Biology subjects

Ginnan, N.

Publications and source records attributed to Ginnan, N..

6 recordsLinked to original sources

bioRxiv2026

Wild Luteibacter populations exhibit climate-associated divergence and distinct genomic strategies for osmotic stress tolerance

Soil bacteria play a crucial role in supporting ecosystem health, yet little is known about how wild populations adapt to abiotic stressors, like limited water availability. We used 186 Luteibacter isolates from maize roots grown in never-irrigated prairie soils collected from a steep precipitation gradient in Kansas, US to test whether climate history is associated with osmotic stress tolerance and genomic differentiation. In vitro, strains from semi-arid sites were more tolerant to osmotic-stress treatment than those from humid sites. Comparative genomics of a subset of 96 isolates identified four strongly biogeographically structured lineages and extensive accessory-genome diversity. Semi-arid climate-associated strains were enriched for genes involved in osmotic homeostasis, oxidative stress protection, motility, and type IV secretion. Humid climate-associated strains were enriched in environmental sensing, metabolic versatility, biofilm formation, iron acquisition, type VI secretion, and resource competition. GWAS identified 22 candidate genes associated with osmotic-stress tolerance, including those related to type IV pili, biofilm production, DNA repair, and phage. No candidates were shared between semi-arid and humid strains, suggesting distinct genetic mechanisms of osmotic tolerance. Predicted prophage composition was also geographically structured, although total prophage gene content did not predict osmotic-stress tolerance. Together, these results show that adaptation to long-term differences in water availability likely involves coordinated shifts in stress physiology, genome content, and ecological interactions in wild bacterial populations, providing insight into predicting microbial responses to changing climates.

microbiology↗

bioRxiv2026

Orchard management alters citrus root and rhizosphere microbiomes with functional consequences for plant performance

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.

systems biology↗

bioRxiv2026

ZeaMiC: a Publicly Available Culture Collection of Maize Root-Associated Bacteria

Plant-associated microbiota are composed of hundreds of microbial species. For many of them, little is known about their individual functions and even less is known about their emergent community-level traits. While culture-independent methods provide valuable insights into the composition, diversity, and functional potential of plant-associated microbiota, culture-dependent methods are essential for reductionist lines of inquiry into the roles of individual species and their interactions within a community. Here, we present ZeaMiC, a publicly available culture collection of root-associated bacteria from Zea mays (maize). This resource comprises 88 isolates obtained from diverse soils and several maize genotypes, with live cultures available through DSMZ (German Collection of Microorganisms and Cell Cultures) both as single stocks and as cost-effective bundles (https://www.dsmz.de/collection/catalogue/microorganisms/microbiota/zeamic). To maximize relevance, isolates were selected to be representative of maize root-associated microbiomes in the Corn Belt of the United States, based on abundance-occupancy patterns from previously published root microbiome data, phylogenetic diversity, and literature-based evidence of functional importance. Whole-genome sequencing and annotation revealed genes associated with root colonization, plant growth promotion, and nutrient cycling, including functions such as chemotaxis, biofilm formation, secretion systems, hormone modulation, and phosphate solubilization. This collection serves as a community resource for future mechanistic studies of plant-microbe and microbe-microbe interactions, filling the gap in our understanding of the ecological interactions in plant microbiomes.

microbiology↗

bioRxiv2024

Spatial chemistry of citrus reveals molecules bactericidal to Candidatus Liberibacter asiaticus

Huanglongbing (HLB), associated with the psyllid-vectored phloem-limited bacterium, Candidatus Liberibacter asiaticus (CLas), is a disease threat to all citrus production worldwide. Currently, there are no sustainable curative or prophylactic treatments available. In this study, we utilized mass spectrometry (MS)-based metabolomics in combination with 3D molecular mapping to visualize complex chemistries within plant tissues to explore how these chemistries change in vivo in HLB-impacted trees. We demonstrate how spatial information from molecular maps of branches and single leaves yields insight into the biology not accessible otherwise. In particular, we found evidence that flavonoid biosynthesis is disrupted in HLB-impacted trees, and an increase in the polyamine, feruloylputrescine, is highly correlated with an increase in disease severity. Based on mechanistic details revealed by these molecular maps, followed by metabolic modeling, we formulated and tested the hypothesis that CLas infection either directly or indirectly converts the precursor compound, ferulic acid, to feruloylputrescine to suppress the antimicrobial effects of ferulic acid and biosynthetically downstream flavonoids. Using in vitro bioassays, we demonstrated that ferulic acid and bioflavonoids are indeed highly bactericidal to CLas, with the activity on par with a reference antibiotic, oxytetracycline, recently approved for HLB management. We propose these compounds should be evaluated as therapeutics alternatives to the antibiotics for HLB treatment. Overall, the utilized 3D metabolic mapping approach provides a promising methodological framework to identify pathogen-specific inhibitory compounds in planta for potential prophylactic or therapeutic applications.

plant biology↗

bioRxiv2022

Arbuscular mycorrhizal fungal composition across US citrus orchards, management strategies, and disease severity spectrum

Arbuscular mycorrhizal fungi (AMF) remain understudied in perennial cropping systems. Citrus is a globally grown fruit tree and under threat by the pandemic Huanglongbing (HLB) disease. Here, we assessed in what capacity geographical location, management strategies and disease affect AMF citrus root communities. Root samples were collected from 88 trees in ten orchards located in the two major citrus producing states in the US. Orchards were selected based on conventional or organic practices in California and based on HLB symptom severity in Florida. We used AMF-specific amplicon sequencing primers to capture community composition and diversity. Taxa names were assigned based on a phylogenetic analysis that comprised a backbone of AMF references sequences from Mycobank and virtual taxa from the MaarjAM database. AMF were detected in 78% of citrus root samples with taxa belonging to six known (Dominikia, Funneliformis, Glomus, Rhizophagus, Sclerocystis, Septoglomus) and unknown Glomeraceae genera. Geographical location affected AMF community composition but not richness, whereas management practice and disease influenced both richness and composition. Our approach indicated that perennial agroecosystems share a set of AMF generalist and specialist taxa. Some taxa could improve environmental fitness and be exploited for agricultural purposes.

microbiology↗

bioRxiv2022

Microbial turnover and dispersal events occur in sync with plant phenology in the perennial evergreen tree crop, Citrus sinensis

Emerging research indicates that plant-associated microbes can alter plant developmental timing. However, it is unclear if host phenology impacts microbial community assembly. Microbiome studies in annuals or deciduous perennial plants face challenges in separating effects of tissue age from phenological driven effects on the microbiome. In contrast, evergreen perennial trees, like Citrus sinensis, retain leaves for years allowing for uniform sampling of similarly aged leaves from the same developmental cohort. This aids in separating phenological effects on the microbiome from impacts due to annual leaf maturation/senescence. Here we used this system to test the hypothesis that host phenology acts as a driver of microbiome composition. Citrus sinensis leaves and roots were sampled during seven phenological stages. Using amplicon-based sequencing, followed by diversity, phylogenetic, differential abundance, and network analyses we examined changes in bacterial and fungal communities. Host phenological stage is the main determinant of microbiome composition, particularly within the foliar bacteriome. Microbial enrichment/depletion patterns suggest that microbial turnover and dispersal were driving these shifts. Moreover, a subset of community shifts were phylogenetically conserved across bacterial clades suggesting that inherited traits contribute to microbe-microbe and/or plant-microbe interactions during specific phenophases. Plant phenology influences microbial community composition. These findings enhance understanding of microbiome assembly and identify microbes that potentially influence plant development and reproduction.

microbiology↗