Dynamics of rhizoplane bacterial communities subjected to physicochemical treatments in hydroponic crops

Chave, Marie; Dabert, Patrick; Brun, Reto; Godon, Jean Jacques; Poncet, C.

doi:10.1016/j.cropro.2007.07.010

Cited by 12 publications

(7 citation statements)

References 33 publications

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“…Root samples were washed following the 4 different protocols described in Table 2b. Two protocols were found in the literature; i.e., root shaking with isotonic water (NaCl) [39] or with (NaPO 3 ) 6 +peptone [40]. The two others were developed in our laboratory and consisted of root shaking (KPBT Sh) or sonication (KPBT So) in KPBT buffer.…”

Section: Microbiota Recoverymentioning

confidence: 99%

Standardization of Plant Microbiome Studies: Which Proportion of the Microbiota is Really Harvested?

et al. 2020

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Studies in plant-microbiome currently use diverse protocols, making their comparison difficult and biased. Research in human microbiome have faced similar challenges, but the scientific community proposed various recommendations which could also be applied to phytobiome studies. Here, we addressed the isolation of plant microbiota through apple carposphere and lettuce root microbiome. We demonstrated that the fraction of the culturable epiphytic microbiota harvested by a single wash might only represent one-third of the residing microbiota harvested after four successive washes. In addition, we observed important variability between the efficiency of washing protocols (up to 1.6-fold difference for apple and 1.9 for lettuce). QIIME2 analysis of 16S rRNA gene, showed a significant difference of the alpha and beta diversity between protocols in both cases. The abundance of 76 taxa was significantly different between protocols used for apple. In both cases, differences between protocols disappeared when sequences of the four washes were pooled. Hence, pooling the four successive washes increased the alpha diversity for apple in comparison to a single wash. These results underline the interest of repeated washing to leverage abundance of microbial cells harvested from plant epiphytic microbiota whatever the washing protocols, thus minimizing bias.

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Section: Microbiota Recoverymentioning

confidence: 99%

Standardization of Plant Microbiome Studies: Which Proportion of the Microbiota is Really Harvested?

et al. 2020

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“…Whatever the hydroponic habitat, the diversity of microorganisms depends on their ability to metabolise the available carbon sources. Although a nutrient film technique system is much simpler than a soil-based culture system, SSCP analyses showed the bacterial diversity of the rhizoplane to be as high as that of the rhizosphere in soil (Chave et al, 2008). However, further studies comparing the microorganisms colonising soil and soilless cultures are needed to draw any conclusion.…”

Section: Influence Of the Rhizosphere On The Microbial Communitiesmentioning

confidence: 99%

Pathogenic and beneficial microorganisms in soilless cultures

Vallance

Déniel

Floch

et al. 2011

Agronomy Sust. Developm.

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HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

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“…Other researchers have omitted sonication entirely, and instead carried out washing with or without additional shaking ( Chave et al, 2008 ; Ofek et al, 2014 ), shaking only ( Nunan et al, 2005 ), bead beating ( Peiffer et al, 2013 ), or combined several mechanical treatments ( Kaiser et al, 2001 ; Wieland et al, 2001 ). A detailed summary of protocols (not including sonication) from studies before 2009 has been compiled by Barillot et al (2013) .…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Strategies to Separate Root-Associated Microbial Communities: A Crucial Choice in Rhizobiome Research

et al. 2016

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Plants shape distinct, species-specific microbiomes in their rhizospheres. A main premise for evaluating microbial communities associated with root-soil compartments is their successful separation into the rhizosphere (soil-root interface), the rhizoplane (root surface), and the endosphere (inside roots). We evaluated different approaches (washing, sonication, and bleaching) regarding their efficiency to separate microbial cells associated with different root compartments of soil-grown rice using fluorescence microscopy and community fingerprinting of 16S rRNA genes. Vigorous washing detached 45% of the rhizoplane population compared to untreated roots. Additional sonication reduced rhizoplane-attached microorganisms by up to 78% but caused various degrees of root tissue destruction at all sonication intensities tested. Treatment with sodium hypochlorite almost completely (98%) removed rhizoplane-associated microbial cells. Community fingerprinting revealed that microbial communities obtained from untreated, washed, and sonicated roots were not statistically distinguishable. Hypochlorite-treated roots harbored communities significantly different from all other samples, likely representing true endospheric populations. Applying these procedures to other root samples (bean and clover) revealed that treatment efficiencies were strongly affected by root morphological parameters such as root hair density and rigidity of epidermis. Our findings suggest that a careful evaluation of separation strategies prior to molecular community analysis is indispensable, especially when endophytes are the subject of interest.

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Dynamics of rhizoplane bacterial communities subjected to physicochemical treatments in hydroponic crops

Cited by 12 publications

References 33 publications

Standardization of Plant Microbiome Studies: Which Proportion of the Microbiota is Really Harvested?

Standardization of Plant Microbiome Studies: Which Proportion of the Microbiota is Really Harvested?

Pathogenic and beneficial microorganisms in soilless cultures

Evaluation of Strategies to Separate Root-Associated Microbial Communities: A Crucial Choice in Rhizobiome Research

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