Publications

3867

AbstractNitrogen (N2) fixation in oligotrophic surface waters is the main source of new nitrogen to the ocean1 and has a key role in fuelling the biological carbon pump2. Oceanic N2 fixation has been attributed almost exclusively to cyanobacteria, even though genes encoding nitrogenase, the enzyme that fixes N2 into ammonia, are widespread among marine bacteria and archaea3–5. Little is known about these non-cyanobacterial N2 fixers, and direct proof that they can fix nitrogen in the ocean has so far been lacking. Here we report the discovery of a non-cyanobacterial N2-fixing symbiont, ‘Candidatus Tectiglobus diatomicola’, which provides its diatom host with fixed nitrogen in return for photosynthetic carbon. The N2-fixing symbiont belongs to the order Rhizobiales and its association with a unicellular diatom expands the known hosts for this order beyond the well-known N2-fixing rhizobia–legume symbioses on land6. Our results show that the rhizobia–diatom symbioses can contribute as much fixed nitrogen as can cyanobacterial N2 fixers in the tropical North Atlantic, and that they might be responsible for N2 fixation in the vast regions of the ocean in which cyanobacteria are too rare to account for the measured rates.

A Gram-stain-positive, rod-shaped, aerobic, motile bacterium, J379T, was isolated from radioactive water spring C1, located in a former silver–uranium mine in the Czech Republic. This slow-growing strain exhibited optimal growth at 24–28 °C on solid media with <1 % salt concentration and alkaline pH 8–10. The only respiratory quinone found in strain J379T was MK-7(H4). C18 : 1 ω9c (60.9 %), C18 : 0 (9.4 %), C16 : 0 and alcohol-C18 : 0 (both 6.2 %) were found to be the major fatty acids. The peptidoglycan contained directly cross-linked meso-diaminopimelic acid. Phylogenetic reconstruction based on the 16S rRNA gene sequences and the core-genome analysis revealed that strain J379T forms a separate phylogenetic lineage within the recently amended order Solirubrobacterales. A comparison of the 16S rRNA gene sequences between strain J379T and other members of the order Solirubrobacterales showed <96 % similarity. This analysis revealed that the closest type strains were Parviterribacter kavangonensis D16/0 /H6T (95.2 %), Capillimicrobium parvum 0166_1T (94.9 %) and Conexibacter arvalis KV-962T (94.5 %). Whole-genome analysis showed that the closest type strain was Baekduia soli BR7-21T with an average nucleotide identity of 78 %, average amino acid identity of 63.2 % and percentage of conserved proteins of 48.2 %. The G+C content of the J379T genomic DNA was 71.7 mol%. Based on the phylogenetic and phylogenomic data, as well as its physiological characteristics, strain J379T is proposed to represent a type strain (DSM 113746T=CCM 9300T) of Svornostia abyssi gen. nov. sp. nov. within the family Baekduiaceae.

Numerous bacteria in the human gut microbiome remains unknown and/or have yet to be cultured. While collections of human gut bacteria have been published, none are publicly accessible. This is partly due to issues with the deposition of strains to public culture collections. We address these key issues (microbial unknowns, lack of public access to isolates) by proposing a framework that facilitates large-scale submission of isolates, exemplified by a rich collection of human gut isolates that is taxonomically described, functionally novel, and made publicly available. An innovative bulk strain submission system was established by large-scale generation and curation of persistent strain identifiers (https://straininfo.dsmz.de). This was used to create the Human intestinal Bacterial Collection (www.hibc.rwth-aachen.de), which contains 340 strains representing 198 species within 29 families and 7 phyla, of which 32 previously unknown taxa are taxonomically described and named. These included three butyrate-producing species of Faecalibacterium and new dominant species associated with health and inflammatory bowel disease. Plasmids were identified to be prolific within the HiBC isolates, with almost half (46%) of strains containing one or more plasmids (up to 6). Megaplasmids were identified within two strains, one of them is globally present within multiple Bacteroidales species. The strain submission framework and public collection of easily searchable and available gut bacterial isolates presented here will facilitate the work of many by enabling functional studies.

A genome-based polyphasic approach was used to determine the taxonomic status of two novel bacterial strains, SCSIO 12594T and SCSIO 12813T, isolated from tissues of a coral. Both strains were Gram-stain-negative and facultatively anaerobic. The genome sizes of strains SCSIO 12594T and SCSIO 12813T were 3.9 Mb and 4.1 Mb, respectively, and they possessed DNA G+C contents of 55.1 and 46.2 mol%, respectively . Both strains were found to be catalase- and oxidase-positive, while SCSIO 12594T also could hydrolyse starch. SCSIO 12594T was observed to grow at between 20 and 37 °C (optimally at 25 °C) and at a pH range from 6 to 7 and in the presence of 3–7 % (w/v) NaCl. The growth of SCSIO 12813T required seawater and occurred at 20–30 °C (optimum, 25 °C), pH 5–8 (optimum, pH 6–7) and in the presence of 3–3.7 % (w/v) NaCl. The results of 16S rRNA gene-based phylogenetic analysis indicated that SCSIO 12594T shared 92.97 % or less sequence similarity with its closest relatives Rhodobium gokarnense JA173T and other members of the order Hyphomicrobiales. The results of 16S rRNA sequences-based phylogenetic analysis of SCSIO 12813T indicated that Croceimicrobium hydrocarbonivorans A20-9T (89.34 %) was the most closely related species. SCSIO 12594T and SCSIO 12813T can be readily separated from their closest relatives, as indicated by the results of phylogenomic analysis, low average nucleotide indexes, average amino acid identity, digital DNA–DNA hybridisation (dDDH) similarities and associated phenotypic and chemical data. Consequently, the two coral isolates are considered to represent two novel genera and species for which the names Coralliovum pocilloporae gen. nov., sp. nov. and Sanyastnella coralliicola gen. nov., sp. nov. are proposed, the type strains are SCSIO 12594T (= JCM 35320T = GDMCC 1.3060T) and SCSIO 12813T (= JCM 35373T = GDMCC 1.3063T), respectively. In addition, two novel families, Coralliovaceae fam. nov. and Sanyastnellaceae fam. nov are proposed to accommodate Coralliovum pocilloporae gen. nov., sp. nov. and Sanyastnella coralliicola gen. nov., sp. nov., respectively.

Terrestrial cyanobacteria are extremely diverse. In urban areas, they can be found as black stains on the surface of building walls, stone monuments, or man-made structures. Many of the terrestrial cyanobacteria are still understudied. To expand knowledge of terrestrial cyanobacterial diversity, a polyphasic characterization was performed to identify 12 strains isolated from campus of University of the Ryukyus, Okinawa, Japan. Multigene phylogenetic analyses based on 16S rRNA gene and 16S-23S rRNA internal transcribed spacer (ITS) region showed that the isolated strains formed two independent subclades within Nodosilinea, and were distantly related to all described Nodosilinea species. The 16S-23S rRNA ITS secondary structures showed variations for D1-D1′ and Box B domain, while V3 domain was almost identical among entire species of Nodosilinea, including the studied strains. In addition, a unique morphological character, i.e. forming nodule or spiral shape, was also observed in certain studied strains. According to polyphasic characterization, Nodosilinea coculeatus sp. nov. and Nodosilinea terrestrialis sp. nov., were proposed as two new species of terrestrial cyanobacteria from Okinawa.

AbstractThe Asian citrus psyllid, Diaphorina citri, is the primary vector of the HLB pathogen, Candidatus Liberibacter asiaticus (CLas). The acquisition of CLas shortens the developmental period of nymphs, accelerating the emergence into adulthood and thereby facilitating the spread of CLas. Cuticular proteins (CPs) are involved in insect emergence. In this study, we investigated the molecular mechanisms underlying CLas‐promoted emergence in D. citri via CP mediation. Here, a total of 159 CP genes were first identified in the D. citri genome. Chromosomal location analysis revealed an uneven distribution of these CP genes across the 13 D. citri chromosomes. Proteomic analysis identified 54 differentially expressed CPs during D. citri emergence, with 14 CPs exhibiting significant differential expression after CLas acquisition. Five key genes, Dc18aa‐1, Dc18aa‐2, DcCPR‐24, DcCPR‐38 and DcCPR‐58, were screened from the proteome and CLas acquisition. The silencing of these 5 genes through a modified feeding method significantly reduced the emergence rate and caused various abnormal phenotypes, indicating the crucial role that these genes play in D. citri emergence. This study provides a comprehensive overview of the role of CPs in D. citri and reveals that CLas can influence the emergence process of D. citri by regulating the expression of CPs. These key CPs may serve as potential targets for future research on controlling huanglongbing (HLB) transmission.

Metcalfa pruinosa (Say, 1830) - новий інвазивний шкідник Humulus lupulus L., який заселяє 130 видів рослин у Києві. Крім того, він є переносником Candidatus Phytoplasma asteris, який інфікує H. lupulus. З огляду на це, ми проаналізували та порівняли літературні дані щодо хазяїв M. pruinosa у Києві та Ca. P. asteris загалом. В результаті ми виявили 13 їхніх спільних рослин-хазяїв: Acer negundo L., Citrus limon (L.) Osbeck, Corylus avellana L., Fraxinus excelsior L., H. lupulus, Musa acuminata Colla, Prunus cerasus L., Prunus domestica L., Rosa canina L., Sonchus oleraceus L., Tilia cordata Mill., Trifolium pratense L., Vitis vinifera L. У подальших дослідженнях слід оцінити інфікованість цих хазяїв Ca. P. asteris.

Diaphorina citri serves as the primary vector for ‘ Candidatus Liberibacter asiaticus’ ( C Las), the bacterium associated with the severe Asian form of huanglongbing. C Las-positive D. citri are more fecund than their C Las-negative counterparts and require extra energy expenditure. Therefore, understanding the molecular mechanisms linking metabolism and reproduction is of particular importance. In this study, we found adipokinetic hormone ( DcAKH ) and its receptor ( DcAKHR ) were essential for increasing lipid metabolism and fecundity in response to C Las infection in D. citri. Knockdown of DcAKH and DcAKHR not only resulted in the accumulation of triacylglycerol and a decline of glycogen, but also significantly decreased fecundity and C Las titer in ovaries. Combined in vivo and in vitro experiments showed that miR-34 suppresses DcAKHR expression by binding to its 3’ untranslated region, whilst overexpression of miR-34 resulted in a decline of DcAKHR expression and C Las titer in ovaries and caused defects that mimicked DcAKHR knockdown phenotypes. Additionally, knockdown of DcAKH and DcAKHR significantly reduced juvenile hormone (JH) titer and JH signaling pathway genes in fat bodies and ovaries, including the JH receptor, methoprene-tolerant ( DcMet ), and the transcription factor, Krüppel homolog 1 (DcKr-h1) , that acts downstream of it, as well as the egg development related genes vitellogenin 1-like ( DcVg-1-like ), vitellogenin A1-like ( DcVg-A1-like ) and the vitellogenin receptor ( DcVgR ). As a result, C Las hijacks AKH/AKHR-miR-34-JH signaling to improve D. citri lipid metabolism and fecundity, while simultaneously increasing the replication of C Las, suggesting a mutualistic interaction between C Las and D. citri ovaries.