Morphological, cultural, physiological and biochemical characteristics
Colonies of strain H3-26T were milky-white, round, moist, translucent, neat edges on R2A solid medium (Fig. 1A). Strain H3-26T was gram-negative, facultative anaerobic, immobile, rod-shaped, single or paired, 0.6–0.9 µm×0.9–2.7 µm (Fig. 1B, 1C and 1D). Strain H3-26T showed many similar phenotypic characteristics with reference strains of Deefgea, but there were a few of differences. Detailed results of the phenotypic and biochemical characterization of strain H3-26T are provided in Table 1 and in the species description.
Table 1
Differential phenotypic characteristics of strain H3-26T and its closely related species of the genus Deefgea
Characteristic
|
1
|
2
|
3
|
Cell size (width×length; µm)
|
0.6–0.9×0.9–2.7
|
0.7–0.9×1.9–3.7
|
0.7–0.9×1.7–3.2
|
Source
|
gills
|
hard-water
|
wetland
|
Temperature range (optimum) (℃)
|
4–30(25)
|
4–32(23–28)
|
15–37 (25–30)
|
pH range (optimum)
|
5.0–11.0(7.0)
|
5.8–8.5(7.3–7.6)
|
6.0–8.0(7.0)
|
Motility
|
-
|
+
|
+
|
Anaerobic growth
|
+
|
+
|
-
|
glucose acidification
|
-
|
-
|
+
|
glucose assimilation
|
+
|
-
|
+
|
gluconate assimilation
|
+
|
+w
|
+
|
N-acetylglucosamine assimilation
|
+
|
+w
|
+
|
Nitrate reduction
|
+
|
+w
|
+
|
mannose assimilation
|
+
|
-
|
+
|
tryptophan deaminase
|
-
|
-
|
+
|
Alkaline phosphatase
|
-
|
ND
|
+
|
trypsin
|
-
|
ND
|
+
|
D-mannose
|
+
|
-
|
+
|
D-sucrose
|
-
|
+
|
-
|
salicin
|
-
|
-
|
+
|
D-cellobiose
|
-
|
-
|
+w
|
D-maltose
|
-
|
-
|
+w
|
D-fucose
|
-
|
-
|
+w
|
Potassium 5-ketogluconate
|
-
|
-
|
+
|
DNA G + C content (mol%)
|
48.74
|
48.50
|
48.29
|
Strains: 1, H3-26T; 2, Deefgea rivuli WB 3.4-79T; 3, Deefgea chitinilytica Nsw-4T. |
+ positive; -, negative; +w, weakly positive; ND, not determined. The data of strain H3-26T were obtained in this study, Data of Deefgea rivuli WB 3.4-79T and Deefgea chitinilytica Nsw-4T were taken from Stackebrandt et al. (2007) and Chen et al.(2010). |
Genomic characteristics and comparative genomics analysis
The draft genome of strain H3-26T contained 26 contigs with an N50 value of 387129 bp and an N90 value of 69269 bp. The genome size of strain H3-26T is 3.26 Mb. A total of 2995 genes were predicted in the draft genome of strain H3-26T. The genomic DNA G + C content of H3-26T is 48.74 mol%, which is similarity with Deefgea rivuli WB 3.4-79T (48.50%) and Deefgea chitinilytica Nsw-4T (48.29%). The dDDH and ANI values between strain H3-26T and Deefgea rivuli WB 3.4-79T, Deefgea chitinilytica Nsw-4T were 21.20–21.90% and 76.29–77.43%, respectively, which were lower than the threshold values of 70% and 95–96% for species discrimination. The homologous genes analysis were shown in a Venn diagram (Fig. 3). 2432, 2604 and 2656 genes were identified in the genomes of strain H3-26T, Deefgea chitinilytica Nsw-4T and Deefgea rivuli WB 3.4-79T, respectively, with 2221 genes shared in all of them. In the genomes of strain H3-26T, Deefgea chitinilytica Nsw-4T and Deefgea rivuli WB 3.4-79T, 10, 16 and 15 genes were identified as unique genes with no detectable homologous in each other. The distribution of genes into COG functional categories revealed that the 4 major functional genes were assigned to cellular processes and signaling (30.79%), metabolism (37.83%), information storage and processing (18.64%) and poorly characterized (12.74%) (Fig. 4).
Fatty acid profiles analysis
The predominant fatty acids of strain H3-26T (>5.0% of the total amounts) were comprised of C16:1 ω7c (40.77%), C16:0 (23.07%), C12:0 (5.89%) and C14:0 (5.88%). The major differences between strain H3-26T and its closely relatives were shown in Table 2. The presence of C13:0 anteiso, C14:0 anteiso, C15:0 3-OH, C17:1 anteiso ω9c and C18:3 ω6c could be used to distinguish strain H3-26T from Deefgea rivuli WB 3.4-79T and Deefgea chitinilytica Nsw-4T.
Table 2
Comparison of fatty acid profiles of strain H3-26T and its closely related species
Fatty acid
|
1
|
2
|
3
|
C12:0
|
5.89
|
3.2
|
3.6
|
C13:0 anteiso
|
2.00
|
–
|
–
|
C12:0 3-OH
|
2.95
|
2.6
|
3.2
|
C14:0 anteiso
|
1.57
|
–
|
–
|
C14:0
|
5.88
|
2.1
|
3.9
|
C15:0 3-OH
|
3.34
|
/
|
–
|
C16:0
|
23.07
|
22.5
|
24.5
|
C16:0 3-OH
|
1.18
|
0.5
|
1.4
|
C16:1 ω7c
|
40.77
|
51.0
|
50.9
|
C17:1 anteiso ω9c
|
–
|
5.1
|
3.7
|
C18:0
|
2.08
|
2.7
|
1.1
|
C18:1 ω7c
|
0.97
|
3.0
|
4.1
|
C18:3 ω6c
|
1.62
|
–
|
–
|
Strains: 1, strain H3-26T; 2, Deefgea rivuli WB 3.4-79T; 3, Deefgea chitinilytica Nsw-4T. Values are percentages of the total fatty acids. Fatty acids that make up<0.5% of the total are not shown. “– ”Not detected or <0.5%. |
Description of Deefgea salmonis sp. nov.
Deefgea salmonis sp. nov. (sal.mo’nis. L.gen.masc.n. salmonis, of salmon, since it was first discovered in salmon)
Cells are gram-negative, facultative anaerobic, immobile, rod-shaped, single or paired, 0.6–0.9 µm in width, and 0.9–2.7 µm in length. Colonies grown on R2A at 25℃for 2 days are milky-white, round, moist, translucent, neat edges and 0.8–1.6 mm in diameter. Growth occurs in the presence of 0–1% (w/v) NaCl (optimum, 0% NaCl), pH 5.0–11.0 (optimum, 7.0), and 4–30℃ (optimum, 25℃). Positive for oxidase, catalase and anaerobic growth. Negative for hydrolysis of starch, motility, tweens 80, β-galactosidases, arginine dihydrolase, lysine decarboxylase, ornithine decarboxylase, citric acid utilization, Voges-Prokauer test, gelatin, urease, hydrogen sulfide and indole production. Positive reactions (API 20NE) for nitrate reduction, eaculin hydrolysis, assimilation of glucose, mannose, N-acetylglucosamine and potassium gluconate. Positive enzyme reactions (API ZYM) for C4 esterase, C8 esterase, leucine aromatase, acid phosphatase, naphthol-AS-BI-phosphohydrolase and N-acetylglucosaminidase. The following compounds are utilized in the API 50CH test system: D-ribose, D-glucose, D-fructose, D-mannose, N-acetylglucosamine and potassium gluconate. The predominant fatty acids of strain H3-26T (>5.0% of the total amounts) were comprised of C16:1 ω7c (40.77%), C16:0 (23.07%), C12:0 (5.89%) and C14:0 (5.88%).
The type strain H3-26T (= JCM 35050T = CICC 25103T) was isolated from gills of Oncorhynchus mykiss in Lhasa, Tibet Autonomous Region, PR China. The genome size of strain H3-26T is 3.26 Mb with a low genomic DNA G + C content of 48.74 mol%. The GenBank accession numbers of 16S rRNA gene sequences and whole genome sequence of strain H3-26T are OK077561 and JAJAWG000000000, respectively.