Publications

4479

AbstractCyanobacteria exhibit a vast diversity from polar to tropical environments. Though much work has been done on elucidating their biodiversity, knowledge on the occurrence, diversity and toxicity of benthic cyanobacteria is limited when compared to the planktonic forms. Integrating molecular techniques with ecological and morphological analyses has become essential in untangling cyanobacterial diversity, particularly for benthic taxa such as the cryptic “Lyngbya.” Molecular markers such as the 16S rRNA gene and whole genome sequencing have significantly improved the taxonomy of cyanobacteria. Building on these advancements, this study characterizes benthic cyanobacterial isolates from various locations in Florida, USA, and Orange Walk, Belize, resulting in the identification of a novel genus, Floridanema, and four new species (F. aerugineum, F. evergladense, F. flaviceps, and F. fluviatile). This new genus commonly occurs in canals, ponds, lakes and rivers. By integrating ecological, morphological, and genomic analyses, this study provides support for the family Aerosakkonemataceae and the establishment of the order Aerosakkonematales. The LC–MS data revealed that Floridanema strains do not produce microcystins, nodularin‐R, or anabaenopeptins.

A Gram-stain-negative, aerobic and rod-shaped bacterium, designated as HZG-20T, was isolated from a tidal flat in Zhoushan, Zhejiang Province, China. The 16S rRNA sequence similarities between strain HZG-20T and Pikeienuella piscinae RR4-56T, Coraliihabitans acroporae NNCM2T, Parvibaculum indicum P31T and Zhengella mangrovi X9-2-2T were 98.9, 91.7, 91.0 and 91.0%, respectively. Colonies of strain HZG-20T were 1.4 mm in diameter, milky white, round, smooth and convex after cultivating on marine agar at 30 °C for 48 h. Cells were catalase and oxidase-negative. Growth occurred at 15–37 ℃ (optimum, 28 ℃), pH 5.0–9.0 (optimum, pH 6.0–8.0) and with 0–8% (w/v) NaCl (optimum, 1–3%). It contained Menaquinone-8 (H2) as the sole respiratory quinone, and C16:0 (11.8–13.6%), C18:1  ω9c (6.8–13.3%) and C15:0 anteiso (10.9–27.7%) as the major cellular fatty acids. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid, one unidentified phosphoglycolipid, two unidentified glycolipids (GL1–GL2) and three unidentified lipids (L1–L3). The genome of strain HZG-20T was 3 835 886 bp in length, comprised 3746 protein-coding genes, with DNA G+C content of 67.1 mol%. The phylogenetic and phylogenomic trees indicated that strain HZG-20T formed an independent and stable clade with P. piscinae RR4-56T. However, the average nucleotide identity, digit DNA–DNA hybridization and average amino acid identity values between strain HZG-20T and P. piscinae RR4-56T, C. acroporae NNCM2T, P. indicum P31T and Z. mangrovi X9-2-2T were 81.6, 71.1, 68.7 and 69.5%; 23.0, 18.5, 17.9 and 17.5%; and 78.2, 56.8, 56.5 and 61.9%, respectively, together with distinct chemotaxonomic features, indicating strain HZG-20T should not be assigned to known genera. As a result, a novel species of a novel genus within the family Paracoccaceae, designated as Paludibacillus litoralis gen. nov., sp. nov., was proposed. The type strain is HZG-20T (MCCC 1K08468T=KCTC 82692T).

AbstractThis study reports the draft genome ofCandidatusPhytoplasma pyri strain P1, isolated from Argentina, marking the first global sequencing of this species. The genome assembly consisted of 16 contigs, with a total length of 575,431 bp, a GC content of 20.35%, and 125X coverage. A total of 536 genes were annotated, including those related to metabolism, genetic information processing, and signaling. Phylogenetic analysis placed ‘CandidatusPhytoplasma pyri’ within the 16SrX group, supporting its classification as a distinct species from ‘CandidatusPhytoplasma mali’ and ‘CandidatusPhytoplasma prunorum’, despite their close evolutionary proximity. The investigation also identified 17 secreted proteins, including homologs of known effectors such as SAP39 and SAP41, as well as conserved proteins associated with virulence mechanisms. A homologue of the Imp immunodominant membrane protein was also characterized, revealing conserved gene organization across related strains. These findings contribute to the understanding of ‘CandidatusPhytoplasma pyri’ pathogenic and provide valuable genomic data for future research. This study highlights the importance of expanding phytoplasma genomics, as it provides a crucial first step in understanding ‘CandidatusPhytoplasma pyri’ and its role in plant pathology

This article describes a new genus and species of cyanobacteria isolated from Laguna Pastos Grandes in the Bolivian Altiplano. This discovery marks the first described species of this phylum from this extreme environment. Additionally, the phylogenetic status of the genus Capilliphycus is reassessed. The analyses are based on 16S rRNA gene maximum likelihood and Bayesian phylogenies, identity (p-distance), morphology and habitat comparisons. The new genus is a Lyngbya-like type from a mat at the margin of a brackish–alkaline lake with borax. It is phylogenetically close to Dapis, Tenebriella and Okeania, but compared to these genera, the maximum 16S rRNA gene identity values reached only 90.9%, 91.1% and 92.5%, respectively. The genus Capilliphycus was found to be polyphyletic. The type species Capilliphycus salinus is clustered with C. guerandensis. However, “C. tropicalis” and “C. flaviceps” form a distinct clade, distant from the Capilliphycus type species. Between the two “Capilliphycus” clades, Sirenicapillaria and Limnoraphis are found.

Abstract The CHAB-I-5 cluster is a pelagic lineage that can comprise a significant proportion of all Roseobacters in surface oceans and has predicted roles in biogeochemical cycling via heterotrophy, aerobic anoxygenic photosynthesis (AAnP), CO oxidation, DMSP degradation, and other metabolisms. Though cultures of CHAB-I-5 have been reported, none have been explored and the best-known representative, strain SB2, was lost from culture after obtaining the genome sequence. We have isolated two new CHAB-I-5 representatives, strains US3C007 and FZCC0083, and assembled complete, circularized genomes with 98.7% and 92.5% average nucleotide identities with the SB2 genome. Comparison of these three with 49 other unique CHAB-I-5 metagenome-assembled and single-cell genomes indicated that the cluster represents a genus with two species, and we identified subtle differences in genomic content between the two species subclusters. Metagenomic recruitment from over fourteen hundred samples expanded their known global distribution and highlighted both isolated strains as representative members of the clade. FZCC0083 grew over twice as fast as US3C007 and over a wider range of temperatures. The axenic culture of US3C007 occurs as pleomorphic cells with most exhibiting a coccobacillus/vibrioid shape. We propose the name Candidatus Thalassovivens spotae, gen nov., sp. nov. for the type strain US3C007T (= ATCC TSD-433T = NCMA B160T).

Abstract Candidatus Patescibacteria is a diverse bacterial phylum that is notable for members with ultrasmall cell size, reduced genomes, limited metabolic capabilities, and dependence on other prokaryotic hosts. Despite the prevalence of the name Ca. Patescibacteria in the scientific literature, it is not officially recognized under the International Code of Nomenclature of Prokaryotes and lacks a nomenclatural type. Here, we rectify this situation by describing two closely related circular metagenome-assembled genomes and by proposing one of them (ABY1TS) to serve as the nomenclatural type for the species Patescibacterium danicumTS gen. nov., sp. nov. according to the rules of the SeqCode. Rank-normalized phylogenomic inference confirmed the stable placement of P. danicumTS in the Ca. Patescibacteria class ABY1. Based on these results, we propose Patescibacterium gen. nov. to serve as the type genus for associated higher taxa, including the phylum Patescibacteriota phyl. nov. We complement our proposal with a genomic characterization, metabolic reconstruction, and biogeographical analysis of Patescibacterium. Our results confirm small genome sizes (<1 Mbp), low GC content (>36%), and the occurrence of long gene coding insertions in the 23S rRNA sequences, along with reduced metabolic potential, inferred symbiotic lifestyle, and a global distribution. In summary, our proposal will provide nomenclatural stability to the fourth-largest phylum in the bacterial domain.