First draft genome assemblies of Pleochaeta shiraiana and Phyllactinia moricola, two tree-parasitic powdery mildew fungi with hemiendophytic mycelia

Powdery mildew fungi (Erysiphaceae) are widespread obligate biotrophic plant pathogens. Thus, applying genetic and omics approaches to study these fungi remains a major challenge, particularly for species with hemiendophytic mycelium. These belong to a distinct phylogenetic lineage within the Erysiphaceae. To date, only a single draft genome assembly is available for this clade, determined in Leveillula taurica. Here, we generated the first draft genome assemblies of Pleochaeta shiraiana and Phyllactinia moricola, two tree-parasitic powdery mildew species with hemiendophytic mycelium, representing two genera that have not been investigated with genomics tools yet. Together with the draft genome of L. taurica, these resources will be pivotal for understanding the molecular basis of the lifestyle of these fungi, which is unique within the Erysiphaceae.

Diversity of Coronaviruses in Wild Representatives of the Aves Class in Poland

The revealed prevalence of coronaviruses in wild bird populations in Poland was 4.15% and the main reservoirs were birds from orders Anseriformes and Charadriiformes, with a prevalence of 3.51% and 5.59%, respectively. Gammacoronaviruses were detected more often than deltacoronaviruses, with detection rates of 3.5% and 0.7%, respectively. Gammacoronaviruses were detected in birds belonging to six orders, including Anseriformes, Charadriiformes, Columbiformes, Galliformes, Gruiformes, and Passeriformes, indicating a relatively wide host range. Interestingly, this was the only coronavirus detected in Anseriformes (3.51%), while in Charadriiformes, the prevalence was 3.1%. The identified gammacoronaviruses belonged to the Igacovirus and Brangacovirus subgeneras. Most of these were igacoviruses and formed a common phylogenetic group with a Duck Coronavirus 2714 and two with an Avian Coronavirus/Avian Coronavirus9203, while the viruses from the pigeons formed a distinct “pigeon-like” group, not yet officially represented. The presence of deltacoronaviruses was detected in birds belonging to three orders, Charadriiformes, Galliformes, and Suliformes indicating a narrower host range. Most identified deltacoronaviruses belonged to the Buldecovirus subgenus, while only one belonged to Herdecovirus. Interestingly, the majority of buldecoviruses were identified in gulls, and they formed a distinct phylogenetic lineage not represented by any officially ratified virus species. Another separate group of buldecoviruses, also not represented by the official species, was formed by a virus identified in a common snipe. Only one identified buldecovirus (from common pheasant) formed a group with the ratified species Coronavirus HKU15. The results obtained indicate the high diversity of detected coronaviruses, and thus also the need to update their taxonomy (establishing new representative virus species). The serological studies performed revealed antibodies against an infectious bronchitis virus in the sera of white storks and mallards.

Mangrovimonas spongiae sp. nov., a novel member of the genus Mangrovimonas isolated from marine sponge

A taxonomic study was carried out on strain HN-E26T, which was isolated from sponge collected from Yangpu Bay, Hainan, PR China. Cells of strain HN-E26T were Gram-stain-negative, motile by gliding, yellow-pigmented and rod-shaped. The strain could grow at 10–40 °C (optimum, 25 °C), at pH 6.0–9.0 (optimum, pH 7.0) and in 0.5–12 % (w/v) NaCl (optimum, 4–7 %). This isolate was positive for oxidase, catalase, and the hydrolysis of starch, xylan, aesculin and gelatin, but negative for indole production and the reduction of nitrate. Strain HN-E26T shared the highest 16S rRNA gene sequence similarity with Mangrovimonas yunxiaonensis LYYY01T (95.5 %), followed by Formosa spongicola A2T (94.4 %), Meridianimaribacter flavus NH57NT (94.3 %) and Winogradskyella exilis 022-2-26T (94.3 %). The phylogenetic tree based on 16S rRNA gene sequences revealed that strain HN-E26T formed a distinct phylogenetic lineage within the cluster comprising Mangrovimonas yunxiaonensis LYYY01T and ‘ Mangrovimonas xylaniphaga ’ ST2L12T. The dominant fatty acids were iso-C15 : 0 and iso-C15 : 1 G. The major polar lipids comprised phosphatidylethanolamine, three unidentified aminolipids and six unidentified lipids. The respiratory lipoquinone was identified as MK-6. The G+C content of the genomic DNA was 33.9 mol%. Based on the phenotypic and phylogenetic data, strain HN-E26T represents a novel species of the genus Mangrovimonas , for which the name Mangrovimonas spongiae sp. nov. is proposed, with the type strain HN-E26T (=MCCC 1K03326T=LMG 30458T).

Erythrobacter spongiae sp. nov., isolated from marine sponge

A taxonomic study was carried out on strain HN-E23T, which was isolated from sponge collected from Yangpu Bay, Hainan, China. Cells of strain HN-E23T were Gram-stain-negative, non-motile, orange-yellow-pigmented, short rods, that could grow at 10–40 °C (optimum, 28 °C), at pH 5–11 (optimun, pH 7) and in 0.5–12 % (w/v) NaCl (optimum, 3 %). This isolate was positive for oxidase, catalase, and the hydrolysis of aesculin, but negative for indole production and the reduction of nitrate. The phylogenetic tree based on 16S rRNA gene sequences revealed that strain HN-E23T formed a distinct phylogenetic lineage within the cluster comprising Erythrobacter strains. Strain HN-E23T shared the highest 16S rRNA gene sequence similarity to Erythrobacter aquimixticola JSSK-14T (97.2 %), followed by Erythrobacter atlanticus s21-N3T (96.6 %), Erythrobacter luteus KA37T (96.5 %) and Erythrobacter citreus RE35F/1T (96.4 %). The digital DNA–DNA hybridization (dDDH) and the average nucleotide identity (ANI) values between strain HN-E23T and JSSK-14T were 18.8 and 74.9 %, respectively. The dDDH and ANI values are below the standard cut-off criteria for delineation of bacterial species. The dominant fatty acids were summed feature 8 (C18 : 1ω7c/ω6c), C16 : 0 and summed feature 3 (C16 : 1ω7c/ω6c). The major polar lipids comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, an unidentified glycolipid and six unidentified lipids. The respiratory lipoquinone was identified as Q-10. The G+C content of the genomic DNA was 65.5 mol%. Based on the phenotypic and phylogenetic data, strain HN-E23T represents a novel species of the genus Erythrobacter , for which the name Erythrobacter spongiae sp. nov. is proposed, with the type strain HN-E23T (=MCCC 1K03331T=LMG 30457T).

Draft Genome Sequence of Agrobacterium sp. Strain R89-1, a Morphine Alkaloid-Biotransforming Bacterium

Agrobacterium sp. strain R89-1 isolated from composted wastes of Papaver somniferum can effectively biotransform codeine/morphine into 14-OH-derivatives. Here, we present a 4.7-Mb assembly of the R89-1 strain genome. The draft shows that the strain R89-1 represents a distinct phylogenetic lineage within the genus Agrobacterium.

Photobacterium aquae sp. nov., isolated from a recirculating mariculture system

A Gram-staining-negative, heterotrophic, facultatively anaerobic bacterium, designated AE6T, was isolated from a grouper (Epinephelus malabaricas) culture tank in a recirculating mariculture system located in Tianjin, China. Strain AE6T was able to grow at 15–40 °C (optimum, 30–35 °C), at pH 5.5–10.0 (optimum, pH 7.0–7.5) and in the presence of 0.5–7 % (w/v) NaCl (optimum, 2–3 %). It contained Q-8 as the predominant respiratory quinone, phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) as the major polar lipids and C16 : 1ω7c/C16 : 1ω6c (40.4 %), C18 : 1ω7c (15.5 %) and C16 : 0 (13.5 %) as the predominant cellular fatty acids. The genomic DNA G+C content was 47.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AE6T belonged to the genus Photobacterium (94.2–96.8 % of 16S rRNA gene sequence similarity) and formed a distinct phylogenetic lineage within the genus and exhibited the highest sequence similarity to Photobacterium aphoticum CECT 7614T (96.8 %). Multilocus sequence analysis (MLSA) using four loci (gyrB, rpoA, pyrH and recA) also revealed that strain AE6T was phylogenetically related to the genus Photobacterium . Based on the phylogenetic, chemotaxonomic and phenotypic evidence, strain AE6T is considered to represent a novel species of the genus Photobacterium , for which the name Photobacterium aquae sp. nov. is proposed. The type strain is AE6T ( = CGMCC 1.12159T = JCM 18480T).

Draft Genome Sequence of Strain P7-3-5, a New Flavobacteriaceae Bacterium Isolated from Intertidal Sand

ABSTRACTTheFlavobacteriaceaebacterium strain P7-3-5 was isolated from intertidal sand of the Yellow Sea, China. Analysis of the 16S rRNA gene sequences showed that strain P7-3-5 formed a distinct phylogenetic lineage within the familyFlavobacteriaceae.The genome of strain P7-3-5 was sequenced to facilitate the physiological, ecological, and evolutionary studies of the bacteria within the familyFlavobacteriaceae.

Characterization of intronic structures and alternative splicing in Phytophthora sojae by comparative analysis of expressed sequence tags and genomic sequences

The oomycetes, a distinct phylogenetic lineage of fungus-like microorganisms, are heterokonts (stramenopiles) belonging to the supergroup Chromalveolata. Although the complete genomic sequences of a number of oomycetes have been reported, little information regarding the introns therein is available. Here, we investigated the introns of Phytophthora sojae , a pathogen that causes soybean root and stem rot, by a comparative analysis of genomic sequences and expressed sequence tags. A total of 4013 introns were identified, of which 96.6% contained canonical splice sites. The P. sojae genome possessed features distinct from other organisms at 5′ splice sites, polypyrimidine tracts, branch sites, and 3′ splice sites. Diverse repeating sequences, ranging from 2 to 10 nucleotides in length, were found at more than half of the intron–exon boundaries. Furthermore, 122 genes underwent alternative splicing. These data indicate that P. sojae has unique splicing mechanisms, and recognition of those mechanisms may lead to more accurate predictions of the location of introns in P. sojae and even other oomycete species.

Cocleimonas flava gen. nov., sp. nov., a gammaproteobacterium isolated from sand snail (Umbonium costatum)

A Gram-stain-negative, aerobic, yellow-pigmented, heterotrophic, sulfur-oxidizing, non-motile, rod-shaped bacterium, designated KMM 3898T, was isolated from an internal tissue of the sand snail Umbonium costatum, collected from the shallow sediments of the Sea of Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KMM 3898T formed a distinct phylogenetic lineage within the class Gammaproteobacteria and was most closely related to Leucothrix mucor DSM 2157T (89.2 % 16S rRNA gene sequence similarity) and members of the genus Thiothrix (86.7–88.5 %). Chemotaxonomically, strain KMM 3898T contained the isoprenoid quinone Q-8, the polar lipids phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown phospholipid and the fatty acids C18 : 1 ω7c, C16 : 1 ω7c and C16 : 0 as predominant components (>10 %). The DNA G+C content of strain KMM 3898T was 43.4 mol%. On the basis of phenotypic features and phylogenetic analysis, strain KMM 3898T represents a novel genus and species, for which the name Cocleimonas flava gen. nov., sp. nov. is proposed. The type strain is KMM 3898T (=NRIC 0757T =JCM 16494T).

Erythrobacter gangjinensis sp. nov., a marine bacterium isolated from seawater

A novel Gram-negative, aerobic, orange-pigmented bacterial strain, designated K7-2T, was isolated from seawater of Gangjin Bay, Korea, and subjected to a polyphasic taxonomic study. Strain K7-2T contained ubiquinone-10 (Q-10) as the predominant respiratory lipoquinone and did not produce bacteriochlorophyll a. Major fatty acids were C18 : 1 ω7c (51.4 %), iso-C15 : 0 2-OH and/or C16 : 1 ω7c (15.0 %) and C17 : 1 ω6c (8.8 %). Major polar lipids were phosphatidylethanolamine and phosphatidylcholine. The DNA G+C content was 61.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain K7-2T formed a distinct phylogenetic lineage within the cluster comprising Erythrobacter strains. Similarities between the 16S rRNA gene sequences of strain K7-2T and the type strains of Erythrobacter species ranged from 95.0 % (Erythrobacter litoralis DSM 8509T) to 96.8 % (Erythrobacter citreus RE35F/1T). On the basis of polyphasic taxonomic data, strain K7-2T (=KCTC 22330T=JCM 15420T) is classified in a novel species within the genus Erythrobacter, for which the name Erythrobacter gangjinensis sp. nov. is proposed.