For reprint orders, please contact: [email protected]

Future Microbiology

Review

Microbiology and epidemiology of Halomonas species Kwang Kyu Kim1, Jung-Sook Lee1 & David A Stevens*2,3,4 Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305–806, Republic of Korea 2 California Institute for Medical Research, 2260 Clove Drive, San Jose, CA 95128, USA 3 Stanford University Medical School, Stanford, CA, USA 4 Division of Infectious Diseases, Department of Medicine, Santa Clara Valley Medical Center, San Jose, CA, USA *Author for correspondence: Tel.: +1 408 885 4302 n Fax: +1 408 885 4306 n [email protected] 1

Halomonas has been organized as a genus since 1980, and comprises halophilic and/or halotolerant Gram-negative aerobic bacteria, typically found in saline environments. The genus is enlarging: at present, 76 species are taxonomically recognized, with more to be added. Increasing industrial uses have been found, largely in bioremediation and the production of desirable compounds. Originally seen as environmental contaminants, pathogenicity was initially not recognized; however, disease in algae, animals and humans has now been described. As the biotechnological use of these species increases, and the ability to isolate and recognize them improves, one might expect further pathogenic encounters with humans to be described.

The genus Halomonas, type genus of the family Halomonadaceae, is a member of the class Gammaproteobacteria [1,101]. At present, the Gammaproteobacteria comprise 16 orders and include several medically, ecologically and scientifically important groups of bacteria, such as the families Enterobacteriaceae, Pseudomonadaceae, Pasteurellaceae and Vibrionaceae. A number of important human pathogens belong to this class, such as Salmonella spp. (agents of enteritis and typhoid fever), Yersinia pestis (plague), Vibrio cholerae (cholera), Pseudomonas aeruginosa (lung infections in hospitalized or cystic fibrosis patients), Haemophilus influenzae (meningitis and otitis), Legionella spp. and Coxiella burnetii (pneumonia), and Shigella spp. and Escherichia coli (diarrhea). The genus Halomonas (from the Greek nouns hals or halos [salt] and monas [a unit or monad]; hence Halomonas, salt [-tolerant] monad) accommodates halophilic/halotolerant bacteria that typically occur in saline or hypersaline environments. Members of the genus Halomonas can be referred to as halomonads. From the variety of habitats in which they are found, in addition to their phenotypic hetero­ geneity, they may be regarded as ubiquitous, versatile chemoheterotrophs [2]. The genus Halomonas was created by Vreeland et al. [3] based on the description of a single species, H. elongata, for a group of Gramnegative, rod-shaped, extremely halotolerant bacteria, which were originally assigned to the family Vibrionaceae [4]. Later, according to decisions made at the meeting of the Subcommittee on the Taxonomy of Vibrionaceae 10.2217/FMB.13.108 © 2013 Future Medicine Ltd

in September 1986 [5], the genus Halomonas was excluded from the family Vibrionaceae. In 1987, two novel species – H. subglaciescola [6] and H. halodurans [7] – were described by numerical taxonomic approaches. Subsequently, the family Halomonadaceae was proposed for the accommodation of the genera Halomonas and Deleya on the basis of results obtained with the 16S rRNA gene cataloging technique of several closely related organisms [8]. This resulted in the transfer of Flavobacterium halmophilum into Halomonas as H. halmophila comb. nov. and shortly afterwards, H. meridiana sp. nov. was described [9]. Volcaniella eurihalina was also reclassified into the genus Halomonas based on phylogenetic ana­lysis of the 16S rRNA gene sequence [10]. Similarly, transfer of the species of the genus Deleya, as well as Halovibrio variabilis and Paracoccus halodenitrificans, to the genus Halomonas, amended the genus Halomonas [11] and increased the number of species to 15. Since then, a huge number of novel species have been validly published in the genus Halomonas. As a result, the genus Halomonas shows considerable intrageneric heterogeneity, which has led to several taxonomic re-evaluations. Arahal et al. transferred two Halomonas species, H. canadensis and H. israelensis, to the genus Chromohalobacter on the basis of 16S rRNA gene sequence comparisons and DNA–DNA hybridization data [12] and reclassified H. marina into a novel genus, Cobetia, based on 16S and 23S rRNA gene sequence analyses [13]. Sánchez-Porro et al. reclassified three Halomonas species, H. marisflavi, H. indalinina and H. avicenniae, to a novel Future Microbiol. (2013) 8(12), 1559–1573

Keywords alkaliphilic n bacteremia bioremediation n dialysis n halomonads n Halomonas n halophilic n halotolerant n saline environment n n

part of

ISSN 1746-0913

1559

Review

Kim, Lee & Stevens

genus, Kushneria, on the basis of a polyphasic taxonomic investigation including a comparison of the complete 16S rRNA and 23S rRNA gene sequences [14]. More recently, de la Haba et al. transferred H. salaria to the genus Salinicola [15] and Romanenko et al. reclassified H. halodurans as a later heterotrophic synonym of Cobetia marina [16] following the same procedures. Despite a series of taxonomic re-evaluations, the genus Halomonas is still phylogenetically heterogeneous (Figure 1). However, phylogenetic studies based on complete 16S and 23S rRNA gene sequences have defined two clearly distinguished clusters. Group 1 includes H. elongata (the type species) and the species H. eurihalina, H. caseinilytica, H. sinaiensis, H. halmophila,

H. sabkhae, H. almeriensis, H. halophila, H. salina, H. smyrnensis, H. organivorans, H. koreensis, H. beimenensis, H. maura, H. nitroreducens and H. stenophila. Group 2 comprises the species H. aquamarina, H. meridiana, H. axialensis, H. magadiensis, H. johnsoniae, H. hamiltonii, H. stevensii, H. hydrothermalis, H. alkaliphila, H. venusta, H. andesensis, H. boliviensis, H. neptunia, H. alkaliantarctica, H. variabilis, H. titanicae, H. sulfidaeris, H. zhanjiangensis, H. subterranea, H. janggokensis, H. gomseomensis, H. arcis, H. vilamensis, H. subglaciescola, H. cibimaris and H. jeotgali [17,18]. There remains more than 30 species that do not phylogenetically fit in the Halomonas sensu stricto cluster (group 1) or group 2. As their positions vary with the different

0.01

Figure 1. Maximum-likelihood phylogenetic tree, based on 16S rRNA gene sequences, showing the relationships between members of the genus Halomonas. An explanation of the methodology followed for sequence ana­lysis can be found in [71] . The arrow points to an outgroup, which has been removed to simplify the figure. Halomonas species that can be ascribed to the 16S rRNA groups 1 and 2 [17] have been marked accordingly. Bar: 0.01 substitutions per nucleotide position. Names found in the literature, but not validly published per taxonomic rules, are in quotation marks.

1560

Future Microbiol. (2013) 8(12)

future science group

Microbiology & epidemiology of Halomonas species

tree-making algorithms applied, they are not considered to be additional groups at present. More recently, multi­locus sequence ana­lysis using the 16S rRNA, 23S rRNA, atpA, gyrB, rpoD and secA genes was applied to species of the family Halomonadaceae, which indicated that a phylo­geny based on concatenated 16S rRNA, gyrB and rpoD genes shows higher levels of intergeneric resolution within the family Halomonadaceae [19]. Nonclinical epidemiology of Halomonas species The range of species in the genus

The genus description of the Halomonas is as follows: Gram-negative cells are rod-shaped, straight or curved (four species [H. alimentaria, H. halodenitrificans, H. kribbensis and “H. aidingensis”] present coccoid or short rod-shaped cells). In the text that follows, we will use the convention to utilize names found in the literature, but not validly published per taxonomic rules, in quotation marks. Such names may be superseded later by validly publishing the novel isolates and assuring they are not identical to validly described species (presented here without quotation marks). Elongated or filamentlike, flexible rods may form in older cultures. Rod-shaped species are motile by means of lateral, polar or peritrichous flagella. Nine species (H. alimentaria, H. almeriensis, H. cerina, H. halocynthiae, H. halodenitrificans, H. maura, H. sabkhae, H. xianhensis and “H. nitrilicus”) do not show motility. Endospores are not observed and most commonly, colonies are white or yellow, becoming light brown after prolonged incubation. All species are mainly aerobic chemoorganotrophs that have a respiratory type of metabolism in which oxygen is a terminal electron acceptor. Some species have a fermentative metabolism; whereas, some are also capable of anaerobic growth in the presence of nitrate or nitrite. All species tested are catalase-positive. Oxidase activity is species-dependent. Carbohydrates, amino acids, polyols and hydrocarbons can be utilized as sole sources of carbon and energy. A minority of species produce exopolysaccharides, and this can also be used to help distinguish among the species. With respect to pH, temperature and range of salinities, interspecific variation can be high. The genus Halomonas is characteristically halophilic or halotolerant. Generally, they are moderately halophilic (alternatively described as slightly halophilic) and prefer to grow in 3–15% (weight/ volume [w/v]) saline. Commonly, 7.5% (w/v) is used to demonstrate the halophilicity. Several future science group

Review

classification schemes have been generated to characterize microbes by the effect of salt upon them. That of Kushner is most used [20]. The moderately halophilic/halotolerant halomonads can usually grow over a wide range of salt concentrations, with a requirement or tolerance for salts [21]. Kushner defined moderate halophiles as organisms growing optimally between 0.5 and 2.5 M NaCl [20]. Although most halomonads are moderately halophilic, H. andesensis, H. axialenesis, H. meridiana, H. neptunia, H. sulfidaeris, “H. glaciei”, “H. nitrilicus” and “H. profundus” are only slightly so [9,22–26]. Most halomonads grow optimally at neutral pH, and, in general, they can grow at a pH of 8–10. More than a fifth of the species are more preferentially alkaliphilic or facultatively alkaliphilic. Bacteria able to grow in the absence of salt as well as in the presence of relatively high salt concentrations are designated halotolerant (or extremely halotolerant if growth can extend above 2.5 M NaCl). Various species are described as growing over a range of 0.1–32.5% w/v salt. Salt tolerance varies to some extent with the temperature used in the growth study. The species H. johnsoniae and H. magadiensis are considered to be halotolerant since they do not require salt for optimum growth [27,28]. Since all halomonads are mesophilic, most of them can grow at 37°C; nearly a fourth of the species grow optimally at 37°C or higher. The predominant respiratory quinone is ubiquinone Q‑9; however, H. campaniensis only possesses Q‑8. The major fatty acids are C16:1, C16:0, C17:0 cyclo, C18:1 and C19:0 cyclo. The 16S rRNA gene sequences contain four signature bases (C at position 1424, U at position 1439, A at position 1462 and C at position 1464 [by conventional method of numbering, as used for E. coli]) in addition to the 15 signature sequences found in the family Halomonadaceae [11]. The G+C content of the DNA is 51.4–74.6 M%. Many have a large extrachromosomal DNA content [2]. The genus Halomonas currently contains 76 species whose names have been validly published (as of July 2013), together with eight species that have previously been effectively, but not validly, published (Table 1). Ecology: where it has been found & why it is found there

During early research on the microbiology of hypersaline environments, halomonad-like organisms were often neglected. They inhabit a wide range of habitats, much less restricted than those the halophilic Archaea thrive in, for www.futuremedicine.com

1561

Review

Kim, Lee & Stevens

Table 1. All published species names of the genus Halomonas (as of July 2013). Species†

Isolation source‡

16S rRNA gene § Strain

Ref. ¶

Accession no.

H. alimentaria

Jeotgal (traditional Korean fermented seafood)

YKJ-16

H. alkaliantarctica

Antarctic salt lake

CRSS

H. alkaliphila

Salt pool in a resort (Italy)

18bAGT

H. almeriensis

Saltern (Spain)

M8

AY858696

H. andesensis

Saline lake (Bolivia)

LC6

H. anticariensis

Saline wetland (Spain)

FP35T

H. aquamarina

Seawater

DSM 30161T

AJ306888

H. arcis

Salt lake (China)

T

AJ282

EF144147

H. axialensis

Low-temperature hydrothermal fluid

T

Althf1

AF212206

H. beimenensis

Abandoned saltern (Taiwan)

NTU-107T

EU159469

H. boliviensis

Hypersaline lake (Bolivia)

LC1

AY245449

H. campaniensis

Mineral pool in a resort (Italy)

5AG

H. campisalis

Saline, alkaline lake (USA)

4AT

H. caseinilytica

Salt lake (China)

AJ261T

H. cerina

Hypersaline soils (Spain)

SP4

H. cibimaris

Jeotgal (traditional Korean fermented seafood)

10-C-3

H. cupida

Marine

DSM 4740T

FN257742

H. daqiaonensis

Saltern (China)

YCSA28T

FJ984862

H. daqingensis

Oil-polluted saline soil (China)

DQD2–30

H. denitrificans

Seawater

M29

H. desiderata

Municipal sewage sludge (Germany)

FB2

H. elongata

Solar salt facility (The Netherlands Antilles)

DSM 2581T

H. eurihalina

Hypersaline habitats (soils, salt ponds) and seawater

ATCC 49336

H. flava

Salt lake (China)

YIM 94343

H. fontilapidosi

Saline wetland (Spain)

5CR

H. gomseomensis

Solar saltern (Korea)

M12T

H. gudaonensis

Oil-polluted saline soil (China)

SL014B-69

H. halmophila

Dead Sea

ATCC 19717

H. halocynthiae

Gill tissue of the ascidian Halocynthia aurantium

H. halodenitrificans

T

T

T

AF211860

[31]

AJ564880

[30,57]

AJ640133

[38]

EF622233

T

[25]

AY489405

T T

[22]

AJ515365

[39]

AF054286

[40]

EF527874 EF613112

T

[32]

GQ232738

T

EF121854

T

AM229317

T

X92417

T

[34]

FN869568 T

[3]

X87218 HQ832736

T

EU541349

T

AM229314 DQ421808

T

AJ306889

[8]

KMM 1376T

AJ417388

[60]

Meat-curing brine

ATCC 13511T

L04942

[35]

H. halophila

Hypersaline soils (Spain)

DSM 4770

FN257740

H. hamiltonii

Dialysis machines of a renal care center (USA)

W1025

H. hydrothermalis

Low-temperature hydrothermal fluid

H. ilicicola

T

T

AM941396

[27]

Slthf2T

AF212218

[22]

Solar saltern (Spain)

SP8

EU218533

H. janggokensis

Solar saltern (Korea)

H. jeotgali H. johnsoniae

T

T T

M24

AM229315

Jeotgal (traditional Korean fermented seafood)

T

Hwa

EU909458

[33]

Dialysis machines of a renal care center (USA)

T68687T

AM941399

[27]

Names found in the literature, but not validly published per taxonomic rules, are in quotation marks. Such names may be superseded later by validly publishing the novel isolates and assuring they are not identical to validly described species (presented here without quotation marks). ‡ Where locations are not provided, the locations were not stated clearly in the original publication or the isolation was made at more than one location. § Bacterial strains and DNA accession numbers used in the 16S rRNA gene-based phylogenetic ana­lysis (Figure 1) are given. A superscript T indicates a type or proposed type strain. ¶ Unless indicated, species information was obtained from [101]. †

1562

Future Microbiol. (2013) 8(12)

future science group

Microbiology & epidemiology of Halomonas species

Review

Table 1. All published species names of the genus Halomonas (as of July 2013) (cont.). Species†

Isolation source‡

16S rRNA gene § Strain

Accession no.

H. kenyensis

Soda lakes (Kenya)

AIR-2

AY962237

H. koreensis

Solar saltern (Korea)

SS20T

AY382579

H. korlensis

Saline, alkaline soil (China)

XK1T

H. kribbensis

Solar saltern (Korea)

BH843

H. lutea

Salt lake (China)

YIM 91125

H. magadiensis

Saline soda lakes (Kenya)

21 MI

H. maura

Solar saltern (Morocco)

S-31T

H. meridiana

Antarctic saline lakes

DSM 5425

H. mongoliensis

Soda lake (Mongolia)

Z-7009

H. muralis

Biofilm covering a wall and a mural (Austria)

LMG 20969

H. neptunia

Hydrothermal plume

H. nitroreducens

T

EU085033

Ref. ¶ [41]

[42]

DQ280368

T

EF674852

T

X92150

T

[28]

FN257741 AJ306891

[9]

AY962236

[41]

AJ320530

[36]

Eplume1T

AF212202

[22]

Solar saltern (Chile)

11S

EF613113

H. organivorans

Saline soils (Spain)

G-16.1

AJ616910

H. pacifica

Marine

DSM 4742T

L42616

H. pantelleriensis

Saline lake (Italy)

AAP

H. qijiaojingensis

Salt lake (China)

YIM 93003

H. ramblicola H. rifensis

T

T

T T

T

X93493

T T

HQ832735

Hypersaline rambla (Spain)

RS-16

T

GU726750

Solar saltern (Morocco)

HK31T

HM026177

H. sabkhae

Salt flat (Algeria)

5–3

H. saccharevitans

Salt lake (China)

AJ275

H. salifodinae

Salt mine (China)

BC7

H. salina

Hypersaline habitats (soils, solar salterns, salt ponds) and F8–11T seawater

AJ295145

H. shengliensis

Oil-polluted saline soil (China)

SL014B-85T

EF121853

H. sinaiensis

Salt lake (Egypt)

Alo SharmT

AM238662

H. smyrnensis

Saltern (Turkey)

AAD6

DQ131909

H. stenophila

Saline wetlands (Spain)

N12

H. stevensii

Patients’ blood and dialysis machines (USA)

S18214T

H. subglaciescola

Organic Lake (Antarctic saline lake)

DSM 4683

H. subterranea

Saline well (China)

ZG16

H. sulfidaeris

Deep-sea metal sulfide rock

Esulfide1

AF212204

H. taeanensis

Solar saltern (Korea)

BH539T

AY671975

H. titanicae

Rusticles of the RMS Titanic wreck

BH1

H. variabilis

Great Salt Lake (USA)

DSM 3051

AJ306893

H. ventosae

Saline soils (Spain)

Al12

AY268080

H. venusta

Marine

DSM 4743T

AJ306894

H. vilamensis

Hypersaline lake (Argentina)

SV325

EU557315

H. xianhensis

Oil-polluted saline soil (China)

A-1

EF442769

T

EF144149

T

EF527873

T

T

HM242216

T

AM941388 T

[6]

EF144148

T T

[22]

FN433898

T T

T

T

AJ306892

[27,72]

T

EF421176

Names found in the literature, but not validly published per taxonomic rules, are in quotation marks. Such names may be superseded later by validly publishing the novel isolates and assuring they are not identical to validly described species (presented here without quotation marks). ‡ Where locations are not provided, the locations were not stated clearly in the original publication or the isolation was made at more than one location. § Bacterial strains and DNA accession numbers used in the 16S rRNA gene-based phylogenetic ana­lysis (Figure 1) are given. A superscript T indicates a type or proposed type strain. ¶ Unless indicated, species information was obtained from [101]. †

future science group

www.futuremedicine.com

1563

Review

Kim, Lee & Stevens

Table 1. All published species names of the genus Halomonas (as of July 2013) (cont.). Species†

Isolation source‡

16S rRNA gene § Strain

Ref.¶

Accession no.

H. xinjiangensis

Salt lake (China)

TRM 0175

H. zhanjiangensis

Sea urchin

JSM 078169

“H. aidingensis”

Salt lake (China)

Ad-1T

“H. chromatireducens”

Salt marshes (Russia)

AGD 8–3T

“H. glaciei”

Antarctic fast ice

DD 39

“H. nitrilicus”

Soda lakes and salt marshes

ANL-aCH3

“H. phocaeensis”

Neonates’ blood (Tunisia)

CCUG 5096

“H. profundus”

Deep-sea hydrothermal vent shrimp

AT1214T

“H. sediminis”

Salt lake (China)

YIM C248

EU822512

T T

T T

T

T

FJ429198

[61]

GQ281062

[73]

EU447163

[74]

AJ431369

[24]

EU447162

[26]

AY922995

[70]

AJ876733

[23]

EU135707

[75]

Names found in the literature, but not validly published per taxonomic rules, are in quotation marks. Such names may be superseded later by validly publishing the novel isolates and assuring they are not identical to validly described species (presented here without quotation marks). ‡ Where locations are not provided, the locations were not stated clearly in the original publication or the isolation was made at more than one location. § Bacterial strains and DNA accession numbers used in the 16S rRNA gene-based phylogenetic ana­lysis (Figure 1) are given. A superscript T indicates a type or proposed type strain. ¶ Unless indicated, species information was obtained from [101]. †

example [29]. Halomonads have been found at a wide range of pH and temperatures as well as at almost any range of salinities (Table 2). Halomonads are found all over the world in saline or hypersaline environments. Many are found in natural brines in arid, coastal and even deepsea locations, as well as in artificial salterns used to mine salts from the sea (Table 1). A total of 16 Halomonas species, including the type species H. elongata [3], were originally found in solar salt facilities; for example, solar salterns or salt mines. A total of 24 species were originally found in saline or salt lakes; H. alkaliantarctica, H. meridiana and H. subglaciescola were isolated from salt or water samples collected in Antarctic salt lakes [6,9,30]. Overall, 17 species were originally found in saline or hypersaline soils. Fifteen species were discovered in marine environments; H. axialensis, H. hydrothermalis, H. neptunia, H. sulfidaeris and “H. profundus” were isolated from deep-sea hydrothermal-vent environments [22,23]. Nine species were discovered in alkaline, saline samples collected in soda lakes and mineral pools, among others. Those found in unusual sources include H. alimentaria [31], H. cibimaris [32] and H. jeotgali [33] (from salted fermented seafood), H. desiderata (from municipal sewage sludge) [34], H. halodenitrificans (from meat-curing brine) [35], H. muralis (from biofilm covering a wall and a mural) [36] and “H. glaciei” (from Antarctic fast ice) [24]. The isolation of H. muralis is particularly intriguing. Mural paintings, particularly if subjected to increasing dampness, contain different hygroscopic salts such as carbonates, chlorides, 1564

Future Microbiol. (2013) 8(12)

nitrates and sulfates, among others, which are locally concentrated or are dispersed within porous materials [37]. As a result of changing physical parameters, these soluble salts migrate with the water through the wall, and after drying out these salts are exposed to the surface of the material. This process leads to the formation of deposits of hygroscopic salts on the surface, socalled ‘salt efflorescence’, which may be a source for the enrichment of halomonads. Of interest, six haloalkaliphilic strains (FB1–FB6) of H. desiderata were obtained from samples taken from the municipal sewage treatment plant (pH: 7.5) without salt supplementation [34]. Alkaliphilic species include the nine species originally isolated from alkaline, saline samples: H. alkaliphila, H. campaniensis, H. campisalis, H. kenyensis, H. korlensis, H. magadiensis, H. mongoliensis, “H. alkalitolerans” and “H. nitrilicus” [26,28,38–43]. High osmolarity in saline or hypersaline conditions can be deleterious to cells since water is lost to the external medium until osmotic equilibrium is achieved [21]. To prevent loss of cellular water under these circumstances, halophilic/halotolerant bacteria generally accumulate high concentrations of organic solutes within the cytoplasm [44]. The types of organic solutes used for osmotic balance include polyols, sugars or amino acids, and the derivatives of these classes of molecules: betaines, ectoines and occasionally peptides suitably altered to remove charges [45]. These osmolytes can either be synthesized by the cell, de novo or from storage material, or transported future science group

Microbiology & epidemiology of Halomonas species

Review

Table 2. Physiological features of members of the genus Halomonas. Species†

Salt range (%, w/v)

Temperature range (°C) pH range

Ref.‡

H. alimentaria

0–30

4–45

5.0–10.0

H. alkaliantarctica

2.2–22.2

10–37

7.4–9.6

[57]

H. alkaliphila

0–20

5–50

7.5–10.0

[38]

H. almeriensis

5–25

15–37

6.0–10.0

H. andesensis

0.5–20

4–45

6.0–11.0

H. anticariensis

0.5–15

20–45

6.0–9.0

H. aquamarina

0.5–20

15–37

5.0–10.0

H. arcis

0–20

4–48

6.0–10.0

H. axialensis

0.5–24

-1–35

5.0–12.0

H. beimenensis

0–15

15–50

5.5–9.5

H. boliviensis

0–25

0–45

6.0–11.0

H. campaniensis

0.5–25

4–45

6.0–10.0

H. campisalis

0.5–15

4–50

8.0–11.0

H. caseinilytica

0.5–15

4–48

5.0–9.0

H. cerina

3–25

4–45

5.0–10.0

H. cibimaris

3–15

15–35

5.5–9.0

H. cupida

0–15

15–37

5.0–10.0

H. daqiaonensis

2–15

5–40

6.0–9.0

H. daqingensis

1–15

10–50

8.0–10.0

H. denitrificans

0–30

4–45

5.0–10.0

H. desiderata

0–20

10–45

7.0–11.0

H. elongata

0–20

4–45

5.0–10.0

H. eurihalina

0.5–25

4–45

5.0–10.0

H. flava

0.5–23

20–40

6.0–9.0

H. fontilapidosi

3–25

15–45

5.0–9.0

H. gomseomensis

1–20

5–45

6.0–10.0

H. gudaonensis

0.5–30

4–45

6.0–10.0

H. halmophila

3–25

15–45

5.0–10.0

H. halocynthiae

0.5–15

7–35

5.0–11.0

[60]

H. halodenitrificans

3–20

5–37

5.0–10.0

[35]

H. halophila

2–25

4–45

5.0–10.0

H. hamiltonii

0–20

10–40

6.0–10.0

[27]

H. hydrothermalis

0.5–22

2–40

5.0–12.0

[22]

H. ilicicola

2–17.5

25–42

6.0–9.0

H. janggokensis

1–20

5–45

6.0–10.0

H. jeotgali

5–25

10–32

5.0–10.0

[33]

H. johnsoniae

0–20

10–40

7.0–10.0

[27]

H. kenyensis

0–13

10–55

7.5–10.6

[41]

[25]

[22]

[32]

[34]

Names found in the literature, but not validly published per taxonomic rules, are in quotation marks. Such names may be superseded later by validly publishing the novel isolates and assuring they are not identical to validly described species (presented here without quotation marks). ‡ Unless indicated, data were taken from [2,59,76,101]. § Only the optimum salt range, temperature or pH has been reported. ND: Not determined; w/v: Weight/volume. †

future science group

www.futuremedicine.com

1565

Review

Kim, Lee & Stevens

Table 2. Physiological features of members of the genus Halomonas (cont.). Species†

Salt range (%, w/v)

Temperature (°C)

pH

Ref.‡

H. koreensis

1–30

15–45

5.0–10.0

H. korlensis

0.5–25

4–43

6.0–10.0

H. kribbensis

1–14

10–40

5.5–9.5

H. lutea

1–20

4–45

5.0–9.0

H. magadiensis

0–20

20–45

5.0–11.0

H. maura

1–20

10–45

5.0–10.0

H. meridiana

0–20

4–45

5.0–10.0

[9]

H. mongoliensis

0–12

15–50

8.0–10.5

[41]

H. muralis

0–15

10–35

5.5–10.0

[36]

H. neptunia

0.5–27

-1–35

5.0–12.0

[22]

H. nitroreducens

0.5–30

4–45

5.0–10.0

H. organivorans

1.5–30

15–45

6.0–10.0

H. pacifica

0–20

4–45

5.0–10.0

H. pantelleriensis

1–15

10–45

6.0–11.0

H. qijiaojingensis

0.5–23

20–40

6.0–9.0

H. ramblicola

1–30

4–41

5.0–10.0

H. rifensis

0.5–20

25–45

5.0–10.0

H. sabkhae

5–25

30–50

6.0–9.0

H. saccharevitans

0.5–15

4–48

5.0–10.0

H. salifodinae

0.5–20

4–48

6.0–9.0

H. salina

2–20

4–45

5.0–10.0

H. shengliensis

0.5–30

4–45

5.0–10.0

H. sinaiensis

0–30

25–50

6.0–9.0

H. smyrnensis

3–25

5–40

5.5–8.5

H. stenophila

3–15

15–37

6.0–8.0

H. stevensii

0–20

10–40

7.0–11.0

H. subglaciescola

0.5–20

0–45

5.0–10.0

H. subterranea

0–15

4–48

6.0–10.0

H. sulfidaeris

0.5–24

-1–35

5.0–10.0

H. taeanensis

1–25

10–45

7.0–10.0

H. titanicae

0.5–25

4–42

5.5–9.5

H. variabilis

1–25

15–37

6.0–9.0

H. ventosae

3–15

15–50

6.0–10.0

H. venusta

0–20

4–45

5.0–10.0

H. vilamensis

1–25

5–40

5.0–10.0

H. xianhensis

0.05–27.5

10–42

5.5–9.0

H. xinjiangensis

0–20

15–50

6.0–9.0

H. zhanjiangensis

1–20

4–40

6.0–10.5

[42]

[28]

[27]

[22]

[61]

Names found in the literature, but not validly published per taxonomic rules, are in quotation marks. Such names may be superseded later by validly publishing the novel isolates and assuring they are not identical to validly described species (presented here without quotation marks). ‡ Unless indicated, data were taken from [2,59,76,101]. § Only the optimum salt range, temperature or pH has been reported. ND: Not determined; w/v: Weight/volume. †

1566

Future Microbiol. (2013) 8(12)

future science group

Microbiology & epidemiology of Halomonas species

Review

Table 2. Physiological features of members of the genus Halomonas (cont.). Species†

Salt range (%, w/v)

Temperature (°C)

pH

Ref.‡

“H. aidingensis”

0.5–25

4–45

5.5–10.5

[73]

“H. alkalitolerans”

1–23

10–50

7.0–11.0

[43]

“H. chromatireducens”

0.53–20.4

8–47

6.8–10.5

[74]

“H. glaciei”

0–15

4–30

6.0–12.0

[24]

“H. nitrilicus”

0.6–20.5

32

7.5–10.5

[26]

“H. phocaeensis”

2.9–11.7

ND

“H. profundus”

2–3

“H. sediminis”

1–15

§

§

§

[70]

ND

32–37

8.0–9.0

§

[23]

4–35

6.0–10.0

[75]

§

Names found in the literature, but not validly published per taxonomic rules, are in quotation marks. Such names may be superseded later by validly publishing the novel isolates and assuring they are not identical to validly described species (presented here without quotation marks). ‡ Unless indicated, data were taken from [2,59,76,101]. § Only the optimum salt range, temperature or pH has been reported. ND: Not determined; w/v: Weight/volume. †

into the cell from the medium. Important organic osmolytes synthesized by halophilic/ halotolerant bacteria are glucosylglycerol, dimethylsulfoniopropionate, the amino acids proline and glutamine, glutamine amide derivatives, N-acetylated diamino acids, ectoine and hydroxyectoine, and glycine betaine. These are polar, highly soluble molecules that carry no net charge [46]. Ectoine and glycine betaine are most common (Ta ble  3). A key feature of

osmolytes is that they do not inhibit overall cellular functions, although they may modulate individual enzyme activities. This behavior led to them being labeled as ‘compatible solutes’ [47]. Halomonads’ tolerance towards any kind of denaturing stress and ubiquitous distribution may be attributed to the presence of compatible solutes. Their accumulation helps to maintain turgor pressure, cell volume and concentration of electrolytes – all essential

Table 3. Organic compatible solutes of members of the genus Halomonas. Species

Solute Glycine etaine Ectoine

H. boliviensis

++

Hydroxyectoine Others

+ ++

++ ++

H. campisalis‡

+

++

+

H. elongata H. elongata‡

++ ++

+

++

H. eurihalina

++

+

H. halmophila H. halmophila‡

++

++ ++

H. halodenitrificans H. halodenitrificans‡ ++

++ ++

H. halophila H. halophila‡

++

++ ++

H. pantelleriensis H. pantelleriensis‡

+ ++

H. variabilis

‡

++

[77]

+

H. campaniensis H. campaniensis‡

H. salina

Ref. †

Glutamate Glutamate

[39] [78]

Glutamate, glucose

[79]

Glutamate

[80]

Glutamate, alanine Alanine, trehalose, glucose

[79]

Glutamate, glucose Trehalose

[79]

+

Glutamate Trehalose, glucose

[79]

++ ++

+

Glutamate Glutamate

[81]

++

+

Glutamate

[80]

++

++

Trehalose

[79]

+

Empty cells signify no data demonstrating the presence of the solutes indicated. † Solutes that never occur as primary osmolytes. ‡ Yeast extract was supplied in the medium. ++: Present in high concentrations; +: Present in minor amounts.

future science group

www.futuremedicine.com

1567

Review

Kim, Lee & Stevens

elements for cell maintenance and proliferation [45]. Furthermore, the advantages of the compatible solute systems are not confined to achieving osmotic balance [48]. The effect of compatible solutes is not only that they may be present inside the cells in molar concentrations without altering the cell’s metabolic functions, but also that they are capable of stabilizing proteins [49]. The protein stabilizing property of compatible solutes under stress conditions is reflected by the fact that they confer increased tolerance towards heating, freezing, drying, radiation and other denaturing agents, as well as towards high salinity [49]. Owing to fact that compatible solutes act as stabilizers of binding structures and enzymes, confer elevated tolerance towards any kind of denaturing agents, and stabilize a protein regardless of its origin [50], the beneficial effect of compatible solutes must relate to a general stabilizing property, not to a specific adaptation to salt stress. Compatible solutes stabilize a protein, keeping it in the native, folded state [49]. The mechanism responsible for stabilization is ‘preferential exclusion’, which means that compatible solutes are preferentially excluded from the immediate vicinity of proteins, implying unfavorable net interactions between the protein fabric and the compatible solute, called the ‘osmophobic effect’ [51]. The osmophobic effect makes denaturation of protein less favorable, and therefore forces proteins to remain correctly folded, since denatured protein exposes much more of the protein fabric to solvent, relative to the folded state [52]. Further detailed studies of this effect demonstrated that the peptide backbone plays a dominant role in protein stabilization, while the side chains favor protein unfolding [53]. The stabilizing effect of compatible solutes applies generally, not specifically, to salt-adapted proteins. Expanding utility of the genus

Industrial uses of the bacteria in this genus are increasing (Box 1) [2,54]. Their extracellular enzymes are of interest to the biotechnology industry. Ectoine and hydroxyectoine are important to the cosmetic industry because of their moisturizing properties. Bioremediation uses include degrading hydrocarbons efficiently under hypersaline conditions, thus raising the important possibility of utility in the elimination of oil spills at sea [55]. Formaldehyde and uranium, for example, can be degraded under hypersaline conditions. The increasing uses by humans in­evitably means that these bacteria will have more encounters with 1568

Future Microbiol. (2013) 8(12)

humans, and increasing possibilities for opportunistic infections. The extracellular production of exopolysaccharides  [30,56,57] would promote biofilm formation, which would be useful for survival of these bacteria in marine environments. Biofilm formation has been demonstrated by members of this genus [36,56]. Biofilm formation could also contribute to persistence in the contaminated environment of humans. Clinical experience with the genus Laboratory microbiology

Isolation from the environment is accomplished with the use of high salt selection media, which will inhibit halointolerant competitors. We developed such a strategy to isolate halomonads from our hospital environment [58]. A range of 6.5–20.5% w/v salt in broths was tested, and we found that 16.5% w/v salt in brain–heart infusion broth was optimal enrichment prior to subculture to agar for our species, H. stevensii, H. hamiltonii and H. johnsoniae. The optimal method for isolation was found to be vortex mixing of a swab sample into a salt enrichment broth, incubation at 35°C for 48–72 h, then subculture to agar plates (without salt supplementation) incubated in room air at 35°C for 24–72 h. Halomonas isolates produced a distinctive purple colony on MacConkey’s agar (without salt supplementation), which became more pronounced with increased time of incubation. In order to avoid excessively high salt concentrations when attempting to culture from salt powders and crystals, we made a 16% w/v solution of each, either in sterile water or brain–heart infusion broth [58]. Samples of these were plated on agar. The remainder was filtered (0.2 µm, cellulose nitrate) and then the filter was placed, filter side up, on a sheep blood agar plate (without salt supplementation). As an alternative method, the unfiltered solutions were added to high salt broth for enrichment, with a large dilution factor. In yet another successful method, enabling the culturing of larger amounts of powder or crystals but avoiding the process of solubilizing these, we vigorously shook them in sterile 0.9% w/v saline (to dislodge any externally adherent bacteria). We then allowed the solids to settle, and directly plated a portion of the fluid onto agar. The remaining solution was filtered, and the filter cultured on sheep blood agar plates (without salt supplementation) [58]. Standard clinical laboratory systems that rely on metabolic patterns will fail to identify or misidentify these organisms, which are uncommonly encountered in patients. There are no clinically future science group

Microbiology & epidemiology of Halomonas species

used antibiotics to which all species are susceptible [58,59]. Conversely, whereas all species are susceptible to the majority of antibiotics tested, no species, with two exceptions, have been shown susceptible to all antibiotics tested. The two exceptions are H. stevensii (27 antibiotics tested) and H. desiderata (16 antibiotics tested) [58,59]. These studies mean that if halomonads are encountered clinically, susceptibility testing will be required and broad-spectrum antibiotic therapy initiated until the test results are available. It is recommended that isolates be maintained on agar slants with 7.5–10% (w/v) NaCl [1,2]. Those with lower salt requirements can be maintained on commercial Marine Agar. It is recommended that isolates be transferred regularly every 3 months.

Box 1. Industrial uses of the genus Halomonas. Bioremediation Waste water treatment „„Fermentation „„Decontamination – Environmental heavy metals – Radioactive compounds „„ „„

Agricultural fungicides Production – Antimicrobials – Biosurfactants – Exopolysaccharides – Enzymes – Moisturizers – Plastics – Polysaccharide polymers

„„ „„

Clinical epidemiology

An initial clue to suggest the possible pathogenic potential of these organisms, namely a host– microbe relationship of any kind, is that three species, H. halocynthiae, H. zhanjiangensis and “H. profundus”, were isolated from marine invertebrates as their symbionts [23,60,61]. Halomonads pathogenic to marine animals or algae have been reported. Halomonas sp. strain 3 causing ‘HoleRotten Disease’ was isolated from diseased sporophytes of Laminaria japonica, a type of seaweed, in a farm cultivating the latter in China [62]. Four strains (B1–B4) belonging to H. cupida (formerly Alcaligenes cupidus) were isolated from dying fish at hatcheries in western Japan, causing mortality in black sea bream fry [63]. A highly exopolysaccharide-producing Halomonas strain (CAM2) causing epizootics was isolated from larval cultures of the Chilean scallop [64]. Leading infectious disease texts do not mention these organisms as human pathogens [65]; furthermore comprehensive and classic older review articles state they are ‘not pathogenic’ [2]. Involvement in human diseases has, however, now been repeatedly documented, and a common theme is bacteremia (Table 4). However, it is possible that this apparent predilection may be explained by culture of blood, normally sterile, yielding a halomonad as a pathogen in pure culture, facilitating recognition, whereas halomonads as part of other, contaminated, body fluids (such as stool or sputum) may not be identified among the other flora. Another theme in these human diseases is hemodialysis, which relies on salts to prepare dialysis fluids of appropriate osmolarity. Such salts (bicarbonates) have been implicated in the dialysis patient-related cases [58]. The last four future science group

Review

line entries in Table 4 are dialysis-related cases (five cases). All had physiologic perturbations, such as fever or hypotension, during dialysis that led to the blood cultures. The halomonads that contaminated the environment in our dialysis unit have persisted for several years, as evidenced by cultures from environmental surfaces, indicating continued introduction from contaminated storage tanks and/or tenacious residence in the environment and/or spread by staff [27,54,58]. Another dialysisrelated isolate is discussed in the next paragraph. It is underappreciated that bacteria can contaminate dialysates [66]. Dialyzer membranes have sticky properties that enable bacterial adhesion; thus, the membranes could act as Table 4. Human infections with Halomonas species. Species†

Infection

H. venusta

Fish bite on leg, wound infection

Ref. [69]

“H. phocaeensis”

Bacteremia in neonates (six cases)

[70]

H. variabilis–H. boliviensis–H. neptunia Presumed bacteremia cluster

[58,82]

H. stevensii

Bacteremia (two cases)

[27,58]

H. johnsoniae

Bacteremia

H. stevensii ‡

Bacteremia (2012)

[Kim KK, Lee JS, Stevens DA, Unpublished Data]

H. stevensii ‡

Bacteremia (2013)

[Stevens DA, Lee JS, Kim KK, Unpublished Data]

[54]

Names found in the literature, but not validly published per taxonomic rules, are in quotation marks. Such names may be superseded later by validly publishing the novel isolates and assuring they are not identical to validly described species (presented here without quotation marks). ‡ Identified by 16S rDNA sequencing. Adapted with permission from [54]. †

www.futuremedicine.com

1569

Review

Kim, Lee & Stevens

concentrators  [67]. An additional concern is that bacteria in a dialysate can traverse the membrane [68]. Although an extensive culture survey of dialysates performed did not uncover any Halomonas species [66], suboptimal culturing methods for these organisms was likely used, as previous sections in our present paper have suggested. A study investigating inflammatory reactions, including fever, in dialysis patients found the dialysate compartment to contain bacterial DNA, even if the dialysates appeared sterile [67]. These investigators digested biofilms in this compartment uncovering a Halomonas DNA, among others [67]. Of the evaluable patients known (Table  4), all six adults responded promptly to broadspectrum antibiotics with clearance of the blood and symptoms, as did four of six neonates [54,58,69,70] [Kim KK et al., Unpublished Data; Stevens DA, Unpublished Data].

The two nonresponding neonates who died had marked comorbidities [70]. As most texts do not yet recognize this genus as a pathogen, there is no body of work on the microbe–host interaction, other than what we have summarized here about the clinical outcome of cases. Antibiotic susceptibilities have been referred to in the preceding section. We hope the medical community becomes more aware of the pathogenic potential of bacteria in this genus. Our experience shows the importance of speciation of Gram-negative organisms from patient cultures that have unusual

or atypical biochemical features, which may not readily conform to usual clinical laboratory identification algorithms. To detect these bacteria in mixed environmental cultures taken in a hospital during an epidemiologic workup will likely require the selective methods we have described here. Finally, we have shown that environmental isolates of this genus do become pathogenic [54,58]. Future perspective

Owing to the unusual environments in which these species are found, the unique products of their adaptive physiology will find increasing industrial uses. Their adaptability will enable them to contaminate various environments utilized by humans. As Table 4 indicates, there is an increasing tempo of recognition as human pathogens over recent years, and it is expected that improved microbiologic techniques and identification will result in more reports of disease. Financial & competing interests disclosure

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties. No writing assistance was utilized in the production of this manuscript.

Executive summary Background „„A total of 76 species have already been validly described. Based on 16S rDNA sequencing, there are two large clusters of 16 and 26 each, the latter including the few valid species that have been described as pathogenic in humans. Nonclinical epidemiology of Halomonas species „„The range of species in the genus: – With respect to pH, temperature and range of salinities, interspecific variation can be high. The genus Halomonas is characteristically halophilic or halotolerant. Ecology: where it has been found and why it is found there? – Halomonads have been found at a wide range of pH and temperatures as well as at almost any range of salinities. Halomonads are found all over the world, commonly in saline or hypersaline environments. They have developed a unique physiology that protects them from these hyperosmotic environments. Their adaptability suggests there will be increasing descriptions of new species.

„„

Expanding utility of the genus: – Their unique physiology has been harnessed by man in bioremediation and production of valuable materials. For some of these uses, members of the genus offer unique advantages.

„„

Clinical experience with the genus „„Laboratory microbiology: – Isolation from the environment is accomplished with the initial use of high salt selection media, which will inhibit halointolerant competitors. Clinical epidemiology: – Contamination of the human environment is increasingly recognized, and disease in algae, animals and humans has now been described. As the industrial uses of these species increase, and the ability to isolate and recognize them improves, further pathogenic encounters with humans may be expected.

„„

1570

Future Microbiol. (2013) 8(12)

future science group

Microbiology & epidemiology of Halomonas species

References Papers of special note have been highlighted as: n of interest nn of considerable interest 1.

2.

nn

3.

n

4.

5.

6.

7.

8.

9.

Garrity GM, Bell JA, Lilburn T. Class III. Gammaproteobacteria class. nov. In: Bergey’s Manual of Systematic Bacteriology (Volume 2, 2nd Edition, Part B). Brenner DJ, Krieg NR, Staley JT, Garrity GM (Eds). Springer, NY, USA, 159–206 (2005). Arahal DR, Ventosa A. The family Halomonadaceae. In: The Prokaryotes (Volume 6, 3rd Edition). Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (Eds). Springer, NY, USA, 811–835 (2006). Most comprehensive review of the genus to date. Vreeland RH, Litchfield CD, Martin EL, Elliot E. Halomonas elongata, a new genus and species of extremely salt-tolerant bacteria. Int. J. Syst. Bacteriol. 30(2), 485–495 (1980). Founding of the genus. Shewin JM, Véron M, Schubert RH, Hendrie MS. Family II. Vibrionaceae Véron 1965, 5245. In: Bergey’s Manual of Determinative Bacteriology (8th Edition). Buchanan RE, Gibbons NE (Eds). The Williams & Wilkins Co., MD, USA, 340–352 (1974). Farmer JJ 3rd. International Committee on Systematic Bacteriology. Subcommittee on the taxonomy of Vibrionaceae. Minutes of the meetings, 8 and 11 September 1986, Manchester, England. Int. J. Syst. Bacteriol. 39(2), 201–212 (1989). Franzmann PD, Burton HR, McMeekin TA. Halomonas subglaciescola, a new species of halotolerant bacteria isolated from Antarctica. Int. J. Syst. Bacteriol. 37(1) 27–34 (1987). Hebert AM, Vreeland RH. Phenotypic comparison of halotolerant bacteria: Halomonas halodurans sp. nov., nom. rev., comb. nov. Int. J. Syst. Bacteriol. 37(4), 347–350 (1987). Franzmann PD, Wehmeyer U, Stackebrandt E. Halomonadaceae fam. nov., a new family of the class Proteobacteria to accommodate the genera Halomonas and Deleya. Syst. Appl. Microbiol. 11(1), 16–19 (1988). James SR, Dobson SJ, Franzmann PD, McMeekin TA. Halomonas meridiana, a new species of extremely halotolerant bacteria isolated from Antarctic saline lakes. Syst. Appl. Microbiol. 13(3), 270–278 (1990).

10. Mellado E, Moore ERB, Nieto JJ, Ventosa A.

Phylogenetic inferences and taxonomic consequences of 16S ribosomal DNA sequence comparison of Chromohalobacter marismortui, Volcaniella eurihalina, and Deleya salina and reclassification of V. eurihalina as Halomonas eurihalina comb.

future science group

nov. Int. J. Syst. Bacteriol. 45(4), 712–716 (1995).

the family Halomonadaceae based on comparative 23S and 16S rRNA gene sequence ana ­lysis. Int. J. Syst. Evol. Microbiol. 60(4), 737–748 (2010).

11. Dobson SJ, Franzmann PD. Unification of the

genera Deleya (Baumann et al. 1983), Halomonas (Vreeland et al. 1980), and Halovibrio (Fendrich 1988) and the species Paracoccus halodenitrificans (Robinson and Gibbons 1952) into a single genus, Halomonas, and placement of the genus Zymobacter in the family Halomonadaceae. Int. J. Syst. Bacteriol. 46(2), 550–558 (1996). 12. Arahal DR, García MT, Ludwig W, Schleifer

KH, Ventosa A. Transfer of Halomonas canadensis and Halomonas israelensis to the genus Chromohalobacter as Chromohalobacter canadensis comb. nov. and Chromohalobacter israelensis comb. nov. Int. J. Syst. Evol. Microbiol. 51(4), 1443–1448 (2001). 13. Arahal DR, Castillo AM, Ludwig W,

Schleifer KH, Ventosa A. Proposal of Cobetia marina gen. nov., comb. nov., within the family Halomonadaceae, to include the species Halomonas marina. Syst. Appl. Microbiol. 25(2), 207–211 (2002). 14. Sánchez-Porro C, de la Haba RR,

Soto-Ramírez N, Márquez MC, Montalvo-Rodríguez R, Ventosa A. Description of Kushneria aurantia gen. nov., sp. nov., a novel member of the family Halomonadaceae, and a proposal for reclassification of Halomonas marisflavi as Kushneria marisflavi comb. nov., of Halomonas indalinina as Kushneria indalinina comb. nov. and of Halomonas avicenniae as Kushneria avicenniae comb. nov. Int. J. Syst. Evol. Microbiol. 59(2), 397–405 (2009). 15. de la Haba RR, Sánchez-Porro C, Márquez

MC, Ventosa A. Taxonomic study of the genus Salinicola: transfer of Halomonas salaria and Chromohalobacter salarius to the genus Salinicola as Salinicola salarius comb. nov. and Salinicola halophilus nom. nov., respectively. Int. J. Syst. Evol. Microbiol. 60(4), 963–971 (2010). 16. Romanenko LA, Tanaka N, Svetashev VI,

Falsen E. Description of Cobetia amphilecti sp. nov., Cobetia litoralis sp. nov. and Cobetia pacifica sp. nov., classification of Halomonas halodurans as a later heterotypic synonym of Cobetia marina and emended descriptions of the genus Cobetia and Cobetia marina. Int. J. Syst. Evol. Microbiol. 63(1), 288–297 (2013). 17. Arahal DR, Ludwig W, Schleifer KH,

Ventosa A. Phylogeny of the family Halomonadaceae based on 23S and 16S rRNA sequence analyses. Int. J. Syst. Evol. Microbiol. 52(1), 241–249 (2002). 18. de la Haba RR, Arahal DR, Márquez MC,

Ventosa A. Phylogenetic relationships within

www.futuremedicine.com

Review

19. de la Haba RR, Marquez MD, Papke RT,

Ventosa A. Multilocus sequence ana­lysis of the family Halomonadaceae. Int. J. Syst. Evol. Microbiol. 62(3), 520–538 (2012). n

Newer approach to resolution of the subgroups in the genus.

20. Kushner DJ. Life in high salt and solute

concentrations: halophilic bacteria. In: Microbial Life in Extreme Environments. Academic Press, London, UK, 317–368 (1978). 21. DasSarma S, Arora P. Halophiles.

In: Encyclopedia of Life Sciences. Nature Publishing Group, London, UK (2001). 22. Kaye JZ, Márquez MC, Ventosa A, Baross JA.

Halomonas neptunia sp. nov., Halomonas sulfidaeris sp. nov., Halomonas axialensis sp. nov. and Halomonas hydrothermalis sp. nov.: halophilic bacteria isolated from deep-sea hydrothermal-vent environments. Int. J. Syst. Evol. Microbiol. 54(2), 499–511 (2004). 23. Simon-Colin C, Raguénès G, Cozien J,

Guezennec JG. Halomonas profundus sp. nov., a new PHA-producing bacterium isolated from a deep-sea hydrothermal vent shrimp. J. Appl. Microbiol. 104(5), 1425–1432 (2008). 24. Reddy GSN, Raghavan PUM, Sarita NB

et al. Halomonas glaciei sp. nov. isolated from fast ice of Adelie Land, Antartica. Extremophiles 7(1), 55–61 (2003). 25. Guzmán D, Quillaguamán J, Muñoz M,

Hatti-Kaul R. Halomonas andesensis sp. nov., a moderate halophile isolated from the saline lake laguna Colorada in Bolivia. Int. J. Syst. Evol. Microbiol. 60(4), 749–753 (2010). 26. Chmura A, Shapovalova AA, van Pelt S et al.

Utilization of arylaliphatic nitriles by haloalkaliphilic Halomonas nitrilicus sp. nov. isolated from soda soils. Appl. Microbiol. Biotechnol. 81(2), 371–378 (2008). 27. Kim KK, Lee KC, Oh HM, Lee JS.

Halomonas stevensii sp. nov., Halomonas hamiltonii sp. nov. and Halomonas johnsoniae sp. nov., isolated from a renal care centre. Int. J. Syst. Evol. Microbiol. 60(2), 369–377 (2010). 28. Duckworth AW, Grant WD, Jones BE, Meijer

D, Márquez MC, Ventosa A. Halomonas magadii sp. nov., a new member of the genus Halomonas, isolated from a soda lake of the East African rift valley. Extremophiles 4(1), 53–60 (2000). 29. Ventosa A, Nieto JJ, Oren A. Biology of

moderately halophilic aerobic bacteria. Microbiol. Mol. Biol. Rev. 62(2), 504–544 (1998).

1571

Review

Kim, Lee & Stevens

30. Poli A, Moriello VS, Esposito E, Lama L,

Gambacorta A, Nicolaus B. Exopolysaccharide production by a new Halomonas strain CRSS isolated from saline lake Cape Russell in Antarctica growing on complex and defined media. Biotechnol. Lett. 26(21), 1635–1638 (2004).

41. Boltyanskaya YV, Kevbrin VV, Lysenko AM

et al. Halomonas mongoliensis sp. nov. and Halomonas kenyensis sp. nov., new haloalkaliphilic denitrifiers capable of N2O reduction, isolated from soda lakes. Microbiology 76(6), 739–747 (2007). korlensis sp. nov., a moderately halophilic denitrifying bacterium isolated from saline and alkaline soil. Int. J. Syst. Evol. Microbiol. 58(11), 2582–2588 (2008). alkalitolerans sp. nov., a novel moderately halophilic bacteriun isolated from soda meadow saline soil in Daqing, China. J. Microbiol. 49(1), 24–28 (2011). halophilic eubacteria: molecular principles, water-solute interactions, stress protection. Experientia 49(6–7), 487–496 (1993).

35. Robinson J, Gibbons NE. The effect of salts

on the growth of Micrococcus halodenitrificans n. sp. Can. J. Bot. 30(2), 147–154 (1952). 36. Heyrman J, Balcaen A, De Vos P, Swings

J. Halomonas muralis sp. nov., isolated from microbial biofilms colonizing the walls and murals of the Saint-Catherine chapel (Castle Herberstein, Austria). Int. J. Syst. Evol. Microbiol. 52(6), 2049–2054 (2002). 37. Ripka, K, Denner EBM, Michaelsen A,

Lubitz W, Piñar G. Molecular characterisation of Halobacillus strains isolated from different medieval wall paintings and building materials in Austria. Int. Biodeter. Biodegr. 58(3–4), 124–132 (2006). 38. Romano I, Lama L, Nicolaus B, Poli A,

Gambacorta A, Giordano A. Halomonas alkaliphila sp. nov., a novel halotolerant alkaliphilic bacterium isolated from a salt pool in Campania (Italy). J. Gen. Appl. Microbiol. 52(6), 339–348 (2006). 39. Romano I, Giordano A, Lama L, Nicolaus B,

Gambacorta A. Halomonas campaniensis sp. nov., a haloalkaliphilic bacterium isolated from a mineral pool of Campania Region, Italy. Syst. Appl. Microbiol. 28(7), 610–618 (2005). 40. Mormile MR, Romine MF, García MT,

Ventosa A, Bailey TJ, Peyton BM. Halomonas campisalis sp. nov., a denitrifying, moderately haloalkaliphilic bacterium. Syst. Appl. Microbiol. 22(4), 551–558 (1999).

1572

Exopolysaccharides produced by the recently described halophilic bacteria Halomonas ventosae and Halomonas anticariensis. Res. Microbiol. 157(9), 827–835 (2006). 57. Poli A, Esposito E, Orlando P et al.

Halomonas alkaliantartica sp. nov., isolated from saline lake Cape Russell in Antarctica, an alkaliphilic moderately halophilic, exopolysaccharide-producing bacterium. System. Appl. Microbiol. 30(1), 31–38 (2007). 58. Stevens DA, Hamilton JR, Johnson N, Kim

45. Roberts M. Organic compatible solutes of

KK, Lee JS. Halomonas, a newly recognized human pathogen, causing infections and contamination in a dialysis center; 3 new species. Medicine 88(4), 244–249 (2009).

halotolerant and halophilic microorganisms. Saline Syst. 1, 5 (2005).

34. Berendes F, Gottschalk G, Heine-Dobbernack

E, Moore ERB, Tindall BJ. Halomonas desiderata sp. nov., a new alkaliphilic, halotolerant and denitrifying bacterium isolated from a municipal sewage works. Syst. Appl. Microbiol. 19(2), 158–167 (1996).

56. Mata JA, Bejar V, Llamas I et al.

44. Galinski EA. Compatible solutes of

33. Kim MS, Roh SW, Bae JW. Halomonas

jeotgali sp. nov., a new moderate halophilic bacterium isolated from a traditional fermented seafood. J. Microbiol. 48(3), 404–410 (2010).

characterization of Halomonas sp. strain C2SS100, a hydrocarbon-degrading bacterium under hypersaline conditions. J. Applied Microbiol. 107(3), 785–794 (2009).

43. Wang S, Yang Q, Liu ZH et al. Halomonas

32. Jeong SH, Lee JH, Jung JY, Lee SH, Park MS,

Jeon CO. Halomonas cibimaris sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Antonie van Leeuwenhoek 103(3), 503–512 (2013).

55. Mnif S, Chamkha M, Sayadi S. Isolation and

42. Li HB, Zhang LP, Chen SF. Halomonas

31. Yoon JH, Lee KC, Kho YH, Kang KH, Kim

CJ, Park YH. Halomonas alimentaria sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int. J. Syst. Evol. Microbiol. 52(1), 123–130 (2002).

growing human importance. Am. J. Med. Sci. 345(5), 335–338 (2013).

46. Galinski EA. Osmoadaptation in bacteria.

Adv. Microb. Physiol. 37, 272–328 (1995). n

nn

Demonstrates how bacteria cope in hypersaline environments.

47. Brown AD. Microbial water stress. Bacteriol.

59. Mata JA, Martínez-Cánovas J, Quesada E,

Béjar V. A detailed phenotypic characterisation of the type strains of Halomonas species. Syst. Appl. Microbiol. 25(3), 360–375 (2002).

Rev. 40(4), 803–846 (1976). 48. Yancey PH, Clark ME, Hand SC, Bowlus

RD, Somero GN. Living with water stress: evolution of osmolyte systems. Science 217(4566), 1214–1222 (1982). 49. Roeßler M, Müller V. Osmoadaptation in

bacteria and archaea: common principles and differences. Environ. Microbiol. 3(12), 743–754 (2001). 50. Barth S, Huhn M, Matthey B, Klimka A,

Galinski EA, Engert A. Compatible solute-supported periplasmic expression of functional recombinant proteins under stress conditions. Appl. Environ. Microbiol. 66(4), 1572–1579 (2000). 51. Bolen DW, Baskakov IV. The osmophobic

effect: natural selection of a thermodynamic force in protein folding. J. Mol. Biol. 310(5), 955–963 (2001). 52. Gekko K, Timasheff SN. Mechanism of

protein stabilization by glycerol: preferential hydration in glycerol–water mixtures. Biochemistry 20(16), 4667–4676 (1981). 53. Liu Y, Bolen DW. The peptide backbone

plays a dominant role in protein stabilization by naturally occurring osmolytes. Biochemistry 34(39), 12884–12891 (1995). 54. Stevens DA, Kim KK, Johnson N, Lee JS,

Hamilton JR. Halomonas johnsoniae: review of a medically underappreciated genus of

Future Microbiol. (2013) 8(12)

Introduces the association between environmental contamination, dialysis and bacteremia.

n

Valuable phenotypic information with respect to possible new isolations.

60. Romanenko LA, Schumann P, Rohde M,

Mikhailov VV, Stackebrandt E. Halomonas halocynthiae sp. nov., isolated from the marine ascidian Halocynthia aurantium. Int. J. Syst. Evol. Microbiol. 52(5), 1767–1772 (2002). 61. Chen YG, Zhang YG, Huang HY et al.

Halomonas zhanjiangensis sp. nov., a halophilic bacterium isolated from a sea urchin. Int. J. Syst. Evol. Microbiol. 59(11), 2888–2893 (2009). 62. Wang G, Shuai L, Li Y, Lin W, Zhao X,

Duan D. Phylogenetic ana­lysis of epiphytic marine bacteria on Hole-Rotten diseased sporophytes of Laminaria japonica. J. Appl. Phychol. 20(4), 403–409 (2008). 63. Kusuda R, Yokoyama J, Kawai K.

Bacteriological study on cause of mass mortalities in cultured black sea bream fry. Bull. Jap. Soc. Sci. Fish. 52(10), 1745–1751 (1986). 64. Rojas R, Miranda CD, Amaro AM.

Pathogenicity of a highly exopolysaccharideproducing Halomonas strain causing epizootics in larval cultures of the Chilean scallop Argopecten purpuratus (Lamarck, 1819). Microb. Ecol. 57(1), 129–139 (2009).

future science group

Microbiology & epidemiology of Halomonas species

65. Mandell GL, Bennett JE, Dolin R. Principles

and Practice of Infectious Diseases (7th Edition). Churchill Livingstone, PA, USA (2010). 66. Bambauer R, Schauer M, Jung WK, Daum V,

Vienkin J. Contamination of dialysis water and dialysate: a survey of 30 centers. ASAIO J. 40(4), 1012–1016 (1994). 67. Cazzavillan S, Ratanarat R, Segala C et al.

Inflammation and subclinical infection in chronic kidney disease: a molecular approach. Blood Purif. 25(1), 69–76 (2007). 68. Hansard PC, Haseeb MA, Manning RA,

Salwen MJ. Recovery of bacteria by continuous renal replacement therapy in septic shock and by ultrafiltration from an in vitro model of bacteremia. Crit. Care Med. 32(4), 932–937 (2004). 69. von Graevenitz A, Bowman J, Del Notaro C,

Ritzler M. Human infection with Halomonas venusta following fish bite. J. Clin. Microbiol. 38(8), 3123–3124 (2000). n

First report of human disease.

70. Berger P, Barguellil F, Raoult D, Drancourt

M. An outbreak of Halomonas phocaeensis sp. nov. bacteraemia in a neonatal intensive care unit. J. Hosp. Infect. 67(1), 79–85 (2007). 71. Kim KK, Lee KC, Lee JS. Patulibacter

ginsengiterrae sp. nov., isolated from soil of a ginseng field. Int. J. Syst. Evol. Microbiol. 62(3), 563–568 (2012).

future science group

72. Kim KK, Lee KC, Jeong H, Stevens DA, Lee

JS. Draft genome sequence of the human pathogen Halomonas stevensii S18214T. J. Bacteriol. 194(18), 5143 (2012). 73. Liu WY, Wang J, Yuan M. Halomonas

aidingensis sp. nov., a moderately halophilic bacterium isolated from Aiding salt lake in Xinjiang, China. Antonie van Leeuwenhoek 99(3), 663–670 (2011). 74. Shapovalova AA, Khijniak TV, Tourova TP,

Sorokin DY. Halomonas chromatireducens sp. nov., a new denitrifying facultatively haloalkalophilic bacterium from solonchak soil capable of aerobic chromate reduction. Microbiology 78(1), 102–111 (2009). 75. Huang HY, Chen YG, Wang YX et al.

Halomonas sediminis sp. nov., a new halophilic bacterium isolated from salt-lake sediment in China. Extremophiles 12(6), 829–835 (2008). 76. González-Domenech CM, Martínez-Checa

F, Béjar V, Quesada E. Denitrification as an important taxonomic marker within the genus Halomonas. Syst. Appl. Microbiol. 33(2), 85–93 (2010). 77. Guzman H, Van-Thuoc D, Martin J,

Hatti-Kaul R, Quillaguaman J. A process for the production of ectoine and poly(3hydroxybutyrate) by Halomonas boliviensis. Appl. Microbiol. Biotechnol. 84(6), 1069–1077 (2009).

www.futuremedicine.com

Review

78. Aston JE, Peyton BM. Response of

Halomonas campisalis to saline stress: changes in growth kinetics, compatible solute production and membrane phospholipid fatty acid composition. FEMS Microbiol. Lett. 274(2), 196–203 (2007). 79. Severin J, Wohlfarth A, Galinski EA.

The predominant role of recently discovered tetrahydropyrimidines for the osmoadaptation of halophilic eubacteria. J. Gen. Microbiol. 138(8), 1629–1638 (1992). 80. Del Moral A, Severin J, Ramos-Cormenzana

A, Trüper HG, Galinski EA. Compatible solutes in new moderately halophilic isolates. FEMS Microbiol. Lett. 122(1–2), 165–172 (1994). 81. Romano I, Nicolaus B, Lama L, Trabasso D,

Caracciolo G, Gambacorta A. Accumulation of osmoprotectants and lipid pattern modulation in response to growth conditions by Halomonas pantelleriense. Syst. Appl. Microbiol. 24(3), 342–352 (2001). 82. Nikkari S, Lopez FA, Lepp PW et al. Broad-

range bacterial detection and the ana­lysis of unexplained death and critical illness. Emerg. Infect. Dis. 8(2), 188–194 (2002).

Website 101. List of prokaryotic names with standing in

nomenclature. www.bacterio.net

1573