Biodiversity Science ›› 2019, Vol. 27 ›› Issue (12): 1320-1329.doi: 10.17520/biods.2019219

• Original Papers:Microbial Diversity • Previous Article     Next Article

Community composition and diversity of cultivable endophytic bacteria isolated from Dongxiang wild rice

Zhiyuan Chen1, Jun Liu1, Xingpeng Yang1, Meng Liu1, Ya Wang2, Zhibin Zhang1, *(), Du Zhu1, 2, *   

  1. 1 Key Laboratory of Protection and Utilization of Subtropical Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang 330022
    2 Key Laboratory of Bioprocess Engineering of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang 330013
  • Received:2019-07-07 Accepted:2019-10-20 Online:2020-02-22
  • Zhang Zhibin,Zhu Du

Endophytic bacteria are essential to the growth and metabolism of their host plants. To better understand the community structure and diversity of endophytic bacteria on plants, we isolated 94 strains of endophytic bacteria from the roots, stems and leaves of Dongxiang wild rice (Oryza rufipogon). Subsequent 16S rRNA sequence alignments and phylogenetic analyses revealed that the 94 strains could be categorized into 17 genera of 14 families in 3 phyla (Proteobacteria, Actinobacteria, and Firmicutes).Bacillus and Microbacterium, accounting for 27.7% and 20.2% of the diversity, respectively, were the two most dominant genera. The distribution and diversity of endophytic bacteria differed across different tissues of Dongxiang wild rice: the roots contained the most endophytic bacteria strains (n = 34, 36.2%), followed by leaves (n = 32, 34.0%), and stems (n = 28, 29.8%). Shannon-Wiener diversity index (H′ = 2.52), Simpson dominance index (D = 0.88) and Pielou evenness index (E = 0.72) were higher in the roots than in the stems or leaves. Meanwhile, the Jaccard similarity index between roots and stems (C = 0.29) was lower than that between roots and leaves (C = 0.47), or that between stems and leaves (C = 0.45). Our efforts to uncover the diversity of endophytic bacteria in Dongxiang wild rice confirms that roots contain the most diverse strains but that the composition of endophytes varies across tissues.

Key words: Oryza rufipogon, endophytes, classification, phylogeny, composition analysis

Table 1

The distribution of endophytic bacteria isolated from different tissues of Dongxiang wild rice"

代表菌株 NCBI库中相似度最高菌种 基因登录号 序列相 分离菌株数 培养基分离菌株数
Representative strains (登录号) GenBank accession 似度 No. of strains No. of strains from medium
Closest relatives in NCBI no. Identity
(GenBank accession no.) (%) NA BPA R2A TSA NA×10
Root Stem Leaf
变形菌门 Proteobacteria
泛菌属 Pantoea 5 1 6 3 2 3 2 2
JXR10 Pantoea sp. (JX994157.1) KP980595 100
JXS8 Pantoea sp. (KJ733870.1) KP980579 100
JXL1 Pantoea sp. (KJ733870.1) KP980566 100
鞘氨醇单胞菌属 Sphingomonas 1 - 1 - 1 - 1 -
JXR34 Sphingomonas yanoikuyae (KJ009425.1) KP980605 100
JXL6 Sphingomonas sanguinis (NR113637.1) KP980568 100
土壤杆菌属 Agrobacterium - 3 1 1 - 1 - 2
JXS10 Agrobacterium sp. (GQ169803.1) KP980581 100
JXL9 Agrobacterium sp. (KJ184856.1) KP980570 100
甲烷细菌属 Methylobacterium 1 1 1 - 1 - 1 1
JXR16 Methylobacterium sp. (KM083547.1) KP980599 100
JXS9 Methylobacterium sp. (AB604650.1) KP980580 100
JXL16 Methylobacterium sp. (KM083546.1) KP980572 100
假单胞菌属 Pseudomonas 1 - 1 - - - - 2
JXR26 Pseudomonas sp. (HE978359.1) KP980602 100
JXL21 Pseudomonas fulva (AY741159.1) KP980573 100
寡养单胞菌属Stenotrophomonas - 3 - - 1 - 1 1
JXS14 Stenotrophomonas maltophilia (JN571747.1) KP980583 100
根瘤菌属 Rhizobium - 1 - 1 - - - -
JXS18 Rhizobium sp. (JN082742.1) KP980584 100
不动杆菌属 Acinetobacter 1 - - 1 - - - -
JXR29 Acinetobacter oleivorans (KJ806471.1) KP980603 100
放线菌门 Actinobacteria
微小菌属 Microbacterium 1 8 10 5 3 6 2 3
JXR14 Microbacterium trichothecenolyticum (KF953537.1) KP980598 100
JXS2 Microbacterium sp. (AB773218.1) KP980577 100
JXL7 Microbacterium sp. (EU741023.1) KP980569 100
JXL12 Microbacterium laevaniformans KP980571 100
短杆菌属 Curtobacterium 1 2 1 - 1 2 - 1
JXR24 Curtobacterium citreum (KC329830.1) KP980601 100
JXS1 Curtobacterium luteum (JQ660182.1) KP980576 97
JXL30 Curtobacterium sp. (KC841444.1) KP980575 100
分支杆菌属 Mycobacterium 2 - - 1 - - - 1
JXR17 Mycobacterium sp. (AB605021.1) KP980600 100
节杆菌属 Arthrobacter 3 - - 1 - - - 2
JXR12 Arthrobacter phenanthrenivorans (KC934897.1) KP980596 100
代表菌株 NCBI库中相似度最高菌种 基因登录号 序列相 分离株数 培养基分离株数
Representative strains (登录号) GenBank accession 似度 No. of strains No. of strains from medium
Closest relatives in NCBI no. Identity
(GenBank accession no.) (%) NA BPA R2A TSA NA×10
Root Stem Leaf
雷弗森菌属 Leifsonia 3 - - - - 1 - 2
JXR6 Leifsonia sp. (KJ944083.1) KP980592 100
红球菌属 Rhodococcus 1 - - - - - 1 -
JXR8 Rhodococcus equi (NR041910.1) KP980594 100
厚壁菌门 Firmicutes
类芽孢杆菌属 Paenibacillus 3 - 1 1 - 1 -
JXR1 Paenibacillus agarexedens (KC355292.1) KP980588 100
JXR5 Paenibacillus sp. (KJ000069.1) KP980591 99
JXR30 Paenibacillus vulneris (KM272755.1) KP980604 100
芽孢杆菌属 Bacillus 7 9 10 8 8 1 2 7
JXR2 Bacillus cereus (KF831402.1) KP980589 100
JXR3 Bacillus sp. (JX566646.1) KP980590 100
JXS6 Bacillus subtilis (KP229430.1) KP980578 100
JXS20 Bacillus sp. (KM555037.1) KP980585 100
JXS25 Bacillus mojavensis (HQ123468.1) KP980587 97
JXL24 Bacillus sp. (KP119613.1) KP980574 100
赖氨酸芽孢杆菌属 Lysinibacillus 4 - 1 1 - 2 1 1
JXR13 Lysinibacillus sphaericus (KM070813.1) KP980597 100
JXL2 Lysinibacillus fusiformis (JN867122.1) KP980567 100
总计 Total 34 28 32 23 18 16 12 25

Fig. 1

The endophytic bacteria isolated by nutrient agar, Baird-Parker agar, Reasoner’s 2A agar Tryptone soy agar and 10-fold nutrient agar from each tissues of Dongxiang wild rice. (A) The amount of endophytic bacterial, derived from any tissues of Dongxiang wild rice, isolated from different mediums; (B) The percentage of the isolated strains from each medium."

Fig. 2

Neighbor-joining tree based on 16S rRNA gene sequences showing the phylogenetic relationships among the strains and their closely related taxa. The thicker branches represent endophytic bacteria of Dongxiang wild rice and the others represent related strains."

Fig. 3

Distribution of endophytic bacteria from different tissues of Dongxiang wild rice at the genus level. (A) Root; (B) Stem; (C) Leaf."

Table 2

Diversity analysis of endophytic bacteria in different tissues of Dongxiang wild rice (according to genera)"

Wiener index
Simpson index
Pielou index
根 Root 14 2.52 0.88 0.72
茎 Stem 8 1.81 0.80 0.54
叶 Leaf 9 2.09 0.74 0.60
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