Sarah L. Strauss

Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus, is the most destructive disease affecting citrus production worldwide. Trunk injection of oxytetracycline (OTC) is increasingly used to suppress the pathogen and improve tree performance, yet its ecological consequences for plant‐associated microbiomes remain poorly understood. Here, we evaluated the compartment‐specific responses of plant growth–promoting microbiomes to systemic OTC treatment in HLB‐affected citrus trees under commercial orchard conditions. Using shotgun metagenomics combined with targeted detection of plant growth–promoting genes, we analyzed functional and taxonomic dynamics across leaves, bark, roots, and rhizosphere at three time points (3 days, 3 weeks, and 3 months) following treatment. OTC injection reduced pathogen abundance in leaves and improved yield, fruit weight, and juice quality. Aggregated plant growth–promoting functional profiles remained largely stable across compartments. However, taxonomic shifts were nonetheless detected within microbial lineages carrying these functions, suggesting that comparable functional potential may be maintained despite changes in the microbial lineages encoding it. Bark communities showed transient enrichment of nutrient acquisition and interaction‐related functions, while the rhizosphere exhibited taxonomic turnover without consistent functional shifts. In contrast, root microbiomes displayed temporally structured reorganization of interaction‐associated functions and were the only compartment where functional composition correlated with plant performance. Genome‐resolved analyses further suggested early enrichment of stress‐tolerant and metabolically versatile taxa following treatment. We conclude that systemic OTC trunk injection in citrus was associated with taxonomic redistribution rather than broad functional loss of plant‐associated microbiomes, with functionally relevant consequences emerging selectively in the root microbiome. These findings highlight the importance of spatially resolved microbiome analyses for understanding the ecological impacts of antibiotic use in perennial crop systems and for evaluating the sustainability of disease‐management strategies.

The role of cover crops in promoting the abundance of beneficial soil microbes is increasingly gaining attention in tree crops. However, soil fungi remain comparatively understudied despite their roles in nutrient cycling and soil organic matter turnover, functions that are directly influenced by cover crops and may, in turn, affect the cash crop. This study compared the effects of cover crop mixtures to a weedy control on soil bacterial and fungal communities in young (< 10 years) and old (> 20 years) citrus orchards-with different lengths of cover cropping-across three soil depths over 2 years. Soil fungi responded to cover crops, whereas soil bacteria showed minimal changes in both orchards. In the young orchard, non-legume cover crop mixtures altered soil fungal communities three months after planting and after 2 years, both cover crop mixtures resulted in distinct community shifts relative to the control. In the old orchard, soil depth shaped fungal communities, with the strongest cover crop effects in the topsoil and subsurface soil. In both orchards, cover crops enriched potentially plant-beneficial microbial taxa, including arbuscular mycorrhizal fungi, highlighting the importance of cover crops as a management tool for driving fungal-mediated ecological processes and soil health benefits in orchard systems.

Statistical and culture-based models propose that environmental disturbances reshape competitive interactions among functionally redundant microbial taxa. However, the mechanisms driving these changes and their impact on biogeochemical processes remain largely untested in soil, owing to the challenge of linking functions to specific taxa in highly diverse and functionally complex soil microbiomes. Here, we simulated environmental disturbance in microcosms containing organic carbon-rich or sandy soils. Using bacterial and archaeal nitrifiers, a functionally tractable microbial guild, we examined how disturbance restructures competition among diverse microbial taxa within this guild. In both soils ammonia-oxidizing archaea (AOA) predominated numerically and functionally under steady climax conditions. Following disturbance, ammonia-oxidizing bacteria (AOB) and complete ammonia oxidizers (comammox) rapidly gained a growth-related competitive advantage, likely due to increased per-cell ammonium availability supporting their intrinsic high growth rates. AOB recolonization was essential for full post-disturbance nitrogen turnover, resulting in elevated nitrification rates and increased nitrous oxide emissions. Nitrification rate did not fully recover when AOB were inhibited. In contrast, AOA and comammox played a dispensable role in recovering post-disturbance nitrification, limited by slower growth and lower per-cell activity, respectively. Competitive regrowth ability of microbial species showed a tradeoff with pre-disturbance abundance, highlighting the enhanced post-disturbance role of rare-abundance AOA, in addition to AOB phylotypes. Our findings demonstrate that bacterial and archaeal nitrifiers constitute a continuous spectrum between r- and K-strategists. Disturbance reshapes competition through differential growth and activity traits among functionally redundant taxa, favoring AOB and thereby transforming community assembly while intensifying nutrient cycling and greenhouse gas fluxes.

Agricultural management practices act as ecological disturbances that can restructure soil and plant-associated microbial communities, but the functional consequences of these microbial shifts on crop performance remain poorly understood. Here, we examined how common orchard inputs, including wood mulch, glyphosate, and humic acid, affect citrus root and rhizosphere microbiomes and tree performance over a three-year field experiment. Mulch emerged as the dominant driver of microbiome structure, significantly altering bacterial and fungal community composition and increasing rhizosphere alpha diversity. Root microbiomes remained comparatively stable, suggesting stronger host selective forces within root tissues. Mulched rhizospheres were enriched with saprotrophic fungi and metabolically diverse bacteria, while non-mulched soils contained taxa typically associated with nutrient cycling, like Rhizobium , Sphingomonas , and Nitrososphaera . Interactions between mulch and glyphosate further reshaped bacterial communities and corresponded with reduced tree physiological performance, including photosynthesis rates. To verify whether these microbial shifts were contributing to these plant phenotype changes, we conducted a greenhouse experiment using field-derived soil microbiota. Active microbiota from mulch-treated soils reduced citrus seedling establishment and root growth relative to microbiota from non-mulched soils, whereas heat-killed controls eliminated these negative effects, demonstrating a causal relationship between management-induced microbiota changes and decreases in plant performance. In contrast, humic acid influenced plant growth primarily through direct abiotic effects rather than microbial community-level traits. Together, our results show that orchard management practices can restructure citrus microbiomes and generate community-level traits that influence plant performance, highlighting the importance of incorporating microbial ecology and microbiome information when designing and testing crop management strategies.

Soil enzyme activities are sensitive biochemical indicators that could benefit soil health assessments, especially in coarse-textured soils. Current protocols are inconsistent for fluorimetric assays and an optimized assay would facilitate comparisons of activities across climates and soils. A factorial experiment was conducted to evaluate how assay conditions affect the activity of three enzymes (acid phosphatase, β-glucosidase, and N-acetyl-β-glucosaminidase) across seven Florida mineral soils (>89% sand) by crossing two temperatures, four pH values, and two reaction termination reagents. Results between microplate fluorimetry and benchtop colorimetry and between air-dried and frozen (−80 °C) soils were also compared. For these soils, a pH of 4.5 with sodium hydroxide termination and a temperature of 25 °C were deemed “optimal” for maximizing activities and maintaining consistent trends. Activities measured with benchtop colorimetry and microplate fluorimetry were related for each enzyme (R² range: 0.58–0.83) and activities from air-dried soils were 50–90% of those from frozen soils (R² range: 0.75–0.91). Enzyme activities were positively correlated with other indicators (total C, nutrients), supporting their use in soil health assessments. As the rankings of soil samples by highest enzyme activities were similar regardless of protocol variations, this suggests that inherent soil properties were the dominant drivers of enzymatic activity.