Publications

4372

‘Candidatus Liberibacter solanacearum’ (Lso) is an uncultured, phloem-associated bacterium causing a severe tuber disease in potato called zebra chip (ZC). Seven haplotypes of Lso have been described in different hosts, with haplotypes A and B found associated with infections in potato and tomato. In the field, Lso is transmitted by the potato psyllid (Bactericera cockerelli), and between 2011 and 2015, a significant change in Lso haplotype prevalence was previously reported in Idaho: from exclusively A haplotype found in tested psyllids in 2012 to mainly B haplotype found in collected psyllids in 2015. However, prevalence of Lso haplotypes in Idaho was not analyzed in potato tubers exhibiting symptoms of ZC. To fill in this knowledge gap, prevalence of Lso haplotypes was investigated in potato tubers harvested in southern Idaho between 2012 and 2018, and it was found to change from exclusively A haplotype in the 2012 season to an almost equal A and B haplotype distribution during the 2016 season. During the same period, haplotype distribution of Lso in psyllid vectors collected using yellow sticky traps also changed, but in psyllids, the shift from A haplotype of Lso to B haplotype was complete, with no A haplotype detected in 2016 to 2018. The changes in the haplotype prevalence of the Lso circulating in potato fields in southern Idaho may be, among other factors, responsible for a decrease in the ZC incidence in Idaho potato fields between an outbreak of the disease in 2012 and a very low level of ZC afterward.

Summary Marine sponges represent one of the few eukaryotic groups that frequently harbour symbiotic members of the Thaumarchaeota , which are important chemoautotrophic ammonia‐oxidizers in many environments. However, in most studies, direct demonstration of ammonia‐oxidation by these archaea within sponges is lacking, and little is known about sponge‐specific adaptations of ammonia‐oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope‐based functional assays. ‘ Candidatus Nitrosospongia ianthellae’ is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbour nitrite‐oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin‐like proteases, a metalloprotease unique among archaea, as well as a putative branched‐chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge‐associated, but not in free‐living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic‐like proteins, and a DNA‐phosporothioation system, represent important adaptations of AOA to life within these ancient filter‐feeding animals.

Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands of cells. They occur worldwide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genomics and metagenomics to retrieve draft genomes of 3 marine Candidatus Electrothrix and 1 freshwater Ca. Electronema species. These genomes contain >50% unknown genes but still share their core genomic makeup with sulfate-reducing and sulfur-disproportionating Desulfobulbaceae, with few core genes lost and 212 unique genes (from 197 gene families) conserved among cable bacteria. Last common ancestor analysis indicates gene divergence and lateral gene transfer as equally important origins of these unique genes. With support from metaproteomics of a Ca. Electronema enrichment, the genomes suggest that cable bacteria oxidize sulfide by reversing the canonical sulfate reduction pathway and fix CO 2 using the Wood–Ljungdahl pathway. Cable bacteria show limited organotrophic potential, may assimilate smaller organic acids and alcohols, fix N 2 , and synthesize polyphosphates and polyglucose as storage compounds; several of these traits were confirmed by cell-level experimental analyses. We propose a model for electron flow from sulfide to oxygen that involves periplasmic cytochromes, yet-unidentified conductive periplasmic fibers, and periplasmic oxygen reduction. This model proposes that an active cable bacterium gains energy in the anodic, sulfide-oxidizing cells, whereas cells in the oxic zone flare off electrons through intense cathodic oxygen respiration without energy conservation; this peculiar form of multicellularity seems unparalleled in the microbial world.

Abstract Me.tha.no.hal'ar.chae.um N.L. neut. n. methanum methane; N.L. pref. methano ‐ pertaining to methane; Gr. masc. n. hals, halos salt; N.L. neut. n. archaeum (pertaining to archaios, ‐e, ‐on) ancient; N.L. neut. n. Methanohalarchaeum a salt‐loving archaeon forming methane. The candidate genus Ca . Methanohalarchaeum includes obligately anaerobic, extremely halophilic, neutrophilic, and moderately thermophilic methanogens with small coccoid cells producing methane by reduction of C 1 ‐methylated compounds using either H 2 or formate as electron donors. Amino acids or acetate is required as C‐source for assimilation. Core membrane lipids are represented by diphytanyl glycerol tetra‐ and diethers. Cells accumulate potassium as a compatible solute. They inhabit hypersaline lakes or salterns with neutral pH. The genus contains a single candidate species Ca . M. thermophilum, which is the type species. It is a member of the class Methanonatronarchaeia within a newly proposed phylum Halobacteriota (formerly part of the phylum Euryarchaeota ). DNA G + C content (mol%) : 35.4 (genome of the type strain). Type species : Ca . Methanohalarchaeum thermophilum Sorokin, Merkel, Abbas, Makarova, Rijpstra et al. 2018, 2206. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Methanohalarchaeum is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Methanobacteriati / Methanobacteriota / Methanonatronarchaeia / Methanonatronarchaeales / Methanonatronarchaeaceae / Candidatus Methanohalarchaeum The genus Candidatus Methanohalarchaeum can also be recovered in the Genome Taxonomy Database (GTDB) as g__Methanohalarchaeum (version v220) ** . GTDB classification: d__Archaea / p__Halobacteriota / c__Methanonatronarchaeia / o__Methanonatronarchaeales / f__Methanonatronarchaeaceae / g__Methanohalarchaeum * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

AbstractTheCampylobacterotais a novel phylum created from the reclassification of the proteobacterial classEpsilonproteobacteriaand orderDesulfurellales(Deltaproteobacteria). The phylum is organized according to phylogenies based on a concatenated alignment of 120 conserved protein marker sequences and the 16S rRNA gene. Like any phylogenetic inference, this road map is a hypothesis based on the data available at the time of writing and may be subject to change as new species are described, or other gene sequences considered. This road map incorporates relative evolutionary divergence to normalize subordinate ranks. It, therefore, includes a number of changes at the rank of order, family, and genus, which would otherwise not be affected by the merging of the former lineages.