Publications

4713

Abstract Anaerobic methanotrophic (ANME) archaea are important players in the microbial methane cycle, mitigating methane emissions from anoxic environments. ANME are found ubiquitously in methane-rich sediments, where they can couple anaerobic methane oxidation (AOM) to different electron acceptors such as sulfate, metal oxides, and natural organic matter (NOM). However, we still lack understanding of the geochemical niches and preferred metabolic pathways of most ANME subclades. Here, we investigated the genomic potential and ecophysiology of ANME-2a with respect to metal-dependent AOM in brackish metal-rich coastal sediments. We assembled several high-quality ANME MAGs from subclades with high strain heterogeneity and analyzed the genomic potential for metal-AOM. Additionally, we monitored long-term enrichments with various electron acceptors from the same sediments. Ultimately, we recovered 8 novel genomes of ANME-2a that clustered with an uncharacterized genus with only 2 representatives in public databases for which we propose the name ‘ Candidatus Methanoborealis’. The analysis of the MAGs showed two different clusters within this genus; one comprising of MAGs from the Baltic Sea that showed high potential for extracellular electron transfer (EET) required for metal-AOM, and another cluster form more diverse environments with less EET potential. The Baltic Sea Ca. Methanoborealis were the only canonical methanotrophs in the incubations during active methane oxidation and metal reduction. Our results contribute to the understanding of the phylogenomic and metabolic diversity in ANME subclades, which will help to further characterize novel ANME lineages from complex sediment samples.

Two species have been named in the provisional genus ‘ Candidatus Nostocoides’: ‘ Ca . Nostocoides limicola’ corrig. Blackall et al . 2000 and ‘ Ca . Nostocoides acidiphilum’ corrig. Kulichevskaya et al . 2012. The type species of the genus, ‘ Ca . Nostocoides limicola’ has since been transferred to Tetrasphaera Maszenan et al . 2000, which was later renamed Nostocoides Deshmukh and Oren 2024. This leaves ‘ Ca . Nostocoides acidiphilum’ as an orphan species. Furthermore, Kulichevskaya et al . did not assign ‘ Ca . Nostocoides acidiphilum’ to ‘ Ca . Nostocoides’ corrig. Blackall et al . 2000. Instead, they proposed a new genus, ‘ Ca . Nostocoides’ corrig. Kulichevskaya et al . 2012, in the phylum Planctomycetota . This is in violation of Rule 51b (4) of the International Code of Nomenclature of Prokaryotes, making ‘ Ca . Nostocoides’ corrig. Kulichevskaya et al . 2012 and ‘ Ca . Nostocoides acidiphilum’ corrig. Kulichevskaya et al . 2012 pro-illegitimate names. To resolve this situation, I propose the replacement names ‘ Ca . Nostocimimus’ gen. nov. and ‘ Ca . Nostocimimus acidiphilus’ comb. nov., respectively.

Abstract Grapevine plants showing symptoms typically induced by phytoplasmas infection, characterized by leaf reddening or yellowing, reduce vigour, delayed growth and shoot proliferation with reduced leaf size, were observed in the state of São Paulo, Brazil. This disorder causes significant damage to grape production by delaying the onset of fruit bearing and reducing yield. Similar symptoms have been reported in grapevines grown in other countries revealing the presence of phytoplasmas in diseased plants. Based on the described symptoms, this study was conducted in order to demonstrate the association between phytoplasma and symptomatic grapevine plants, as well as characterize molecularly the detected pathogen. Molecular analysis was performed using PCR and RFLP assays, followed by phylogenetic analysis. Amplifications of genomic fragments of 1.2 evidenced the presence of phytoplasma in tissue of symptomatic samples confirming the preliminary diagnosis based on the symptoms. Molecular characterisation identified the phytoplasma as a ‘ Ca Phytoplasma prunorum’ strain, belonging to the 16SrX-B subgroup. This is the first report of a phytoplasma belonging to the 16SrX-B group infecting grapevine plants in Brazil.

Abstract Hemotropic mycoplasmas (hemoplasmas) infecting cattle were first detected in France in 2019 during a clinical outbreak, but their prevalence both at the species and strain levels remains unknown. This study therefore aimed to determine the prevalence of hemoplasmas and their coinfections, and to identify associated risk factors using a fixed-effect logistic regression model. Detection was performed using 16S rRNA qPCR, as well as three strain-specific rnpB qPCR assays targeting Candidatus Mycoplasma haematobovis (CMh, formerly Ca . M. haemobos), Mycoplasma wenyonii strain Mexico (Mex), and Mycoplasma wenyonii strain Massachusetts (Mass). A total of 1011 cattle were sampled, of which 88.7% (897/1011) tested positive by 16S rRNA qPCR. Prevalence rates for CMh, Mex, and Mass were 67.7% (684/1011), 65.9% (666/1011), and 19.8% (200/1011), respectively. Concordance between 16S rRNA qPCR and strain-specific rnpB qPCR was 92% (931/1011). Coinfections were detected in 67.8% (565/833) of infected animals, with the CMh + Mex combination being the most frequent. The Mass strain was predominantly found in triple infections. Risk factors for infection included coinfections, age (except for Mass), and climatic conditions for CMh and Mass. Further studies are needed to elucidate transmission routes and pathogenicity mechanisms of hemoplasmas.

Abstract Cassava is a key food and energy crop in the tropical and subtropical regions. In South America, oversprouting disease (OVSPD) and cassava frogskin disease (CFSD) occur frequently, however, their etiologies remain unknown. OVSPD is characterized by excessive shoot proliferation, chlorosis, and dwarfism, whereas CFSD largely affects roots, causing cork-like tissues with honeycomb patterns and reduced starch content. In Brazil, phytoplasma organisms were found to be associated with both diseases, with sequences of the 16SrIII-B subgroup phytoplasmas linked to OVSPD and the 16SrIII-L and 16SrIII-A subgroups linked to CFSD. To clarify the identity and taxonomic position of the putative phytoplasma in the diseases, high-throughput sequencing (HTS) of total plant DNA from cassava plants with OVSPD and others with CFSD symptoms was performed, and the complete genome of a novel phytoplasma was assembled from OVSPD plants. In contrast, HTS from CFSD affected plants revealed short sequence fragments of diverse phytoplasmas, however, the assembly of larger scaffolds failed. Genome analyses of two OVSPD phytoplasma assemblies confirmed a novel phytoplasma species within the 16SrIII group. It has an average nucleotide identity (ANI), below the 95% species demarcation threshold relative to the genomes of other phytoplasma species and we propose the name ' Candidatus Phytoplasma manihotii' sp. nov. A broader screening showed that this phytoplasma occurs only in OVSPD plants, suggesting that the genome fragments detected in CFSD plants may have resulted from other sources, such as genomic integration or horizontal gene transfer.

Desmodium styracifolium (Osb.) Merr., a member of the Leguminosae family, is an important medicinal plant widely used in traditional Chinese medicine. In September 2024, D. styracifolium plants exhibiting symptoms of little leaf and stunted growth were observed in a field of Zhanjiang, Guangdong province, China. Since the symptoms resembled those associated with phytoplasma infections, total DNA was extracted from the leaves of four symptomatic plants and one healthy plant for molecular identification. Universal primer pairs (P1/P7, R16mF2/mR1) for phytoplasma detection were used to amplify the 16S rDNA fragments (~1.8 kb and ~1.4 kb), while a specific primer pair secY-F/secY-R was employed to amplify a ~1.4 kb segment of the secY gene. Target fragments were successfully amplified from all symptomatic samples but not from the healthy control. These amplicons were cloned and sequenced. The obtained 16S rDNA sequence of D. styracifolium little leaf phytoplasma (DsLFP-GDZJ) showed the highest identity (99.67–100%) with strains of ‘Ca. Phytoplasma australasiaticum’ (subgroup 16SrII-A and 16SrII-D). Phylogenetic analysis also indicated that DsLFP-GDZJ formed a small evolutionary branch with strains of ‘Ca. Phytoplasma australasiaticum’ (subgroup 16SrII-A and 16SrII-D). Virtual RFLP (restriction fragment length polymorphism) analysis of the 16S rDNA sequence demonstrated DsLFP-GDZJ belongs to the 16SrII-A subgroup (GenBank accession number L33765). The secY gene sequence of DsLFP-GDZJ also showed the highest similarity and the closest relationship with those of the 16SrII-A subgroup phytoplasma strains. These results showed that DsLFP-GDZJ is a strain of ‘Ca. Phytoplasma australasiaticum’ (16SrII-A subgroup). To our knowledge, this is the first report of ‘Ca. Phytoplasma australasiaticum’—related phytoplasma associated with D. styracifolium little leaf disease in China, thereby establishing D. styracifolium (Osb.) Merr. as a new host plant of phytoplasma.

Abstract Magnetoreception is a remarkable ability found across a diverse range of organisms, including bacteria, birds, fish, insects, and mammals, enabling them to detect and harness the Earth’s geomagnetic field. Recently, the recruitment of biomineralizing ectosymbionts by euglenozoans was evidenced as an ecological strategy for microeukaryotes to acquire this sense. Here, we report a case of magnetosymbiosis involving a ciliate and four populations of endosymbiotic bacteria experiencing genome reduction. Among these bacteria, one group of sulphate-reducing Desulfovibrionales was found to biomineralize bundles of bullet-shaped magnetite crystals. The ciliate’s magnetotaxis mirrors that of free-living magnetotactic bacteria and euglenozoans, enabling efficient navigation in chemically stratified aquatic environments. However, in this case, magnetotaxis arises from an endosymbiotic interaction. Using a combination of optical-, confocal-, electron- and X-ray-based microscopy techniques, together with genomic analyses, these findings demonstrate that magnetosymbiosis can emerge in unicellular eukaryotic lineages through endosymbiotic integration, expanding our understanding of such interactions in aquatic ecosystems. More broadly, this work contributes to the ongoing debate on the origins of magnetoreception in eukaryotes.

Abstract The African citrus triozid (ACT), Trioza erytreae (Del Guercio, 1918) (Hemiptera: Triozidae), is a significant pest of citrus in southern Africa serving as a vector of African citrus greening disease associated with the phloem-limited gram-negative bacterium “Candidatus Liberibacter africanus” (CLaf). ACT can also vector another Liberibacter species, “Ca. Liberibacter asiaticus” (CLas) associated with Asian citrus greening. Given the confirmed presence of CLas on the African continent, efforts to monitor populations of ACT as well as associated liberibacters in citrus environments have been enhanced since 2021. Trapping and active collections in citrus surroundings indicated the presence of two triozid species with similar morphology to ACT and five other triozids which were morphologically distinct. This study aimed to characterise the diversity of triozid species around citrus and determine their association with liberibacter. Morphological characters and nucleotide sequence phylogeny of the mitochondrial cytochrome c oxidase I (COI) gene region supported the distinction of seven triozid species including ACT. CLaf was only detected in ACT. None of the other triozid species had any liberibacter species associated with them. Our results suggest the presence of other triozid species in other African countries, which probably were misidentified as ACT. Our findings highlight the need for a comprehensive taxonomic revision of triozids associated with citrus. Integrating morphological and molecular characters in a revised classification will be essential for accurate identification of ACT. Molecular confirmation is needed for confidence in distinguishing ACT from closely related non-pest species.

Abstract Segmented filamentous bacteria (SFB) describe morphologically similar gut commensals found in mammals, fish and birds. In mice, SFB intimately colonizes the ileal epithelium at the time of weaning and elicits a strong pleiotropic immune activation that fosters colonization resistance while augmenting disease severity in various disease models. SFB is therefore critical in both health and disease but information regarding SFB in humans remains limited. Here, we first identify and characterize a human SFB species with SFB-specific morphology, including the hook-like tip structure that mediates attachment, and unique genome features, including a starch and glycogen degradation module. This species, which we name Anisomitus miae and establish as the nomenclature type for the SFB genus, is common across Africa. We then bioinformatically identify, based on the 16S rRNA gene V3-V4 variable region sequence, four major, and two minor, human SFB lineages in forty-four countries distributed across all six inhabited continents. We provide evidence towards the co-colonization potential of the SFB lineages and their colonization dynamics, including a potent but short-lived colonization peak in children between one to five years of age. This study establishes the presence of multiple SFB species in the human population and SFB as a minor but wide-spread group of commensals in humans.