In vitro domestication of halophyte microbiota for future SynCom application

IF 4.1 2区农林科学 Q1 AGRONOMY Plant and Soil Pub Date : 2025-02-15 DOI:10.1007/s11104-024-07198-1

Nada A. Moner, Tarek R. Elsayed, Wafaa M. Amer, Mervat A. Hamza, Hanan H. Youssef, Randa M. Abdel-Fatah, Mahmoud S. Abdelwahab, Omar M. Shahat, Gehan H. Youssef, Mahmoud El-Tahan, Mohamed Fayez, Florian Fricke, Silke Ruppel, Nabil A. Hegazi

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Abstract

Background and aims

Microbiome-mediated strategies for future stressed-agriculture entail exploration of repertoires of halophyte microbiota. Culturomics strategies are advanced to improve culturability and extend diversity of microbiota of Salicornia europaea L.

Methods

The plant broth-based-seawater-culture medium (PBSW) was advanced for in vitro domestication of microbiota of endo-rhizosphere/endo-phyllosphere of S. europaea. Populations (Colony Forming Units, CFUs) and biomass production (Optical Density, OD) were monitored throughout successive steps of in vitro cultivation/domestication in liquid batch cultures. Culture-dependent methods were applied to cultivate and identify (16S rRNA gene sequencing) representative isolates; and culture-independent analyses (DGGE/qPCR) for community composition.

Results

PBSW supported higher CFUs counts; and related to 16S rRNA gene copy numbers (qPCR), increased (> 40 fold) culturability compared to NaCl-salted-standard culture medium. Successive in vitro domestication/batch cultures boosted bacterial growth, diminished differences among tested culture media and shortened doubling times (DT). PCR-DGGE showed divergence in culturable community composition primarily attributed to culture media. 16S rRNA gene sequencing of representative isolates indicated: a) greater diversity in endo-phyllosphere than endo-rhizosphere; b) abundant phyla were Pseudomonadota/Bacillota /Actinomycetota; c) dominance of Halomonas among 15 genera identified; d) Gracilibacillus, Metabacillus, Mixta, Salinicoccus, Zhihengliuella, Marinobacter, Marinimicrobium and Planomicrobium were first reported/cultivated for S. europaea. In vitro domestication resulted in dominance of genera of Pseudomonadota/Bacillota for endo-phyllosphere and Halomonas sp. of Pseudomonadota for endo-rhizosphere.

Conclusion

PBSW created in situ similis milieu for cultivation of halophyte bacteria, and enabled in vitro domestication for propagating microbiota, instead of laborious construction of consortia of single isolates, for future SynCom applications.

Graphical Abstract

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盐生菌群的体外驯化及其在SynCom中的应用

背景和目的微生物组介导的未来胁迫农业策略需要探索盐生植物微生物群的多样性。提出了培养组学策略，以提高欧洲海参的可培养性和扩大微生物群的多样性。方法提出了植物肉汤-海水培养基（PBSW）对欧洲海参根际/根层内微生物群的体外驯化。在试管培养/驯化的连续步骤中监测种群（菌落形成单位，cfu）和生物量（光密度，OD）。采用培养依赖法培养鉴定（16S rRNA基因测序）代表性分离株；和培养独立分析（DGGE/qPCR）的群落组成。结果spbsw支持较高的cfu计数；与16S rRNA基因拷贝数（qPCR）有关，与nacl盐标准培养基相比，可培养性提高（>； 40倍）。连续的体外驯化/批量培养促进了细菌的生长，减少了被试培养基之间的差异，缩短了倍增时间（DT）。PCR-DGGE结果显示，可培养群落组成的差异主要归因于培养基。代表性分离株的16S rRNA基因测序结果表明：a)根际内比根际内具有更大的多样性；b)丰富的门为假单胞菌门/杆菌门/放线菌门；c)盐单胞菌在15个属中占优势；d)在欧洲葡萄球菌中首次报道培养到Gracilibacillus、Metabacillus、Mixta、Salinicoccus、Zhihengliuella、Marinobacter、marinimicroum和Planomicrobium。在离体驯化中，层内以假单胞菌属/芽孢杆菌属为主，根内以假单胞菌属为主。结论pbsw为盐生菌的原位培养创造了相似的环境，并为今后SynCom的应用提供了体外驯化繁殖微生物群的条件，而不是费力地构建单个菌株的群体。图形抽象

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来源期刊

Plant and Soil 农林科学-农艺学

CiteScore

8.20

自引率

8.20%

发文量

543

审稿时长

2.5 months

期刊介绍： Plant and Soil publishes original papers and review articles exploring the interface of plant biology and soil sciences, and that enhance our mechanistic understanding of plant-soil interactions. We focus on the interface of plant biology and soil sciences, and seek those manuscripts with a strong mechanistic component which develop and test hypotheses aimed at understanding underlying mechanisms of plant-soil interactions. Manuscripts can include both fundamental and applied aspects of mineral nutrition, plant water relations, symbiotic and pathogenic plant-microbe interactions, root anatomy and morphology, soil biology, ecology, agrochemistry and agrophysics, as long as they are hypothesis-driven and enhance our mechanistic understanding. Articles including a major molecular or modelling component also fall within the scope of the journal. All contributions appear in the English language, with consistent spelling, using either American or British English.