Publications

4368

ABSTRACT Candidatus Saccharimonadia is a class‐level lineage of ultrasmall bacteria within the phylum Minisyncoccota (formerly Candidate Phyla Radiation or Ca . Patescibacteria), commonly found in activated sludge processes treating municipal wastewater. In this study, we aimed to elucidate the metabolic potential of Ca . Saccharimonadia by using shotgun metagenomic sequencing combined with a filtration‐based size‐fractionation approach for activated sludge from five wastewater treatment plants. A total of 65 high‐quality metagenomic bins were recovered, belonging to four orders and 19 families of Ca . Saccharimonadia, including previously unreported lineages in activated sludge. These bins had small genomes (approximately 0.46–1.73 Mbp) with limited metabolic capabilities, indicating dependency on other microorganisms. Notably, the order Ca . Saccharimonadales retained a type IV secretion system and effector gene cluster for parasitic interactions with the hosts, suggesting that Ca . Saccharimonadales bacteria may exhibit a parasitic lifestyle. Co‐occurrence network analysis showed that members of the order Ca . Saccharimonadales were significantly correlated with multiple lineages, including Actinobacteriota , for which a parasitic relationship has been previously demonstrated. Our results shed light on the potential ecophysiology of the diverse members of Ca . Saccharimonadia, providing a comprehensive understanding of Ca . Saccharimonadia in activated sludge.

ABSTRACT Biogas, a mix of CO 2 , CH 4 and small proportions of other gases, is a biofuel obtained by anaerobic digestion (AD). Biogas production is often considered a black box process, as the role and dynamics of some of the microorganisms involved remain undisclosed. Previous metataxonomic studies in the frame of the MICRO4BIOGAS project ( www.micro4biogas.eu ) revealed that MBA03, an uncharacterised and uncultured bacterial taxon belonging to phylum Bacillota , was very prevalent and abundant in industrial full‐scale AD plants. Despite the efforts, this taxon has not yet been cultivated, which makes the analysis of its taxonomy, ecology and metabolism even more challenging. In the present work, 30 samples derived from anaerobic digesters were sequenced, allowing the reconstruction of 108 metagenome‐assembled genomes (MAGs) potentially belonging to MBA03. According to phylogenetic analyses and genomic similarity indices, MBA03 was classified as a new bacterial order, proposed as ‘ Candidatus Darwinibacteriales’ ord. nov., which includes ‘ Candidatus Darwinibacter acetoxidans’ gen. nov., sp. nov. of ‘ Candidatus Darwinibacteriaceae’ fam. nov., along with ‘ Candidatus Wallacebacter cryptica’ gen. nov., sp. nov. of the ‘ Candidatus Wallacebacteriaceae’ fam. nov. Ecotaxonomic studies determined that AD processes are the main ecological niche of ‘ Candidatus Darwinibacteriales’. Moreover, metabolic predictions identified Darwinibacteraceae members as putative syntrophic acetate‐oxidising bacteria (SAOB), as they encode for the reversed Wood–Ljungdahl (W–L) pathway coupled to the glycine cleavage system. This suggests that Darwinibacteraceae members could work in collaboration with hydrogenotrophic methanogenic archaea to produce methane in industrial biogas plants. Overall, our findings present ‘ Candidatus Darwinibacteriales’ as a potential key player in anaerobic digestion and pave the way towards the complete characterisation of this newly described bacterial taxon, which has not yet been cultured.

Mulberries (Morus spp.) are important crops valued for berry and silk production (Baciu et al., 2023). In March 2025, a mulberry tree in Dongshi, Taichung, Taiwan, was found bearing fruits showing phyllody symptoms. To determine whether the disease was associated with phytoplasma infection, symptomatic fruits were collected from five branches and tested. For the controls, asymptomatic berries were sampled from three symptomless mulberry trees in Wufeng, Taichung in April 2025. DNA was extracted from five symptomatic fruits collected from different branches and three symptomless berries obtained from separate asymptomatic trees. DNA was extracted with a Synergy 2.0 Plant DNA Extraction Kit (OPS Diagnostics). To ensure that DNA qualities were sufficient for PCR assays, the samples were tested with primers 28KJ and 28C targeting the plant’s 26S rDNA (Cullings 1992). PCR was conducted with the GoTaq Green Master Mix (Promega), and every sample produced the expected amplicon (~685 bp). Nested PCR tests were conducted using universal phytoplasma primer pairs P1/ P7 (outer; Schneider et al. 1995) and R16F2n/R16R2 (inner; Gundersen and Lee 1996). Four out of five symptomatic samples amplified the 1.25-kb target fragment in the nested assay, while none of the asymptomatic samples did. The 16S rDNA of a representative symptomatic sample was sequenced (GenBank/DDBJ accession no. LC897699) and subjected to analysis using iPhyClassifier (https://plantpathology.ba.ars.usda.gov/cgi-bin/resource/iphyclassifier.cgi). The detected phytoplasma was classified to the 16SrI-B subgroup with a similarity coefficient of 1.0 (compared to a reference pattern; ‘Candidatus Phytoplasma asteris’ OY; accession no. AP006628) and was found to share 99.68% 16S rDNA sequence similarity with a ‘Ca. Phytoplasma asteris’ reference strain (accession no. M30790). To validate this finding, the sample was also tested with other phytoplasma gene-specific nested primers targeting the elongation factor Tu (tuf) and ribosomal protein (rp) genes. For tuf, primer pairs fTuf1/rTuf1 and fTufAy/rTufAy were respectively used for the first and second round of PCR (Schneider and Gibb 1997). For rp, the outer and inner primer pairs were rpF1/rpR1 and rp(I)F1A/rp(I)R1A, respectively (Martini et al. 2007). Both target gene fragments were successfully amplified, and the inner amplicons were sequenced. BLASTn (core_nt) searches using quality-trimmed sequences showed that the obtained tuf sequence (accession no. LC896430) was most similar to that of ‘Ca. Phytoplasma asteris’ OY (accession no. AP006628; 99.9%; 830/831 bp) and those of various 16SrI strains. The detected rp sequence (accession no. LC896429) shared the highest identity with that of a ‘Ca. Phytoplasma asteris’ strain infecting Boehmeria pannosa (16SrI‑B; accession no. MT739521; 99.9%; 1,056/1,057 bp) and those of other 16SrI strains, and was very similar to that of ‘Ca. Phytoplasma asteris’ OY (accession no. AP006628; 99.6%; 1,053/1,057 bp). Accordingly, the phytoplasma detected in this study was identified as a ‘Ca. Phytoplasma asteris’-related strain belonging to subgroup 16SrI-B. In Taiwan, 16SrI phytoplasmas have been reported affecting plants such as Murraya exotica (Tseng et al. 2022). This is the first report of a 16SrI phytoplasma related with Morus symptoms in Taiwan. Since the disease directly impacts the commercial value of the berries, the pathogen should be carefully monitored in mulberry-producing areas.

Abstract Background Globally, the disease ecology of reptiles remains understudied, even for threatened and iconic species such as the Galápagos marine iguana ( Amblyrhynchus cristatus ). Although marine iguanas are parasitized by distinct species of ticks and mites, research on vector-borne diseases for this species is limited. Methods In this study, we detected 16S ribosomal RNA (rRNA) sequences of Candidatus Allocryptoplasma in transcriptomic data from marine iguana blood samples. These 16S rRNA sequences were further characterized through phylogenetic analysis and a haplotype network. Results Our analysis revealed the first molecular evidence for the infection of marine iguanas with Candidatus Allocryptoplasma, a candidate genus in the family Anaplasmataceae with unknown pathogenic potential, likely transmitted by ticks. Phylogenetic analysis of the novel 16S rRNA sequences together with available Anaplasmataceae sequences confirmed their assignment to this candidate genus. A haplotype network analysis indicated that the agent infecting the marine iguana represents a distinct lineage within the known Ca . Allocryptoplasma diversity. Conclusions Candidatus Allocryptoplasma had a high prevalence within marine iguanas, infecting individuals across most of the geographical range of this species. To elucidate the transmission dynamics of this bacterium in the Galápagos ecosystem, ectoparasites of the marine iguana and shared vertebrate hosts should be screened for infection with Ca . Allocryptoplasma. Graphical Abstract

Abstract The DPANN superphylum is a deep-branching radiation of Archaea with small cell and genome sizes. Most DPANN lineages are predicted or validated to be host-dependent. However, certain lineages have substantial biosynthetic capacities and are potentially less dependent on hosts or even free-living. Here, we reconstructed 163 Micrarchaeota genomes, comprising 48 assigned to previously undescribed orders and 115 affiliated with known orders. Investigation of their genetic repertoire revealed substantial metabolic capacity in Norongarragalinales, Anstonellales, and the newly proposed Wunengiarchaeales-associated lineages, including complete or near-complete glycolysis and de novo biosynthetic pathways for nucleotides, amino acids, co-factors, and cell envelopes. We classified these genes related to central metabolism, but which are uncommon in DPANN archaea as putative free-living associated genes (pFLAGs). The extensive presence of pFLAGs in Norongarragalinales suggests a potential host-independent lifestyle. Reconstruction of evolutionary history revealed that these pFLAGs were not ancestral within the DPANN superphylum. Instead, we suggest that less host-dependent organisms evolved from symbionts through the gradual acquisition of pFLAGs through horizontal gene transfer, whereas other Micrarchaeota lineages with streamlined genomes experienced reductive evolution due to thermal adaptation. Our analyses demonstrate that host dependency is not always an evolutionary dead end, but can be reversed through acquisition of new metabolic capabilities by horizontal transfer.

Phloem feeders, such as the psyllid Diaphorina citri ( D. citri ), feed on plants by inserting their stylet bundle followed by probing the apoplast before reaching the phloem. The psyllids secrete watery saliva containing various proteins into the phloem, which can act as effectors to facilitate their feeding or modulate host defense responses. Concomitantly, feeding is the main mode of transmitting the Candidatus Liberibacter asiaticus ( C Las) bacteria to the phloem. C Las produces several effectors that have been hypothesized to contribute to Huanglongbing (HLB) virulence. Here, we aimed to identify putative effector proteins from both D. citri and C Las. To achieve this, we used different omics techniques on different tissues and organs from both plants and insects. More specifically, we performed transcriptomics on the heads of healthy and C Las-infected D. citri and proteomics of artificial diet and of phloem of four different plant species fed on by healthy and C Las-infected D. citri. Subsequently, we used various criteria and bioinformatics tools to predict putative effectors. This resulted in the identification of four proteins from D. citri [ferritin, prisilkin, CG31997-PA, and pterin-4-alpha-carbinolamine dehydratase-like protein (PCBD)] and two Sec-dependent effectors from C Las, CLIBASIA_04560 and CLIBASIA_05320, that were used for further functional studies. The expression of these six proteins in Nicotiana benthamiana modified the ROS burst triggered by flagellin, indicating that they can indeed function as effector proteins in planta . In addition, expression of the psyllid effectors in planta significantly reduced the growth of Pseudomonas syringae pv. tabaci ( Pta ).