Publications

4681

ABSTRACT The Sphaerotilus-Leptothrix group of bacteria includes one of the first described microorganisms, Leptothrix ochracea , an uncultured type strain, plus isolates of Leptothrix and Sphaerotilus . This group is unified by the ability to form sheaths and oxidize metals, although L. ochracea exhibits obvious ecological, morphological, and functional differences from the rest of Sphaerotilus-Leptothrix . Recently, there have been calls to combine the group into one genus, Sphaerotilus ; however, these studies lacked adequate genomic representation of L. ochracea . Here, we present a comprehensive comparative genomic analysis of the Sphaerotilus-Leptothrix group, including expanded representation of L. ochracea , a closely related novel species, Leptothrix toolikensis , and two new isolates ( Leptothrix mechoopdaensis ). Analysis of 38 genomes resolves three phylogenetic and functional groups: the ochracea -type Leptothrix (Group 1), the mobilis -type Leptothrix (Group 2), and Sphaerotilus (Group 3). Group 1 genomes form a separate genus based on average nucleotide identity and alignment fraction. The genomes clearly diverge from the rest of Sphaerotilus-Leptothrix in phylogeny, size, and metabolic potential. Group 1 genomes are much smaller (2.59–3.04 Mb) than those of Groups 2 (4.55–6.06 Mb) and 3 (3.94–5.07 Mb), while encoding more metal oxidases and fewer carbohydrate-active enzymes. Group 2 clusters with Group 3 phylogenetically and is similar in organic carbon metabolisms but maintains more metal oxidation genes. Group 2 members lack homogeneity in phenotype and genotype, suggesting that additional isolates and genomes are needed for confident classification. However, Group 1 genomes ( L. ochracea and L. toolikensis ) show clear divergence, precluding their inclusion in Sphaerotilus and supporting the retention of the genus Leptothrix . IMPORTANCE Researchers have long noted differences in metal oxidation, morphology, and ecology among Sphaerotilus-Leptothrix , but longstanding confusion over phylogeny and genus boundaries led to inconsistent taxonomic classification between the two genera. This confusion stems from previous work that used isolates that are unavailable or lost distinguishing traits in culture, and from limited genomic data. Furthermore, the Leptothrix type strain L. ochracea has never been isolated. This study provides molecular evidence that substantiates calls to reassign some Leptothrix members to the genus Sphaerotilus but adds to an emerging body of evidence that Group 1 L. ochracea and now L. toolikensis represent a functionally distinct lineage. While genomic similarity metrics left taxonomic divisions unclear, integrating metabolic potential with phylogeny resolved genus boundaries based on clear functional groupings. This polyphasic approach for delineating genera clarifies longstanding taxonomic confusion and refines our understanding of functional diversity both across and within Sphaerotilus-Leptothrix lineages.

Psyllids harbour the obligate nutritional symbiont ‘ Candidatus Carsonella ruddii’ ( Ca Cr), yet complete Ca Cr genomes remain unevenly sampled across Psylloidea, limiting both comparative analysis and temporal inference. Here, seven complete Ca Cr genomes (165–174 kb) were assembled and annotated from psyllid hosts representing four families, including lineages for which genome-grade resources had previously been unavailable. We integrated whole-genome phylogenomics, pangenome analysis, fossil-calibrated relaxed-clock dating and quantitative PCR (based on 16S rRNA) screening of secondary symbionts. Across hosts, Ca Cr retained an extremely reduced, AT-rich (>82%) and gene-dense (>90% coding) genome architecture with a conserved core of 155 genes, while the accessory fraction was limited and lineage-specific. Most variable genes belonged to amino-acid metabolism or proteins of unknown function, suggesting differential erosion of peripheral functions around a stable translational and informational core. Phylogenomically, Ca Cr diversification broadly tracked deep host diversification, although the Ca Cr lineage from Diaphorina citri grouped with Triozidae-associated lineages rather than with other sampled Psyllidae. Using two host fossil-informed soft calibrations, we estimated that major Ca Cr divergences occurred mainly from the Paleogene to the Miocene, with crown diversification of Cacopsylla -associated Ca Cr at 15.95–18.99 Ma. In contrast to the stability of the primary symbiosis, secondary symbionts showed patchy host distributions: Wolbachia- and Arsenophonus -like lineages occurred in multiple hosts, ‘ Candidatus Profftella armatura’ was restricted to D. citri , and no secondary symbiont was detected in Cacopsylla chinensis . These results provide a time-resolved comparative framework for Ca Cr evolution in psyllids and underscore the different evolutionary stability of primary and facultative associates.

Soils are critical microbial habitats that support terrestrial ecosystem functioning and harbor numerous uncultured and functionally uncharacterized microbial groups. The black soil region in northeast China is a key agricultural ecosystem globally, yet the classification and functional understanding of its crucial microbial groups remain underexplored. In this study, we identified three high-completeness metagenome-assembled genomes (MAGs) from the Global Mollisols Genomic Atlas (GMGA). Phylogenetic and comparative genomic analyses identified these genomes as representing a novel evolutionary branch within the genus Flavobacterium, classified under the phylum Bacteroidota. Their novel taxonomic position is further supported by average nucleotide identity (ANI) and average amino acid identity (AAI) thresholds, demonstrating significant divergence from all known reference genomes. Functional annotation indicated that this species possesses strong plant polysaccharide degradation potential and a chemoheterotrophic lifestyle, together with environmental stress tolerance and a specialized nitrogen metabolic network adapted to agricultural inputs, thereby conferring a metabolic advantage in black soil environments characterized by high organic matter input and marked seasonal fluctuations. In addition, global distribution analysis showed that this lineage is widely distributed across diverse ecosystems and is significantly enriched in soil habitats, particularly in environments with fluctuating carbon sources and high organic matter inputs. The new species is most abundant in temperate soils, with the northeast black soil region of China emerging as a key hotspot. Based on these findings, and because no pure culture is currently available, we propose Candidatus Flavobacterium genomatis based on genome-resolved metagenomic evidence and in alignment with the International Code of Nomenclature of Prokaryotes rules for uncultivated prokaryotes. Our results expand the known species diversity of the genus Flavobacterium and suggest potential ecological roles of uncultured black-soil microbes in carbon and nitrogen cycling, including possible involvement in N2O reduction under suitable environmental conditions.

GroE is a chaperonin folding system consisting of GroEL (Cpn60, a 60 kDa chaperonin), and the smaller co-chaperonin GroES (Cpn10). Many ‘client’ proteins require GroE to fold properly, including several that are essential for cell viability. GroE is found in nearly all bacteria and eukaryotes. Mollicutes are the only micro-organisms that lack GroE in almost all cases. Only two clades of Mollicutes have retained the ancestral GroE system, or perhaps reacquired one; these exceptions include the family Acholeplasmataceae , consisting of the genera Acholeplasma and ‘ Candidatus Phytoplasma’. The role of GroEL in these unique Mollicutes is a source of speculation, given how many non-canonical ‘moonlighting’ roles have been ascribed to this protein. GroEL has been suggested to play a role in pathogenesis in plant and animal pathogenic Mollicutes by binding to host cells and facilitating invasion. However, in one further layer of exception, the phytopathogenic taxon ‘ Candidatus Phytoplasma pruni’ (ribosomal group 16SrIII) was reported in 2012 to lack a GroE system. This study confirms the lack of a functional GroE system in 16SrIII by providing two new, high-quality, non-fragmented genome assemblies, as well as a thorough survey of other 16SrIII genomes for genes encoding GroEL/GroES, including those that may not resemble phytoplasma GroEL (i.e. acquired by horizontal gene transfer, HGT). We discuss the implications of a clearly phytopathogenic, invasive group of Mollicutes that nevertheless lacks GroE, in light of the presumed role of GroEL for this species. We determined that multiple genomes of 16SrIII contain short, non-functional groEL pseudogenes, while most of the reported genomes lack any semblance of a GroE system. Examination of the new assemblies allowed us to rule out HGT as a means of GroE acquisition.

“Candidatus Sarcina troglodytae” (“Ca. S. troglodytae”), a proposed bacterial species in the family Clostridiaceae, has been epidemiologically associated with a lethal disease in sanctuary chimpanzees in Sierra Leone, epizootic neurologic and gastroenteric syndrome (ENGS). As sarcinae are known to be difficult to culture, a lack of viable in vitro growth conditions has limited further characterization of this bacterium. Such studies are critical to elucidating the relationship between “Ca. S. troglodytae” and ENGS.  Here, we isolate a Gram-stain-positive, endospore-forming, coccus and anaerobic bacterial strain, designated JB3T, from brain tissue of a western chimpanzee (Pan troglodytes verus) using a reinforced clostridial medium. We describe the growth of strain JB3T at a pH range of 6 to 9 (optimum 6) at 37°C in an atmosphere composed of 5% H2, 5% CO2, and 90% N2 and demonstrate endospore production under alkaline conditions, suggesting the possibility of an environmental reservoir. We identify ethanol as the primary non-gaseous fermentation byproduct which we hypothesize to have relevance for ENGS. Antibiotic susceptibility testing shows susceptibility to common antimicrobial agents with notable resistance to ceftriaxone. By establishing in vitro conditions for the viable culture, propagation, and storage of “Ca. S. troglodytae”, this study lays the groundwork for future infection studies to test hypotheses about pathogenic mechanisms and prevention/treatment measures for ENGS.

Abstract Bacterial symbionts were shown to have significant beneficial impacts on the fitness of their host in insects, but little is known on the symbionts of spiders and their interactions with their hosts. Here, we assembled and investigated the circular 575 kb genome of Candidatus Argioplasma dusa, a novel bacterial symbiont of the wasp spider Argiope bruennichi . Phylogenomic analysis placed this species within the phylum Tenericutes, in a poorly characterized clade that may represent a new order-level lineage or affiliate with the Mycoplasmatales order. With 559 predicted genes, the genome is relatively small compared to other Tenericutes genomes (on average 969 genes) and has a low GC content of ~24%. While the genome encodes genes for proteins involved in glycolysis and fermentative acetate production, it revealed minimal biosynthetic capabilities with pathways for nucleotide, amino acid and vitamin biosynthesis being absent in Ca . Argioplasma dusa. This suggests an intracellular endosymbiotic lifestyle within the spider host. The symbiont was detected in A. bruennichi populations across the distribution range of the spider but appears to be absent in certain populations.

‘Candidatus Liberibacter asiaticus’ (CLas), the causal agent of citrus huanglongbing, is transmitted by the Asian citrus psyllid Diaphorina citri. While CLas-positive (CLas+) females exhibit increased fecundity and metabolic demands, their neuroendocrine regulation mechanisms remain unclear. We propose CLas manipulates dopamine (DA) signaling to enhance psyllid fecundity and CLas proliferation. Metabolomics revealed elevated DA in CLas+ females. Silencing DA synthesis genes and receptor DcDop2 via RNAi reduced lipid reserves, fecundity, and ovarian CLas titers. Through combined in vivo and in vitro experiments, we demonstrated that the microRNA miR-31a suppresses DcDop2 expression by binding to its 3’ untranslated region. Overexpression of miR-31a resulted in decreased DcDop2 expression and CLas titers in the ovaries, eliciting phenotypic defects akin to DcDop2 knockdown. Furthermore, DcDop2 knockdown and miR-31a overexpression reduced juvenile hormone (JH) levels and adipokinetic hormone (AKH) signaling in fat bodies and ovaries. Consequently, CLas regulates the DA-DcDop2 signaling axis to improve D. citri lipid metabolism and fecundity, while simultaneously promoting its replication. These findings reveal a coevolution between CLas proliferation and ovarian development in the insect host. This discovery enhances our understanding of the molecular interplay between plant pathogens and vector insects and offers novel targets and strategies for HLB field management.