The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small

Applying phylogenetic methods for species delimitation to distinguish B-cell clonal families

The adaptive immune system generates a diverse array of B-cell receptors through the processes of V(D)J recombination and somatic hypermutation. B-cell receptors that bind to an antigen will undergo clonal expansion, creating a Darwinian evolutionary dynamic within individuals. A key step in studying these dynamics is to identify sequences derived from the same ancestral V(D)J recombination event (i.e. a clonal family). There are a number of widely used methods for accomplishing this task but a major limitation of all of them is that they rely, at least in part, on the ability to map sequences to a germline reference set. This requirement is particularly problematic in non-model systems where we often know little about the germline allelic diversity in the study population. Recognizing that delimiting B-cell clonal families is analogous to delimiting species from single locus data, we propose a novel strategy of reconstructing the phylogenetic tree of all B-cell sequences in a sample and using a popular species delimitation method, multi-rate Poisson Tree Processes (mPTP), to delimit clonal families. Using extensive simulations, we show that not only does this phylogenetically explicit approach perform well for the purpose of delimiting clonal families when no reference allele set is available, it performs similarly to state-of-the-art techniques developed specifically for B-cell data even when we have a complete reference allele set. Additionally, our analysis of an empirical dataset shows that mPTP performs similarly to leading methods in the field. These findings demonstrate the utility of using off-the-shelf phylogenetic techniques for analyzing B-cell clonal dynamics in non-model systems, and suggests that phylogenetic inference techniques may be potentially combined with mapping based approaches for even more robust inferences, even in model systems.

Exploration of a multifunctional biocontrol agent Streptomyces sp. JCK-8055 for the management of apple fire blight

Apple fire blight, caused by the bacterium Erwinia amylovora, is a devastating disease of apple and pear trees. Biological control methods have attracted much attention from researchers to manage plant diseases as they are eco-friendly and viable alternatives to synthetic pesticides. Herein, we isolated Streptomyces sp. JCK-8055 from the root of pepper and investigated its mechanisms of action against E. amylovora. Streptomyces sp. JCK-8055 produced aureothricin and thiolutin, which antagonistically affect E. amylovora. JCK-8055 and its two active metabolites have a broad-spectrum in vitro activity against various phytopathogenic bacteria and fungi. They also effectively suppressed tomato bacterial wilt and apple fire blight in in vivo experiments. Interestingly, JCK-8055 colonizes roots as a tomato seed coating and induces apple leaf shedding at the abscission zone, ultimately halting the growth of pathogenic bacteria. Additionally, JCK-8055 can produce the plant growth regulation hormone indole-3-acetic acid (IAA) and hydrolytic enzymes, including protease, gelatinase, and cellulase. JCK-8055 treatment also triggered the expression of salicylate (SA) and jasmonate (JA) signaling pathway marker genes, such as PR1, PR2, and PR3. Overall, our findings demonstrate that Streptomyces sp. JCK-8055 can control a wide range of plant diseases, particularly apple fire blight, through a combination of mechanisms such as antibiosis and induced resistance, highlighting its excellent potential as a biocontrol agent. KEY POINTS: • JCK-8055 produces the systemic antimicrobial metabolites, aureothricin, and thiolutin. • JCK-8055 treatment upregulates PR gene expression in apple plants against E. amylovora. • JCK-8055 controls plant diseases with antibiotics and induced resistance.

Flavobacterium nakdongensis sp. nov., Isolated from Fresh Water during the Cyanobacterial Bloom Period

A novel Gram-negative bacterial strain, 20NA77.7T, was isolated from fresh water of the Nakdong River. Strain 20NA77.7T shared the highest similarity with Flavobacterium indicum GPTSA100-9T (97.91%) and Flavobacterium urocaniciphilum DSM 27078T (96.24%) in the 16S rRNA gene sequence. The digital DNA-DNA hybridization and average nucleotide identity values for strain 20NA77.7T with Flavobacterium species were below 20.8% and 77.33%, respectively. The major fatty acids of strain 20NA77.7T were identified as iso-C15:0, iso-C16:0, iso-C15:1 G, anteiso-C15:0, iso-C15:0 3OH, and iso-C16:0 3OH. Strain 20NA77.7T contained phosphatidylethanolamine, one unidentified aminolipid, and three unidentified lipids as polar lipids and menaquinone-6 as menaquinone. The polyphasic evidence supports the classification of strain 20NA77.7T as a novel species belonging to the genus Flavobacterium, for which the name Flavobacterium nakdongensis is proposed. The type strain is 20NA77.7T (= KCTC 102000T = LMG 33137T).

Roseateles microcysteis sp. nov., Isolated from Co-cultivation of Microcystis aeruginosa and Myriophyllum spicatum

A novel rod-shaped, Gram-stain-negative bacterial strain MS17T was obtained from a co-culture of Microcystis aeruginosa and Myriophyllum spicatum. The examination of the 16S ribosomal RNA gene sequence showed a significant degree of similarity between strain MS17T and Paucibacter sediminis S2-9T (98.4%), Roseateles violae PFR6T (98.1%), 'Roseateles cellulosilyticus' P8T (98.0%), Roseateles aquae APW11T (97.9%), Roseateles oligotrophus CHU3T (97.7%), Roseateles saccharophilus DSM 654T (97.6%), Kinneretia aquatilis CR182T (97.7%), Pelomonas aquatica CCUG 52575T (97.6%), and Roseateles toxinivorans 2C20T (97.0%). Between strain MS17T and the type strains of closely related species, digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values were below 21.9% and 78.48%. The respiratory quinone was ubiquinone Q-8. The main fatty acids (> 10.0%) were C15:1 ω6c, C16:0, C17:0, and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The polar lipids comprised phosphatidylethanolamine, unidentified phospholipid, phosphatidylglycerol, unidentified aminophospholipid, unidentified aminolipid, and three unidentified lipids. The genomic G + C content was 65.9%. According to phenotypic characteristics, phylogenetic relationships, and chemotaxonomic data, strain MS17T has been categorized as a newly discovered species belonging to the Roseateles genus, and the name Roseateles microcysteis sp. nov. is suggested. It exhibits distinct biochemical properties that differentiate it from closely related species. The type strain is MS17T (=KCTC 8001T = LMG 33142T).

Undibacterium cyanobacteriorum sp. nov., an auxin-producing bacterium isolated from fresh water during cyanobacterial bloom period

A novel Gram-negative, white-pigmented, and auxin-producing strain, 20NA77.5T, was isolated from fresh water during cyanobacterial bloom period. Pairwise comparison of the 16S rRNA gene sequences showed that strain 20NA77.5T belonged to the genus Undibacterium and exhibited the highest sequence similarity to the type strains of Undibacterium danionis (98.00%), Undibacterium baiyunense (97.93%), Undibacterium macrobrachii (97.92%), and Undibacterium fentianense (97.71%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain 20NA77.5T and its related type strains were below 79.93 and 23.80%, respectively. The predominant fatty acids (> 10% of the total fatty acids) were C16:0 and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The genomic DNA G + C content of strain 20NA77.5T was found to be 48.61%. Based on the phylogenetic distinctness, chemotaxonomic features, and phenotypic features, strain 20NA77.5T is considered to represent a novel species of the genus Undibacterium, for which the name Undibacterium cyanobacteriorum sp. nov is proposed. The type strain is 20NA77.5T (= KCTC 8005T = LMG 33136T).

Sphingobium cyanobacteriorum sp. nov., isolated from fresh water

A novel Gram-stain-negative, yellow-pigmented, short rod-shaped bacterial strain, HBC34T, was isolated from a freshwater sample collected from Daechung Reservoir, Republic of Korea. The results of 16S rRNA gene sequence analysis indicated that HBC34T was affiliated with the genus Sphingobium and shared the highest sequence similarity to the type strains of Sphingobium vermicomposti (98.01 %), Sphingobium psychrophilum (97.87 %) and Sphingobium rhizovicinum (97.59 %). The average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values between HBC34T and species of the genus Sphingobium with validly published names were below 84.01 and 28.1 %, respectively. These values were lower than the accepted species-delineation thresholds, supporting its recognition as representing a novel species of the genus Sphingobium. The major fatty acids (>10 % of the total fatty acids) were identified as summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The main polar lipids were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, two phospholipids and two unidentified polar lipids. The respiratory quinone was Q-10. The genomic DNA G+C content of HBC34T was 64.04 %. The polyphasic evidence supports the classification of HBC34T as the type strain of a novel species of the genus Sphingobium, for which the name Sphingobium cyanobacteriorum sp. nov is proposed. The type strain is HBC34T (= KCTC 8002T= LMG 33140T).

Strategies for describing myxozoan pathogens, dreadful fish diseases in aquaculture

Myxozoans are obligate endoparasites, cosmopolitan in distribution with both vertebrate and invertebrate hosts. Their myxospores consist of shell valves, polar capsules with coiled polar tubules that are extrudible, and infective amoeboid germs. Myxozoan parasites are most abundant, and due to their increasing number in recent years, they can pose an emerging threat to the fish industry worldwide. Hence, the immediate need is to devise a strategy to understand and detect parasites and parasitism. They may proliferate to different organs with the advancement of infection. This all warrants the development/devising of strategies and results of integrative studies in order to identify these dreadful parasites and resolve taxonomic issues. Different methods whether classical methods including gross morphology or advanced methods such as electron microscopy (SEM, TEM, STEM), Confocal laser scanning microscopy (CLSM), histopathological studies, site preference, host and tissue specificity, a molecular approach using new markers can be clubbed for identification because these parasites are hidden and are difficult to recognize. This group was earlier classified only on the basis of myxospores morphology, but due to the high structural variability of this group advanced methods and approaches have to be implied which can minimize the problems in assigning new species.

Comparative Genome analysis of the Genus Curvibacter and the Description of Curvibacter microcysteis sp. nov. and Curvibacter cyanobacteriorum sp. nov., Isolated from Fresh Water during the Cyanobacterial Bloom Period

The three Gram-negative, catalase- and oxidase-positive bacterial strains RS43T, HBC28, and HBC61T, were isolated from fresh water and subjected to a polyphasic study. Comparison of 16S rRNA gene sequence initially indicated that strains RS43T, HBC28, and HBC61T were closely related to species of genus Curvibacter and shared the highest sequence similarity of 98.14%, 98.21%, and 98.76%, respectively, with Curvibacter gracilis 7-1T. Phylogenetic analysis based on genome sequences placed all strains within the genus Curvibacter. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the three strains and related type strains supported their recognition as two novel genospecies in the genus Curvibacter. Comparative genomic analysis revealed that the genus possessed an open pangenome. Based on KEGG BlastKOALA analyses, Curvibacter species have the potential to metabolize benzoate, phenylacetate, catechol, and salicylate, indicating their potential use in the elimination of these compounds from the water systems. The results of polyphasic characterization indicated that strain RS43T and HBC61T represent two novel species, for which the name Curvibacter microcysteis sp. nov. (type strain RS43T =KCTC 92793T=LMG 32714T) and Curvibacter cyanobacteriorum sp. nov. (type strain HBC61T =KCTC 92794T =LMG 32713T) are proposed.

The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection

BACKGROUND

Accessory proteins have diverse roles in coronavirus pathobiology. One of them in SARS-CoV (the causative agent of the severe acute respiratory syndrome outbreak in 2002-2003) is encoded by the open reading frame 8 (ORF8). Among the most dramatic genomic changes observed in SARS-CoV isolated from patients during the peak of the pandemic in 2003 was the acquisition of a characteristic 29-nucleotide deletion in ORF8. This deletion cause splitting of ORF8 into two smaller ORFs, namely ORF8a and ORF8b. Functional consequences of this event are not entirely clear.

RESULTS

Here, we performed evolutionary analyses of ORF8a and ORF8b genes and documented that in both cases the frequency of synonymous mutations was greater than that of nonsynonymous ones. These results suggest that ORF8a and ORF8b are under purifying selection, thus proteins translated from these ORFs are likely to be functionally important. Comparisons with several other SARS-CoV genes revealed that another accessory gene, ORF7a, has a similar ratio of nonsynonymous to synonymous mutations suggesting that ORF8a, ORF8b, and ORF7a are under similar selection pressure.

CONCLUSIONS

Our results for SARS-CoV echo the known excess of deletions in the ORF7a-ORF7b-ORF8 complex of accessory genes in SARS-CoV-2. A high frequency of deletions in this gene complex might reflect recurrent searches in "functional space" of various accessory protein combinations that may eventually produce more advantageous configurations of accessory proteins similar to the fixed deletion in the SARS-CoV ORF8 gene.

Computational Reproducibility of Molecular Phylogenies

Repeated runs of the same program can generate different molecular phylogenies from identical data sets under the same analytical conditions. This lack of reproducibility of inferred phylogenies casts a long shadow on downstream research employing these phylogenies in areas such as comparative genomics, systematics, and functional biology. We have assessed the relative accuracies and log-likelihoods of alternative phylogenies generated for computer-simulated and empirical data sets. Our findings indicate that these alternative phylogenies reconstruct evolutionary relationships with comparable accuracy. They also have similar log-likelihoods that are not inferior to the log-likelihoods of the true tree. We determined that the direct relationship between irreproducibility and inaccuracy is due to their common dependence on the amount of phylogenetic information in the data. While computational reproducibility can be enhanced through more extensive heuristic searches for the maximum likelihood tree, this does not lead to higher accuracy. We conclude that computational irreproducibility plays a minor role in molecular phylogenetics.

Description of Brachybacterium sillae sp. nov., a thermophilic bacterium isolated from a hot spring

The taxonomic position of strain EF45031^T, isolated from the Neungam Carbonate hot spring, was examined using the polyphasic taxonomic approach. Strain EF45031^T shared the highest percentage of 16S rRNA gene sequence with Brachybacterium nesterenkovii CIP 104813 ^T (97.7%). The average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values between strain EF45031^T and the type strains B. nesterenkovii CIP 104813 ^T and B. phenoliresistens Phenol-A^T were 77.0%, 69.15%, 21.9% and 75.73%, 68.81%, 20.5%, respectively. Phylogenomic analysis using an up-to-date bacterial core gene (UBCG) set revealed that strain EF45031^T belonged to the genus Brachybacterium. Growth occurred between 25 and 50 ℃ at pH 6.0-9.0 and could tolerate salinity up to 5% (w/v). Strain had anteiso-C_15:0 and anteiso-C_17:0 as major fatty acids. Menaquinone-7 (MK-7) was the predominant respiratory menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, three aminolipids, and two unidentified glycolipids. The cell-wall peptidoglycan contained meso-diaminopimelic acid as a diagnostic diamino acid. The genome comprised 2,663,796 bp, with a G + C content of 70.9%. Stress-responsive periplasmic chaperone/protease coding genes were identified in the genome of EF45031^T and were not detected in other Brachybacterium species. The polyphasic taxonomic properties indicate that the strain represents a novel species within the genus Brachybacterium, for which the name Brachybacterium sillae sp. nov. is proposed. The type strain is EF45031^T (= KCTC 49702 ^T = NBRC 115869 ^T).

Genomic evidence reveals intraspecific divergence of the hot-spring snake (Thermophis baileyi), an endangered reptile endemic to the Qinghai-Tibet plateau

Understanding how and why species evolve requires knowledge on intraspecific divergence. In this study, we examined intraspecific divergence in the endangered hot-spring snake (Thermophis baileyi), an endemic species on the Qinghai-Tibet Plateau (QTP). Whole-genome resequencing of 58 sampled individuals from 15 populations was performed to identify the drivers of intraspecific divergence and explore the potential roles of genes under selection. Our analyses resolved three groups, with major intergroup admixture occurring in regions of group contact. Divergence probably occurred during the Pleistocene as a result of glacial climatic oscillations, Yadong-Gulu rift, and geothermal fields differentiation, while complex gene flow between group pairs reflected a unique intraspecific divergence pattern on the QTP. Intergroup fixed loci involved selected genes functionally related to divergence and local adaptation, especially adaptation to hot spring microenvironments in different geothermal fields. Analysis of structural variants, genetic diversity, inbreeding, and genetic load indicated that the hot-spring snake population has declined to a low level with decreased diversity, which is important for the conservation management of this endangered species. Our study demonstrated that the integration of demographic history, gene flow, genomic divergence genes, and other information is necessary to distinguish the evolutionary processes involved in speciation.

Mucilaginibacter straminoryzae sp. nov., isolated from rice straw used for growing periphyton

A rod-shaped, non-motile, Gram-negative bacterium, strain RS28^T, was isolated from rice straw used as material for periphyton growth. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain RS28^T was affiliated with the genus Mucilaginibacter and had the highest sequence similarity to Mucilaginibacter ginkgonis HMF7856^T (96.47 %) and Mucilaginibacter polytrichastri DSM 26907^T (96.12 %). Strain RS28^T was found to grow at pH 5.5-8.0, 17-40 °C and in the presence of 0-1.5 % (w/v) NaCl. Strain RS28^T contained summed feature 3 (comprising C_16 : 1  ω7c and/or C_16 : 1  ω6c), iso-C_15 : 0 and iso-C_17 : 0 3-OH as the major fatty acids (> 10.0 %). The major polar lipids were phosphatidylethanolamine, two unidentified phospholipids, two unidentified aminophospholipids, three unidentified aminolipids and one unidentified lipid. The respiratory quinone was menaquinone 7. The genomic DNA G+C content was 44.7 mol%. Strain RS28^T possessed six putative secondary metabolite gene clusters involved in the synthesis of resorcinol, NRPS-like, terpene, lassopeptide, T3PKS and arylpolyene. On the basis of the phenotypic, chemotaxonomic, and phylogenetic characteristics, strain RS28^T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter straminoryzae sp. nov. is proposed. The type strain is RS28^T (=KCTC 92039^T=LMG 32424^T).

Mucilaginibacter aquariorum sp. nov., Isolated from Fresh Water

A Gram-stain-negative, rod-shaped bacterial strain, JC4^T, was isolated from a freshwater sample and determined the taxonomic position. Initial identification based on 16S rRNA gene sequences revealed that strain JC4^T is affiliated to the genus Mucilaginibacter with a sequence similarity of 97.97% to Mucilaginibacter rigui WPCB133^T. The average nucleotide identity and digital DNA-DNA hybridization values between strain JC4^T and Mucilaginibacter species were estimated below 80.92% and 23.9%, respectively. Strain JC4^T contained summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c) and iso-C_15:0 as predominant cellular fatty acids. The dominant polar lipids were identified as phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, and two unidentified lipids. The respiratory quinone was MK-7. The genomic DNA G+C content of strain JC4^T was determined to be 42.44%. The above polyphasic evidences support that strain JC4^T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter aquariorum sp. nov. is proposed. The type strain is JC4^T (= KCTC 92230^T = LMG 32715^T).

Description of Microbacterium neungamense sp. nov. isolated from a hot spring

The Gram-positive, nonmotile, rod-shaped bacterium EF45044^T was isolated from a hot spring in Chungju, South Korea. The strain was able to grow at concentrations of 0‒5% (w/v) NaCl, at pH 6.0‒10.0 and in the temperature range of 18‒50 °C. Strain EF45044^T showed the highest 16S rRNA gene sequence similarity (98.2%) with Microbacterium ketosireducens DSM 12510^T, and the digital DNA‒DNA hybridization (dDDH), average amino acid identity (AAI), and average nucleotide identity (ANI) values were all lower than the accepted species threshold. Strain EF45044^T contained MK‒12 and MK‒13 as the predominant respiratory quinones and anteiso‒C_17:0, anteiso‒C_15:0, and iso‒C_16:0 as the major fatty acids. Diphosphatidylglycerol, phosphatidylglycerol, and glycolipid were detected as the major polar lipids. The cell-wall peptidoglycan contained ornithine. The DNA G + C content was 71.4 mol%. Based on the polyphasic data, strain EF45044^T (= KCTC 49703^T) presents a novel species of the genus Microbacterium, for which the name Microbacterium neungamense sp. nov. is proposed.

Biogeography and eye size evolution of the ogre-faced spiders

Net-casting spiders (Deinopidae) comprise a charismatic family with an enigmatic evolutionary history. There are 67 described species of deinopids, placed among three genera, Deinopis, Menneus, and Asianopis, that are distributed globally throughout the tropics and subtropics. Deinopis and Asianopis, the ogre-faced spiders, are best known for their giant light-capturing posterior median eyes (PME), whereas Menneus does not have enlarged PMEs. Molecular phylogenetic studies have revealed discordance between morphology and molecular data. We employed a character-rich ultra-conserved element (UCE) dataset and a taxon-rich cytochrome-oxidase I (COI) dataset to reconstruct a genus-level phylogeny of Deinopidae, aiming to investigate the group's historical biogeography, and examine PME size evolution. Although the phylogenetic results support the monophyly of Menneus and the single reduction of PME size in deinopids, these data also show that Deinopis is not monophyletic. Consequently, we formally transfer 24 Deinopis species to Asianopis; the transfers comprise all of the African, Australian, South Pacific, and a subset of Central American and Mexican species. Following the divergence of Eastern and Western deinopids in the Cretaceous, Deinopis/Asianopis dispersed from Africa, through Asia and into Australia with its biogeographic history reflecting separation of Western Gondwana as well as long-distance dispersal events.

Hymenobacter cyanobacteriorum sp. nov., isolated from a freshwater reservoir during the cyanobacterial bloom period

A Gram-negative, red-colored, and rod-shaped bacterial strain, DH14^T, was isolated from a eutrophic reservoir. The 16S rRNA gene sequence analysis showed that strain DH14^T was most closely related to Hymenobacter terrigena (98.3% similarity) and Hymenobacter terrae (98.1%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain DH14^T and its related type strains were below 82.9% and 27.2%, respectively. Strain DH14^T contained iso-C_15:0 (32.6%), anteiso-C_15:0 (14.0%), and summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c) (25.8%) as major cellular fatty acids. The main polar lipids were phosphatidylethanolamine, two unidentified aminophospholipids, and one unidentified lipid. The respiratory quinone was menaquinone 7 (MK-7). The genomic DNA G + C content was 62.1%. These evidences support the classification of strain DH14^T as a novel species in the genus Hymenobacter, for which the name Hymenobacter cyanobacteriorum sp. nov. is proposed. The type strain is DH14^T (= KCTC 92040^T = LMG 32425^T).

Caenimonas aquaedulcis sp. nov., Isolated from Freshwater of Daechung Reservoir during Microcystis Bloom

A Gram-stain-negative, white-coloured, and rod-shaped bacterium, strain DR4-4^T, was isolated from Daechung Reservoir, Republic of Korea, during Microcystis bloom. Strain DR4-4^T was most closely related to Caenimonas terrae SGM1-15^T and Caenimonas koreensis EMB320^T with 98.1% 16S rRNA gene sequence similarities. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain DR4-4^T and closely related type strains were below 79.46% and 22.30%, respectively. The genomic DNA G+C content was 67.5%. The major cellular fatty acids (≥10% of the total) were identified as C_16:0, cyclo C_17:0, summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). Strain DR4-4^T possessed phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol as the main polar lipids and Q-8 as the respiratory quinone. The polyamine profile was composed of putrescine, cadaverine, and spermidine. The results of polyphasic characterization indicated that the isolated strain DR4-4^T represents a novel species within the genus Caenimonas, for which the name Caenimonas aquaedulcis sp. nov. is proposed. The type strain is DR4-4^T (=KCTC 82470^T =JCM 34453^T).

Senecavirus A Enhances Its Adaptive Evolution via Synonymous Codon Bias Evolution

Synonymous codon bias in the viral genome affects protein translation and gene expression, suggesting that the synonymous codon mutant plays an essential role in influencing virulence and evolution. However, how the recessive mutant form contributes to virus evolvability remains elusive. In this paper, we characterize how the Senecavirus A (SVA), a picornavirus, utilizes synonymous codon mutations to influence its evolution, resulting in the adaptive evolution of the virus to adverse environments. The phylogenetic tree and Median-joining (MJ)-Network of these SVA lineages worldwide were constructed to reveal SVA three-stage genetic development clusters. Furthermore, we analyzed the codon bias of the SVA genome of selected strains and found that SVA could increase the GC content of the third base of some amino acid synonymous codons to enhance the viral RNA adaptive evolution. Our results highlight the impact of recessive mutation of virus codon bias on the evolution of the SVA and uncover a previously underappreciated evolutionary strategy for SVA. They also underline the importance of understanding the genetic evolution of SVA and how SVA adapts to the adverse effects of external stress.

Panacibacter microcysteis sp. nov., isolated from a eutrophic reservoir during the Microcystis bloom period

A Gram-stain-negative, rod-shaped bacterial strain DH6^T was isolated from fresh water of the Daechung Reservoir during the Microcystis bloom period. The strain grew at pH 6.0-8.5, at temperature 17-40 °C, and at 0-1% (w/v) NaCl concentration. Comparison of 16S rRNA gene sequence indicated that strain DH6^T exhibits the highest similarity with Panacibacter ginsenosidivorans Gsoil 1550^T (96.6%). The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values of strain DH6^T compared to its related type strains were below 74.2%, 22.3%, and 74.8%, respectively. The predominant fatty acids (> 5.0%) were identified as iso-C_17:0 3-OH, iso-C_13:0, iso-C_15:0, C_17:0 2-OH, iso-C_11:0, anteiso-C_13:0, and iso-C_15:1 G. The polar lipid profile contained phosphatidylethanolamine, four unidentified aminolipids, and three unidentified lipids. The respiratory quinone was menaquinone 7 (MK-7). The genomic DNA G + C content was 42.6%. Collectively, strain DH6^T should be classified as a novel species within the genus Panacibacter, for which the name Panacibacter microcysteis sp. nov. is proposed. The type strain is DH6^T (= KCTC 82471^T = LMG 32426^T).

Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus

Discovery and study of viruses carried by migratory birds are tasks of high importance due to the host's ability to spread infectious diseases over significant distances. With this paper, we present and characterize the first complete genome sequence of atadenovirus from a tern bird (common tern, Sterna hirundo) preliminarily named tern atadenovirus 1 (TeAdV-1). TeAdV-1 genome is a linear double-stranded DNA molecule, 31,334 base pairs which contain 30 methionine-initiated open reading frames with gene structure typical for Atadenovirus genus, and the shortest known inverted terminal repeats (ITRs) within the Atadenovirus genus consisted of 25 bases. The nucleotide composition of the genome is characterized by a low G + C content (33.86%), which is the most AT-rich genome of known avian adenoviruses within Atadenovirus genus. The nucleotide sequence of the TeAdV-1 genome shows high divergence compared to known representatives of the Atadenovirus genus with the highest similarity to the duck atadenovirus 1 (53.7%). Phylogenetic analysis of the protein sequences of core genes confirms the taxonomic affiliation of the new representative to the genus Atadenovirus with the degree of divergence from the known representatives exceeding the interspecies distance within the genus. Thereby we proposed a novel TeAdV-1 to be considered as a separate species.

Molecular phylogeny of the Anopheles hyrcanus group (Diptera: Culicidae) based on rDNA-ITS2 and mtDNA-COII

BACKGROUND

The Anopheles hyrcanus group, which includes 25 species, is widely distributed in the Oriental and Palaearctic regions. Given the difficulty in identifying cryptic or sibling species based on their morphological characteristics, molecular identification is regarded as an important complementary approach to traditional morphological taxonomy. The aim of this study was to reconstruct the phylogeny of the Hyrcanus group using DNA barcoding markers in order to determine the phylogenetic correlations of closely related taxa and to compare these markers in terms of identification efficiency and genetic divergence among species.

METHODS

Based on data extracted from the GenBank database and data from the present study, we used 399 rDNA-ITS2 sequences of 19 species and 392 mtDNA-COII sequences of 14 species to reconstruct the molecular phylogeny of the Hyrcanus group across its worldwide range. We also compared the performance of rDNA-ITS2 against that of mtDNA-COII to assess the genetic divergence of closely related species within the Hyrcanus group.

RESULTS

Average interspecific divergence for the rDNA-ITS2 sequence (0.376) was 125-fold higher than the average intraspecies divergence (0.003), and average interspecific divergence for the mtDNA-COII sequence (0.055) was eightfold higher than the average intraspecies divergence (0.007). The barcoding gap ranged from 0.015 to 0.073 for rDNA-ITS2, and from 0.017 to 0.025 for mtDNA-COII. Two sets of closely related species, namely, Anophels lesteri and An. paraliae, and An. sinensis, An. belenrae and An. kleini, were resolved by rDNA-ITS2. In contrast, the relationship of An. sinensis/An. belenrae/An. kleini was poorly defined in the COII tree. The neutrality test and mismatch distribution revealed that An. peditaeniatus, An. hyrcanus, An. sinensis and An. lesteri were likely to undergo hitchhiking or population expansion in accordance with both markers. In addition, the population of an important vivax malaria vector, An. sinensis, has experienced an expansion after a bottleneck in northern and southern Laos.

CONCLUSIONS

The topology of the Hyrcanus group rDNA-ITS2 and mtDNA-COII trees conformed to the morphology-based taxonomy for species classification rather than for that for subgroup division. rDNA-ITS2 is considered to be a more reliable diagnostic tool than mtDNA-COII in terms of investigating the phylogenetic correlation between closely related mosquito species in the Hyrcanus group. Moreover, the population expansion of an important vivax malaria vector, An. sinensis, has underlined a potential risk of malaria transmission in northern and southern Laos. This study contributes to the molecular identification of the Anopheles hyrcanus group in vector surveillance.

Mariniflexile maritimum sp. nov., isolated from seawater of the South Sea in the Republic of Korea

A novel Gram-stain-negative, rod-shaped, aerobic, non-motile bacterial strain, designated M5A1M^T, was isolated from seawater collected from the South Sea of the Republic of Korea. Based on 16S rRNA gene sequence similarity, strain M5A1M^T was closely related to Mariniflexile gromovii KMM 6038^T (95.3 %), Mariniflexile fucanivorans SW5^T (95.2 %), Mariniflexile soesokkakense RSSK-9^T (95.1 %), Yeosuana aromativorans GW1-1^T (94.6 %) and Confluentibacter lentus HJM-3^T (94.6 %). Genome-based phylogenetic analyses revealed that strain M5A1M^T formed a distinct cluster with the type strains of the genus Mariniflexile. The major cellular fatty acid constituents (>5 % of the total fatty acids) were iso-C_15:0, anteiso-C_15 : 0, iso-C_15 : 0 3-OH, iso-C_15 : 1 G, iso-C_16:03-OH and iso-C_17 : 0 3-OH. The respiratory quinone was identified as MK-6. The major polar lipids were phosphatidylethanolamine and one unidentified polar lipid. The genomic DNA G+C content of strain M5A1M^T was determined to be 37.7 mol%. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain M5A1M^T is considered to represent a novel species within the genus Mariniflexile, for which the name Mariniflexile maritimum sp. nov. is proposed. The type strain is M5A1M^T (=KCTC 72895^T=JCM 33982^T).

Mucilaginibacter inviolabilis sp. nov., isolated from the phycosphere of Haematococcus lacustris NIES 144 culture

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterial strain, designated HC2^T, was isolated from the phycosphere of Haematococcus lacustris NIES 144 culture. Strain HC2^T was able to grow at pH 4.5-8.0, at 4-32 °C and in the presence of 0-2 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain HC2^T was affiliated to the genus Mucilaginibacter and shared the highest sequence similarity with Mucilaginibacter lappiensis ANJKI2^T (98.20 %) and Mucilaginibacter sabulilitoris SMS-12^T (98.06 %). Strain HC2^T contained summed feature 3 (C_16 : 1 ω7c and/or C_16 : 1 ω6c) and iso-C_15 : 0 as the major fatty acids (>10.0 %). The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, two unidentified aminolipids and four unidentified lipids. The respiratory quinone was menaquinone 7 (MK-7). The genomic DNA G+C content was 42.0 %. On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, strain HC2^T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter inviolabilis sp. nov. is proposed. The type strain is HC2^T (=KCTC 82084^T=JCM 34116^T).

Novosphingobium aquimarinum sp. nov., isolated from seawater

A novel Gram-stain-negative, aerobic, and rod-shaped bacterial strain, M24A2M^T, was isolated from seawater in the Republic of Korea. On the basis of the 16S rRNA gene phylogeny, strain M24A2M^T was found to be closely related to Novosphingobium pentaromativorans US6-1^T and Novosphingobium mathurense SM117^T with pair-wise sequence similarities of 97.4 and 96.9 %, respectively. Phylogenetic analysis of 16S rRNA sequences indicated that M24A2M^T formed a branch with Novosphingobium pentaromativorans US6-1^T and represented a member of the genus Novosphingobium. The predominant cellular fatty acids were C_14 : 0 2-OH, summed feature 3 (C_16 : 1 ω7c and/or C_16 : 1 ω6c), and summed feature 8 (C_18 : 1 ω7c and/or C_18 : 1 ω6c). The polar lipids of strain M24A2M^T consisted mainly of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid, and two unidentified lipids. The respiratory quinone was ubiquinone Q-10. The genomic DNA G+C content was 63.9 %. Given the phenotypic characteristics along with the phylogenetic distinctness and chemotaxonomic features, strain M24A2M^T is considered to represent a novel species within the genus Novosphingobium, for which the name Novosphingobium aquimarinum sp. nov. is proposed. The type strain of Novosphingobium aquimarinum sp. nov. is M24A2M^T (=KCTC 72894^T=JCM 33983^T).

Babesial infection in the Madagascan flying fox, Pteropus rufus É. Geoffroy, 1803

Background

Babesiae are erythrocytic protozoans, which infect the red blood cells of vertebrate hosts to cause disease. Previous studies have described potentially pathogenic infections of Babesia vesperuginis in insectivorous bats in Europe, the Americas and Asia. To date, no babesial infections have been documented in the bats of Madagascar, or in any frugivorous bat species worldwide.

Results

We used standard microscopy and conventional PCR to identify babesiae in blood from the endemic Madagascan flying fox (Pteropus rufus). Out of 203 P. rufus individuals captured between November 2013 and January 2016 and screened for erythrocytic parasites, nine adult males (4.43%) were infected with babesiae. Phylogenetic analysis of sequences obtained from positive samples indicates that they cluster in the Babesia microti clade, which typically infect felids, rodents, primates, and canids, but are distinct from B. vesperuginis previously described in bats. Statistical analysis of ecological trends in the data suggests that infections were most commonly observed in the rainy season and in older-age individuals. No pathological effects of infection on the host were documented; age-prevalence patterns indicated susceptible-infectious (SI) transmission dynamics characteristic of a non-immunizing persistent infection.

Conclusions

To our knowledge, this study is the first report of any erythrocytic protozoan infecting Madagascan fruit bats and the first record of a babesial infection in a pteropodid fruit bat globally. Given the extent to which fruit bats have been implicated as reservoirs for emerging human pathogens, any new record of their parasite repertoire and transmission dynamics offers notable insights into our understanding of the ecology of emerging pathogens.

Electronic supplementary material

The online version of this article (10.1186/s13071-019-3300-7) contains supplementary material, which is available to authorized users.

Salicibibacter kimchii gen. nov., sp. nov., a moderately halophilic and alkalitolerant bacterium in the family Bacillaceae, isolated from kimchi

A moderately halophilic and alkalitolerant bacterial strain NKC1-1^T was isolated from commercial kimchi in Korea. Strain NKC1-1^T was Gram-stain-positive, aerobic, rod-shaped, non-motile, and contained diaminopimelic acid-type murein. Cell growth was observed in a medium containing 0-25% (w/v) NaCl (optimal at 10% [w/v]), at 20-40°C (optimal at 37°C) and pH 6.5-10.0 (optimal at pH 9.0). The major isoprenoid quinone of the isolate was menaquinone-7, and the major polar lipids were phosphatidylglycerol and unidentified phospholipids. Cell membrane of the strain contained iso-C_17:0 and anteiso-C_15:0 as the major fatty acids. Its DNA G + C content was 45.2 mol%. Phylogenetic analysis indicated the strain to be most closely related to Geomicrobium halophilum with 92.7-92.9% 16S rRNA gene sequence similarity. Based on polyphasic taxonomic evaluation with phenotypic, phylogenetic, and chemotaxonomic analyses, the strain represents a novel species in a new genus, for which the name Salicibibacter kimchii gen. nov., sp. nov. is proposed (= CECT 9537^T; KCCM 43276^T).

Ketobacter alkanivorans gen. nov., sp. nov., an n-alkane-degrading bacterium isolated from seawater

Strain GI5^T was isolated from a surface seawater sample collected from Garorim Bay (West Sea, Republic of Korea). The isolated strain was aerobic, Gram-stain-negative, rod-shaped, motile by means of a polar flagellum, negative for catalase and weakly positive for oxidase. The optimum growth pH, salinity and temperature were determined to be pH 7.5-8.0, 3 % NaCl (w/v) and 25 °C, respectively; the growth ranges were pH 6.0-9.0, 1-7 % NaCl (w/v) and 18-40 °C. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that GI5^T clustered within the family Alcanivoracaceae, and most closely with Alcanivorax dieseloleiB-5^T and Alcanivorax marinusR8-12^T (91.9 % and 91.6 % similarity, respectively). The major cellular fatty acids in GI5^T were C18 : 1ω7c/C18 : 1ω6c (44.45 %), C16 : 1ω6c/C16 : 1ω7c (14.17 %) and C16 : 0 (10.19 %); this profile was distinct from those of the closely related species. The major respiratory quinone of GI5^T was Q-8. The main polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Two putative alkane hydroxylase (alkB) genes were identified in GI5^T. The G+C content of the genomic DNA of GI5^T was determined to be 51.2 mol%. On the basis of the results of phenotypic, chemotaxonomic and phylogenetic studies, strain GI5^T represents a novel species of a novel genus of the family Alcanivoracaceae, for which we propose the name Ketobacter alkanivorans gen. nov., sp. nov.; the type strain is GI5^T (=KCTC 52659^T=JCM 31835^T).

Virgibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi

A Gram-stain-positive, halophilic, rod-shaped, non-motile, spore forming bacterium, strain NKC1-2^T, was isolated from kimchi, a Korean fermented food. Comparative analysis based on 16S rRNA gene sequence demonstrated that the isolated strain was a species of the genus Virgibacillus. Strain NKC1-2^T exhibited high level of 16S rRNA gene sequence similarity with the type strains of Virgibacillus xinjiangensis SL6-1^T (96.9%), V. sediminis YIM kkny3^T (96.8%), and V. salarius SA-Vb1^T (96.7%). The isolate grew at pH 6.5-10.0 (optimum, pH 8.5-9.0), 0.0-25.0% (w/v) NaCl (optimum, 10-15% NaCl), and 15-50°C (optimum, 37°C). The major menaquinone in the strain was menaquinone-7, and the main peptidoglycan of the strain was meso-diaminopimelic acid. The predominant fatty acids of the strain were iso-C_14:0, anteisio-C_15:0, iso- C_15:0, and iso-C_16:0 (other components were < 10.0%). The polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G + C content of NKC1-2^T was 42.5 mol%. On the basis of these findings, strain NKC1-2^T is proposed as a novel species in the genus Virgibacillus, for which the name Virgibacillus kimchii sp. nov. is proposed (=KACC 19404^T =JCM 32284^T). The type strain of Virgibacillus kimchii is NKC1-2T.

Structural characterization of a putative chitin synthase gene in Phytophthora spp. and analysis of its transcriptional activity during pathogenesis on potato and soybean plants

Although chitin is a major component of the fungal cell wall, in oomycetes (fungal-like organisms), this compound has only been found in very little amounts, mostly in the cell wall of members of the genera Achlya and Saprolegnia. In the oomycetes Phytophthora infestans and P. sojae the presence of chitin has not been demonstrated; however, the gene putatively encoding chitin synthase (CHS), the enzyme that synthesizes chitin, is present in their genomes. The evolutionary significance of the CHS gene in P. infestans and P. sojae genomes is not fully understood and, therefore, further studies are warranted. We have cloned and characterized the putative CHS genes from two Phytophthora spp. and multiple isolates of P. infestans and P. sojae and analyzed their phylogenetic relationships. We also conducted CHS inhibition assays and measured CHS transcriptional activity in Phytophthora spp. during infection of susceptible plants. Results of our investigations suggest that CHS contains all the motifs that are typical in CHS genes of fungal origin and is expressed, at least at the mRNA level, during in vitro and in planta growth. In infected tissues, the highest levels of expression occurred in the first 12 h post inoculation. In addition, results from our inhibition experiments appear to suggest that CHS activity is important for P. infestans normal vegetative growth. Because of the considerable variation in expression during infection when compared to basal expression observed in in vitro cultures of non-sporulating mycelium, we hypothesize that CHS may have a meaningful role in Phytophthora pathogenicity.

Molecular phylogeny of Anopheles hyrcanus group members based on ITS2 rDNA

Background

The Anopheles hyrcanus group includes 25 species, and is widely distributed in the Oriental and Palaearctic regions. Several species within this group are vectors of malaria, lymphatic filariasis and Japanese encephalitis. It is difficult or impossible to identify cryptic species based on their morphological characteristics, with some closely related species of the Hyrcanus Group have similar adult morphological characteristics. Thus, their molecular identification has been an important complementary method to traditional morphological taxonomy.

Methods

We used 461 ribosomal DNA (rDNA) internal transcribed spacer 2 (ITS2) sequences relating to 19 species to reconstruct the molecular phylogeny of the Hyrcanus Group across its range. In addition, we compared the performance of rDNA ITS2 to that of mitochondrial DNA (mtDNA) cytochrome c oxidase subunit 1 gene (cox1) to assess the genetic divergence of Hyrcanus Group sibling species.

Results

Based on Kimura’s 2-parameter (K2P) distance model, the average conspecific ITS2 divergence was 0.003, whereas sequence divergence between species averaged 0.480. Average ITS2 sequence divergences were almost 160 times higher among the Hyrcanus Group members than within each species. Two sets of sibling species, An. lesteri Baisas & Hu, 1936 and An. paraliae Sandosham, 1959; and An. sinensis Wiedemann, 1828, An. belenrae Rueda, 2005, and An. kleini Rueda, 2005, were resolved by ITS2. Each of these species was represented as an independent lineage in the phylogenetic tree. Results suggest that An. pseudopictus Grassi, 1899 and An. hyrcanus (Pallas, 1771) are most likely a single species. We uncovered two new ITS2 lineages that require further study before resolving their true taxonomic status, and designed a diagnostic polymerase chain reaction (PCR) assay to distinguish five morphologically similar species.

Conclusions

Nuclear and mitochondrial genes generally provided consistent results for subgroup division. Compared to cox1, ITS2 is a more reliable tool for studying phylogenetic relationships among closely related mosquito taxa. Based on species-specific differences in ITS2 sequences, the multiplex PCR assay developed here can be used to improve the efficiency of vector identification. Thus, this research will promote the progress of malaria vector surveillance in both epidemic and non-epidemic areas of South and East Asia.

Electronic supplementary material

The online version of this article (10.1186/s13071-017-2351-x) contains supplementary material, which is available to authorized users.

Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi

A novel halophilic bacterium, strain K7(T), was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0-25.0% (w/v) NaCl (optimum 10-15% NaCl), pH 5.5-8.5 (optimum pH 7.0-7.5), and 15-42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone-7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio-C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7(T) and Gracilibacillus orientalis XH-63(T) (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7(T) is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7(T) (KACC 18669(T); JCM 31344(T)).

Calculibacillus koreensis gen. nov., sp. nov., an anaerobic Fe(III)-reducing bacterium isolated from sediment of mine tailings

A strictly anaerobic bacterium, strain B5(T), was isolated from sediment of an abandoned coal mine in Taebaek, Republic of Korea. Cells of strain B5(T) were non-spore-forming, straight, Gram-positive rods. The optimum pH and temperature for growth were pH 7.0 and 30°C, respectively, while the strain was able to grow within pH and temperature ranges of 5.5-7.5 and 25-45°C, respectively. Growth of strain B5(T) was observed at NaCl concentrations of 0 to 6.0% (w/v) with an optimum at 3.0-4.0% (w/v). The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid and three unknown polar lipids. Strain B5(T) grew anaerobically by reducing nitrate, nitrite, ferric-citrate, ferric-nitrilotriacetate, elemental sulfur, thiosulfate, and anthraquinone-2-sulfonate in the presence of proteinaceous compounds, organic acids, and carbohydrates as electron donors. The isolate was not able to grow by fermentation. Strain B5(T) did not grow under aerobic or microaerobic conditions. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B5(T) is most closely related to the genus Tepidibacillus (T. fermentans STGH(T); 96.3%) and Vulcanibacillus (V. modesticaldus BR(T); 94.6%). The genomic DNA G+C content (36.9 mol%) of strain B5(T) was higher than those of T. fermentans STGH(T) (34.8 mol%) and V. modesticaldus BR(T) (34.5 mol%). Based on its phenotypic, chemotaxonomic, and phylogenetic properties, we describe a new species of a novel genus Calculibacillus, represented by strain B5(T) (=KCTC 15397(T) =JCM 19989(T)), for which we propose the name Calculibacillus koreensis gen. nov., sp. nov.

Structural and biological function of NYD-SP15 as a new member of cytidine deaminases

Recent studies were mainly focus on the cytidine deaminase family genes, which contained a lot of members that varied on the function of catalytic deamination in RNA or DNA and were involved in the process of growth maintenance, host immunity, retroviral infection, tumorigenesis, and drug resistance with a feature of C-U deamination. In this study, we identified a new member of cytidine deaminase family, NYD-SP15. Previous work showed that the deduced structure of the protein contained two dCMP_cyt_deam domains, which were involved in zinc ion binding. NYD-SP15 was expressed variably in a wide range of tissues, indicating its worthy biological function and creative significances. Sequence analysis, RT-PCR, western blot, flow cytometry, direct-site mutation and GST pull-down assay were performed to analyze the construction and function of NYD-SP15. The results in our studies showed that NYD-SP15 was closely related to deoxycytidylate deaminase and cytidine deaminase, with authentic cytidine deaminase activity in vivo and vitro as well as homo dimerization effects. NYD-SP15 contained nuclear localization sequence (NLS) and nuclear export-signal (NES) and could dynamically shuttle between the nucleus and cytoplasm. Furthermore, NYD-SP15 gene over-expression reduced the cells growth and blocked G1 to S phase, which implied a potential inhibition effect on cell growth.

Differential Evolutionary Selection and Natural Evolvability Observed in ALT Proteins of Human Filarial Parasites

The abundant larval transcript (ALT-2) protein is present in all members of the Filarioidea, and has been reported as a potential candidate antigen for a subunit vaccine against lymphatic filariasis. To assess the potential for vaccine escape or heterologous protection, we examined the evolutionary selection acting on ALT-2. The ratios of nonsynonymous (K(a)) to synonymous (K(s)) mutation frequencies (ω) were calculated for the alt-2 genes of the lymphatic filariasis agents Brugia malayi and Wuchereria bancrofti and the agents of river blindness and African eyeworm disease Onchocerca volvulus and Loa loa. Two distinct Bayesian models of sequence evolution showed that ALT-2 of W. bancrofti and L. loa were under significant (P<0.05; P < 0.001) diversifying selection, while ALT-2 of B. malayi and O. volvulus were under neutral to stabilizing selection. Diversifying selection as measured by ω values was notably strongest on the region of ALT-2 encoding the signal peptide of L. loa and was elevated in the variable acidic domain of L. loa and W. bancrofti. Phylogenetic analysis indicated that the ALT-2 consensus sequences formed three clades: the first consisting of B. malayi, the second consisting of W. bancrofti, and the third containing both O. volvulus and L. loa. ALT-2 selection was therefore not predictable by phylogeny or pathology, as the two species parasitizing the eye were selected differently, as were the two species parasitizing the lymphatic system. The most immunogenic regions of L. loa and W. bancrofti ALT-2 sequence as modeled by antigenicity prediction analysis did not correspond with elevated levels of diversifying selection, and were not selected differently than predicted antigenic epitopes in B. malayi and O. volvulus. Measurements of ALT-2 evolvability made by χ2 analysis between alleles that were stable (O. volvulus and B. malayi) and those that were under diversifying selection (W. bancrofti and L. loa) indicated significant (P<0.01) deviations from a normal distribution for both W. bancrofti and L. loa. The relationship between evolvability and selection in L. loa followed a second order polynomial distribution (R2 = 0.89), indicating that the two factors relate to one another in accordance with an additional unknown factor. Taken together, these findings indicate discrete evolutionary drivers acting on ALT-2 of the four organisms examined, and the described variation has implications for design of novel vaccines and diagnostic reagents. Additionally, this represents the first mathematical description of evolvability in a naturally occurring setting.

Effect of time and diet change on the bacterial community structure throughout the gastrointestinal tract and in faeces of the northern brown bandicoot, Isoodon macrourus

A significant gap, in not only peramelid nutritional physiology but marsupial nutrition as a whole, is the lack of information relating to microorganisms of the gastrointestinal tract. This research is a preliminary investigation that will provide a baseline for comparisons among peramelids. The high degree of 16S rRNA gene clones identified in this research that are closely related to culturable bacteria suggests that additional research will enable a more complete description of the gastrointestinal bacteria of I. macrourus. Most identifiable clones belonged to Clostridium and Ruminococcus. This research has confirmed that the hindgut of I. macrourus, the caecum, proximal colon and distal colon, are the main sites for microbial activity.

Occurrence of viable, red-pigmented haloarchaea in the plumage of captive flamingoes

Flamingoes (Phoenicopterus spp.) whose plumage displays elegant colors, inhabit warm regions close to the ocean throughout the world. The pink or reddish color of their plumage originates from carotenoids ingested from carotenoid-abundant food sources, since flamingoes are unable to synthesize these compounds de novo. In this study, viable red-colored archaeal strains classified as extremely halophilic archaea (i.e., haloarchaea) and belonging to the genera Halococcus and Halogeometricum were isolated from the plumage of flamingoes in captivity. Detailed analysis for haloarchaeal community structure in flamingo feathers based on metagenomic data identified several haloarchaeal genera and unclassified sequences of the class Halobacteria at the genus level. Carotenoid pigment analyses showed that a bacterioruberin precursor carotenoid in haloarchaea was identical to one of the pigments found in flamingo plumage. To the best of our knowledge, this is the first report of viable extremophilic archaea in avian plumage, thus contributing to our understanding of the ecology of haloarchaea. The potential influence of haloarchaea as an environmental factor determining avian plumage coloration should be investigated in further studies.

Anaerosolibacter carboniphilus gen. nov., sp. nov., a strictly anaerobic iron-reducing bacterium isolated from coal-contaminated soil

A strictly anaerobic, mesophilic, iron-reducing bacterial strain, IRF19T, was isolated from coal-contaminated soil in the Republic of Korea. IRF19T cells were straight, rod-shaped, Gram-staining-negative and motile by means of flagella. The optimum pH and temperature for their growth were determined to be pH 7.5–8.0 and 40 °C, while the optimum range was pH 6.5–10.0 and 20–45 °C, respectively. Strain IRF19T did not require NaCl for growth but it tolerated up to 2 % (w/v). Growth was observed with yeast extract, d-glucose, d-fructose, d-ribose, d-mannitol, d-mannose, l-serine, l-alanine and l-isoleucine. Fe(III), elemental sulfur, thiosulfate and sulfate were used as electron acceptors. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain IRF19T is affiliated to the family Clostridiaceae and is most closely related to Salimesophilobacter vulgaris Zn2T (93.5 % similarity), Geosporobacter subterraneus VNs68T (93.2 %) and Thermotalea metallivorans B2-1T (92.3 %). The major cellular fatty acids of strain IRF19T were C14 : 0, iso-C15 : 0 and C16 : 0, and the profile was distinct from those of the closely related species. The major respiratory quinone of strain IRF19T was menaquinone MK-5 (V-H2). The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid and two unknown polar lipids. The G+C content of the genomic DNA of strain IRF19T was determined to be 37.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic results, strain IRF19T is considered to represent a novel species of a novel genus of the family Clostridiaceae , for which we propose the name Anaerosolibacter carboniphilus gen. nov., sp. nov., with the type strain IRF19T ( = KCTC 15396T = JCM 19988T).

Genetic variability and evolutionary diversification of membrane ABC transporters in plants

BACKGROUND

ATP-binding cassette proteins have been recognized as playing a crucial role in the regulation of growth and resistance processes in all kingdoms of life. They have been deeply studied in vertebrates because of their role in drug resistance, but much less is known about ABC superfamily functions in plants.

RESULTS

Recently released plant genome sequences allowed us to identify 803 ABC transporters in four vascular plants (Oryza. sativa, Solanum lycopersicum, Solanum tuberosum and Vitis vinifera) and 76 transporters in the green alga Volvox carteri, by comparing them with those reannotated in Arabidopsis thaliana and the yeast Saccharomyces cerevisiae. Retrieved proteins have been phylogenetically analysed to infer orthologous relationships. Most orthologous relationships in the A, D, E and F subfamilies were found, and interesting expansions within the ABCG subfamily were observed and discussed. A high level of purifying selection is acting in the five ABC subfamilies A, B, C, D and E. However, evolutionary rates of recent duplicate genes could influence vascular plant genome diversification. The transcription profiles of ABC genes within tomato organs revealed a broad functional role for some transporters and a more specific activity for others, suggesting the presence of key ABC regulators in tomato.

CONCLUSIONS

The findings achieved in this work could contribute to address several biological questions concerning the evolution of the relationship between genomes of different species. Plant ABC protein inventories obtained could be a valuable tool both for basic and applied studies. Indeed, interpolation of the putative role of gene functions can accelerate the discovering of new ABC superfamily members.

Draconibacterium filum sp. nov., a new species of the genus of Draconibacterium from sediment of the east coast of the Korean Peninsula

A Gram-stain negative, long rod shaped, facultatively anaerobic bacterium, designated strain F2(T), was isolated from coastal sediment of the Korean Peninsula. Strain F2(T) was found to grow at 10-40 °C (optimum 30 °C), at pH 6.0-8.5 (optimum pH 7.5) and at 0.0-8.0 % (w/v) NaCl (optimum 3.0 %). Phylogenetic analysis of the 16S rRNA gene sequence showed that strain F2(T) is closely related to Draconibacterium orientale FH5(T) (with 97.9 % 16S rRNA gene similarity) of the family Prolixibacteraceae of the phylum Bacteroidetes. The major isoprenoid quinone was identified as MK-7 and the main fatty acids as iso-C15:0 (24.1 %), anteiso-C15:0 (15.4 %), C16:0 (10.7 %), iso-C17:0 3-OH (7.6 %) and iso-C16:0 3-OH (5.9 %). The major polar lipids were identified as phosphatidylethanolamine, phosphatidylinositol and four unidentified polar lipids. The genomic DNA G+C content of strain F2(T) was determined to be 44.7 mol% and the DNA-DNA relatedness of strain F2(T) with D. orientale DSM 25947(T) was 34.6 ± 4.3 %. Nitrate reduction capability and cell morphology of strain F2(T) are distinct from those of the closest relative, D. orientale DSM 25947(T). Based on these properties, we propose strain F2(T) represents a novel species within the genus Draconibacterium, with the name Draconibacterium filum sp. nov. The type strain of D. filum is F2(T) (=KCTC 32486(T) = JCM 19986(T)).

Unusual tandem expansion and positive selection in subgroups of the plant GRAS transcription factor superfamily

BACKGROUND

GRAS proteins belong to a plant transcription factor family that is involved with multifarious roles in plants. Although previous studies of this protein family have been reported for Arabidopsis, rice, Chinese cabbage and other species, investigation of expansion patterns and evolutionary rate on the basis of comparative genomics in different species remains inadequate.

RESULTS

A total of 289 GRAS genes were identified in Arabidopsis, B. distachyon, rice, soybean, S. moellendorffii, and P. patens and were grouped into seven subfamilies, supported by the similarity of their exon-intron patterns and structural motifs. All of tandem duplicated genes were found in group II except one cluster of rice, indicating that tandem duplication greatly promoted the expansion of group II. Furthermore, segment duplications were mainly found in the soybean genome, whereas no single expansion pattern dominated in other plant species indicating that GRAS genes from these five species might be subject to a more complex evolutionary mechanism. Interestingly, branch-site model analyses of positive selection showed that a number of sites were positively selected under foreground branches I and V. These results strongly indicated that these groups were experiencing higher positive selection pressure. Meanwhile, the site-specific model revealed that the GRAS genes were under strong positive selection in P. patens. DIVERGE v2.0 was used to detect critical amino acid sites, and the results showed that the shifted evolutionary rate was mainly attributed to the functional divergence between the GRAS genes in the two groups. In addition, the results also demonstrated the expression divergence of the GRAS duplicated genes in the evolution. In short, the results above provide a solid foundation for further functional dissection of the GRAS gene superfamily.

CONCLUSIONS

In this work, differential expression, evolutionary rate, and expansion patterns of the GRAS gene family in the six species were predicted. Especially, tandem duplication events played an important role in expansion of group II. Together, these results contribute to further functional analysis and the molecular evolution of the GRAS gene superfamily.

Desulfotomaculum tongense sp. nov., a moderately thermophilic sulfate-reducing bacterium isolated from a hydrothermal vent sediment collected from the Tofua Arc in the Tonga Trench

A novel, strictly anaerobic, moderately thermophilic, endospore-forming, sulfate-reducing bacterium, designated TGB60-1T, was isolated from a hydrothermal sediment vent collected from the Tofua Arc in the Tonga Trench. The strain was characterized phenotypically and phylogenetically. The isolated strain was observed to be Gram-positive, with slightly curved rod-shaped cells and a polar flagellum. Strain TGB60-1T was found to grow anaerobically at 37–60 °C (optimum, 50 °C), at pH 6.0–8.5 (optimum, pH 7.0) and with 1.0–4.0 % (w/v) NaCl (optimum, 3.0 %). The electron acceptors utilised were determined to be sulfate, sulfite, and thiosulfate. Strain TGB60-1T was found to utilise pyruvate and H2 as electron donors. Strain TGB60-1T was determined to be related to representatives of the genus Desulfotomaculum and the closest relatives within this genus were identified as Desulfotomaculum halophilum SEBR 3139T, Desulfotomaculum alkaliphilum S1T and Desulfotomaculum peckii LINDBHT1T (92.7, 92.1, and 91.8 % 16S rRNA gene sequence similarity, respectively). The major fatty acids (>20 %) were identified as C16:0 and C18:1 ω7c. The G+C content of the genomic DNA of this novel bacterium was determined to be 53.9 mol%. Based on this polyphasic taxonomic study, strain TGB60-1T is considered to represent a novel species in the genus Desulfotomaculum, for which the name Desulfotomaculum tongense sp. nov. is proposed. The type strain of D. tongense is strain TGB60-1T (= KTCT 4534T = JCM 18733T).

Halolamina rubra sp. nov., a haloarchaeon isolated from non-purified solar salt

Two Gram-stain negative, rod-shaped and motile extreme halophiles, designated CBA1107(T) and CBA1108, were isolated from non-purified solar salt. Based on the phylogenetic analysis, strains CBA1107(T) and CBA1108 were shown to belong to the genus Halolamina, with similarities for the 16S rRNA gene sequences between strains CBA1107(T) and Halolamina pelagica TBN21(T) , Halolamina salina WSY15-H3(T) and Halolamina salifodinae WSY15-H1(T) of 98.3, 97.6 and 97.3 %, respectively; the similarities for the rpoB' gene sequences between the same strains were 96.0, 95.3 and 94.6 %, respectively. The colonies of both strains were observed to be red pigmented on growth medium. Strain CBA1107(T) was observed to grow at 20-50 °C, in the presence of 15-30 % NaCl, at pH 6.0-9.0, and with 0.005-0.5 M Mg(2+). The cells of both strains lysed in distilled water. The DNA-DNA hybridization experiments showed that strain CBA1107(T) shared 97 % relatedness with CBA1108 and <50 % relatedness with H. pelagica JCM 16809(T), H. salina JCM 18549(T) and H. salifodinae JCM 18548(T). The genomic DNA G+C content of strain CBA1107(T) was determined to be 65.1 mol%. The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and glycolipids including sulfated mannosyl glucosyl diether and mannosyl glucosyl diether. Based on the polyphasic taxonomic analyses, the strains are considered to represent a new taxon for which the name Halolamina rubra sp. nov. is proposed, with the type strain CBA1107(T) (=CECT 8421(T) =JCM 19436(T)).

Halobellus rufus sp. nov., an extremely halophilic archaeon isolated from non-purified solar salt

A halophilic archaeon, designed strain CBA1103(T), was isolated from non-purified solar salt. The cells of strain CBA1103(T) were observed to be Gram-stain negative and pleomorphic, and the colonies appear red. Strain CBA1103(T) was observed to grow between 20 and 55 °C (optimum 37 °C), and in NaCl concentrations of 10-30 % (w/v) (optimum 15 %) with 0-0.5 M MgSO4·7H2O (optimum 0.1 M) and at pH 6.0-9.0 (optimum pH 7.0). Additionally, the cells lyse in distilled water. The major polar lipids of strain CBA1103(T) are phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and two glycolipids chromatographically identical to sulfated mannosyl glucosyl diether and manosyl glucosyl diether. Strain CBA1103(T) is shown to belong to the Halobellus genus and exhibits similarity to related taxa; the 16S rRNA gene sequence similarity between strain CBA1103(T) and Halobellus rarus 18362(T), Hbs. limi 16811(T), Hbs. litoreus JCM 17118(T), Hbs. inordinatus YC20(T), Hbs. clavatus TNN18(T) and Hbs. salinus CSW2.24.4(T) is 97.3, 96.5, 96.5, 94.5, 94.5 and 93.7 %, respectively. The RNA polymerase subunit B gene sequence of strain CBA1103(T) shows 93.7 % similarity with the sequence of Hbs. litoreus JCM 17118(T); the similarity is lower with sequences from the type strains of other species of Halobellus. The genomic DNA G+C content of strain CBA1103(T) was determined to be 67.0 mol% a value which is in the range of the genomic DNA G+C content of members of the genus Halobellus (61.5-69.2 mol%). These results suggest that strain CBA1103(T) should be considered to represent a new taxon for which the name Halobellus rufus sp. nov. is proposed, with the type strain CBA1103(T) (=CECT 8423(T) =JCM 19434(T)).

Halorubrum halophilum sp. nov., an extremely halophilic archaeon isolated from a salt-fermented seafood

A novel, red-pigmented, pleomorphic and short rod-shaped haloarchaeon, designated B8(T), was isolated from a salt-fermented seafood. Strain B8(T) was found to be able to grow at 20-45 °C, in the presence of 15-30 % (w/v) NaCl and at pH 7.0-9.0. The optimum requirements were found to be a temperature range of 35-40 °C, pH 8.0 and the presence of 25 % NaCl. The cells of strain B8(T) were observed to be Gram-staining negative and lysed in distilled water. Anaerobic growth did not occur in the presence of nitrate, L-arginine, dimethyl sulfoxide or trimethylamine N-oxide. The catalase and oxidase activities were found to be positive and nitrate was reduced in aerobic conditions. Tween 20, 40 and 80 were found to be hydrolyzed, whereas casein, gelatin and starch were not hydrolyzed. Indole or H2S was not formed and urease activity was not detected. A phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain B8(T) is most closely related to members of the genus Halorubrum in the family Halobacteriaceae. Strain B8(T) was found to have three 16S rRNA genes, rrnA, rrnB and rrnC; similarities between the 16S rRNA gene sequences are 99.0-99.8 %. Strain B8(T) shared 99.0 % 16S rRNA gene sequence similarity with Halorubrum (Hrr.) lipolyticum JCM 13559(T) and Hrr. saccharovorum DSM 1137(T), 98.8 % with Hrr. kocurii JCM 14978(T), 98.3 % with Hrr. lacusprofundi DSM 5036(T), 98.0 % with Hrr. arcis JCM 13916(T), 97.7 % with Hrr. aidingense JCM 13560(T) and 97.0 % with Hrr. aquaticum JCM 14031(T), as well as 93.7-96.5 % with other type strains in the genus Halorubrum. The RNA polymerase subunit B' gene sequence similarity of strain B8(T) with Hrr. kocurii JCM 14978(T) is 97.2 % and lower with other members of the genus Halorubrum. DNA-DNA hybridization experiments showed that strain B8(T) shared equal or lower than 50 % relatedness with reference species in the genus Halorubrum. The genomic DNA G+C content of strain B8(T) was determined to be 64.6 mol%. The major isoprenoid quinone of strain B8(T) was identified as menaquinone-8 and the major polar lipids as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, sulfated mannosyl glucosyl diether and an unidentified phospholipid. Based on this polyphasic taxonomic study, strain B8(T) is considered to represent a new species in the genus Halorubrum, for which the name Hrr. halophilum sp. nov. is proposed. The type strain is B8(T) (=JCM 18963(T) = CECT 8278(T)).