Publications

4448

First sugar beet varieties with reasonable yield stability under infection with Candidatus Arsenophonus phytopathogenicus (ARSEPH), the causal agent of the syndrome “Basses Richesses” (SBR), were discovered, but the mechanisms behind this have not been described yet. Thus, this research aimed at analyzing different morphological, physiological and quality related traits of ARSEPH infected sugar beet taproots to identify methods for SBR variety screening. In a greenhouse experiment, one susceptible and two tolerant varieties were infected with ARSEPH via the vector Pentastiridius leporinus (reed glass-winged cicada) under controlled conditions. In the susceptible variety, an infection with ARSEPH caused an average reduction in volume (~40%), length (~6%), width (~21%), fresh mass (~41%) and an increase in dry matter content (~5%). The tolerant varieties exhibited a lower effect on these parameters but showed a greater increase in alcohol insoluble residues (cellulose, hemicellulose, pectin, lignin) and marc content. The significant enhancement in flexural taproot tissue strength observed in the tolerant varieties may be linked to increased levels of structural cell components. The susceptible and one tolerant variety exhibited reduced periderm puncture resistance after infection. This first study of physiological and morphological traits provides deeper insights into host-pathogen interaction and potential variety response. To confirm the relevance and implications of the results as new parameters for screening of SBR-tolerant varieties, further analysis with additional varieties across a larger number of samples is necessary.

Abstract Dermatophilaceae polyphosphate-accumulating organisms (PAOs), formerly classified as Tetrasphaera PAOs, play pivotal roles in enhanced biological phosphorus removal (EBPR). However, their phylogenetic diversity, ecological preferences, and metabolic traits remain poorly characterized, and a robust marker gene for their classification is lacking. Here, we performed an extensive phylogenomic and metabolic analysis of Dermatophilaceae PAOs utilizing 46 newly recovered metagenome-assembled genomes (MAGs) from a laboratory-scale EBPR reactor treating high-strength wastewater and full-scale wastewater treatment plants. These analyses revealed a previously uncharacterized PAO genus, named Candidatus Dermatophostum, which is adapted to high-phosphorus environments. Its representative species, Ca. D. ammonifactor, was enriched in the EBPR reactor and its PAO phenotype was confirmed by polyphosphate staining and fluorescence in situ hybridization. Genomic, transcriptomic, and protein structure analyses revealed its specialized metabolic capabilities for phosphate metabolism, glycogen synthesis and dissimilatory nitrate reduction to ammonium. Moreover, Ca. Dermatophostum was found to be widely distributed across WWPTs worldwide, underscoring both its ecological importance and its potential role in mitigating nitrous oxide (N 2 O) emissions. Finally, we propose a ppk1 -based classification framework that resolves Dermatophilaceae PAOs into six distinct clades, consistent with whole-genome phylogeny, and demonstrates that ppk1 can serve as a reliable marker gene for tracking these populations. Together, these findings expand the ecological and functional understanding of Dermatophilaceae PAOs and highlight their promise for advancing sustainable wastewater treatment and resource recovery.

ABSTRACT Recent discoveries of aerobic methanotrophs in non-seep carbonate-rich environments in the deep sea suggest that these organisms may persist as part of the rare biosphere. Recovering rare, active methanotrophs through targeted culturing is essential for understanding their persistence under the oligotrophic non-seep conditions and for uncovering their genomic adaptations related to the survival in energy-limited ecosystems. In our study, using metagenomic analysis of enrichment cultures from the Alpha Crucis Carbonate Ridge, we discovered Methylotuvimicrobium crucis sp. nov., a novel methanotroph representing the rare biosphere in native sediments, described in accordance with the SeqCode rules. Recent discoveries of aerobic methanotrophs in non-seep carbonate-rich environments in the deep sea suggest that these organisms may persist as part of the rare biosphere. Recovering rare, active methanotrophs through targeted culturing is essential for understanding their persistence under the oligotrophic non-seep conditions, and for uncovering their genomic adaptations related to the survival in energy-limited ecosystems. In our study, using metagenomic analysis of enrichment cultures from the Alpha Crucis Carbonate Ridge, we discovered Methylotuvimicrobium crucis sp. nov., a novel methanotroph representing the rare biosphere in native sediments, described in accordance with the SeqCode rules. Phylogenomic analysis revealed <95% of Average Nucleotide Identity (ANI) to described species, with genomic evidence of deep-sea specialization including: (i) stress adaptation through cold-shock proteins (CspA) and DNA repair systems (UvrD/LexA), (ii) metabolic versatility via complete methane oxidation (pmoABC), nitrogen fixation (nifHDK), and sulfur cycling (sox/sqr) pathways, and (iii) niche partitioning through biofilm formation (GGDEF/EAL) and heavy metal resistance (CopZ/CzcD). Comparative genomics identified a 1,234-gene deep-sea core shared with Methylotuvimicrobium sp. wino1, enriched in mobile elements (TnpA, prophages) suggesting horizontal gene transfer drives adaptation. While undetected in situ amplicon surveys, Methylotuvimicrobium crucis exhibited enrichment under methane availability, demonstrating its role as a latent methane filter. These findings contribute to the understanding of the ecological significance of aerobic methanotrophs in deep-sea systems, revealing how rare microbial taxa with genomic plasticity have the potential to influence biogeochemical cycling in deep carbonate-rich environments. IMPORTANCE Microbial communities in deep-sea sediments play crucial roles in global biogeochemical cycles, yet they remain poorly characterized due to the challenges of sampling and culturing under extreme conditions. This study provides a comprehensive overview of microbial diversity and functional potential in carbonate-rich deep-sea sediments, with an emphasis on methane-oxidizing bacteria. By combining high-throughput metagenomics and comparative genomics, we reconstructed high-quality genomes from previously uncharacterized microbial consortia, including novel members of the genus Methylotuvimicrobium . Our findings shed light on the ecological strategies of methanotrophs in oxygen-limited environments and expand the genomic representation of key players in carbon cycling.

Abstract Deciphering the genomic basis of ecological diversification in activated sludge microbiomes is essential for optimizing treatment technology and advancing microbial ecology. Here, we present a global genome-resolved investigation of Candidatus Accumulibacter, the primary functional agent of enhanced biological phosphorus removal, based on 828 metagenomes from wastewater treatment plants across six continents. We recovered 104 high-quality Candidatus Accumulibacter metagenome-assembled genomes, discovering a new clade (Clade IV), substantially expanding the known phylogenetic diversity and revealing a ubiquitous yet geographically heterogeneous global distribution. Phylogenomic and pangenome analyses uncovered extensive clade-specific gene gain and loss, particularly in nitrogen metabolism, suggesting divergent evolutionary trajectories shaped by relaxed selection and niche adaptation. Genome-wide patterns of convergent streamlining and enriched antiviral defense systems indicate selective pressures from strong competition and viral predation. Constraint-based metabolic modeling revealed pervasive amino acid autotrophies and metabolic complementarity, coupled with distinct carbon utilization strategies that support ecological specialization across operational settings. Experimental validation reconciled model-phenotype discrepancies, highlighting the importance of transporter promiscuity and gene regulation in carbon substrate assimilation. Collectively, our findings redefine Candidatus Accumulibacter as a dynamic model of microbial genome plasticity, metabolic adaptation, and ecological resilience, providing an insight for understanding how microbial communities adapt and respond under engineered environmental conditions.

Background/Objective. This study analyzed for the first time the asymptomatic condition induced by CLas in Citrus sinensis / C. aurantium based on initial reports in the Central Gulf region of Mexico. The objective was to analyze with a mechanistic approach the spatial-temporal concentration of CLas at the plant level in commercial orchards to demonstrate the possible implication of a prolonged incubation period in the asymptomatic expression of HLB. Materials and Methods. Two out of three trees (A1-A3) (>30 years old) of asymptomatic Valencia sweet orange trees positive for CLas, identified through official diagnostic protocols in San José Acateno, Puebla, were confined. On trees A2 and A3, 13 and 16 secondary branches were marked, with a total of 112 and 108 foliage/samples per month, respectively (total 646 samples), obtained from the distal and proximal parts of each branch. Seven monthly samplings of plant material were carried out between May and December. At the root level, three categories were sampled by diameter/function and by a combination of six distal trunk sectors (0 - 280 cm) by 4 in depth (0 x 110 cm) with a total of 111 samples. DNA extraction was performed with 2% CTAB and quantification by RT-qPCR (oligos, HLBp/HLBas). Results. In canopy, the incidence/branches in A3 was 52.2% (Ct = 22.7 – 34.9), and in A2 47.8% (Ct = 23.4 –35), with no statistical difference (p = 0.48). The inoculum load was 1.6 (±1.3) log-CLas, equivalent to 109 copies/reaction in 100 mL (range in number of copies 6.3 to 68,870.7). CLas did not differ between distal (1.6 log) and proximal (1.5 log) samples (p = 0.33). Significative temporal fluctuation was found between June and October in positive samples (37 – 87, p < 0.0001), but not in CLas concentration (1.6 – 3.5 log-CLas, p > 0.72). The distribution of CLas by branch had a temporal effect (p = 0.0001) and by sector (p = 0.07), showing high mobility and seasonality. The maximum concentration (Ymax) was associated with the middle-upper sector of the canopy, and high mobility towards the lower and upper sectors in Yinitial and Yfinal. In roots, 38.7% positivity was found. The detectability of CLas was homogeneous among root types (p < 0.0001) but variable in concentration (p = 0.04). The 47.6%, 15.4%, and 38.7% incidence was associated with 38.3, 43.4, and 9.5 average CLas copies for support, conduction, and absorption roots, respectively (p = 0.0001). Two sections with higher CLas intensity-concentration (80 – 144 copies) were associated with roots in the middle drip zone (160 – 240 cm) and medium depth strata (50 – 80 cm). Conclusion. CLas was significantly and consistently detected in plant and root tissue throughout the experimental period, but at fluctuating, non-incremental concentration, analogous between trees A2 and A3. The wide canopy-root distribution suggests a chronic systemic effect. Consequently, the incubation period does not determine the asymptomatic condition in the sweet orange/sour orange productive system investigated. Other factors, e.g. inherent to pathogen variability, could be involved. These results contribute to optimizing a surveillance-monitoring system considering seasonality, zone-branch, sector-canopy and type of tissue, with a greater probability of detection of CLas even in an eventual asymptomatic condition and generate new insights for Clas management.