Bacterial diversity and community structural changes in rhizosphere soil of naked barley disturbed by root rot

doi:10.11686/cyxb2024255

Abstract

Abstract:

The occurrence and spread of naked barley （Hordeum vulgare var. nudum） root rot are known to be closely related to the dynamics of the rhizosphere soil bacterial community. This study systematically investigated naked barley root rot in fields of the Tibetan Gannan Autonomous Prefecture， Gansu Province， to clarify the influences on the diversity and structure of the rhizosphere soil bacterial community disturbed by naked barley root rot. Rhizosphere soil samples with different root rot incidences were collected， and genetic characterization of the bacterial community was obtained by high-throughput sequencing. The structural dynamics and the diversity of the bacterial community were thus analyzed. Additionally， the various bacterial functional genes were annotated using COG databases. The results revealed a rich and evenly distributed bacterial species composition in the rhizosphere soil of naked barley， which comprehensively mirrors the bacterial community structure of the samples. The bacterial community of healthy samples was closest to samples with 5% incidence of root rot. Additionally， as the incidence rate of root rot increased， the bacterial communities diverged more significantly from those of healthy samples. The number of bacterial species in diseased rhizosphere soil samples increased initially and then decreased， as the root rot incidence increased. Also， the relative abundance of Proteobacteria initially increased and then decreased with increased root rot， incidence， while a contrasting trend was observed for Chloroflexi， Acidobacteria， Bacteroidetes， Actinobacteria and Gemmatimonadetes. Similarly， the relative abundance of Bacillales， Nitrospirales， and their commonly-present families Gemmatimonadaceae， Bacillaceae， Nitrospiraceae， as well as the genera Gemmatimonas， Bacillus， and Nitrospira， including Bacillus simplex， showed an initial increase followed by a decrease. Conversely， the relative abundance of Acinetobacter calcoaceticus and Stenotrophomonas rhizophila initially decreased and then increased. The abundance of functional genes related to bacterial amino acid transport and metabolism， transcription， lipid transport and metabolism， posttranslational modification， protein turnover， chaperones in the rhizosphere soil of naked barley decreased due to the occurrence of root rot， while the abundance of genes involved in signal transduction mechanisms and energy production and conversion increased.

Key words: naked barley, root rot, community structure, species diversity, high-throughput

Xue-ping LI, Shi-yang XU, Jian-jun LI, Yong-hong QI. Bacterial diversity and community structural changes in rhizosphere soil of naked barley disturbed by root rot[J]. Acta Prataculturae Sinica, 2025, 34(5): 118-129.

Figures/Tables 9

Fig.1 Bacterial OTUs in naked barley rhizosphere soil

Table 1 Bacterial diversity indexes in rhizosphere soil of naked barley with different root rot incidences

样本 Samples	谱系多样性 PD_whole_tree	丰富度估计量指数 Chao1	测序深度指数Goods_coverage	种类丰富度维度 Observed_species	香浓指数 Shannon index	辛普森指数 Simpson index
AH	54.95	1975.18	0.96	1598.00	9.25	0.99
AR₁	54.70	1892.30	0.97	1598.60	9.32	0.99
AR₂	54.52	1889.42	0.97	1597.20	9.26	0.99
AR₃	55.62	1933.35	0.96	1607.00	9.32	0.99
AR₄	54.67	1926.21	0.97	1608.90	9.37	0.99

Fig.2 Bacterial species richness and evenness in rhizosphere soil of naked barley with different root rot incidences

Fig. 3 Bacterial genetic cluster analysis in rhizosphere soil of naked barley with different root rot incidences

Fig.4 Bacterial community structure at phylum and class level in rhizosphere soil of naked barley with different root rot incidences

Fig.5 Community structure of bacteria at order and family level in rhizosphere soil of naked barley with different root rot incidences

Fig.6 Bacterial community structure and correlation analysis at genus level in rhizosphere soil of naked barley with different root rot incidences

Fig.7 Bacterial community structure at species level in rhizosphere soil of naked barley with different root rot incidences

Fig. 8 Functions of the annotated bacterial genes in rhizosphere soil of naked barley with different root rot incidences

References 44

1	Li X P. Naked barley root rot diseases and influence on its rhizosphere microecology in Qinghai-tibet plateau， China. Lanzhou： Gansu Agricultural University， 2017： 1-3.
	李雪萍. 青藏高原青稞根腐类病害及其对根际土壤微生态的影响. 兰州：甘肃农业大学， 2017： 1-3.
2	Li M J， Shan L， Tong L T， et al. Effect of pearling on composition， microstructure， water migration and cooking quality of highland barley （Hordeum vulgare var. Coeleste linnaeus）. Food Chemistry， 2022， 395： 133581.
3	Gong W F， Wei L P， Du J， et al. Structure and diversity of the bacterial community in the rhizosphere of highland barley in Xizang. Acta Microbiologica Sinica， 2023， 63（10）： 4034-4050.
	巩文峰，魏丽萍，杜娟，等. 西藏青稞根际细菌群落结构及多样性. 微生物学报， 2023， 63（10）： 4034-4050.
4	Li X P， Xu S Y， Wang X M， et al. Field survey and pathogen identification of naked barley root rot in Qinghai Province. Journal of Plant Protection， 2021， 48（4）： 757-765.
	李雪萍，许世洋，汪学苗，等. 青海省青稞根腐病调查及病原菌鉴定. 植物保护学报， 2021， 48（4）： 757-765.
5	Li X P， Liu M J， Xu S Y， et al. Investigation and pathogen identification of common root rot of Qingke barley （Hordeum vulgare var. nudum）.Acta Prataculturae Sinica， 2021， 30（7）： 190-198.
	李雪萍，刘梅金，许世洋，等. 青稞普通根腐病的调查与病原鉴定. 草业学报， 2021， 30（7）： 190-198.
6	Li X P， Li M Q， Xu S Y， et al. Pathogens identification and pathogenicity analysis of Fusarium root rot on naked barley. Journal of Triticeae Crops， 2022， 42（9）： 1149-1161.
	李雪萍，李敏权，许世洋，等. 青稞镰孢根腐病病原鉴定及致病性分析. 麦类作物学报， 2022， 42（9）： 1149-1161.
7	Xu S Y， Li X P， Liu M J， et al. Study on the screening of disease prevention pesticides for naked barley root rot. Journal of Cold-Arid Agricultural Sciences， 2023， 2（5）： 458-463.
	许世洋，李雪萍，刘梅金，等. 青稞根腐病防治药剂筛选研究. 寒旱农业科学， 2023， 2（5）： 458-463.
8	Xu S Y， Li M Q， Liu M J， et al. Screening of highland barley root rot resistant varieties. Gansu Agricultural Science and Technology， 2022， 53（3）： 25-30.
	许世洋，李敏权，刘梅金，等. 青稞根腐病抗性品种筛选. 甘肃农业科技， 2022， 53（3）： 25-30.
9	Xu S Y， Li M Q， Liu M J， et al. Screening of bacteria with biocontrol effects against naked barley root rot accompany with plant growth-promoting properties and the biocontrol effects of the bacterial inoculant. Microbiology China， 2022， 49（7）： 2575-2586.
	许世洋，李敏权，刘梅金，等. 青稞根腐病防病促生细菌的筛选及其菌剂防效. 微生物学通报， 2022， 49（7）： 2575-2586.
10	Yang Z， Dai C C， Wang X X， et al. Advance in research on rhizosphere microbial mechanisms of crop soil-borne fungal diseases. Acta Pedologica Sinica， 2019， 56（1）： 12-22.
	杨珍，戴传超，王兴祥，等. 作物土传真菌病害发生的根际微生物机制研究进展. 土壤学报， 2019， 56（1）： 12-22.
11	Ling N， Wang T， Kuzyakov Y. Rhizosphere bacteriome structure and functions. Nature Communications， 2022， 13（1）： 836.
12	De Corato U. Soil microbiota manipulation and its role in suppressing soil-borne plant pathogens in organic farming systems under the light of microbiome-assisted strategies. Chemical and Biological Technologies in Agriculture， 2020， 7（1）： 17.
13	Liu J W， Li X Z， Yao M J. Research progress on assembly of plant rhizosphere microbial community. Acta Microbiologica Sinica， 2021， 61（2）： 231-246.
	刘京伟，李香真，姚敏杰. 植物根际微生物群落构建的研究进展. 微生物学报， 2021， 61（2）： 231-246.
14	Xu S Y， Li X P， Li M Q， et al. Effects of root rot disease at seedling stage on bacterial community structure in the rhizosphere soil of naked barley. Grassland and Turf， 2023， 43（5）： 120-128.
	许世洋，李雪萍，李敏权，等. 青稞苗期根腐病对根际土壤细菌群落结构的影响. 草原与草坪， 2023， 43（5）： 120-128.
15	Shi X， Zhao Y， Xu M， et al. Insights into plant-microbe interactions in the rhizosphere to promote sustainable agriculture in the new crops era. New Crops， 2024， 1： 1-17.
16	Fang Z D. Research methods of plant pathology. Beijing： China Agriculture Press， 1998： 6-18.
	方中达. 植病研究方法. 北京：中国农业出版社， 1998： 6-18.
17	Bolger A M， Lohse M， Usadel B. Trimmomatic： a flexible trimmer for Illumina sequence data. Bioinformatics， 2014， 30（15）： 2114-2120.
18	Magoč T， Salzberg S L. FLASH： fast length adjustment of short reads to improve genome assemblies. Bioinformatics， 2011， 27（21）： 2957-2963.
19	Caporaso J G， Kuczynski J， Stombaugh J， et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods， 2010， 7（5）： 335-336.
20	Edgar R C， Haas B J， Clemente J C， et al. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics， 2011， 27（16）： 2194-2200.
21	Rognes T， Flouri T， Nichols B， et al. VSEARCH： a versatile open source tool for metagenomics. PeerJ， 2016， 4： e2584.
22	Wang Q， Garrity G M， Tiedje J M， et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied & Environmental Microbiology， 2007， 73（16）： 5261-5267.
23	Desantis T Z， Hugenholtz P， Larsen N， et al. Greengenes， a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied & Environmental Microbiology， 2006， 72（7）： 5069-5072.
24	Langille M G， Zaneveld J， Caporaso J G， et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnology， 2013， 31（9）： 814-821.
25	Zhang J， Wei Z， Chen J. A distance-based approach for testing the mediation effect of the human microbiome. Bioinformatics， 2018， 34（11）： 1875-1883.
26	Santoyo G. How plants recruit their microbiome？ New insights into beneficial interactions. Journal of Advanced Research， 2022， 40： 45-58.
27	Qi Y H， Cao S F， Li X P， et al. Study on the relationship between root rot disease and nutrient content， enzyme activity and microbial quantity in rhizosphere soil of naked barley in Lintan County， Gannan State. Acta Agrestia Sinica， 2018， 26（4）： 877-884.
	漆永红，曹素芳，李雪萍，等. 甘南州临潭县青稞根际土壤养分含量、酶活性和微生物数量与根腐病的关系研究. 草地学报， 2018， 26（4）： 877-884.
28	Liu H， Dong Y H， Shen M C， et al. Characteristics of rhizosphere microbial communities in a disease suppressive soil of tomato bacterial wilt and its disease-suppressive transmission mechanism. Acta Pedologica Sinica， 2022， 59（4）： 1125-1135.
	刘洪，董元华，申民翀，等. 番茄青枯病抑病土壤根际微生物群落特征及其抑制性传递机制. 土壤学报， 2022， 59（4）： 1125-1135.
29	Sharma V， Vashishtha A， Jos A L M， et al. Phylogenomics of the phylum Proteobacteria： Resolving the complex relationships. Current Microbiology， 2022， 79（8）： 224.
30	Xian W D， Zhang X T， Li W J. Research status and prospect on bacterial phylum Chloroflexi. Acta Microbiologica Sinica， 2020， 60（9）： 1801-1820.
	鲜文东，张潇橦，李文均. 绿弯菌的研究现状及展望. 微生物学报， 2020， 60（9）： 1801-1820.
31	Wang G H， Liu J J， Yu Z H， et al. Research progress of Acidobacteria ecology in soils. Biotechnology Bulletin， 2016， 32（2）： 14-20.
	王光华，刘俊杰，于镇华，等. 土壤酸杆菌门细菌生态学研究进展. 生物技术通报， 2016， 32（2）： 14-20.
32	Pan X， Raaijmakers J M， Carrión V J. Importance of bacteroidetes in host-microbe interactions and ecosystem functioning. Trends in Microbiology， 2023， 31（9）： 959-971.
33	Yang Y， Li H L， Ma K L， et al. Actinomycetes and their metabolites： visual analysis based on CiteSpace. Acta Microbiologica Sinica， 2022， 62（10）： 3825-3843.
	杨阳，李海亮，马凯丽，等. 放线菌及其代谢产物研究进展-基于CiteSpace可视化分析. 微生物学报， 2022， 62（10）： 3825-3843.
34	Mujakić I， Piwosz K， Koblížek M. Phylum Gemmatimonadota and its role in the environment. Microorganisms， 2022， 10（1）： 151.
35	Liu H， Wei L L， Zhu L F， et al. Research progress of Sphingomonas. Microbiology China， 2023， 50（6）： 2738-2752.
	刘辉，韦璐璐，朱龙发，等. 鞘氨醇单胞菌的研究进展. 微生物学通报， 2023， 50（6）： 2738-2752.
36	Liu G H， Liu B， Wang J P， et al. Advances in taxonomy and application of Bacillus. Microbiology China， 2017， 44（4）： 949-958.
	刘国红，刘波，王阶平，等. 芽胞杆菌分类与应用研究进展. 微生物学通报， 2017， 44（4）： 949-958.
37	Zhou Y F， Bai Y S， Yue T， et al. Research progress on the growth-promoting characteristics of plant growth-promoting rhizobacteria. Microbiology China， 2023， 50（2）： 644-666.
	周益帆，白寅霜，岳童，等. 植物根际促生菌促生特性研究进展. 微生物学通报， 2023， 50（2）： 644-666.
38	Wu H M， Sha B C， Zhang J Y， et al. Effects of bacterial root rot on photosynthetic characteristics in Panax notoginseng. Chinese Journal of Eco-Agriculture， 2020， 28（11）： 1739-1752.
	武洪敏，沙本才，张金燕，等. 细菌性根腐病对三七光合特性的影响. 中国生态农业学报， 2020， 28（11）： 1739-1752.
39	Boussageon R， Sportes A， Lemaitre J P， et al. A bacillaceae consortium positively impacts arbuscular mycorrhizal fungus colonisation， plant phosphate nutrition， and tuber yield in Solanum tuberosum cv. Jazzy. Symbiosis， 2023， 89（2）： 235-250.
40	Daims H， Lebedeva E， Pjevac P， et al. Complete nitrification by Nitrospira bacteria. Nature， 2015（528）： 504-509.
41	Sun Y， Wang M， Mur L A J， et al. Unravelling the roles of nitrogen nutrition in plant disease defences. International Journal of Molecular Sciences， 2020， 21（2）： 572.
42	Huang C， Jiang L， Liang Y P， et al. Acinetobacter calcoaceticus promotes the seedling growth of Lespedeza daurica under saline-alkaline stress. ActaMicrobiologica Sinica， 2023， 63（8）： 3264-3278.
	黄臣，蒋霖，梁银萍，等. 醋酸钙不动杆菌对盐碱胁迫下达乌里胡枝子促生效应研究. 微生物学报， 2023， 63（8）： 3264-3278.
43	Wu W， Zhang P F， Zhang G P， et al. Screening， identification and growth promoting characteristics of high efficient organic phosphate-mineralizing bacterium from rhizosphere soils of Forsythia suspensa. Journal of Southwest Forestry University （Natural Sciences）， 2018， 38（3）： 93-100.
	吴伟，张鹏飞，张桂萍，等. 连翘根际高效解有机磷细菌的筛选鉴定及促生长特性研究. 西南林业大学学报（自然科学）， 2018， 38（3）： 93-100.
44	Song M， Yun H Y， Kim Y H. Antagonistic Bacillus species as a biological control of ginseng root rot caused by Fusarium cf. incarnatum. Journal of Ginseng Research， 2014， 38（2）： 136-145.

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