Plant Growth Promotion Potential Is Equally Represented in Diverse Grapevine Root-Associated Bacterial Communities from Different Biopedoclimatic Environments

Table 2

Identification of the dominant bands in the PCR-DGGE fingerprinting profiles (marked in Figure 1). The codes of the different fractions of the grapevine root systems are as follows: E, Endosphere; R, rhizosphere; S, root-surrounding soil; B, bulk soil.

Frac.	DGGE band	Closest relative; (NCBI database)	Acc. N°	%	Closest describe relative; (Ez Taxon database)	Acc. N°	%	Class
B	IT-01	Ramlibacter sp.	AY429716	88	Curvibacter fontanus	AB120963	87	Betaproteobacteria
B	IT-02	Unc. Comamonadaceae	AY360707	86	Curvibacter fontanus	AB120963	85	Betaproteobacteria
B	IT-03	Unc. Variovorax sp.	JN590646	90	Xylophilus ampelinus	AF078758	89	Betaproteobacteria
B	IT-04	Unc. Acidobacteria	EF651005	95	Desulfomonile limimaris	AF230531	81	Acidobacteria
B	IT-05	Unc. bacterium	HQ393158	98	Massilia plicata	AY966000	96	Betaproteobacteria
B	IT-06	Massilia sp.	JF279920	99	Massilia niabensis	EU808006	99	Betaproteobacteria
B	IT-07	Unc. bacterium	AY274152	97	Solibacter usitatus	CP000473	92	Acidobacteria
B	IT-08	Unc. Acidobacteria	GU257870	94	Chloracidobacterium thermophilum	CP002514	80	Acidobacteria
E	IT-09	Micromonospora sp.	FR692086	92	Micromonospora peucetia	X92603	90	Actinobacteria
E	IT-10	Chloroplast	U189132	99	Chloroplast	AM711640	99	Eukarya
E	IT-11	Chloroplast	HQ325745	100	Chloroplast	DQ386163	99	Eukarya
E	IT-12	Chloroplast	HQ325745	100	Chloroplast	DQ386163	100	Eukarya
R	IT-13	Unc. Rhodocyclaceae	EF643420	97	Thiobacter subterraneus	AB180657	91	Betaproteobacteria
R	IT-14	Unc. bacterium	FR853277	91	Steroidobacter denitrificans	EF605262	89	Gammaproteobacteria
R	IT-15	Unc. bacterium	JN855310	98	Bradyrhizobium pachyrhizi	AY624135	97	Alphaproteobacteria
R	IT-16	Unc. Pseudomonadales	FJ889292	97	Steroidobacter denitrificans	EF605262	96	Gammaproteobacteria
R	IT-17	Unc. bacterium	HM445266	92	Rubrivivax gelatinosus	D16213	90	Betaproteobacteria
R	IT-18	Unc. bacterium	EU881322	99	Thiobacter subterraneus	AB180657	90	Betaproteobacteria
R	IT-19	Unc. Rhizobium sp.	EF074979	92	Rhizobium giardinii	U86344	91	Alphaproteobacteria
R	IT-20	Sphingobacterium sp.	EU580525	97	Dyadobacter hamtensis	AJ619978	93	Sphingobacteria
R	IT-21	Unc. bacterium	EF019453	86	Methylogaea oryzae	EU672873	79	Gammaproteobacteria
R	IT-22	Unc. bacterium	EF392989	96	Steroidobacter denitrificans	EF605262	87	Gammaproteobacteria
R	IT-23	Unc. bacterium	FR853277	95	Steroidobacter denitrificans	EF605262	93	Gammaproteobacteria
R	IT-24	Unc. bacterium	GU568879	87	Novosphingobium resinovorum	EF029110	82	Alphaproteobacteria
R	IT-25	Unc. bacterium	FJ479326	93	Steroidobacter denitrificans	EF605262	91	Gammaproteobacteria
R	IT-26	Unc. bacterium	JN855310	99	Bradyrhizobium pachyrhizi	AY624135	98	Alphaproteobacteria
R	IT-27	Unc. bacterium	JN855310	95	Nitrobacter hamburgensis	CP000319	94	Alphaproteobacteria
R	IT-28	Unc. bacterium	DQ643675	93	Rubrivivax gelatinosus	D16213	91	Betaproteobacteria
R	IT-29	Unc. bacterium	GU291531	94	Novosphingobium resinovorum	EF029110	94	Alphaproteobacteria
R	IT-30	Unc. Alphaproteobacteria	JN371328	81	Blastochloris sulfoviridis	D86514	78	Alphaproteobacteria
R	IT-31	Unc. Steroidobacter	FN297970	100	Steroidobacter denitrificans	EF605262	98	Gammaproteobacteria
S	IT-32	Unc. Acidobacteria	HQ597613	97	Chloracidobacterium thermophilum	CP002514	81	Acidobacteria
S	IT-33	Unc. bacterium	JN855310	91	Nitrobacter winogradskyi	CP000115	90	Alphaproteobacteria
S	IT-34	Unc. bacterium	FJ479326	99	Steroidobacter denitrificans	EF605262	97	Gammaproteobacteria
S	IT-35	Unc. Alphaproteobacteria	FJ568851	95	Donghia mobilis	FJ455532	91	Alphaproteobacteria
B	TN-01	Unc. bacterium	KC541101	100	Massilia aurea	AM231588	99	Betaproteobacteria
B	TN-02	Unc. bacterium	HM186197	99	Ohtaekwangia koreensis	GU117702	93	Sphingobacteria
B	TN-03	Chryseobacterium indoltheticum	AY468448	99	Chryseobacterium indoltheticum	AY468448	98	Flavobacteria
B	TN-04	Unc. bacterium	HF546519	83	Xenophilus azovorans	AF285414	77	Betaproteobacteria
E	TN-05	Unc. bacterium	FN667504	97	Streptomyces sodiiphilus	AY236339	96	Actinobacteria
E	TN-06	Chloroplast	HQ336404	99	Chloroplast	DQ386163	99	Cyanobacteria
E	TN-07	Chloroplast	HQ336404	99	Chloroplast	DQ386163	99	Cyanobacteria
E	TN-08	Chloroplast	HQ336404	100	Chloroplast	DQ386163	99	Cyanobacteria
E	TN-09	Chloroplast	EU189132	99	Chloroplast	AM711640	99	Cyanobacteria
E	TN-10	Chloroplast	HQ336404	99	Chloroplast	DQ386163	99	Cyanobacteria
E	TN-11	Chloroplast	HQ336404	100	Chloroplast	DQ386163	92	Cyanobacteria
E	TN-12	Chloroplast	HQ336404	99	Chloroplast	DQ386163	99	Cyanobacteria
E	TN-13	Chloroplast	EU118126	100	Chloroplast	EU118126	99	Cyanobacteria
E	TN-14	Chloroplast	EU118126	100	Chloroplast	EU118126	99	Cyanobacteria
E	TN-15	Chloroplast	EU118126	100	Chloroplast	EU118126	100	Cyanobacteria
E	TN-16	Chloroplast	EU118126	99	Chloroplast	EU118126	98	Eukarya
E	TN-17	Rhizobium radiobacter	AJ389904	100	Rhizobium radiobacter	AJ389904	100	Alphaproteobacteria
E	TN-18	Hydrogenophilus thermoluteolus	AB680730	98	Hydrogenophilus hirschii	FR749905	98	Betaproteobacteria
E	TN-19	Chloroplast	HQ325745	99	Chloroplast	L37580	96	Eukarya
E	TN-20	Chloroplast	HQ325745	99	Chloroplast	DQ386163	99	Eukarya
R	TN-21	Unc. bacterium	JF198689	89	Steroidobacter denitrificans	EF605262	84	Gammaproteobacteria
R	TN-22	Rhizobium sullae	NR_029330	89	Rhizobium sullae	Y10170	82	Alphaproteobacteria
R	TN-23	Rhizobium giardinii	JX869993	91	Rhizobium selenitireducens	EF440185	74	Alphaproteobacteria
R	TN-24	Rhizobium huautlense	HQ538618	99	Rhizobium huautlense	AF025852	99	Alphaproteobacteria
R	TN-25	Unc. bacterium	HM328693	99	Novosphingobium resinovorum	EF029110	95	Alphaproteobacteria
R	TN-26	Rhizobium etli	NR_029184	100	Rhizobium vallis	FJ839677	99	Alphaproteobacteria
R	TN-27	Unc. Betaproteobacteria	EU266802	92	Hydrogenophaga palleronii	AF019073	78	Betaproteobacteria
R	TN-28	Rhizobium giardinii	EU410948	99	Rhizobium endophyticum	EU867317	98	Alphaproteobacteria
R	TN-29	Unc. bacterium	HF546519	85	Piscinibacter aquaticus	DQ664244	81	Betaproteobacteria
R	TN-30	Unc. bacterium	HE586741	85	Hydrogenophaga palleronii	AF019073	78	Betaproteobacteria
R	TN-31	Unc. bacterium	JF175892	93	Niastella populi	EU877262	81	Sphingobacteria
R	TN-32	Unc. bacterium	JF175892	93	Chitinophaga arvensicola	D12657	84	Sphingobacteria
R	TN-33	Unc. Flavobacterium sp.	EU017400	99	Flavobacterium reichenbachii	AM177616	84	Flavobacteria
R	TN-34	Flavobacterium sp.	EF601822	99	Flavobacterium pectinovorum	AM230490	98	Flavobacteria
R	TN-35	Unc. Betaproteobacteria	EF662768	97	Azoarcus buckelii	AJ315676	88	Betaproteobacteria
R	TN-36	Sphingobacterium sp.	EU580525	96	Dyadobacter hamtensis	AJ619978	94	Sphingobacteria
R	TN-37	Reichenowi ornate	AY316684	82	Aurantimonas altamirensis	DQ372921	80	Alphaproteobacteria
R	TN-38	Unc. Gammaproteobacteria	JN648252	97	Steroidobacter denitrificans	EF605262	88	Gammaproteobacteria
R	TN-39	Rhizobium sp.	FN546874	98	Rhizobium endophyticum	EU867317	97	Alphaproteobacteria
R	TN-40	Rhizobium sp.	AM922181	99	Rhizobium endophyticum	EU867317	98	Alphaproteobacteria
R	TN-41	Unc. bacterium	FJ719038	97	Dyadobacter hamtensis	AJ619978	95	Sphingobacteria
R	TN-42	Rhizobium leguminosarum	HQ853453	99	Rhizobium vallis	FJ839677	98	Alphaproteobacteria
S	TN-43	Unc. bacterium	AF423222	99	Thiobacter subterraneus	AB180657	89	Betaproteobacteria
S	TN-44	Unc. Comamonadaceae	AY360707	99	Acidovorax konjaci	AF078760	97	Betaproteobacteria
S	TN-45	Unc. Sphingobacteriales	AM934931	99	Ohtaekwangia koreensis	GU117702	93	Sphingobacteria
S	TN-46	Unc. bacterium	GQ023702	91	Hydrogenophilus hirschii	FR749905	91	Betaproteobacteria
S	TN-47	Unc. Burkholderiaceae	AM935484	99	Thiobacter subterraneus	AB180657	90	Betaproteobacteria
S	TN-48	Pedobacter sp.	AY599662	85	Pedobacter metabolipauper	AM491370	84	Sphingobacteria
S	TN-49	Pedobacter africanus	NR_028977	99	Pedobacter africanus	AJ438171	98	Sphingobacteria
S	TN-50	Unc. bacterium	HM049699	88	Pedobacter africanus	AJ438171	87	Sphingobacteria
S	TN-51	Unc. bacterium	HM049699	99	Pedobacter steynii	AM491372	98	Sphingobacteria
S	TN-52	Flavobacterium sp.	HM149210	99	Flavobacterium pectinovorum	AM230490	98	Flavobacteria
B	ET-01	Unc. Betaproteobacteria	JF806989	99	Thiobacter subterraneus	AB180657	90	Betaproteobacteria
B	ET-02	Bacillus sp.	FM992819	99	Bacillus pocheonensis	AB245377	98	Bacilli
B	ET-03	Bacillus sp.	FM992819	87	Bacillus alcalophilus	X60603	85	Bacilli
B	ET-04	Unc. bacterium	DQ398884	86	Hydrogenophaga flava	AF078771	84	Betaproteobacteria
B	ET-05	Unc. Sphingobacteriales	AM934931	99	Ohtaekwangia koreensis	GU117702	92	Sphingobacteria
B	ET-06	Unc. bacteria	JF681924	90	Sterolibacterium denitrificans	AJ306683	84	Gammaproteobacteria
E	ET-07	Unc. bacterium	JQ357881	99	Chitinophaga pinensis	CP001699	98	Sphingobacteria
E	ET-08	Unc. bacterium	JQ358300	99	Chitinophaga sancti	AB078066	98	Sphingobacteria
E	ET-09	Chryseobacterium wanjuense	AB682410	100	Chryseobacterium wanjuense	DQ256729	100	Flavobacteria
E	ET-10	Flavobacterium sp.	JF915324	99	Flavobacterium subsaxonicum	AM934666	96	Flavobacteria
E	ET-11	Chitinophaga sp.	JQ659659	98	Chitinophaga ginsengisoli	AB245374	96	Sphingobacteria
E	ET-12	Chitinophaga sp.	JQ659659	98	Chitinophaga ginsengisoli	AB245374	96	Sphingobacteria
E	ET-13	Novosphingobium sp.	EU984513	99	Novosphingobium resinovorum	EF029110	99	Alphaproteobacteria
E	ET-14	Unc. bacterium	FN667504	97	Streptomyces sodiiphilus	AY236339	96	Actinobacteria
E	ET-15	Glycomyces scopariae	JQ342894	99	Glycomyces scopariae	EU200682	99	Actinobacteria
E	ET-16	Variovorax paradoxus	AB680784	99	Variovorax paradoxus	D88006	99	Betaproteobacteria
E	ET-17	Pseudoxanthomonas sp.	JF703645	99	Pseudoxanthomonas	AB008507	98	Gammaproteobacteria
E	ET-18	Rhizobium sp.	AM922181	99	Rhizobium radiobacter	AJ389904	99	Alphaproteobacteria
E	ET-19	Chloroplast	HQ325745	99	Chloroplast	DQ386163	99	Eukarya
E	ET-20	Rhizobium sp.	AM922181	85	Rhizobium radiobacter	AJ389904	83	Alphaproteobacteria
E	ET-21	Chloroplast	HQ325745	100	Chloroplast	DQ386163	99	Eukarya
R	ET-22	Chitinophaga terrae	AB267724	98	Chitinophaga niabensis	EU714259	95	Sphingobacteria
R	ET-23	Chitinophaga sp.	GQ281772	99	Chitinophaga niabensis	EU714259	97	Sphingobacteria
R	ET-24	Chitinophaga sp.	JQ659659	97	Chitinophaga sancti	AB078066	96	Sphingobacteria
R	ET-25	Novosphingobium sp.	AB453877	90	Novosphingobium resinovorum	EF029110	88	Alphaproteobacteria
R	ET-26	Unc. bacterium	GQ074926	99	Novosphingobium resinovorum	EF029110	97	Alphaproteobacteria
R	ET-27	Unc. bacterium	GQ169020	90	Blastochloris sulfoviridis	D86514	88	Alphaproteobacteria
R	ET-28	Unc. bacterium	DQ814032	99	Mesorhizobium thiogangeticum	AJ864462	99	Alphaproteobacteria
R	ET-29	Pseudoxanthomonas mexicana	JQ660737	100	Pseudoxanthomonas japonensis	AB008507	99	Gammaproteobacteria
R	ET-30	Mesorhizobium sp.	JN688938	94	Sinorhizobium americanum	AF506513	93	Alphaproteobacteria
R	ET-31	Unc. bacterium	AB540382	82	Steroidobacter denitrificans	EF605262	79	Gammaproteobacteria
R	ET-32	Sphingopyxis chilensis	JF459975	98	Sphingopyxis panaciterrae	AB245353	98	Alphaproteobacteria
R	ET-33	Chitinophaga sp.	JN680879	89	Chitinophaga niabensis	EU714259	79	Sphingobacteria
R	ET-34	Unc. bacterium	GU291531	100	Novosphingobium resinovorum	EF029110	99	Alphaproteobacteria
R	ET-35	Devosia chinhatensis	EF433462	99	Devosia chinhatensis	EF433462	99	Alphaproteobacteria
R	ET-36	Ensifer sp.	JF450188	99	Ensifer adhaerens	AM181733	98	Alphaproteobacteria
R	ET-37	Sinorhizobium fredii	HQ836172	98	Sinorhizobium americanum	AF506513	97	Alphaproteobacteria
R	ET-38	Mesorhizobium loti	HQ424911	93	Mesorhizobium plurifarium	Y14158	92	Alphaproteobacteria
R	ET-39	Mesorhizobium loti	HQ424911	88	Mesorhizobium plurifarium	Y14158	87	Alphaproteobacteria
S	ET-40	Cupriavidus sp.	AB266608	99	Cupriavidus oxalaticus	AF155567	98	Betaproteobacteria
S	ET-41	Unc. Burkholderiaceae	JF681924	95	Thiobacter subterraneus	AB180657	79	Betaproteobacteria
S	ET-42	Unc. Bacteroidetes	FM877553	87	Ohtaekwangia koreensis	GU117702	85	Sphingobacteria
S	ET-43	Unc. Bacteroidetes	FM877553	99	Ohtaekwangia kribbensis	GU117703	92	Sphingobacteria

Frac.: Fraction analysed; Unc.: Uncultured.