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Int J Syst Evol Microbiol 57 (2007), 900-905; DOI  10.1099/ijs.0.64818-0
© 2007 International Union of Microbiological Societies

Halomonas avicenniae sp. nov., isolated from the salty leaves of the black mangrove Avicennia germinans in Puerto Rico

Nelís Soto-Ramírez1, Cristina Sánchez-Porro2, Soniris Rosas1, Wildaomaris González1, Marian Quiñones1, Antonio Ventosa2 and Rafael Montalvo-Rodríguez1

1 Biology Department Box 9012, University of Puerto Rico, Mayagüez 00681, Puerto Rico
2 Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain

Correspondence
Rafael Montalvo-Rodríguez
titomontal{at}yahoo.com


    ABSTRACT
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 REFERENCES
 
A Gram-negative, short rod to oval-shaped bacterium (strain MW2aT) was isolated from the surface of leaves of the black mangrove Avicennia germinans and subjected to a polyphasic taxonomic study. Strain MW2aT was moderately halophilic, growing at NaCl concentrations in the range 0–25 % (w/v) with optimum growth at 5 % (w/v) NaCl. Growth occurred at 12–40 °C (optimum, 30–35 °C) and at pH 5.0–9.0 (optimum, pH 7.0–8.0). Strain MW2aT was strictly aerobic. Phylogenetic analysis based on the 16S rRNA gene showed that the strain belongs to the genus Halomonas. The closest relative was Halomonas marisflavi, with 98.6 % 16S rRNA gene sequence similarity. The DNA G+C content of strain MW2aT was 61.5 mol%, which is in the range of values for Halomonas species. DNA–DNA hybridization with H. marisflavi showed a relatedness of 42 % and lower values were obtained with respect to other related Halomonas species. The major fatty acids were C16 : 0, C19 : 0 cyclo {omega}8c, C18 : 1{omega}7c and C12 : 0 3-OH. Overall, the phenotypic, genotypic and phylogenetic results presented in this study demonstrate that strain MW2aT represents a novel species within the genus Halomonas. The name Halomonas avicenniae sp. nov. is proposed, with strain MW2aT (=CECT 7193T=CCM 7396T) as the type strain.


The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain MW2aT is DQ888315.


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The genus Halomonas belongs to the family Halomonadaceae within the Gammaproteobacteria and at the time of writing comprised 35 species that had been isolated mainly from saline or hypersaline environments (Arahal et al., 2002Go; Bouchotroch et al., 2001Go; Dobson & Franzmann, 1996Go; Garcia et al., 2004Go; Lee et al., 2005Go; Lim et al., 2004Go; Martínez-Cánovas et al., 2004Go; Martínez-Checa et al., 2005Go; Mata et al., 2002Go; Mormile et al., 1999Go; Quillaguaman et al., 2004Go; Romanenko et al., 2002Go; Ventosa et al., 1998Go; Vreeland et al., 1980Go; Yoon et al., 2001Go, 2002Go) or from unusual habitats such as dry mural paintings (Heyrman et al., 2002Go) and deep-sea hydrothermal vents (Kaye et al., 2004Go). Phylogenetic analysis using the 16S and 23S rRNA gene sequences and phenotypic studies demonstrated that this genus is very heterogeneous (Arahal et al., 2002Go; Mata et al., 2002Go). One distinct group is represented by a single species, Halomonas marisflavi (Yoon et al., 2001Go). To date, there have been no reports of the occurrence of members of this genus being associated with mangroves that thrive on saline habitats. Avicennia germinans is a type of mangrove that has developed mechanisms to tolerate high salt concentrations in unstable substrates, to obtain oxygen in almost anoxic sediments and to reproduce in harsh areas. One of these mechanisms consists of the secretion of salt crystals on the leaves when the concentration is in excess of that normally present in the vascular system (Lugo & Snedaker, 1975Go). In this study, we determined the taxonomic position of strain MW2aT, which was isolated from the surface of leaves of the black mangrove A. germinans during a microbial diversity study. As a result of our studies, the name Halomonas avicenniae sp. nov. is proposed for this novel micro-organism.

Strain MW2aT was isolated from the surface of leaves of A. germinans. For isolation, a total of 40 leaves were collected randomly from four trees growing near the solar salterns of Cabo Rojo, Puerto Rico. The leaves were placed in sterile bags (Whirl Pak) containing 1 % phosphate buffer at pH 7 with 15 % (w/v) NaCl and mixed. This procedure allowed suspension of the micro-organisms present in the salt crystals on the surface of the leaves. Ten millilitres of the suspension was then used to generate serial dilutions. The dilutions were poured into agar plates containing Seghal–Gibbons (SG) medium at 15 % NaCl (Seghal & Gibbons, 1960Go). The inoculated plates were incubated at 30 °C. After 3 days of incubation, colonies were selected and purified by using the quadrant streak plate method. Pure cultures were transferred to SG medium for further analysis.

The morphology of the cells was examined by using the Nomarsky technique and scanning electron microscopy with cells at the exponential phase of growth under optimal conditions. Electron microscopy was performed as described previously (Díaz-Muñoz & Montalvo-Rodríguez, 2005Go). Gram stain was performed using both heat-fixed smears and smears fixed in 5 % acetic acid (Dussault, 1955Go). Macroscopic properties were determined using the classical characterization of colony appearance. Optimal conditions for growth were determined by growing strain MW2aT in SG broth supplemented with 0, 5, 10, 15, 20, 25 and 30 % (w/v) NaCl at temperatures of 20, 25, 30, 35 and 40 °C. The pH range for growth was tested using SG medium containing 5 % NaCl and adjusted to pH 4.0, 5.0, 6.0, 7.0, 8.0, 9.0 and 10.0, with the addition of the appropriate buffering capacity to each medium as described previously (Montalvo-Rodríguez et al., 2000Go). The cells were cultivated with constant agitation (150 r.p.m.) and growth was monitored by measuring the absorbance at 600 nm. Cells of strain MW2aT are Gram-negative, non-spore-forming, motile short rods or ovals. At the exponential phase of growth in SG medium with 5 % NaCl at 30 °C, cells were 2–2.6 µm long and 1–2 µm wide. On SG medium with 5 % NaCl, colonies were orange, smooth, circular/slightly irregular and convex, with an entire margin. Strain MW2aT grew at NaCl concentrations in the range 0–25 % (w/v) in SG medium. Growth did not occur at concentrations of NaCl greater than 25 % (w/v). The temperature range for growth was 12–40 °C and the pH range was 5.0–9.0. Optimal growth occurred in SG medium with 5 % (w/v) NaCl at 30–35 °C and pH 7.0–8.0. This combination of conditions produced the shortest generation time (1.42 h).

All of the biochemical tests were carried out with 5 % NaCl and at 30 °C, unless stated otherwise. Catalase activity was determined by addition of a 1 % (w/v) H2O2 solution to colonies on SG agar medium. Oxidase activity was tested using the Dry Slide (Difco) biochemical test (Montalvo-Rodríguez et al., 1998Go). Hydrolysis of starch, Tween 80 and aesculin was determined as described by Cowan & Steel (1965)Go, with the addition of basal salts [5 % NaCl, 2 % MgSO4.7H2O and 0.2 % KCl (w/v)] to the medium. Hydrolysis of gelatin and production of urease were determined according to Cowan & Steel (1965)Go. Citrate utilization was determined on Simmons' citrate medium (Simmons, 1926Go) supplemented with basal salts. Acid production from carbohydrates was determined using a phenol red base supplemented with 0.7 % of the carbohydrate tested and basal salts. Motility was determined using SIM medium, supplemented with basal salts. Production of H2S was determined using the API 20E system, as described previously (Yoon et al., 2001Go). Growth under anaerobic conditions was determined by incubating strain MW2aT in an anaerobic chamber in SG medium with 5 % NaCl. Tests for sugar fermentation and enzymes (qualitative) were carried out using API 20 NE and API ID 32E (bioMérieux), according to the manufacturer's instructions, with the inoculated fluid at 5 % NaCl and incubation at 30 °C. Nutritional features were determined using Koser medium (Koser, 1923Go), as modified by Ventosa et al. (1982)Go, which contains the basal salts described above and (%, w/v): KNO3, 0.1; (NH4)2HPO4, 0.1; and KH2PO4, 0.05. The filter-sterilized substrate was added to this medium at a final concentration of 0.1 % (w/v), with the exception of carbohydrates, which were used at a final concentration of 0.2 % (w/v). Strain MW2aT was able to use L-arabinose, D-cellobiose, D-fructose, D-galactose, D-glucose, maltose, D-mannose and glycerol as carbon and energy sources. Antibiotic susceptibility was determined according to the conventional Kirby–Bauer method (Bauer et al., 1966Go). The phenotypic characteristics of strain MW2aT are summarized and compared with those of the type strains of related Halomonas species in Table 1Go and in the species description.


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Table 1. Phenotypic characteristics that distinguish strain MW2aT from the type strains of other species of the genus Halomonas

Strains: 1, MW2aT; 2, H. marisflavi KCCM 80003T; 3, H. elongata ATCC 33173T; 4, H. salina ATCC 49509T; 5, H. halodurans DSM 5160T; 6, Halomonas halmophila DSM 5349T; 7, Halomonas marina DSM 4741T; 8, Halomonas eurihalina DSM 5720T. Data from Arahal et al. (2001Go, 2002)Go, Baumann et al. (1983)Go, Franzmann et al. (1988)Go, Hebert & Vreeland (1987)Go, Mata et al. (2002)Go, Mellado et al. (1995)Go, Yoon et al. (2001)Go and this study. +, Positive; –, negative; +/–, weak reaction; ND, no data.

 
For the characterization and sequencing of the 16S rRNA gene, strain MW2aT was grown in SG medium with 5 % NaCl and incubated at 30 °C. Genomic DNA was extracted from cells in lysis buffer followed by phenol/chloroform extraction and ethanol precipitation. The DNA was used as a template for subsequent PCR amplification. Reaction conditions and amplification protocols used were as described elsewhere (Hezayen et al., 2002Go). The resulting amplicon was purified using a MinElute PCR purification kit, according to the manufacturer's instructions. Purified PCR products were sequenced at a DNA sequencing facility (Macrogen, Korea). Distance analysis of the resulting DNA sequence was performed using the PHYLIP program (version 3.63; Felsenstein, 1993Go). Multiple-sequence alignment was performed by using the CLUSTAL W program with 16s rrna gene sequences of closely related organisms (as determined by BLAST analysis) (Maidak et al., 1996Go). The 16S rRNA gene similarity values were calculated by pairwise comparison of the sequences within the alignment. SEQBOOT was used to generate 100 bootstrapped datasets. Distance matrices were calculated with DNADIST. One hundred trees were inferred by using the neighbour-joining software. Any bias introduced by the order of sequence addition was minimized by randomizing the input order. The program CONSENSE was used to determine the most frequent branching order. The final tree was drawn using TREEVIEW (Page, 1996Go).

In silico analysis of strain MW2aT using the BLAST program (National Center for Biotechnology) with an almost complete 16S rRNA gene sequence (1433 bp) revealed that this strain was related to the genus Halomonas, with the closest sequence similarity to H. marisflavi KCCM 80003T (98.6 %), a species that represents one of the various groups of this genus. 16S rRNA gene sequence similarities between strain MW2aT and Halomonas elongata ATCC 33173T, Halomonas salina DSM 5928T and Halomonas halodurans DSM 5160T were 92.8, 92.8 and 91.7 %, respectively. Strain MW2aT also showed low sequence similarity to Chromohalobacter salexigens DSM 3043T (93.7 %). Phylogenetic analysis using the neighbour-joining algorithm revealed that strain MW2aT was closely related to H. marisflavi, forming a branch in this cluster with a boostrap value of 100 % (Fig. 1Go). The phylogenetic position of strain MW2aT was also confirmed in a tree generated using the maximum-parsimony algorithm.


Figure 1
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Fig. 1. Neighbour-joining distance tree based on the 16S rRNA gene sequences of strain MW2aT and closely related species. Bar, 1 substitution per 100 nucleotides. Bootstrap values greater than 40 % are shown. Zymobacter palmae DSM 10491T was used as the outgroup.

 
Fatty acids were analysed by using GC at the Belgian Co-ordinated Collections of Microorganisms, Laboratory of Microbiology of Gent (BCCM/LMG), Gent, Belgium (Kämpfer & Kroppenstedt, 1996Go; Miller, 1982Go). Cells were cultured on SW10 medium [8.1 % NaCl, 0.7 % MgCl2, 0.96 % MgSO4, 0.036 % CaCl2, 0.2 % KCl, 0.006 % NaHCO3, 0.0026 % NaBr, 0.5 % yeast extract, w/v (Difco)] (Ventosa et al., 1982Go) for 24 h at pH 7.0 and 30 °C. The predominant fatty acids of strain MW2aT were C16 : 0, C19 : 0 cyclo {omega}8c, C18 : 1{omega}7c and C12 : 0 3-OH. This composition is very similar to those described for other Halomonas species (Table 2Go).


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Table 2. Cellular fatty acid compositions (%) of strain MW2aT, the closely related species H. marisflavi and the type species of the genus, H. elongata

The strains were grown on SW10 medium for 24 h at pH 7.0 and 30 °C. –, Not detected.

 
The G+C content of genomic DNA was determined from the mid-point value (Tm) of the thermal denaturation profile (Marmur & Doty, 1962Go) using the equation of Owen & Hill (1979)Go, as described in detail by Ventosa et al. (1999)Go. The DNA G+C content of strain MW2aT was 61.5 mol%, which is in the range for species belonging to the genus Halomonas (Arahal & Ventosa, 2005Go; Franzmann et al., 1988Go).

DNA–DNA hybridization studies were performed by using the competition procedure of the membrane method (Johnson, 1994Go), as described in detail by Mormile et al. (1999)Go. The hybridization temperature used was 57.3 °C, which is within the limit of validity for the filter method (De Ley & Tijtgat, 1970Go) and the percentage DNA–DNA relatedness was calculated according to Johnson (1994)Go. The experiments were carried out in triplicate. The DNA–DNA relatedness between strain MW2aT and H. marisflavi KCCM 80003T was 42 %, whereas the relatedness with H. elongata ATCC 33173T and H. salina DSM 5928T was 23 and 13 %, respectively. These levels of DNA–DNA relatedness are low enough to classify strain MW2aT as representing a genotypically distinct species within the genus Halomonas (Wayne et al., 1987Go; Stackebrandt & Goebel, 1994Go).

Overall, the phenotypic, phylogenetic, chemotaxonomic and genotypic results presented in this study demonstrate that strain MW2aT represents a novel species within the genus Halomonas, for which the name Halomonas avicenniae sp. nov. is proposed.

Description of Halomonas avicenniae sp. nov.
Halomonas avicenniae [a.vi.cen.ni'ae. N.L. n. Avicennia scientific name of a botanical genus which encompasses Avicennia germinans (the black mangrove); N.L. gen. n. avicenniae of Avicennia, isolated from leaves of Avicennia germinans].

Cells are Gram-negative, motile, non-spore-forming short rods or oval-shaped, 2–2.6 µm long and 1–2 µm wide. Colonies are orange, smooth, circular/slightly irregular and convex, with an entire margin. Moderately halophilic, growing at NaCl concentrations in the range 0–25 % (w/v) with optimum growth at 5 % (w/v) NaCl. Growth occurs at 12–40 °C (optimum, 30–35 °C) and pH 5.0–9.0 (optimum, pH 7.0–8.0). Strictly aerobic. Catalase-positive and gelatin and aesculin are hydrolysed. Production of indole and H2S, hydrolysis of starch, DNA and Tween 80, and urease and oxidase are negative. Nitrate is not reduced. Acid is produced from D-glucose, sucrose, xylose, D-fructose and L-arabinose and weakly produced from maltose. Negative for arginine dihydrolase, ornithine decarboxylase and lysine decarboxylase. beta-Galactosidase, beta-glucosidase and {alpha}-glucosidase activities are present. Negative for beta-glucuronidase, N-acetyl-beta-glucosaminidase, {alpha}-galactosidase, {alpha}-maltosidase and L-aspartic acid arylamidase. L-Arabinose, D-cellobiose, D-fructose, D-galactose, D-glucose, maltose, D-mannose and glycerol are used as carbon and energy sources. Shows intermediate resistance to erythromycin (15 µg). Resistant to penicillin (10 units), bacitracin (10 units), cephalothin (30 µg), tetracycline (30 µg), rifampicin (5 µg), streptomycin (10 µg), neomycin (30 µg), kanamycin (30 µg), vancomycin (30 µg), nalidixic acid (30 µg), novobiocin (30 µg) and chloramphenicol (30 µg). Major fatty acids are C16 : 0, C19 : 0 cyclo {omega}8c, C18 : 1{omega}7c and C12 : 0 3-OH. The DNA G+C content of the type strain is 61.5 mol%.

The type strain is MW2aT (=CECT 7193T=CCM 7396T), which was isolated from the leaf surface of Avicennia germinans (black mangrove).


    ACKNOWLEDGEMENTS
 
The authors would like to thank Donato Seguí, Magaly Zapata, José Almodóvar and other members of Montalvo-Rodríguez's laboratory for technical assistance on this study. We would also like to thank Dr Jean P. Euzéby for his help with the etymology. This study was supported by grants from the Quality of Life and Management of Living Resources programme of the European Commission (Project ‘Multigenome Access Technology for Industrial Catalysts’, QLK3-CT-2002-01972), Spanish Ministerio de Educación y Ciencia (BMC2003-01344) and from the Junta de Andalucia, and by the Dean of Arts and Sciences Seed Money programme at the University of Puerto Rico-Mayagüez Campus and the University of Puerto Rico AlaCiMa Program.


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