Roseomonas bella sp. nov., isolated from lake sediment Zhang, Jin-Yu; Jiang, Xiao-Bing; Zhu, Di ...
International journal of systematic and evolutionary microbiology,
10/2020, Letnik:
70, Številka:
10
Journal Article
Recenzirano
Odprti dostop
A Gram-stain-negative, non-motile, coccus-shaped, catalase- and oxidase-positive, facultatively anaerobic and pink-pigmented bacterium, designated strain CQN31
T
, was isolated from sediment of ...Changqiaohai Lake, Yunnan Province, China. Growth occurred at 4–45 °C (optimum, 37 °C), at pH 6.5–9.5 (optimum, pH 8.0) and with 0–1 % (w/v) NaCl (optimum, 0 %). C
18 : 1
ω
7
c
/C
18 : 1
ω
6
c
and C
16 : 0
were the predominant fatty acids. Phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidyldimethylethanolamine (PME) and one unidentified aminolipid (AL) were the major polar lipids. The G+C content of the genomic DNA was 71.5 %. 16S rRNA gene sequence comparisons indicated that strain CQN31
T
shared 96.8 % similarity with
Roseomonas wooponensis
JCM 19527
T
and 95.9 % with
R. terricola
EM0302
T
. Digital DNA–DNA hybridization values between strain CQN31
T
and
Roseomonas stagni
DSM 19981
T
,
R. rosea
DSM 14916
T
and
R. mucosa
NCTC 13291
T
were 21.0, 19.4 and 19.8 %, respectively. Average amino acid identity and average nucleotide identity values between strain CQN31
T
and
R. stagni
DSM 19981
T
,
R. rosea
DSM 14916
T
and
R. mucosa
NCTC 13291
T
were 73.7, 63.4 and 61.9 %, and 79.2, 77.1 and 77.5%, respectively. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain CQN31
T
as a representative of a novel species in the genus
Roseomonas
, for which the name
Roseomonas bella
sp. nov. is proposed. The type strain is CQN31
T
(=KCTC 62447
T
=MCCC 1H00309
T
).
In the present study, the genomes of B. subtilis EM-A7 and B. velezensis EM-A8 were sequenced and annotated. The Illumina sequencing platform (NovaSeq PE150) was used to sequence the genomic DNA. ...There were 6 277 054 raw reads for EM-A7, with a Q20 of 97.52 % and 43.78 % GC, and 8 030 262 raw reads for EM-A8, with a Q20 of 97.53 % and 46.21 % GC. Annotation was carried out by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). The strains were classified taxonomically on the basis of an average nucleotide identity analysis (ANI), as well as through a dDDh analysis on the Genome-to-Genome Distance Calculator (GGDC v3.0). The pipeline predicted 4062 protein-coding sequences (CDSs) and 73 RNA genes (62 tRNA and 6 rRNA) for EM-A7, and 3797 protein-coding sequences (CDSs) and 80 RNA genes for EM-A8. These findings enhance our understanding of the two strains’ potential as biocontrol agents to manage disease in maize.
•Reports the draft genome sequences of B. subtilis strain EM-A7 and B. velezensis strain EM-A8, two biocontrol agents isolated from the maize phyllosphere.•The taxonomic classification of EM-A7 and EM-A8 strains was performed with an average nucleotide identity analysis (ANI) and the Genome-to-Genome Distance Calculator.•In EM-A7, 4062 protein-coding sequences (CDSs) were predicted, and 73 RNA genes (62 tRNA and 6 rRNA).•The PGAP predicted EM-A8 3797 protein-coding sequences (CDSs) and 80 RNA genes.
A novel bacterial strain, N1Y112
T
, was isolated from coastal sediment collected in Weihai, PR China. This Gram-stain-negative, facultatively anaerobic, motile rod-shaped bacterium exhibited the ...ability to oxidize thiosulphate to sulphate and reduce nitrate to ammonia through its Sox system and nitrate reduction pathway, respectively. The strain grew at 20–35 °C (optimum, 28 °C), pH 6.0–10.0 (optimum, pH 7.5) and in the presence of 1.0–5.0 % (w/v) NaCl (optimum, 3.0 %). Major fatty acids present in the strain included summed feature 8 (comprising C
18 : 1
ω
7
c
and/or C
18 : 1
ω
6
c
), summed feature 3 (comprising C
16 : 1
ω
7
c
and/or C
16 : 1
ω
6
c
) and C
16 : 0
. Its polar lipid profile consisted of one phosphatidylethanolamine, two unknown aminolipids, one aminophosphoglycolipid, one diphosphatidylglycerol, one phosphatidylglycerol, two unknown phospholipids and two unknown lipids. Strain N1Y112
T
contained ubiquinone-7 and ubiquinone-8 as isoprenoid quinones, with a genomic G+C content of 50.6 mol%. Based on phylogenetic analysis, strain N1Y112
T
clustered with
Pontibacterium granulatum
JCM 30316
T
being its closest relative at 97.1 % 16S rRNA gene sequence similarity. The average nucleotide identity and digital DNA–DNA hybridization values were 77.1 and 20.7 %, respectively, which suggest significant differences between genomes of N1Y112
T
and
P. granulatum
JCM 30316
T
. Based on the findings from its phenotypic, genotypic and phylogenetic analyses, N1Y112
T
is considered to represent a novel species of the genus
Pontibacterium
, for which the name
Pontibacterium sinense
sp. nov. is proposed. The type strain is N1Y112
T
(=KCTC 72927
T
=MCCC 1H00429
T
).
The Lemon shark
is an important species experiencing conservation issues that is in need of genomic resources. Herein, we conducted a genome survey sequencing in
and determined genome size, explored ...repetitive elements, assembled and annotated the 45S rRNA DNA operon, and assembled and described in detail the mitochondrial genome. Lastly, the phylogenetic position of
in the family Carcharhinidae was examined using translated protein coding genes. The estimated haploid genome size ranged between 2.29 and 2.58 Gbp using a k-mer analysis, which is slightly below the genome size estimated for other sharks belonging to the family Carcharhinidae. Using a k-mer analysis, approx. 64-71 % of the genome of
was composed of repetitive elements. A relatively large proportion of the 'repeatome' could not be annotated. Taking into account only annotated repetitive elements, Class I - Long Interspersed Nuclear Element (LINE) were the most abundant repetitive elements followed by Class I - Penelope and Satellite DNA. The nuclear ribosomal operon was fully assembled. The AT-rich complete mitochondrial genome was 16,703 bp long and encoded 13 protein coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes.
is closely related to the genera
,
and
in the family Carcharinidae. This new genomic resources will aid with the development of conservation plans for this large coastal shark.
Three Gram-stain-negative, facultatively anaerobic, rod-shaped, catalase-positive, oxidase-negative bacterial strains were designated as hw1
T
, hw8
T
and hw3
T
. Strains hw1
T
, hw8
T
and hw3
T
grew ...at 15–28 °C (optimum, 25 °C), 15–35 °C (optimum, 30 °C) and 4–28 °C (optimum, 20 °C), respectively, and at pH 7.0–12.0 (optimum, pH 9.0), pH 6.0–11.0 (optimum, pH 9.0) and 5.0–12.0 (optimum, pH 7.0), respectively. Additionally, strains hw1
T
and hw8
T
only grew when the NaCl concentration was 0 %, while strain hw3
T
grew at between 0 and 0.5 % (w/v; optimum, 0 %). The average nucleotide identity (ANI) values between strains hw1
T
, hw8
T
and the
Roseateles
type strains ranged from 73.8 to 84.2 %, while the digital DNA–DNA hybridization (dDDH) values ranged from 19.7 to 27.5 %. The ANI values between strain hw3
T
and the
Janthinobacterium
type strains ranged from 78.7 to 80.7 %, while dDDH values ranged from 22.3 to 23.0 %. The draft genomes of strains hw1
T
, hw8
T
and hw3
T
consisted of 5.5, 4.4 and 5.9 Mbp, with DNA G+C contents of 61.7, 61.8 and 66.0 mol%, respectively. The results of the dDDH, ANI, phylogenetic, biochemical and physiological analyses indicated that the novel strains were distinct from other members of their genera. Thus, we proposed the names
Roseateles albus
sp. nov. (type strain hw1
T
= KACC 22887
T
= TBRC 16613
T
),
Roseateles koreensis
sp. nov. (type strain hw8
T
= KACC 22885
T
= TBRC 16614
T
) and
Janthinobacterium fluminis
sp. nov. (type strain hw3
T
= KACC 22886
T
= TBRC 16615
T
).
The whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) is among the 100 worst invasive species in the world. As one of the most important crop pests and virus vectors, B. tabaci causes substantial crop ...losses and poses a serious threat to global food security.
We report the 615-Mb high-quality genome sequence of B. tabaci Middle East-Asia Minor 1 (MEAM1), the first genome sequence in the Aleyrodidae family, which contains 15,664 protein-coding genes. The B. tabaci genome is highly divergent from other sequenced hemipteran genomes, sharing no detectable synteny. A number of known detoxification gene families, including cytochrome P450s and UDP-glucuronosyltransferases, are significantly expanded in B. tabaci. Other expanded gene families, including cathepsins, large clusters of tandemly duplicated B. tabaci-specific genes, and phosphatidylethanolamine-binding proteins (PEBPs), were found to be associated with virus acquisition and transmission and/or insecticide resistance, likely contributing to the global invasiveness and efficient virus transmission capacity of B. tabaci. The presence of 142 horizontally transferred genes from bacteria or fungi in the B. tabaci genome, including genes encoding hopanoid/sterol synthesis and xenobiotic detoxification enzymes that are not present in other insects, offers novel insights into the unique biological adaptations of this insect such as polyphagy and insecticide resistance. Interestingly, two adjacent bacterial pantothenate biosynthesis genes, panB and panC, have been co-transferred into B. tabaci and fused into a single gene that has acquired introns during its evolution.
The B. tabaci genome contains numerous genetic novelties, including expansions in gene families associated with insecticide resistance, detoxification and virus transmission, as well as numerous horizontally transferred genes from bacteria and fungi. We believe these novelties likely have shaped B. tabaci as a highly invasive polyphagous crop pest and efficient vector of plant viruses. The genome serves as a reference for resolving the B. tabaci cryptic species complex, understanding fundamental biological novelties, and providing valuable genetic information to assist the development of novel strategies for controlling whiteflies and the viruses they transmit.
We report the draft genome sequence of Bacillus thuringiensis serovar aizawai AS23, an insecticidal strain targeting lepidopteran pests, which was isolated from the rhizosphere of Korean melon ...(Cucumis melo L.). The genome of strain AS23 comprising 6,846,584 bp with a G + C content of 34.83% was assembled to 11 contigs obtained using hybrid assembly. Additionally, we mined the genome for pesticidal genes, identifying several insecticidal genes, including Cry1Aa3, Cry1Ca9, Cry1Da2, Cry1Ia44, Cry2Ab41, Cry9Ea9, Spp1Aa1, and Vip3Aa86.
In this study, we present the draft genome of Aureobasidium pullulans strain MHAU2101, which is the first strain to effectively control fire blight caused by Erwinia amylovora in Korea. The genome of ...strain MHAU2101 was composed of 28,669,322 base pairs, with a C+G content of 50.4%. The assembly comprised 17 contigs and had 99.22% completeness. The results of this study will be a valuable resource for future research on the biocontrol mechanism of A. pullulans strain MHAU2101.
We report the draft genome sequence of Bacillus thuringiensis serovar aizawai AS23, an insecticidal strain targeting lepidopteran pests, which was isolated from the rhizosphere of Korean melon ...(Cucumis melo L.). The genome of strain AS23 comprising 6,846,584 bp with a G + C content of 34.83% was assembled to 11 contigs obtained using hybrid assembly. Additionally, we mined the genome for pesticidal genes, identifying several insecticidal genes, including Cry1Aa3, Cry1Ca9, Cry1Da2, Cry1Ia44, Cry2Ab41, Cry9Ea9, Spp1Aa1, and Vip3Aa86. KCI Citation Count: 0
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