Filling the gaps: missing taxon names at the ranks of class, order and family

Novel metagenomics analysis of stony coral tissue loss disease

Stony coral tissue loss disease (SCTLD) has devastated coral reefs off the coast of Florida and continues to spread throughout the Caribbean. Although a number of bacterial taxa have consistently been associated with SCTLD, no pathogen has been definitively implicated in the etiology of SCTLD. Previous studies have predominantly focused on the prokaryotic community through 16S rRNA sequencing of healthy and affected tissues. Here, we provide a different analytical approach by applying a bioinformatics pipeline to publicly available metagenomic sequencing samples of SCTLD lesions and healthy tissues from four stony coral species. To compensate for the lack of coral reference genomes, we used data from apparently healthy coral samples to approximate a host genome and healthy microbiome reference. These reads were then used as a reference to which we matched and removed reads from diseased lesion tissue samples, and the remaining reads associated only with disease lesions were taxonomically classified at the DNA and protein levels. For DNA classifications, we used a pathogen identification protocol originally designed to identify pathogens in human tissue samples, and for protein classifications, we used a fast protein sequence aligner. To assess the utility of our pipeline, a species-level analysis of a candidate genus, Vibrio, was used to demonstrate the pipeline's effectiveness. Our approach revealed both complementary and unique coral microbiome members compared to a prior metagenome analysis of the same dataset.

Isolation and Characterization of Paracoccus maritimus sp. nov., from Intertidal Sediment

A novel Paracoccus-related strain, designated YLB-12T, was isolated from a sediment sample from the tidal zone of Shapowei Port, Xiamen, Fujian Province, PR China. The novel strain is a Gram-stain-negative, short, rod-shaped, nonmotile, catalase- and oxidase-positive strain that grows at 10-37 °C and pH 5.0-9.0 in the presence of 0-12.0% (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain belongs to the genus Paracoccus and that its highest sequence similarity was to Paracoccus homiensis DD-R11T (98.5%), followed by Paracoccus zeaxanthinifaciens ATCC 21588T (97.4%), Paracoccus rhizosphaerae LMG 26205T (97.2%), Paracoccus beibuensis CGMCC 1.7295T (97.1%) and Paracoccus halotolerans CFH 90064T (97.0%). The DNA‒DNA hybridization values between strain YLB-12T and the five closely related type strains ranged from 20.4 to 22.4%. The genomic G+C content of strain YLB-12T was 63.7%. In addition to diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol, the polar lipids of the strain YLB-12T also consisted of an unidentified glycolipid and four unidentified polar lipids. The cells contained summed feature 8 (C18: 1ω6c /C18: 1ω7c, 62.7%) as the major cellular fatty acid and ubiquinone-10 as the predominant menaquinone. On the basis of its phenotypic and genotypic characteristics, strain YLB-12T represents a novel species within the genus Paracoccus, for which the name Paracoccus maritimus sp. nov. is proposed. The type strain was YLB-12T (= MCCC 1A17213T = KCTC 82197T).

Streptomyces herbicida sp. nov., a novel actinomycete with antibacterial and herbicidal activity isolated from soil

A novel actinobacterial strain (NEAU-HV9T) showing antibacterial activity against Ralstonia solanacearum and herbicidal activity against Amaranthus retroflexus L. was isolated from soil sampled in Bama yao Autonomous County, Hechi City, Guangxi Zhuang Autonomous Region. The strain is aerobic and Gram-positive. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NEAU-HV9T belonged to the genus Streptomyces and showed high 16S rRNA sequence similarity to Streptomyces panaciradicis 1MR-8T (98.90 %), Streptomyces sasae JR-39T (98.89 %) and Streptomyces barringtoniae JA03T (98.69 %) and less than 98.5 % similarity to other members of the genus Streptomyces. The cell wall of strain NEAU-HV9T contained ll-diaminopimelic acid and the whole-cell hydrolysates were galactose, mannose and ribose. The predominant menaquinones were composed of MK-9(H2) and MK-9(H8). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. The major fatty acids were C16 : 0, iso-C16 : 0 and C17 : 1  ω8c. The genomic DNA G+C content of strain NEAU-HV9T was 70.6 mol%. Furthermore, the strain could be clearly distinguished from its closely related type strains by the combination of DNA-DNA hybridization results and some phenotypic characteristics. Meanwhile, strain NEAU-HV9T displayed herbicidal activity. Therefore, strain NEAU-HV9T represents a novel species within the genus Streptomyces, for which the name Streptomyces herbicida sp. nov. is proposed, with strain NEAU-HV9T (=CCTCC AA 2019088T=DSM 113364T) as the type strain.

Kitasatospora fiedleri sp. nov., a novel antibiotic-producing member of the genus Kitasatospora

Strain TÜ4103T was originally sampled from Java, Indonesia and deposited in the Tübingen strain collection under the name 'Streptomyces sp.'. The strain was found to be an antibiotic producer as strain TÜ4103T showed bioactivity against Gram-positive bacteria, such as Bacillus subtilis and Kocuria rhizophila in bioassays. Strain TÜ4103T showed 16S rRNA gene sequence similarity of 99.65 % to Kitasatospora cheerisanensis DSM 101999T and 98.82 % to Kitasatospora niigatensis DSM 44781T and Kitasatospora cineracea DSM 44780T. Genome-based phylogenetic analysis revealed that strain TÜ4103T is closely related to K. cineracea DSM 44780T and K. niigatensis DSM 44781T. The digital DNA-DNA hybridization values between the genome sequences of strain TÜ4103T and its closest phylogenomic relatives, strains DSM 44780T and DSM 44781T, were 43.0 and 42.9 %, respectively. Average nucleotide identity (ANI) values support this claim, with the highest ANI score of 91.14 % between TÜ4103T and K. niigatensis being closely followed by an ANI value of 91.10 % between K. cineracea and TÜ4103T. The genome of TÜ4103T has a size of 7.91 Mb with a G+C content of 74.05 mol%. Whole-cell hydrolysates of strain TÜ4103T are rich in meso-diaminopimelic acid, and rhamnose, galactose and mannose are characteristic as whole-cell sugars. The phospholipid profile contains phosphatidylethanolamine, diphosphatidylglycerol and glycophospholipid. The predominant menaquinones (>93.5 %) are MK-9(H8) and MK-9(H6). Based on the phenotypic, genotypic and genomic characteristics, strain TÜ4103T (=DSM 114396T=CECT 30712T) merits recognition as the type strain of a novel species of the genus Kitasatospora, for which the name Kitasatospora fiedleri sp. nov. is proposed.

Phylotaxonomic assessment based on four core gene sets and proposal of a genus definition among the families Paracoccaceae and Roseobacteraceae

The families Paracoccaceae and Roseobacteraceae comprise metabolically, phenotypically and genotypically diverse members, and their descriptions rely heavily on 16S rRNA gene analysis. Hundreds of genera have been reported within the two families and misclassifications have been a reoccurring problem, even when the taxonomies have been established based on genome-scale phylogenetic reconstructions. In this study, we conducted a comprehensive phylotaxonomic assessment of the families Paracoccaceae and Roseobacteraceae based on four ubiquitous gene sets, bac120 (120 genes in Bacteria), rhodo268 (268 genes in ‘ Rhodobacteraceae ’, defined in this study), rp1 (16 ribosomal protein genes in Prokaryote) and rp2 (23 ribosomal protein genes in Prokaryote), using two tree-inferring applications and two approaches (supermatrix and consensus). The results suggested that the four supermatrix trees based on bac120 and rhodo268 shared a high proportion of common nodes (>88.4 %) and the topology was reproducible among all the trees within most of the genera. The evolutionary distance (ED) analysis showed significant overlapping between the intergeneric and intrageneric comparisons, implying that the proposal of some genera seemed to be unnecessary. In addition, the bac120 gene set and the FastTree program were found to be the most cost-effective way to conduct phylogenomic analysis of the families Paracoccaceae and Roseobacteraceae . An ED threshold of 0.21–0.23 based on either bac120 or rhodo268 was proposed as one standard for later genus delimitation in these families. A comprehensive phylogenetic framework is presented in this study and the proposed genus definition will help to establish a more reasonable taxonomy in the families Paracoccaceae and Roseobacteraceae .

Methylacidiphilum caldifontis gen. nov., sp. nov., a thermoacidophilic methane-oxidizing bacterium from an acidic geothermal environment, and descriptions of the family Methylacidiphilaceae fam. nov. and order Methylacidiphilales ord. nov

Strain IT6T, a thermoacidophilic and facultative methane-oxidizing bacterium, was isolated from a mud-water mixture collected from Pisciarelli hot spring in Pozzuoli, Italy. The novel strain is white when grown in liquid or solid media and forms Gram-negative rod-shaped, non-flagellated, non-motile cells. It conserves energy by aerobically oxidizing methane and hydrogen while deriving carbon from carbon dioxide fixation. Strain IT6T had three complete pmoCAB operons encoding particulate methane monooxygenase and genes encoding group 1d and 3b [NiFe] hydrogenases. Simple carbon-carbon substrates such as ethanol, 2-propanol, acetone, acetol and propane-1,2-diol were used as alternative electron donors and carbon sources. Optimal growth occurred at 50-55°C and between pH 2.0-3.0. The major fatty acids were C18 : 0, C15 : 0 anteiso, C14 : 0 iso, C16 : 0 and C14 : 0, and the main polar lipids were phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol, diphosphatidylglycerol, some unidentified phospholipids and glycolipids, and other unknown polar lipids. Strain IT6T has a genome size of 2.19 Mbp and a G+C content of 40.70 mol%. Relative evolutionary divergence using 120 conserved single-copy marker genes (bac120) and phylogenetic analyses based on bac120 and 16S rRNA gene sequences showed that strain IT6T is affiliated with members of the proposed order 'Methylacidiphilales' of the class Verrucomicrobiia in the phylum Verrucomicrobiota. It shared a 16S rRNA gene sequence identity of >96 % with cultivated isolates in the genus 'Methylacidiphilum' of the family 'Methylacidiphilaceae', which are thermoacidophilic methane-oxidizing bacteria. 'Methylacidiphilum sp.' Phi (100 %), 'Methylacidiphilum infernorum' V4 (99.02 %) and 'Methylacidiphilum sp.' RTK17.1 (99.02 %) were its closest relatives. Its physiological and genomic properties were consistent with those of other isolated 'Methylacidiphilum' species. Based on these results, we propose the name Methylacidiphilum caldifontis gen. nov., sp. nov. to accommodate strain IT6T (=KCTC 92103T=JCM 39288T). We also formally propose that the names Methylacidiphilaceae fam. nov. and Methylacidiphilales ord. nov. to accommodate the genus Methylacidiphilum gen. nov.

Biosynthetic gene profiling and genomic potential of the novel photosynthetic marine bacterium Roseibaca domitiana

Shifting the bioprospecting targets toward underexplored bacterial groups combined with genome mining studies contributes to avoiding the rediscovery of known compounds by revealing novel, promising biosynthetic gene clusters (BGCs). With the aim of determining the biosynthetic potential of a novel marine bacterium, strain V10T, isolated from the Domitian littoral in Italy, a comparative phylogenomic mining study was performed across related photosynthetic bacterial groups from an evolutionary perspective. Studies on polyphasic and taxogenomics showed that this bacterium constitutes a new species, designated Roseibaca domitiana sp. nov. To date, this genus has only one other validly described species, which was isolated from a hypersaline Antarctic lake. The genomic evolutionary study linked to BGC diversity revealed that there is a close relationship between the phylogenetic distance of the members of the photosynthetic genera Roseibaca, Roseinatronobacter, and Rhodobaca and their BGC profiles, whose conservation pattern allows discriminating between these genera. On the contrary, the rest of the species related to Roseibaca domitiana exhibited an individual species pattern unrelated to genome size or source of isolation. This study showed that photosynthetic strains possess a streamlined content of BGCs, of which 94.34% of the clusters with biotechnological interest (NRPS, PKS, RRE, and RiPP) are completely new. Among these stand out T1PKS, exclusive of R. domitiana V10T, and RRE, highly conserved only in R. domitiana V10T and R. ekhonensis, both categories of BGCs involved in the synthesis of plant growth-promoting compounds and antitumoral compounds, respectively. In all cases, with very low homology with already patented molecules. Our findings reveal the high biosynthetic potential of infrequently cultured bacterial groups, suggesting the need to redirect attention to microbial minorities as a novel and vast source of bioactive compounds still to be exploited.

Pseudophaeobacter profundi sp. nov., isolated from the Western Pacific Ocean

A novel Gram-stain-negative, facultatively anaerobic and heterotrophic bacterium, designated strain ZH257T, was isolated from in situ enrichment samples incubated on the seamount floor of the Western Pacific Ocean. Cells were rod-shaped, oxidase- and catalase- positive, and motile by means of polar flagella. Strain ZH257T grew at 4-37 °C (optimum, 28-32 °C), pH 6.0-9.0 (optimum, pH 7.0) and with 2.0-9.0 % (w/v) NaCl (optimum, 3.0-4.0 %). Strain ZH257T was most closely related to members of the genus Pseudophaeobacter, sharing 99.13, 98.27 and 96.89 % 16S rRNA gene sequence identities with Pseudophaeobacter flagellatus GDMCC 1.2988T, Pseudophaeobacter arcticus DSM 23566T and Pseudophaeobacter leonis DSM 25627T, respectively. The DNA G+C content was 59.2 mol%. The estimated average nucleotide identity and digital DNA-DNA hybridization values between strain ZH257T and its closely related species were 79.61-93.04 % and 23.10-50.20 %, respectively. Strain ZH257T harboured complete denitrification and nitrate assimilation pathways. Strain ZH257T contained summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) as major fatty acids (>5 %), and Q-10 as the major respiratory quinone. The polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and four unidentified lipids. The combined phenotypic, genotypic and chemotaxonomic data showed that strain ZH257T represents a novel species of the genus Pseudophaeobacter, for which the name Pseudophaeobacter profundi sp. nov. is proposed, with the type strain ZH257T (=MCCC M29024T=KACC 23147T).

Gymnodinialimonas phycosphaerae sp. nov., a phycosphere bacterium isolated from Karlodinium veneficum

A facultative anaerobic, Gram-negative, non-motile, rod-shaped bacterial strain, designated N5^T, was obtained from the phycosphere microbiota of the marine planktonic dinoflagellate, Karlodinium veneficum. Strain N5^T showed growth on marine agar at 25 °C, pH 7 and 1 % (w/v) NaCl and produced a yellow colour. According to a phylogenetic study based on 16S rRNA gene sequences, strain N5^T has a lineage within the genus Gymnodinialimonas. The G+C content in the genome of strain N5^T is 62.9 mol% with a total length of 4 324 088 bp. The NCBI Prokaryotic Genome Annotation Pipeline revealed that the N5^T genome contained 4230 protein-coding genes and 48 RNA genes, including a 5S rRNA, 16S rRNA, 23S rRNA, 42 tRNA, and three ncRNAs. Genome-based calculations (genome-to-genome distance, average nucleotide identity and DNA G+C content) clearly indicated that the isolate represents a novel species within the genus Gymnodinialimonas. The predominant fatty acids were C_19 : 0 cyclo ω8c and feature 8 (comprising C_18 : 1 ω6c and/or C_18 : 1 ω7c). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The main respiratory quinone was Q-10. Based on its phenotypic, phylogenetic, genomic and chemotaxonomic features, strain N5^T represents a novel species of the genus Gymnodinialimonas, for which the name Gymnodinialimonas phycosphaerae sp. nov. is proposed. The type strain is N5^T (=KCTC 82362^T=NBRC 114899^T).