Publications

4688

Abstract The candidate phylum Cloacimonadota is frequently detected in anoxic environments such as anaerobic digestion (AD) reactors, hydrothermal vents, and deep-sea sediments, yet its metabolism remains poorly understood. Metagenomic evidence suggests capacities for amino acid fermentation, carbohydrate degradation, as well as a potential role in syntrophic propionate oxidation (SPO), a key bottleneck in AD. However, a complete methylmalonyl-CoA (mmc) pathway, central to SPO, has not been previously identified in Cloacimonadota genomes. Here, we report results from an acidified lab-scale anaerobic baffled reactor fed with sugar beet pulp, where an increase in the relative abundance of Cloacimonadota correlated with recovery of methanogenesis, resulting in increased methane content in the produced biogas. Metagenomic and metatranscriptomic analyses enabled metabolic reconstruction of the dominant Cloacimonadota operational taxonomic unit (OTU). Furthermore, using a curated database of 204 genome-resolved Cloacimonadota species, we characterized the phylum-level metabolic potential. Comparative genomics revealed alternative proteins, including 2-oxoglutarate:ferredoxin oxidoreductase and aspartate aminotransferase, likely to substitute for missing enzymes in the classical mmc pathway. These proteins were widely distributed and highly conserved across the analyzed Cloacimonadota genomes, suggesting that this variant of the SPO pathway could represent a phylum-specific trait. Moreover, we hypothesize that these alternative pathway steps may link propionate metabolism to protein degradation and poly-γ-glutamate biosynthesis. Network analysis identified the methanogenic archaeon Methanothrix as a potential syntrophic partner, an interaction further supported by propionate-fed enrichment cultures showing co-occurrence of Cloacimonadota and Methanothrix species. Our study sheds light on the Cloacimonadota metabolism, advancing our understanding of their ecological roles and potential for biotechnological applications.

An anaerobic, salt-tolerant, rod-shaped bacterium, strain JL216-2 T , was isolated from the shell of the hydrothermal gastropod Alviniconcha marisindica in the Tianxiu hydrothermal field on the Carlsberg Ridge, Indian Ocean. Cells of strain JL216-2 T were motile and 0.5×3–6 µm in size. Strain JL216-2 T grew at 10–32 °C (optimal 28 °C), pH 6.0–9.0 (optimal pH 7.0) and 0.5–12.0% (w/v) sodium chloride(NaCl, optimal 2.5%). Strain JL216-2 T exhibited metabolic versatility, being capable of heterotrophic growth on complex organic compounds. It also performed autotrophic growth by utilizing carbon dioxide (CO₂) fixation or sodium bicarbonate (NaHCO 3 ) as the sole carbon source, driven by hydrogen oxidation coupled with Fe(III) reduction. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to Helicovermis profundi S502 T (90.43% sequence similarity). The genome size of strain JL216-2 T was 4.91 Mb, with a G+C content of 39.54 mol%. Phylogenomic analysis and overall genome relatedness indices values indicated a close relatedness of strain JL216-2 T to H. profundi S502 T and Fusibacter spp. The combined genotypic and phenotypic data showed that strain JL216-2 T represents a novel genus within the order Eubacteriales . The type strain is JL216-2 T (=MCCC M30262 T =KACC 23553 T ).

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 X‐disease, caused by strains in the 16SrIII‐A subgroup of ‘ Candidatus Phytoplasma pruni’, is a devastating disease of Prunus species (stone fruits). Multiple outbreaks of this disease have occurred across much of North America for more than a century, with the most recent one beginning around 2010 in the Pacific Northwest of the United States, causing severe damage to the stone fruit industry. Sensitive and specific detection of X‐disease is critical to prevent the propagation and spread of infected plant material; however, current PCR‐based detection workflows lack specificity to X‐disease and require one or more PCR assays followed by additional testing to confirm the species identity. In this study, two real‐time PCR assays, one targeting the secY gene and the other targeting the tuf gene, were developed for specific detection of X‐disease in stone fruits. The CPH‐TXD assay targeting the tuf gene provided high‐sensitivity target detection of as few as five target copies with significantly reduced cross‐reactivity compared to current methods. The CPH‐SXD assay targeting the secY gene detected a minimum of 30 target copies and showed no cross‐reaction with closely related strains. The repeatability and reproducibility of both assays were verified with acceptable results. Together, these assays provide efficient and high‐specificity detection methods to combat the growing threat of X‐disease in North America.