Diversity of endophytic bacteria of Dendrobium officinale based on culture-dependent and culture-independent methods

Figures & data

Table 1. The identification and classification of endophytic bacteria based on culture-dependent and DGGE methods.

Method	Phylum	Genus	WZR	WZS	WZL
Culture	Firmicutes	Bacillus	5	0	1
		Sporosarcina	1	0	0
		Paenibacillus	1	0	0
	Proteobacteria	Burkholderia	0	5	0
		Methylobacterium	0	0	2
	Actinobacteria	Brevibacterium	1	0	0
		Curtobacterium	0	0	1
	Total		8	5	4
DGGE	Firmicutes	Tissierella	1	1	1
		Clostridium	2	0	1
		Virgibacillus	1	1	0
		Enterococcus	1	0	0
		Brevibacillus	1	0	0
		Streptococcus	0	1	0
		Staphylococcus	0	0	1
	Proteobacteria	Rhizobium	1	0	0
		Ochrobactrum	1	0	0
		Pseudaminobacter	2	2	2
		Delftia	1	1	2
		Klebsiella	1	0	0
		Brevundimonas	0	2	0
		Burkholderia	0	5	0
		Enterobacteriales	0	2	0
		Pseudochrobactrum	0	1	2
		Unidentified	2	2	3
		Total	14	17	13

Figure 1. Comparison of phylum level distributions for three tissue types from culture and DGGE methods.

Figure 2. Comparison of phylum level distributions for three tissue types based on the metagenome method.

Table 2. Comparison of percentage (%) of the metagenome sequences affiliated with the dominant bacterial genera (average abundance >1%) for three tissue sample types.

Phylum	Genus	WZR	WZS	WZL
Proteobacteria	Aquamicrobium	0.44	18.25	12.77
	Brucella	0.2	18.53	10.13
	Pseudochrobactrum	0.34	11.91	8.83
	Burkholderia	9.34	10.93	0.02
	Acinetobacter	0.14	1.31	11.57
	Delftia	0.26	2.95	6.50
	Aminobacter	0.06	4.23	3.50
	Brevundimonas	0.07	2.10	4.07
	Rhodanobacter	6.29	0	0
	Methylovirgula	5.82	0	0
	Pseudaminobacter	0.2	2.11	2.27
	Rhodoblastus	3.92	0	0
	Dyella	3.88	0.01	0
	Rhizobium	2.53	0.71	0.28
	Rhodoplanes	3.17	0	0.01
	Pseudomonas	0.04	0.83	2.02
	Frateuria	3.01	0.01	0.01
Firmicutes	Tissierella	0.09	3.82	3.32
	Bacillus	0.11	0.39	4.76
	Falsibacillus	0.1	0.49	4.58
	Anaerobacter	0.06	2.50	2.23
Actinobacteria	Marmoricola	6.30	0.01	0.01
	Streptacidiphilus	3.76	0	0

Figure 3. Comparison of genus levels using metagenome, culture-dependent, and DGGE methods.