Publications

4509

[Pasteurella] langaaensis has been found to be polyphyletic in relation to the type species Pasteurella multocida, as endicated by 16S rRNA gene sequence comparisons and a number of other comparisons (enclosing the genus name in brackets). 16S rRNA gene sequence-based phylogeny confirmed that [P.] langaaensis is unrelated to other members of Pasteurellaceae at the genus level and may be a candidate for a new genus with 95% 16S rRNA gene sequence identity to the closest related sequence belonging to the type strain of [Actinobacillus] rossii. The highest digital DNA–DNA hybridization value predicted from the whole-genomic sequence of the type strain of [P.] langaaensis was to the type strain of Acinobacillus suis with 26%, confirming a separate taxonomic status at the species level. The phylogenetic comparison of concatenated conserved protein sequences determined in a previous study showed a unique position of the taxon investigated, which qualified for the status of a new genus since the highest conserved protein sequence identity was found to [A.] rossii with 86%. A new genus with one species, Alitibacter langaaensis gen. nov., comb. nov., is proposed. The genus can be separated from other genera in the family Pasteurellaceae by from 1 up to 12 phenotypic characters, and it is monotypic from other genera with respect to analysis of 16S rRNA gene sequences as well as of predicted core genomic proteins. The type strain of Alitibacter langaaensis is F73T (=NCTC 11411T=CCUG 15566T=DSM 22999T=CPI 102678T=ATCC 43328T).

Abstract Citrus Huanglongbing (HLB) is one of the most devastating diseases in the citrus industry and is caused primarily by ‘Candidatus Liberibacter asiaticus’ (CLas), a phloem-restricted gram-negative bacterium transmitted via citrus psyllids in the field. Precise CLas detection is crucial for HLB control, particularly during extensive surveys in new emerging regions. Unfortunately, the lack of a practical on-site detection method for CLas due to the limited specificity of immunostrips and the costive non-user friendliness approaches prevent the effective disease control. In this study, a probe-based recombinase polymerase amplification (RPA) targeting the CLas five-copy nrdB gene (β-subunit of ribonucleotide reductase, RNR) was developed and evaluated for its specificity, sensitivity, and reliability. To enhance user-friendliness and facilitate widely use, an All-in-one kit was premade as freeze-dried pellets in individual tubes, containing all necessary components except DNA template. The applicability of the All-in-one kit for CLas detection was confirmed using plant or psyllid crude DNA extracts. Collectively, the All-in-one kit offers a specific, sensitive, rapid, cost-effective, and practical alternative for diagnosing CLas in field conditions when coupled with simplified crude DNA extraction method, providing an alternative approach for on-site CLas detection in the context of HLB.

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.

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.