Publications

4947

Abstract Enhanced biological phosphorus removal (EBPR) relies on polyphosphate-accumulating organisms that experience dynamic fluctuations in redox conditions and substrate availability. How these organisms regulate metabolism across molecular layers under cyclic operation remains incompletely understood. Here, we investigated molecular regulation in a long-term, stable aerobic granular sludge system dominated by Candidatus Accumulibacter . We combined metagenomics, time-resolved metatranscriptomics, and matched metaproteomics across three consecutive operational cycles. Genome-resolved metagenomics revealed an Accumulibacter -dominated community encoding canonical EBPR functions. Time-resolved metatranscriptomics revealed extensive and reproducible transcriptional dynamics affecting hundreds of genes. These dynamics did not align with discrete EBPR phases or instantaneous environmental transitions, but instead unfolded gradually over the cycle. Despite pronounced transcript-level heterogeneity, aggregation at the functional level revealed strong consolidation, with only a limited number of KEGG orthologs exhibiting coherent temporal regulation. Quantitative metaproteomics revealed a stable proteome across EBPR cycles, with no individual proteins or functional categories showing significant differential abundance despite direct transcript-protein mapping and time-matched sampling. This indicated that transcriptional dynamics did not translate into measurable changes in protein pool size on the time scale of individual cycles, consistent with slow, growth-coupled proteome turnover relative to cycle duration. Together, these results support a hierarchical model of regulation in Candidatus Accumulibacter , in which dynamic transcriptional responses are buffered at both the functional and protein levels. This organization provides a plausible basis for stable EBPR performance under predictable cyclic operation and demonstrates how time-resolved multi-omics can be used to resolve regulatory dynamics across molecular layers in engineered microbial ecosystems.

Abstract In northeastern Argentina, wild canids such as the pampas fox ( Lycalopex gymnocercus ) and the crab‐eating fox ( Cerdocyon thous ) coexist with domestic dogs ( Canis lupus familiaris ) across rural and peri‐urban landscapes, creating opportunities for tick and pathogen exchange. Characterizing tick assemblages and associated pathogens in these hosts is essential to assess potential public health risks at the wildlife–domestic interface. Ticks were collected opportunistically from domestic dogs and road‐killed foxes near two protected areas in Corrientes Province. Specimens were identified using morphological and molecular approaches and screened for Rickettsia spp. by PCR. A total of 30 adult ticks were obtained from 12 dogs and 8 foxes, representing four species: Amblyomma tigrinum , A. ovale , A. dubitatum and Rhipicephalus sanguineus . Amblyomma tigrinum was the most frequent species (50%). Seven individual ticks were confirmed as Candidatus Rickettsia andeanae in A. tigrinum , while one pooled sample was positive by screening only and was not confirmed. These findings expand the known geographic distribution of Ca. R. andeanae and provide molecular evidence of its circulation in ticks collected from both wild and domestic canids in northeastern Argentina. Our results highlight the importance of these hosts as sentinels for tick‐borne pathogens and underscore the need for integrated One Health surveillance to better anticipate emerging potential risks in interface areas.

Huanglongbing (HLB) is one of the most devastating diseases of citrus nowadays. The etiological agent is a fastidious and non-culturable bacterium known as Candidatus Liberibacter asiaticus ( C Las). C Las is a phloem-restricted pathogen, which makes the efficient delivery of antimicrobial compounds to control it a major challenge for citriculture. Therefore, the development of formulations capable of penetrating plant barriers and reducing the bacterial population within the phloem is critical for the control of HLB. Here we report on the development of a novel formulation loaded with oregano essential oil, hexyl gallate and eugenol, described in the literature as a transdermal permeation enhancer. The most effective formula was selected in vitro against bacterial surrogates ( Rhizobium tropici and Rhizobium phaseoli ), displaying bactericidal concentrations of 0.25 and 0.5% (v/v), respectively, of bactericidal concentration. The selected formulation was characterized as a near-Newtonian fluid, with 98.5% of particles measuring around 50 nm, a Polydispersity Index of 0.31, and zeta potential of -17.5 mV. Furthermore, Scanning electron microscopy revealed the presence of nanoparticles, alongside microscopic aggregates. The formulation maintained its bactericidal activity over 120-day storage period. During the root-drenching assays, the formulation significantly reduced overall C Las titres by 1.29 and 2.46 log 10 over a period of 300 days, in two independent experiments. Furthermore, ecotoxicological assessments revealed no acute toxicity in Tenebrio molitor or significant effects in the survival of Melipona scutellaris under the tested conditions. Our findings demonstrate the potential of this non-synthetic formulation as an effective and safe alternative for HLB management, without disrupting non-target organisms.

‘ Candidatus Liberibacter asiaticus’ ( C Las) is a phloem-limited bacterium that causes Huanglongbing (HLB), the devastating citrus greening disease that has led to billions of dollars in losses throughout global citrus production. There is very little epidemiological data available regarding fine-scale molecular variability of C Las populations in different regions of the world or their distribution across various geographical landscapes. Here, we present an assessment of C Las genetic diversity using a hypervariable variable number tandem repeat (VNTR) marker (AGACACA) at the CLIBASIA_01645 locus of 344 genomic sequence data obtained from GenBank from five regions of the world (India-177, China-113, Saudi Arabia-37, Bhutan-10, and Nepal-7). The findings revealed high evolutionary plasticity and non-random distribution of TRN within four distinct classes, significantly deviating from a uniform distribution ( p  < 0.05). The analyzed populations were stratified into four distinct classes: Class I (TRN ≤ 5), Class II (TRN > 5 ≤ 10), Class III (TRN > 10 ≤ 15), and Class IV (TRN > 15). The predominant type of subpopulation for all field samples was intermediate variants, with the highest frequencies observed for TRN6 (25%) and TRN7 (17.15%), possibly indicating genomic stability and/or adaptive advantages of specific tandem repeats. On the other hand, lower frequency rare variants (e.g., TRN17, TRN18, and TRN20 at 0.29%) represent some form of continued low frequency micro evolutional replication slippage and corresponding absence of some individual TRs indicates evidence of local purging forces. Crucially, the Indian C Las populations exhibited significantly greater densities of molecular diversity than populations from China, Saudi, Bhutan, and Nepal examined in this study. The distinct TRN signature profiles of these populations’ subpopulations exhibit strong geographic correlation with ecological regions, reinforcing the CLIBASIA_01645 locus as a strong marker for epidemiological surveillance for tracking global strain movement to develop target-specific HLB management programs.

Abstract The evolution of phototrophy and carbon fixation in the phylum Chloroflexota remains incompletely understood, largely due to the scarcity of cultured mesophilic representatives. Here, we report the isolation and genomic characterization of a novel filamentous anoxygenic phototrophic bacterium from a microbial mat in the mesothermal Lake Umkhey (Southern Siberia). Although the original culture was lost, its genome was recovered via metagenome-assembled genome reconstruction from environmental samples, enabling a detailed phylogenomic and metabolic analysis. The genome of umkhey_bin13 (proposed as ‘Candidatus Viridifilum namsaraevi’ gen. nov., sp. nov.) encodes a complete 3-hydroxypropionate bicycle for autotrophic CO₂ fixation, a type II sulfide:quinone oxidoreductase, but lacks nitrogenase and chemolithotrophic markers. Comparative genomics across 18 Chloroflexota genomes reveals that this new lineage occupies an intermediate phylogenetic position, with distinct gene content for sulfur, nitrogen, and hydrogen metabolism, and highlights a complex evolutionary history within the group. Our findings provide new insights into the evolutionary transitions of photosynthetic and carbon-fixation pathways, and underscore the value of integrating cultivation-independent genomics with classical microbiology. The proposed novel genus and species contribute to a revised framework of Chloroflexota evolution and offer a genomic reference for studying metabolic adaptation in alkaline, sulfide-influenced microbial mats.

In Germany, maize (Zea mays L.) is cultivated on approximately 2.4 Mha, making it one of the most widely grown arable crops alongside wheat and barley (German Federal Statistical Office, 2025). Although maize has previously been identified as a host of Candidatus Phytoplasma solani (PHYPSO, 16SrXII-A), particularly in relation to maize redness (MR) disease detected in southeastern Europe (Jović et al., 2009), its role as a host of ‘Candidatus Arsenophonus phytopathogenicus’ (ARSEPH) has not been reported previously. The planthopper Pentastiridius leporinus (Hemiptera: Cixiidae) is the major vector for transmitting both pathogens in many crops in Germany (Rinklef et al., 2024). MR symptoms include patchy premature drying, reddish discoloration of leaves and midribs, poorly filled or aborted ears, and malformed kernels. In August and September 2025, maize plants showing MR-like symptoms were observed in different fields in Otzberg 49°48'25.3"N, 8°52'28.8"E (South Hesse), Bellheim 49°10′19.9N, 8°15′50.8E, Bockenheim 49°36'18.6"N, 8°11'30. E"O, Ibersheim 49°43′36.5″N, 8°24′34.6″E (Rhineland-Palatinate) and Ettling 48°48'50.0"N, 11°40'17.2"E (Baden-Württemberg). Samples from roots (25), leaves (10), ears (14) and kernels (9) of 14 selected symptomatic plants were collected for molecular analysis. DNA was extracted using a CTAB-based protocol. ARSEPH was detected by qPCR targeting the manA gene according to Zübert and Kube (2021). Positive results were obtained from ears of six plants from Ibersheim and Ettling, leaves of three plants from Bockenheim and Otzberg, kernels of two plants from Bellheim, and roots of one plant from Bockenheim. Four ARSEPH-positive samples (two ears and two kernels) were further analyzed using the Fra4/Fra5 PCR assay (Zreik et al. 1998). Sanger sequencing of the resulting amplicons followed by BLAST analysis confirmed all four sequences as ‘Candidatus Arsenophonus phytopathogenicus’ with 100% identity to reference sequence PP400342. The sequences have been deposited in GenBank under accession numbers PZ623476, PZ623478, PZ623483, and PZ626926. Furthermore, all samples were screened for PHYPSO using the qPCR assay described by Behrmann et al. (2022) with primers KL464/KL465. Seven ear samples from Ibersheim yielded positive qPCR signals. To further validate these results, DNA from qPCR-positive samples was subjected to nested PCR targeting the 16S rRNA gene using primer pairs P1/P7 (Schneider et al., 1995) and R16F2n/R16R2 (Gundersen and Lee, 1996), followed by Sanger sequencing and BLAST analysis against the NCBI GenBank database. However, repeated sequencing did not provide sufficient sequence identity to the reference strain STOL11 (GenBank accession number AF248959) to confirm the qPCR-positive samples as PHYPSO. To our knowledge, this is the first report of ARSEPH in maize in Germany. Its detection in maize extends the known host range of this phloem-limited bacterium. The high ARSEPH loads in ears and kernels detected in reproductive tissues are consistent with preferential accumulation in sink organs during grain filling. Whether maize contributes to pathogen persistence and transmission within the Pentastiridius leporinus or other potential vectors’ pathosystem remains to be investigated.

SUMMARY The ubiquitin proteasome system (UPS) and autophagy cooperatively orchestrate plant immune homeostasis, while diverse phytopathogens deploy secreted effectors to disrupt their crosstalk for successful colonization. Proteaphagy, the autophagic turnover of intact 26S proteasome holoenzymes, is a conserved stress response co‐opted by Pseudomonas syringae effector HopM1 to cripple host proteolysis. However, how the Huanglongbing (HLB) pathogen ‘ Candidatus Liberibacter asiaticus’ ( C Las) simultaneously manipulates UPS and autophagy to subvert citrus immunity remains largely uncharacterized. Here, we functionally characterize the secreted C Las effector SDE5640, which exacerbates HLB susceptibility in sweet orange ( Citrus sinensis ). SDE5640 directly binds the 19S proteasome chaperone CsPSMD10, whose homodimerization via Cys163/Cys190 disulfide bonds is required for immune suppression. CsPSMD10 overexpression enhances citrus susceptibility to C Las, whereas the dimerization‐deficient CsPSMD10‐C190S mutant confers robust HLB resistance. Mechanistically, CsPSMD10 targets CsATG8 isoforms for UPS‐dependent degradation to restrain autophagic flux; SDE5640 competitively occupies the Ank2/Ank3 domains of CsPSMD10 to disrupt CsPSMD10‐CsATG8c complexes, thereby stabilizing CsATG8c and triggering autophagy dependent on CsPSMD10. Moreover, SDE5640‐induced autophagy drives selective autophagic degradation of the 20S proteasome catalytic subunit CsPBA1, which ultimately disrupts cellular proteasome activity and attenuates salicylic acid‐mediated citrus immunity. Collectively, our findings identify a novel SDE5640‐CsPSMD10‐CsATG8c‐CsPBA1 regulatory cascade, illustrating how a single C Las effector synchronously rewires the UPS‐autophagy crosstalk to facilitate pathogen proliferation.

Abstract The archaeal symbiotic Nanobdellales have been isolated with their hosts from a shallow hot marine vent off Iceland and from terrestrial hot springs in Yellowstone National Park and Japan. They have highly reduced genomes and rely on their archaeal hosts for most of their metabolic needs. Here, to provide further insights into the ecology and evolution of this order, we greatly expand their phylogenomic distribution using metagenome assembled genomes from deep-sea hydrothermal vents in the Atlantic, Pacific and Indian Oceans, and the Gulf of California. We show that at least 11 novel genus-level lineages occur at deep-sea vents. We conservatively propose two new genera with their nomenclatural types, Nanoprofundum liuii Rb-1Ts gen. nov. sp. nov. and Nanojejuna irisiana Rb-38Ts gen. nov. sp. nov. We also describe a second species of Nanoarchaeum, N. abyssimaris 17S-22Ts sp. nov. Our genomic and metabolic characterisation of the high-quality metagenome-assembled genomes confirm their highly reduced metabolic capabilities and likely symbiotic lifestyle. With the exception of Nanoarchaeum, all deep-sea genera resemble their terrestrial relatives in that they have genes that encode for archaella and RNAase P protein subunits, and have several genes involved in glycolysis and gluconeogenesis. Using an inferred lateral gene transfer analysis, our data suggest that deep-sea Nanobdellales may potentially associate with a greater taxonomic breadth of hosts than previously reported, spanning members of the Sulfolobales (Ignicoccaceae), the Archaeoglobales and Methanococcales.