Publications

4852

The genus Pseudalkalibacillus, created by the reclassification of specific deep-branching Alkalihalobacillus species, exhibits polyphyletic branching. The Genome Taxonomy Database (GTDB) also assigns Pseudalkalibacillus species into two families and three genera. To clarify the evolutionary relationships and classification of Pseudalkalibacillus species, we report detailed investigations using phylogenomic and molecular signature-based approaches. In phylogenomic trees, Pseudalkalibacillus species are distributed within two family-level lineages. One of these clades, containing the type species of Pseudalkalibacillus (viz. Pseudalkalibacillus decolorationis), represents the genus Pseudalkalibacillus, groups within the family Fictibacillaceae. Ten novel conserved signature indels (CSIs) identified in this study are specific for this clade, providing a robust means for the differentiation of the emended genus Pseudalkalibacillus. The remaining Pseudalkalibacillus species form a separate family-level clade, designated as f_HBI72195 in the GTDB. Within this clade, all species except Pseudalkalibacillus caeni form a robust clade designated as Pseudalkalibacillus clade −2 in our work and g_Anaerobacillus_A in the GTDB. We have also identified 15 novel CSIs specific to this clade. As the Pseudalkalibacillus clade −2 is distinct from Pseudalkalibacillus, we propose transferring species from this clade into a new genus, Guptibacillus gen. nov. The species P. caeni branches distinctly from other Pseudalkalibacillus species, and the GTDB considers it a novel genus (g_Bacillus_BR). Six newly identified CSIs are specific to this species, and we are proposing the transfer of this species into a new genus, Exobacillus gen. nov. Two additional identified CSIs are shared by members of the novel family-level taxon (f_HBI72195) comprising the proposed genera Guptibacillus and Exobacillus, for which we are proposing the name Guptibacillaceae fam. nov. Lastly, the results presented here also show that ‘Pseudalkalibacillus hemicentroti’ and ‘Pseudalkalibacillus macyae’ are later heterotypic synonyms of Guptibacillus hwajinpoensis. These changes, which reliably depict the evolutionary relationships among Pseudalkalibacillus species, should be helpful in future studies of these organisms.

AbstractBackgroundRickettsiaare obligate intracellular gram-negative bacteria of the class Alphaproteobacteria and are vector-borne species that cause diseases in humans and animals. NewRickettsiaspecies have been involved as human pathogens; however, the pathogenic potential of other species is unknown.CandidatusRickettsia colombiensis is a new species in the spotted fever group of unknown pathogenicity that is phylogenetically related to other pathogenic species.ObjetiveTo evaluate the pathogenic potential ofCa. R. colombiensis in Syrian hamsters (Mesocricetus auratus) and analyzed its cross-reactivity against other SFG rickettsia species in human and Syrian hamster sera.MethodsCa. R. colombiensis was isolated fromAmblyomma dissimileusing a shell vial. Subsequently, five male hamsters were inoculated intraperitoneally (IP) and five intradermally (ID) with 1 × 106 Vero cells infected withCa. R. colombiensis. One control animal was used in each group of the study. The health status of the animals was assessed daily, and necropsies were performed on days 5, 10, 15, and 16 DPI. Serum samples for indirect immunofluorescence and tissues were processed for qPCR and immunohistochemistry.ResultsAll animals remained healthy during the trial and showed no changes in their physiological parameters. No Rickettsia DNA was detected in any of the tissues. Animals infected withCa. R. colombiensis showed IgG antibody titers ranging from 1:64 to 1:1024. The control animals were negative. Regarding human sera, 56% (84/150) had IgG antibodies against Ca. R. colombiensis antigen. Sera with titers equal to or higher than 1:64 were 100% seroreactive.ConclusionsCa. R. colombiensis caused a subclinical infection in hamsters, suggesting the possibility of infecting other mammals. However, the clinical, pathological, and molecular findings are inconclusive in establishing thatCa.R. colombiensis is a pathogenic species. Regarding cross-reactivity, it is possible to serologically diagnose Rickettsial infection usingCa. R. colombiensis as antigens.Author summaryRickettsiosis is a human and animal disease caused by the bacterial Rickettsia species, which are mainly transmitted by arthropods. The clinical spectrum of rickettsiosis ranges from asymptomatic infection to severe and fatal diseases, such as Rocky Mountain spotted fever caused by Rickettsia rickettsii. In recent years, the number of species belonging to the genus Rickettsia has increased, in part due to the progress in the detection and identification of these agents by the application of modern molecular techniques. Much of this newRickettsiaspecies, known as Candidatus, has been involved as animal and human pathogens; however, for other Candidatus Rickettsia species, the ability to cause diseases is unknown.CandidatusRickettsia colombiensis is a new species phylogenetically related to pathogenic species. Here, we evaluated, for the first time, the pathogenic potential of this microorganism in a hamster animal model and analyzed its cross-reactivity against other members of the Rickettsia genus in human and hamster sera to determine the possibility of usingCandidatusRickettsia colombiensis as antigens to diagnose rickettsiosis in regions where immunologic reagents are scarce and high biosafety level laboratories do not exist. In this report, we demonstrate thatCandidatusRickettsia colombiensis causes an inapparent infection in hamsters and cross-reactivity between other members of the Rickettsia genus.

Abstract The genus “Candidatus Kouleothrix” (Eikelboom type 1851) is the major filamentous bacterium responsible for activated sludge bulking in Japanese activated sludge plants, where it is present in many in unusually high abundances. Global surveys have shown this genus embraces several species, although the contribution each of these makes to bulking is not known. This study followed their population dynamics in a full-scale bulking sludge plant in Japan over a 12-month period, which required the development of species-specific FISH probes, used to measure their relative abundances. Six of the 9 recognised species of “Ca. Kouleothrix” were detected there, two of which (midas_s_3423 and midas_s_35412) were at consistently high abundances and responsible for increases in the sludge volume index (SVI). Their abundances were also statistically correlated with their filament lengths, which showed higher correlations with SVI increases than did species abundances. This study examined the impacts of both operational parameters and other communities on the abundances of these two species over the 12-month period and showed marked interspecies differences in responses to both. Together these findings stress the importance in studies of this kind to identify populations to species level to reveal possible important ecological differences not seen at the genus level.

ABSTRACT Although the high-altitude limit for microbial survival in the Earth–atmosphere system has remained a scientific curiosity and topic of study, the ecological significance of long-distance microbial dispersal in the atmosphere has been perceived to have marginal relevance. Here, we report the characterization of novel plant pathogenic species of Curtobacterium that were isolated from samples collected at altitudes ranging from 1.5 to 29 km above sea level. Whole genome-based phylogenies of three strains, paired with plant challenge assays, indicate that each is a previously unrecognized species and causes disease on beans comparable to Curtobacterium flaccumfaciens . Isolates from the stratosphere (strain L6-1) and agricultural millet (G77) were identified to be the same species and designated as Curtobacterium aetherium sp. nov. C. aetherium displays high levels of tolerance to desiccation and UV radiation, which are stresses that increase in intensity with altitude. Back trajectory air mass analysis implied that the phytopathogens may have had an intercontinental source, but regional origins in the continental US cannot be excluded. The environmentally robust phytopathogens we have documented in the upper atmosphere provide new perspective on the role that high-altitude transport may play in microbial dispersal, gene flow, and the epidemiology of aerially dispersed plant disease. IMPORTANCE Enormous quantities and varieties of microorganisms are continually aerosolized and transported in the atmosphere, yet there is a limited understanding of the consequences to downwind ecosystems. While studying bacteria that survive extreme conditions at altitudes up to 29 km in the atmosphere, we discovered new species that have the capacity to cause disease in agriculturally relevant bean varieties. The hardiest isolate we characterized from the stratosphere is a member of the same species as an isolate from an agricultural source, which we have designated Curtobacterium aetherium . C. aetherium is a phytopathogen capable of enduring high-altitude and long-distance atmospheric transport while also possessing the potential to opportunistically infect crops in deposition locations.

Abstract Numerous bacteria in the human gut microbiome remain unknown and/or have yet to be cultured. While collections of human gut bacteria have been published, few strains are accessible to the scientific community. We have therefore created a publicly available collection of bacterial strains isolated from the human gut. The Human intestinal Bacteria Collection (HiBC) ( https://www.hibc.rwth-aachen.de ) contains 340 strains representing 198 species within 29 families and 7 phyla, of which 29 previously unknown species are taxonomically described and named. These included two butyrate-producing species of Faecalibacterium and new dominant species associated with health and inflammatory bowel disease, Ruminococcoides intestinale and Blautia intestinihominis , respectively. Plasmids were prolific within the HiBC isolates, with almost half (46%) of strains containing plasmids, with a maximum of six within a strain. This included a broadly occurring plasmid (pBAC) that exists in three diverse forms across Bacteroidales species. Megaplasmids were identified within two strains, the pMMCAT megaplasmid is globally present within multiple Bacteroidales species. This collection of easily searchable and publicly available gut bacterial isolates will facilitate functional studies of the gut microbiome.

Abstract Defining the minimal genetic requirements for cellular life remains a fundamental question in biology. Genomic exploration continually reveals novel microbial lineages, often exhibiting extreme genome reduction, particularly within symbiotic relationships. Here, we report the discovery ofCandidatusSukunaarchaeum mirabile, a novel archaeon with an unprecedentedly small genome of only 238 kbp —less than half the size of the smallest previously known archaeal genome— from a dinoflagellate-associated microbial community. Phylogenetic analyses place Sukunaarchaeum as a deeply branching lineage within the tree of Archaea, representing a novel major branch distinct from established phyla. Environmental sequence data indicate that sequences closely related to Sukunaarchaeum form a diverse and previously overlooked clade in microbial surveys. Its genome is profoundly stripped-down, lacking virtually all recognizable metabolic pathways, and primarily encoding the machinery for its replicative core: DNA replication, transcription, and translation. This suggests an unprecedented level of metabolic dependence on a host, a condition that challenges the functional distinctions between minimal cellular life and viruses. The discovery of Sukunaarchaeum pushes the conventional boundaries of cellular life and highlights the vast unexplored biological novelty within microbial interactions, suggesting that further exploration of symbiotic systems may reveal even more extraordinary life forms, reshaping our understanding of cellular evolution. Graphical Abstract

Diaphorina citri (Hemiptera: Liviidae) is the main vector for the bacterium ‘ Candidatus Liberibacter asiaticus’, which is associated with citrus greening, also known as Huanglongbing. D. citri transmits ‘ Ca. L. asiaticus’ during its feeding on citrus phloem sap. Transmission occurs in a circulative, propagative, and persistent manner. ‘ Ca. L. asiaticus’ has a small genome (1.2 Mb). Therefore, it acquires most of its nutrients and energetic nucleotides from its hosts. The objective of this study was to assess the effect of ‘ Ca. L. asiaticus’ infection on the level of the free fatty acids in its vector. The fatty acids were extracted from adult D. citri using ethyl acetate, derivatized with boron trifluoride-methanol, and analyzed using gas chromatography-mass spectrometry. Nine fatty acids were identified in the D. citri extracts. Oleic acid was the most predominant fatty acid, followed by stearic and palmitic acid, whereas the rest of the fatty acids were present in low amounts. In general, the levels of the detected fatty acids in ‘ Ca. L. asiaticus’-infected D. citri were lower than those found in healthy psyllids. Our findings showed that the reduction of fatty acids in ‘ Ca. L. asiaticus’-infected psyllids resulted from the higher activity of β-oxidation to generate acetyl-coenzyme A, which causes more production of ATP. Our results indicated that ‘ Ca. L. asiaticus’ may enhance the β-oxidation of fatty acids in its vector insect to fulfill its nutrient and energetic nucleotide requirements.

Citrus Huanglongbing, caused by ‘ Candidatus Liberibacter asiaticus’ (CLas), is the most devastating citrus disease worldwide. The CLas genome is much smaller than those of its relatives, such as Sinorhizobium meliloti, due to its reductive evolution. Because CLas has not been cultured in artificial media, despite some progress in co-cultivating, and because genetic manipulation of CLas remains impossible, the understanding of CLas biology is very limited. Usually, 10% of total genes in bacteria are regulatory genes, but only 2% of CLas genes encode transcriptional factors. Here, 20 transcriptional regulators were predicted, including nine genes ( lsrB, ldtR, rem, visR, visN, ctrA, mucR, pelD, and atoC) directly or indirectly involved in regulating motility, and five genes ( rpoH, prbP, phrR, rirA, and lsrB) involved in oxidative stress response. We demonstrated that rem, lsrB, and visNR of CLas can complement the corresponding mutants of S. meliloti in their reduced motility. We further investigated traits controlled by Rem in S. meliloti and CLas using RNA sequencing analyses of rem mutant versus complementation strains with remSmc or remLas. Transcriptomic analysis showed that RemLas significantly regulates the expression of genes in S. meliloti, which was used to infer its regulation of CLas genes by identification of homologous genes. We found that Rem is involved in regulating motility, chemotaxis, transporters, and oxidative phosphorylation in S. meliloti and regulating flagellar and transporter genes in CLas. Among the 39 putative RemLas-regulated genes in CLas, 16 contain the Rem-binding motif, including 10 genes involved in flagellar assembly. Taken together, this study offers valuable insights regarding CLas regulatory genes, with many of them involved in regulating motility and oxidative stress response. The regulation of flagellar genes by Rem in CLas unravels critical information regarding motility in CLas infection of hosts.