Morphological and phenotypical properties
Strain M0105T exhibits some common morphological properties with L. halophilum CAU 1123T, such as irregular rod-shaped, non-motile and non-spore forming. Cells of strain M0105T were 0.3–0.5 µm in width and 1-1.7 µm in length (Fig. S1). Growth occurs on R2A agar supplemented with 1–7% NaCl (optimum 3–5%), at the temperature of 15–46℃ (optimum 37–40℃, Fig. S2). It could grow at a pH range of 6.0 to 10.0 (optimum pH 8.0–9.0). The phylogenetically closely related species are positive for oxidase and catalase, whereas strain M0105T is negative for oxidase. All different phenotypic characteristics between strain M0105T and other type strains were listed in Table 2.
Table 2. Different phenotypic characteristics between strain M0105T and four type species.
Strains: 1, M0105T; 2, A. brevis 34079T; 3, M. xiamenense YBY-7T; 4, D. nitratireducens 25810_4T; 5, L. halophilum CAU 1123T. Data were obtained in this study. *data from [Shin et al. 2017; Yin et al. 2012]. +, Positive; -, negative; w, weakly positive.
Characteristics
|
1
|
2
|
3
|
4
|
5
|
Growth conditions
|
|
|
|
|
|
Growth temperature range (℃)
|
15-46 (37-40)
|
10-50 (35)
|
28-65 (50-58)*
|
8-40 (28-30)
|
20-40 (37)
|
NaCl tolerance (optimum %, w/v)
|
1-7 (3-5)
|
2-10 (5-6)
|
1-6 (3)
|
2-7 (4-5)
|
1-10 (5-6)
|
pH range (optimum)
|
6-10 (8-9)
|
7-10 (8)
|
6-9 (8)
|
6-9 (7)
|
6-9 (7)
|
Oxidase
|
-
|
+
|
+
|
w
|
+
|
Carbon source utilization
|
|
|
|
|
|
D-arabinose
|
+
|
-
|
-
|
-
|
-
|
L-arabinose
|
+
|
-
|
-
|
-
|
-
|
D-ribose
|
+
|
-
|
+
|
-
|
+
|
D-xylose
|
-
|
-
|
w
|
+
|
-
|
L-xylose
|
+
|
-
|
-
|
-
|
-
|
D-glucose
|
-
|
-
|
-
|
+
|
-
|
D-mannitol
|
-
|
-
|
-
|
+
|
-
|
D-cellobiose
|
-
|
-
|
w
|
-
|
-
|
D-maltose
|
-
|
-
|
-
|
+
|
-
|
sucrose
|
-
|
-
|
-
|
+
|
-
|
D-trehalose
|
-
|
-
|
-
|
+
|
-
|
glycogen
|
+
|
-
|
-
|
-
|
-
|
D-arabinitol
|
-
|
-
|
-
|
+
|
-
|
2-ketogluconate
|
+
|
-
|
-
|
-
|
-
|
Turanose
|
-
|
-
|
-
|
+
|
-
|
D-lyxose
|
+
|
-
|
-
|
-
|
-
|
Enzyme activities
|
|
|
|
|
|
α-chymotrypsin
|
+
|
-
|
-
|
w
|
-
|
acid phosphatase
|
+
|
-
|
+
|
+
|
+
|
naphthol-AS-BI-phosphohydrolase
|
-
|
w
|
-
|
w
|
w
|
α-galactosidase
|
-
|
-
|
+
|
-
|
-
|
β-galactosidase
|
-
|
-
|
+
|
-
|
-
|
β-glucuronidase
|
-
|
w
|
-
|
w
|
-
|
α-glucosidase
|
-
|
-
|
+
|
w
|
-
|
β-glucosidase
|
-
|
-
|
+
|
-
|
-
|
N-acetyl-β-glucosaminidase
|
+
|
-
|
-
|
-
|
-
|
Cystine arylamidase
|
-
|
-
|
w
|
w
|
-
|
Alkaline phosphatase
|
+
|
-
|
+
|
+
|
+
|
Lipase (C14)
|
-
|
-
|
w
|
w
|
w
|
Polar lipids
|
DPG, PG, PC, PGL, PL, L, AL
|
DPG, PG, PC, PGL, PL, L, AL
|
DPG, PG, PC, PGL, PL, L
|
DPG, PG, PC, PGL, PL, L
|
PG, PE, PL, L, AL*
|
The polar lipid profile pattern on thin-layer chromatography of strain M0105T (Fig. S6) was similar with A. brevis 34079T, containing unidentified aminolipid (AL), phosphoglycolipids (PGL), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), unidentified phospholipids (PL), unknown lipid (L) and phosphatidylcholine (PC). The sole respiratory quinone Q-10 is frequently found in the family ‘Rhodobacteraceae’ that was also detected as the major respiratory quinone in the isolate. The major fatty acids were C18:1ω7c and C16:0 DMA in strain M0105T, which were in accordance with the closely related species A. brevis 34079T, D. nitratireducens 25810_4T and L. halophilum CAU 1123T. Other main cellular fatty acids (> 5%) of the isolate were C16:0 DMA (12.5%), C16:0 (8.6%) and C18:1ω7c 10-methyl (6.0%).
Genome characteristics
Genome sequencing revealed a genome of 4,055,176 bp and an N50 contig length of 318,302 bp with a DNA G + C content of 67.9 mol%. A total of 3808 protein-coding genes, 45 tRNA genes and 3 rRNA genes were consisted in the sequence. The genome of strain M0105T comprised 99 genes associated with carbohydrate-active enzymes, including auxiliary activities (12), carbohydrate esterases (17), glycosyl transferases (46), polysaccharide lyases (1), carbohydrate-binding modules (5) and glycoside hydrolases (18). Functional gene category analysis revealed that most of genes involved in Global and overview maps (249), amino acid metabolism (265) and energy metabolism (200), Three putative secondary metabolite biosynthetic gene clusters involving in biosynthesis of terpene, type I PKS and arylpolyene were identified.
As compared with other non-mangrove dwelling bacteria, the genes associated with “Replication and repair”, “Protein families: metabolism”, “Energy metabolism” “Metabolism of cofactors and vitamins”, “Transport and catabolism”, “Metabolism of other amino acids”, “Cellular community” and “Amino acid metabolism” were abundance in the mangrove-derived bacteria strain M0105T and A. solimangrovi HB172011T (Fig. 3). Mangrove sediments are known to be rich in various organic substrates such as amino acids, carbohydrates, polysaccharides, phenolics and other related compounds. Microbe in mangrove sediment involved in carbon and energy process by the degradation and utilization of organic matter, thus implying genes associated with carbohydrate metabolism, energy metabolism and amino acid metabolism were abundant in the mangrove-dwelling bacteria [Zhao et al. 2019; Lin et al. 2019]. The abundance of “carbohydrate metabolism” genes in A. solimangrovi HB172011T were higher than strain M0105T. This might be caused by the distribution of carbon source, which was influenced by tidal flow and estuary water flow. The high abundance of DNA-repaired-related genes and heat-shock-related genes (Table S2) were detected in strain M0105T that were highly responsive to cellular stress, such as salt stress, heat stress, radiation and oxidative stresses.
Description of Thermohalobaculum gen. nov.
Thermohalobaculum (Ther.mo.ha.lo,ba’cu.lum Gr. fem. n, therme, heat; Gr. masc. n. hals, salt; L. neut. n. baculum, small rod; N.L. neut. n. Thermohalobaculum, a thermophilic, halophilic rod). A moderately thermophilic, halophilic and Gram-negative bacterium. The major fatty acids are C18:1ω7c and C16:0 DMA. The major menaquinone is Q-10. The type species is Thermohalobaculum xanthum.
Description of Thermohalobaculum xanthum sp. nov.
Thermohalobaculum xanthum (xan.thum. N.L. neut. adj. xanthum yellow. xanthum, a yellow-colony-forming organism).
Cells are non-motile, rod shaped with width of 0.3–0.5 µm and length of 1-1.7 µm. Test for catalase is positive, but for oxidase is negative. Negative for hydrolysis of cellulose, starch, Tweens (20, 40, 60 and 80), urea and gelatin, as well as for H2S production. It can utilize D-tagatose, 5-ketogluconate, D-arabinose, L-arabinose, D-ribose, L-xylose, glycogen, 2-ketogluconate and D-lyxose, but cannot use glycerol, meso-erythritol, D-xylose, D-adonitol, methyl beta-D-xylopyranoside, D-galactose, D-glucose, D-fructose, D-mannose, L-sorbose, L-rhamnose, dulcitol, Myo-inositol, D-mannitol, sorbitol, methyl α-D-mannopyranoside, methyl α-D-glucopyranoside, N-acetyl-D-glucosamine, amygdalin, arbutin, salicin, D-cellobiose, D-maltose, D-lactose, D-melibiose, sucrose, D-trehalose, inulin, D-melezitose, D-raffinose, starch, xylitol, gentiobiose, turanose, D-fucose, L-fucose, D-arabinitol, L-arabinitol and potassium gluconate. Negative for catalase. Shows positive reactions for α-chymotrypsin, acid phosphatase, alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, N-acetyl-β-glucosaminidase and valine arylamidase, but negative reactions for lipase (C14), cystine arylamidase, trypsin, naphthol-ASBI-phosphohydrolase, α-galactosidase, β-galactosidase, β-glucuronidase, α-glucosidase, β-glucosidase, α-mannosidase, β-fucosidase. Colonies are pale-yellow. Temperature range for growth is 15–46℃, with an optimum of 37–40℃. Growth occurs at pH 6.0–10.0, with an optimum of pH 8.0–9.0. NaCl concentration range for growth is 1–7% (optimum, 3–5%, w/v). The DNA G + C content of the type species is 67.9%.
The type strain, M0105T (= BGMRC 2019T = KCTC 52118T = MCCC 1K03767T = NBRC 112057T) was isolated from the mangrove sediments, which were collected from Beibu Gulf in Beihai, Guangxi province. The GenBank accession numbers for the 16S rRNA gene sequence of strain M0105T is MT613384 and the genome sequence is JAEHHL000000000.