Publications

4502

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 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.

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.

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.

Citrus Huanglongbing (HLB), a devastating disease caused by the Gram-negative bacterium ‘ Candidatus Liberibacter asiaticus’ ( C Las), poses serious threats to global citrus production and lacks effective control strategies. Previously, SDE2470 (CLIBASIA_02470) was identified as a Sec-dependent effector that contributes to C Las pathogenesis, although its underlying molecular mechanisms were not fully elucidated. In this study, SDE2470 was found to target a citrus vascular one-zinc-finger transcription factor CsVOZ2. CsVOZ2 overexpression ( CsVOZ2- OE) in transgenic citrus plants significantly suppressed C Las colonization, whereas its RNA interference (RNAi) in citrus hairy roots enhanced susceptibility to C Las. Additionally, CsVOZ2 -OE significantly increased reactive oxygen species (ROS) and abscisic acid (ABA) contents accumulation and activated related genes expression. Further investigation revealed that the E3 ligase CsBTS1 directly interacts with CsVOZ2 and promotes its degradation via the 26S proteasome pathway. CsBTS1E3 -OE in citrus hairy roots markedly enhanced C Las proliferation. Importantly, SDE2470 directly interacts with CsBTS1E3 and strengthen CsBTS1E3-CsVOZ2 interaction. Meanwhile, SDE2470 strengthened the E3 ligase activity of CsBTS1, promoting CsVOZ2 degradation. Taken together, these findings support a model in which SDE2470 hijacks CsBTS1 to destabilize CsVOZ2, thereby disrupting ROS- and ABA-dependent immunity and promoting C Las infection in citrus.

Abstract At the dawn of modern microbiology, Cohn observed abundant filamentous bacteria in drinking water wells that he named Crenothrix polyspora . Subsequent research has revealed the methanotrophic metabolism of Crenothrix bacteria and their disproportionately high activity in stratified lakes compared to unicellular strains, yet laboratory cultivation has proven elusive, leaving the ecophysiology of Crenothrix bacteria largely unknown. Here we report the isolation of two methanotroph strains of the “lacustrine Crenothrix” clade from an iron-rich wetland and reveal their highly unique cell biologies and potential ecological roles. Using physiological approaches, we demonstrate that the strains perform a microaerobic methane metabolism while growing distinct filaments having wide and directionally oriented connective structures. The strains further have broad genomic repertoires for addressing redox stress that we show are uniquely associated with lacustrine Crenothrix compared to related methanotrophs based on genome data. Aligning with laboratory observations, we identify lacustrine Crenothrix bacteria along potential redox gradients in the wetland at iron-rich snow sites, and we further detect such bacteria in diverse global ecosystems based on public metagenome searches. Together, our data strongly point to an ecophysiology of lacustrine Crenothrix bacteria that is tightly linked to redox stress, and we propose these bacteria may uniquely store or share metabolic intermediates via their filamentous lifestyle to thrive under such conditions. Our results provide a fresh view of the diversity, evolution, and ecology of aerobic methanotrophs, connecting over 150 years of microbiology research opening vast new opportunities to probe bacterial adaptations that drive global methane cycling under redox stress.