High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of “Beijing” hybrid maize planted in China

Liu, Yang; Wang, Ronghuan; Li, Yinhu; Cao, Yanhua; Chen, Chuanyong; Qiu, Chuangzhao; Bai, Feirong; Xu, Tianjun; Zhang, Xin; Dai, Wenkui; Zhao, Jiuran; Cheng, Chi

doi:10.1007/s10725-016-0208-5

Cited by 33 publications

(26 citation statements)

References 34 publications

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“…Unfrozen roots were surface-sterilized as indicated by Liu et al ( 2017 ). Essentially, roots were immersed in 70% ethanol for 3 min, washed with fresh sodium hypochlorite solution (2.5% available Cl − ) for 5 min, rinsed with 70% ethanol for 30 s and finally washed thoroughly with sterile distilled water.…”

Section: Methodsmentioning

confidence: 99%

“…Previous studies have analyzed bacterial taxa associated with maize. Most of the work has been done by using culture-dependent methods (Rai et al, 2007 ; Rijavec et al, 2007 ; Pereira et al, 2009 , 2011 ; Ikeda et al, 2013 ; Celador-Lera et al, 2016 ; Menéndez et al, 2016 ; Sandhya et al, 2017 ) or assessed bacterial diversity independently of culture approaches (Schmalenberger and Tebbe, 2003 ; Herschkovitz et al, 2005a , b ; Pereira et al, 2011 ; Correa-Galeote et al, 2016 ; Liu et al, 2017 ). The high-throughput pyrosequencing technology introduced by 454 Life Science (Margulies et al, 2005 ; Rothberg and Leamon, 2008 ) has been used to assess diversity in cultivar-specific bacterial endophyte communities in potato roots (Manter et al, 2010 ), leaf vegetables (Jackson et al, 2013 ), the spermosphere and phyllosphere of spinach (López-Velasco et al, 2013 ), tomato leaves (Romero et al, 2014 ), grapevine leaves and stems (Yousaf et al, 2014 ) and roots and shoots of cucumber (Eevers et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

“…Most of the works has been done toward understand the effect of an engineered varieties of maize in the bacterial diversity in maize rhizosphere (Schmalenberger and Tebbe, 2003 ; Ikeda et al, 2013 ; Liu et al, 2017 ) or to analyse the changes in the rhizosphere of maize after the application of an inoculant (Herschkovitz et al, 2005a , b ; Sanguin et al, 2006a , b ; Alves et al, 2015 ). In recent years, sustainability agriculture methods have also been considered as great potential source of new information and perspective in agriculture and food systems (Wezel et al, 2011 ).…”

Section: Introductionmentioning

confidence: 99%

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Maize Endophytic Bacterial Diversity as Affected by Soil Cultivation History

2018

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The bacterial endophytic communities residing within roots of maize (Zea mays L.) plants cultivated by a sustainable management in soils from the Quechua maize belt (Peruvian Andes) were examined using tags pyrosequencing spanning the V4 and V5 hypervariable regions of the 16S rRNA. Across four replicate libraries, two corresponding to sequences of endophytic bacteria from long time maize-cultivated soils and the other two obtained from fallow soils, 793 bacterial sequences were found that grouped into 188 bacterial operational taxonomic units (OTUs, 97% genetic similarity). The numbers of OTUs in the libraries from the maize-cultivated soils were significantly higher than those found in the libraries from fallow soils. A mean of 30 genera were found in the fallow soil libraries and 47 were in those from the maize-cultivated soils. Both alpha and beta diversity indexes showed clear differences between bacterial endophytic populations from plants with different soil cultivation history and that the soils cultivated for long time requires a higher diversity of endophytes. The number of sequences corresponding to main genera Sphingomonas, Herbaspirillum, Bradyrhizobium and Methylophilus in the maize-cultivated libraries were statistically more abundant than those from the fallow soils. Sequences of genera Dyella and Sreptococcus were significantly more abundant in the libraries from the fallow soils. Relative abundance of genera Burkholderia, candidatus Glomeribacter, Staphylococcus, Variovorax, Bacillus and Chitinophaga were similar among libraries. A canonical correspondence analysis of the relative abundance of the main genera showed that the four libraries distributed in two clearly separated groups. Our results suggest that cultivation history is an important driver of endophytic colonization of maize and that after a long time of cultivation of the soil the maize plants need to increase the richness of the bacterial endophytes communities.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Maize Endophytic Bacterial Diversity as Affected by Soil Cultivation History

2018

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“…However, the relative abundance of Proteobacteria and Firmicutes increased, while that of Acidobacteria decreased from the rhizosphere to the endosphere. These findings are consistent with observations from other plants such as rice (Edwards et al, 2015), maize (Liu et al, 2017), grapes (Zarraonaindia et al, 2015), agave (Coleman-Derr et al, 2015), Brassica stricta (Wagner et al, 2016), Oxyria digyna, and Saxifraga oppositifolia (Kumar et al, 2017). Taken together, these results indicate that there may be some factors that shape the structure of endophytic bacteria acting in different environments and host species.…”

Section: Difference Between Plant Compartments and Sampling Locationssupporting

confidence: 91%

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“…Many studies have also emphasized the importance of microbial metabolism and microbial functional genes in cell behavior and activity, natural product biosynthesis, and other metabolic processes. The presence of H. nitritophilus and P. viridiflava on maize balanced cell osmotic pressure and antagonized the pathogen Ustilago maydis [39]. Abia et al (2017) analyzed river water and sediment microbial diversity through high-throughput analysis and predicted its functional genes through functional maps [40].…”

Section: Discussionmentioning

confidence: 99%

Assessment of endophytic bacterial diversity in rose by high-throughput sequencing analysis

Xia

Kang

et al. 2020

PLoS ONE

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The endophytic bacterial diversity of rose was analyzed by high-throughput sequencing of 16S rDNA and functional prediction of the bacterial community. The number of bacterial sequence reads obtained from 18 rose samples ranged from 63,951 to 114,833, and reads were allocated to 1982 OTUs based on sequences of the V3-V4 region. The highest Shannon Index was found in Luogang rose (1.93), while the lowest was found in Grasse rose (0.35). The bacterial sequence reads were grouped into three different phyla: Firmicutes, Proteobacteria, and Actinobacteria. At the genus level, Bacillus and Staphylococcus had the highest abundance across all 18 samples; Bacillus was particularly abundant in Daguo rose (99.09%), Rosa damascena (99.65%), and Fenghua rose (99.58%). Unclassified OTUs were also found in all samples. PICRUSt gene prediction revealed that each endophyte sample contained multiple KEGG functional modules related to human metabolism and health. A high abundance of functional genes were involved in (1) Amino Acid Metabolism, (2) Carbohydrate Metabolism, (3) Cellular Processes and Signaling, (4) Energy Metabolism, and (5) Membrane Transport, indicating that the endophytic community comprised a wide variety of microorganisms and genes that could be used for further studies. The rose endophytic bacterial community is rich in diversity; community composition varies among roses and contains functional information related to human health.

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High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of “Beijing” hybrid maize planted in China

Cited by 33 publications

References 34 publications

Maize Endophytic Bacterial Diversity as Affected by Soil Cultivation History

Maize Endophytic Bacterial Diversity as Affected by Soil Cultivation History

Untitled

Assessment of endophytic bacterial diversity in rose by high-throughput sequencing analysis

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