timing. Next-generation sequencing analysis indicated the presence of Pseudomonas, Kitasatospora, and Sebacina, genera associated with pathogen suppression and nutrient cycling; alpha-diversity measures further supported synergistic interactions between the two waste-derived amendments. Collectively, waste-derived biochar and Bok-L enhance rhizosphere functions (nutrient retention, carbon storage, disease suppression) and reduce reactive N loss. This offers a scalable method for resilient, climate-smart nursery substrates and sustainable agroecosystems.

Applying bokashi (Bok) at 10% volume/volume (v/v), biochar (BC) at 10% v/v, and their combination (Bok_BC) as soil amendments significantly enhances citrus nursery production, improving plant growth and soil health, alongside offering notable economic benefits. Our greenhouse experiment evaluated these treatments across two fertilizer doses, at half (700 μS/cm) and full (1400 μS/cm) electrical conductivity (EC) levels, compared to a control mix, demonstrating improved nutrient availability, water retention, growth rates, and potential for carbon sequestration. Based on the results of this experiment, a cost–benefit analysis was performed; the BC treatment yielded substantial savings, particularly in large nurseries where BC at 700 μS/cm electrical conductivity (EC) saved USD 1356.38 per day and the same treatment at 1400 μS/cm EC saved USD 1857.53. These savings stem from increased nutrient contents (N, P, and K) and improved water retention, reducing irrigation; shortened growth cycles due to enhanced growth rates were observed, indirectly suggesting reduced electricity costs for greenhouse operations. Additionally, the increased carbon content within the soil points toward long-term benefits from carbon sequestration, further contributing to the sustainability and economic viability of these practices. These findings highlight the economic advantage of incorporating Bok and BC into soil mixes, providing a cost-effective strategy for enhancing greenhouse agriculture sustainability.

The global production of food waste is a far-reaching problem with sizable financial, ethical, social, and environmental costs. Over 66 million tons of food waste is produced annually in the United States alone. This waste can be converted into valuable digestate by-products that promote a circular economy within agri-food systems. The present work investigated the use of two liquid digestates of microaerobic fermentation from mixed food waste and beer mash, respectively, as biostimulants for non-bearing citrus plants (nursery stock) grown in a zero-runoff greenhouse system with recirculating irrigation. The digestates' impact on the structure and diversity of the microbiota was determined on the irrigation water, soil, leaves, roots, and rhizosphere of citrus plants. A combination of culture-dependent (selective media) and culture-independent approaches (Next-Generation Sequencing) was used to assess the composition of the microbial communities and to single out the presence of foodborne pathogens. Our results suggest that the use of digestates is safe (i.e., no human or plant pathogens were present in the digestates or enriched in the plant production system following amendments). Digestates application to the irrigation water reduced the bacterial diversity within 24–48 h and selectively and significantly stimulated beneficial resident host-associated microorganisms (Pseudomonas putida) by two to three orders of magnitude. Carbon dynamics were analyzed in the nutrient solutions by measuring dissolved organic carbon and characterizing carbon species through gas chromatography-electron ionization-mass spectrometry. Our results indicate that dissolved organic carbon in the recirculating irrigation water spikes after each digestate amendment and it is quickly metabolized by bacteria, plateauing 24 h after application. Soil carbon, nitrogen, and nutrient dynamics were also analyzed, and results suggest that digestates increased the concentration of some plant nutrients in soils without causing a surge of potentially toxic elements. This study represents a proof-of-concept for the safe re-use of organic wastes, from farming and consumers, in agriculture. Implementing this type of integrated plant production system could reduce the environmental impact of food waste and benefit the public by improving soil health, reducing agricultural footprint, and increasing crop fitness by deploying a method based on a circular economy and sustainable food production approaches.

Objectives: Spiroplasma citri is a bacterium with a wide host range and is the causal agent of citrus stubborn and brittle root diseases of citrus and horseradish, respectively. S. citri is transmitted in a circulative, persistent manner by the beet leafhopper, Neoaliturus (Circulifer) tenellus (Baker), in North America. Five strains of S. citri were cultured from citrus, horseradish, and N. tenellus from different habitats and times. DNA from cultures were sequenced and genome assembled to expand the database to improve detection assays and better understand its genetics and evolution. Data description: The whole genome sequence of five strains of S. citri are described herein. The S. citri chromosome was circularized for all five strains and ranged from 1,576,550 to 1,742,208 bp with a G + C content of 25.4–25.6%. Characterization of extrachromosomal DNAs resulted in identification of one or two plasmids, with a G + C content of 23.3 to 27.6%, from plant hosts; and eight or nine plasmids, with a G + C content of 21.65 to 29.19%, from N. tenellus. Total genome size ranged from 1,611,714 to 1,832,173 bp from plants and 1,968,976 to 2,155,613 bp from the leafhopper. All sequence data has been deposited in DDBJ/ENA/GenBank under the accession numbers CP046368-CP046373 and CP047426-CP047446.

Spiroplasma citri is a bacterium that causes stubborn disease of citrus and infects other crops, ornamentals, and weeds. It is transmitted by leafhoppers in a circulative manner. Due to limited sequence data on S. citri, the bacterium was isolated from naturally infected Chinese cabbage grown on a farm in Fresno County, CA. DNA from S. citri CC-2 was extracted from a pure culture in LD8 and subjected to PacBio sequencing. Four contigs were obtained with a single circular chromosome of 1,709,192 bp and three plasmids of 40,210, 39,313, and 2,921 bp in size. The genome developed herein extends the sequence database of S. citri and is the first whole-genome sequence record of S. citri from California.

Rice blast, caused by the ascomycete Magnaporthe oryzae, is one of the most destructive rice diseases worldwide. Even though the disease has been present in California since 1996, there is no data for the pathogen population biology in the state. Using amplified fragment length polymorphisms and mating-type markers, the M. oryzae population diversity was investigated using isolates collected when the disease was first established in California and isolates collected a decade later. While in the 1990 samples, a single multilocus genotype (MLG) was identified (MLG1), over a decade later, we found 14 additional MLGs in the 2000 isolates. Some of these MLGs were found to infect the only rice blast-resistant cultivar (M-208) available for commercial production in California. The same samples also had a significant decrease of MLG1. MLG1 was found infecting the resistant rice cultivar M-208 on one occasion whereas MLG7 was the most common genotype infecting the M-208. MLG7 was identified in the 2000 samples, and it was not present in the M. oryzae population a decade earlier. Our results demonstrate a significant increase in genotypic diversity over time with no evidence of sexual reproduction and suggest a recent introduction of new virulent race(s) of the pathogen. In addition, our data could provide information regarding the durability of the Pi-z resistance gene of the M-208. This information will be critical to plant breeders in developing strategies for deployment of other rice blast resistance genes/cultivars in the future.