Substrates specialization in lipid compounds and hydrocarbons of Marinobacter genus.

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Substrates specialization in lipid compounds and

hydrocarbons of Marinobacter genus.

Patricia Bonin, Christophe Vieira, Régis Grimaud, Cécile Militon, Philippe

Cuny, Oscar Lima, Sophie Guasco, Corina P D Brussaard, Valerie Michotey

To cite this version:

Patricia Bonin, Christophe Vieira, Régis Grimaud, Cécile Militon, Philippe Cuny, et al.. Substrates specialization in lipid compounds and hydrocarbons of Marinobacter genus.. Environmental Science and Pollution Research, Springer Verlag, 2015, 22 (20), pp.15347-15359. �10.1007/s11356-014-4009-y�. �hal-01201711�

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Table 1

List of Marinobacter strains used in this study

Species Strains

Location

of

isolation

Type of

sample

Reference

Physiological

(P), genomic

(G) analysis

VT8, DSM

11845

Vietnam

Oil producing

well

(Huu et al.

1999

)

P, G

DN1

Gulf of

Fos, Med

Sea

sediment

(Bonin et al.

1987

)

P

17 ATCC

49840

Gulf of

Fos, Med

Sea

sediment

(Gauthier et

al.

1992

)

P, G

CAB

Gulf of

Fos, Med

Sea

sediment

(Gilewicz et

al.

1997

)

P

BC36,

BC38, R153

Berre

lagoon,

Med Sea

sediment

(Goregues

et al.

2004

)

P

M.

hydrocarbonoclasticus

23W2B,

CUBW5A,

CUBW5B,

23tet5B

North Sea Water column This study P

M. vinifirmus

BC45,

NBC44,

NBC35,

NBC34,

NBC33,

NBC32,

BC43,

BC34

Berre

lagoon,

Med Sea

sediment

(Goregues

et al.

2004

)

P

M. maritimus

2Sq31,

1sq53

Gulf of

Fos, Med

Sea

sediment

(Rontani et

al.

2002

)

P

M. flavimari M.

adhaerens M.

manganoxydans

Cubtrip2B,

Cubtet1B

North Sea Water column This study P

M. adhaerens

HP15 DSM

23420

German

Wadden

Sea

Diatom

interaction

(Gärdes et

al.

2010

)

G

M. manganoxydans

MnI7-9

Indian

Ocean

Deep-sea

hydrothermal

vent sediment

(Wang et al.

2012

)

G

Species Strains

Location

of

isolation

Type of

sample

Reference

Physiological

(P), genomic

(G) analysis

lagoon,

Med Sea

et al.

2004

)

DG893 Culture

Dinoflagellates

(Green et al.

2006

)

P, G

HL-58 –

Microbial

mat

unpublished

G

M. algicola

MCTG268 –

Microbila

mat unpublished

G

M. xestospongiae

BP42

Berre

lagoon,

Med Sea

sediment

(Goregues

et al.

2004

)

P

M. daepoensis

SW-156

(DSM

16072)

South

Korea

Water column

(Yoon et al.

2004

)

G

M. santoriniensis

NKSG1

Santorini,

Med Sea

Shallow marine

hydrothermal

sediment;

(Handley et

al.

2013

)

G

SM19

Spain saline

soil

(Papke et al.

2013

)

G

M. lipolyticus

BF04_CF-4 –

–

unpublished G

M. nanhaiticus

D15-8 W

South

China Sea

Sediment

(Cui et al.

2013

)

G

M. excellens

HL-55 –

–

unpublished

G

ELB17 Antarctica

Waters of a

permanently

ice-covered

lake

unpublished G

M. psychrophilus

BSs20148

Arctic

Ocean

Sediment

(Song et al.

2013

)

G

M. strain AK21

AK21 India Water

column

unpublished

G

M. sp. phylotype no. 2

BP45,

NBP42

Berre

lagoon,

Med Sea

Sediment

(Goregues

et al.

2004

)

P

M. sp. phylotype no. 8

U32, S64,

T33, U31

Berre

lagoon,

Med Sea

Sediment

(Goregues

et al.

2004

)

P

M. sp. phylotype no. 9 R53

Berre

lagoon

Med Sea

Sediment

(Goregues

et al.

2004

)

P

Table 2

Comparison of different PCR primers or probes for detection of Marinobacter 16S rDNA

using probe-match (RDP probe match tool)

Marinob300F-Marinob600R

Mab451f-Mab573r CARD-FISH

probe

Primer set

Number of hits (%

recovery)

Number of hits (%

recovery)

Number of hits (%

recovery)

Reference

This study

(Gray et al.

2011

)

(Karner and Fuhrman

1997

)

Bacteria 2414/2879170

242/2879170

885/2879170

Marinobacter genus 2374/3639 (64.5 %)

235/3639 (6.4 %)

714/3639 (20.6 %)

Marinobacter type

strains

27/30 (90 %)

1/30 (3 %)

8/30 (26.6 %)

Non-target matches 30/ 2414 (1.2 %)

7/242 (2.8 %)

171/885 (20 %)