Publications

4481

Abstract Microbial interactions are fundamental to global ecological and evolutionary processes, exemplified by endosymbiosis between prokaryotes and single-cell eukaryotes that gave rise to organelles. While such associations remain widespread and ecologically important, the diversity and evolutionary dynamics of intracellular symbioses in many microbial ecosystems remain poorly understood. Here, we uncover a hidden layer of microbial complexity in the rumen ecosystem by identifying multiple endosymbiotic associations between ciliate protozoa and bacteria. Using genome-resolved metagenomics on protozoa enriched rumen fractions, we reveal diverse bacterial genomes exhibiting hallmarks of an obligate intracellular lifestyle. These candidate symbionts span several bacterial phyla and include close relatives of known endosymbionts and parasites of protists as well as previously unclassified or presumed free-living bacterial lineages that likely represent overlooked symbiont specialists. Our findings therefore expand the known distribution of bacterial endosymbiosis, establish the rumen – a key site of global carbon and nitrogen cycling – as a promising model for symbiosis research, and demonstrate the power of our approach to uncover hidden symbiotic associations across complex microbial communities. Overall, our results highlight the ubiquity and evolutionary significance of intracellular symbiosis as a shaping force in microbial ecosystems.

Abstract Manc.ar.chae'um. L. masc. adj. mancus , crippled, maimed; N.L. neut. n. archaeum , an archaeon; N.L. neut. n. Mancarchaeum , a crippled archaeon, an archaeon with absence of many pathways in the genome. Microcaldota / Microcaldia / Candidatus Micrarchaeales / Candidatus Micrarchaeaceae / Candidatus Mancarchaeum The archaeon Candidatus Mancarchaeum was identified in a binary culture during the isolation of Cuniculiplasma divulgatum strain PM4. The culture was established with water saturated sediment sample from acidic stream flowing on Parys Mountain copper mine, Isle of Anglesey, UK. The proportion of genomic reads of Ca . Mancarchaeum in the binary culture was ca. 10%. Ca . Mancarchaeum is phylogenetically affiliated with members of the phylum Microcaldota , class Microcaldia , order Ca . Micrarchaeales, family Ca . Micrarchaeaceae. The cultivation experiments and analysis of the 952,257 bp genome suggest aerobic/microaerobic, organoheterotrophic (proteolytic/peptidolytic), acidophilic, and mesophilic lifestyle. The genome analysis showed the lack of complete central pathways and limited respiratory capacities, indicating reliance on the host, in that particular case, C. divulgatum PM4. The metagenomic analysis also suggested the lateral gene transfer events between the Ca . Mancarchaeum and host in situ . Ca . Mancarchaeum was found as a minor member of microbial community of Parys Mountain acid mine drainage stream. Further environmental distribution of representatives of this Candidatus genus showed preferences to habitats with low pHs and temperatures between 35 and 50°C. DNA G + C content (mol%) : 39.5 (genome sequence). Type species : Candidatus Mancarchaeum acidiphilum Golyshina et al. 2017, CL1.

Abstract Fer.men.ti.micr.ar.chae'um. L. gen. neut. n. fermenti , of a fermentation process; N.L. masc. adj. micros , small [probably better: micrus]; N.L. neut. n. archaeum , ancient one, archaeon; from Gr. adj. archaîos ‐a ‐on , ancient; N.L. neut. n. Fermentimicrarchaeum , a small archaeon performing fermentation processes. Microcaldota / Microcaldia / Candidatus Fermentimicrarchaeales / Candidatus Fermentimicrarchaeaceae / Candidatus Fermentimicrarchaeum The genus Candidatus Fermentimicrarchaeum was established based on complete genome sequence assembled from a freshwater lake sediment metagenome. Ca . Fermentimicrarchaeum is phylogenetically affiliated with the phylum Microcaldota (previously known as Candidatus Micrarchaeota) of the archaeal DPANN superphylum. Analysis of the 1.2 Mb genome of Ca . Fermentimicrarchaeum suggests that, contrary to the ARMAN group of Microcaldota and most DPANN members, this organism has complete glycolytic pathways and ATP generation mechanisms in substrate phosphorylation, the capacities to utilize some sugars and amino acids as substrates, and pathways for de novo nucleotide biosynthesis but lacks an aerobic respiratory chain. We suppose that Ca . Fermentimicrarchaeum is a free‐living scavenger rather than an obligate parasite or symbiont, and its functional role in lake sediments consists of the fermentation of low molecular weight organic compounds. 16S rRNA gene sequences and metagenome‐assembled genomes affiliated with Ca . Fermentimicrarchaeum were recovered from freshwater lake sediments and soils. DNA G + C content (mol%) : 46.4–48.5 (genome sequence). Type species : Candidatus Fermentimicrarchaeum limneticum Kadnikov et al. 2020, CL3.

Introducción: La Punta Morada de la Papa (PMP) es una de las enfermedades más graves que afectan al cultivo de la papa en diversos países de América y del mundo; Candidatus Liberibacter solanacearum (CaLso) es el agente causal de esta enfermedad que en los últimos años en el Ecuador ha sido causante de importantes pérdidas económicas. El manejo de la PMP está enfocado en el control del insecto vector Bactericera cockerelli a través de la aplicación periódica de insecticidas. Sin embargo, el uso de semilla proveniente de plantas enfermas puede también ser causante de la diseminación de la enfermedad. Objetivos: este estudio complementa las investigaciones que buscan establecer el porcentaje de transmisión de la enfermedad a través del uso de tubérculos-semilla provenientes de plantas con diferente sintomatología, causadas por CaLso en el cultivo de papa variedad Superchola. Metodología: se evaluó la transmisión de CaLso mediante la siembra de tubérculos-semilla provenientes de plantas con diferente sintomatología bajo condiciones controladas. Las plantas emergidas de estas semilas, fueron monitoreadas para detectar síntomas, recolectando muestras para ser analizadas mediante pruebas PCR. Los resultados permitieron estimar el porcentaje de transmisión a partir de tubérculos-semilla. La metodología aplicada, ayudó a determinar la viabilidad del patogeno en el material vegetativo y su potencial para establecer infecciones en una nueva generación de plantas. Resultados: de esta manera se encontró que el porcentaje de transmisión fue del 11.07% cuando se utiliza como semilla a los tubérculos provenientes de plantas con síntomas severos y si se utiliza semilla libre de la enfermedad, la transmisión es del 0.06 %. Conclusiones: se logró determinar una escala fenotípica según el grado de infección de la enfermedad en plantas progenitoras. Área de estudio general: Agronomía. Área de estudio específica: Sanidad Vegetal. Tipo de artículo: original.

Sunhemp (Crotalaria juncea L.) is a tropical leguminous crop valued for its multifaceted utility in fiber production, green manuring, and as a raw material in the manufacture of paper and rope. One of the major biotic stresses affecting sunhemp is phyllody disease, caused by a phytoplasma, specifically belonging to the “Candidatus Phytoplasma” spp. These are obligate intracellular pathogens classified under the class Mollicutes, and are primarily transmitted by sap-sucking insect vectors such as leafhoppers, and psyllids. Phyllody-infected plants exhibit a range of morphological abnormalities, including malformed floral structures, chlorosis, stunted growth, and proliferation of axillary shoots, resulting in significant agronomic losses. In the present study, the sunhemp genotype NTPSH 11-02 was subjected to gamma irradiation at doses of 20 kR, 30 kR, 40 kR, and 50 kR to induce genetic variability. The M₂ generation lines derived from these treatments were evaluated under natural field conditions to assess their resistance to phyllody. Out of 44 mutant genotypes, two genotypes, NTPSH 63 and NTPSH 32 exhibited moderate resistance to phyllody, while nine genotypes—NTPSH 24, NTPSH 31, NTPSH 36, NTPSH 39, NTPSH 41, NTPSH 48, NTPSH 53, NTPSH 56, and NTPSH 60 demonstrated a tolerant reaction under natural infestation. Phyllody infection was found to negatively impact key yield-contributing traits, including plant height, number of pods per plant, and 100-seed weight (test weight). A significant reduction in these parameters was observed in infected plants compared to healthy controls, underscoring the detrimental effect of phyllody on overall productivity and crop performance.