Real-time PCR for quantification in soil of glycoside hydrolase family 6 cellulase genes

Merlin, Chloé; Besaury, Ludovic; Niepceron, Maïté; Mchergui, Chokri; Riah, Wassila; Bureau, Fabrice; Gattin, Isabelle; Bodilis, Josselin

doi:10.1111/lam.12273

Cited by 14 publications

(8 citation statements)

References 23 publications

(26 reference statements)

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“…not using commercial kits) were used in the majority of studies (e.g. Callejas et al 2011;Barberan & Casamayor 2014;Mao et al 2014) DNA in a number of studies, but only twice since 2014 (Merlin et al 2014;Wasaki et al 2015).…”

Section: Summary Of Dna Extraction Methodsmentioning

confidence: 99%

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

107

112

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Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil ® and PowerMax ® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil ® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater ® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

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Section: Summary Of Dna Extraction Methodsmentioning

confidence: 99%

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

107

112

View full text Add to dashboard Cite

show abstract

“…Four target genes were quantified, including bacterial 16S rRNA genes and three bacterial functional genes (i.e., cbb M , amylase , and cellulose ). The cbb M gene encodes key enzymes of the Calvin‐Benson‐Bassham (CBB) cycle .…”

Section: Methodsmentioning

confidence: 99%

“…These include a parallel barrel structure and enzymatic reactions that act on α‐glycosidic bonds that are hydrolyzed to yield α‐anomeric mono‐ or oligosaccharides . Cellulose‐degrading enzymes ( cellulose ) have been described as members of the superfamily of glycoside hydrolases (GH) in at least ten GH families . Abundances of these genes represent the potential functions of bacterial communities.…”

Section: Methodsmentioning

confidence: 99%

Environmental filtering drives bacterial community structure and function in a subalpine area of northern China

et al. 2018

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Microbial community assembly is affected by the trade-off between deterministic and stochastic processes, but the mechanisms underpinning their relative influences remain elusive. This knowledge gap strongly limits our ability to predict the effect of environmental filtering on microbial community structure and function. To improve the understanding of mechanisms underlying community assembly processes, we investigated bacterial community structure and function on a subalpine shady slope and a sunny slope in the Pangquangou National Nature Reserve in North China. By integrating the results of a null model and the RC metric, we inferred that a deterministic process, that is, environmental filtering, drove bacterial community biogeographical patterns. Edaphic factors caused the largest contribution to microbial community structure, followed by vegetation and spatial variables. Among edaphic factors, total carbon (TC) and total nitrogen (TN) were the most important factors as determined by redundancy analysis (RDA). Moreover, network analysis suggested that the status of bacterial community co-occurrence was significantly greater than that of exclusive relationships. Under environmental stress, there was no significant difference in the overall bacterial community structure on the different slopes, while significant differences were observed in relation to community functions. Given this, we inferred that the degrees of response of bacterial community structure and function to varying environments were not consistent. In conclusion, our results contribute to the understanding of deterministic versus stochastic balance in bacterial community assembly and the response mechanisms of community structure and function to environmental heterogeneity.

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“…Also, bacteria can produce "plant hormones", signaling molecules that elicit systemic resistance in plants [5]. Moreover, some bacteria outcompete, antagonize, or inhibit plant pathogens [6,7], and can produce enzymes which transform complex and inaccessible substrates into available ones [8,9].…”

Section: Introductionmentioning

confidence: 99%

Characterization of bacteria with plant growth promotion and antagonistic activity associated to rhizosphere and phyllosphere of Platanus mexicana and Persea shiedeana trees natural hosts of ambrosial beetle

Ferrera-Rodríguez

Alarcón-González

Caballero-Reyes

et al. 2023

Preprint

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It is well established that bacteria belonging to microbiota of plants, contribute to the better development of their hosts by different mechanisms, such as, growth promotion, nutrient facilitation, stimulation of plant defenses, antagonizing pathogens or pest, and some of them are also, some microorganisms show enzymatic activities with biotechnological application in the agricultural and industrial sector. In the present study we identified and characterized fourteen bacterial strains isolated from the rhizosphere and phyllosphere of Platanus mexicana and Persea schiedeana trees; the aim of this research was to evaluate bacterial biological activities over plant growth promotion on Arabidopsis thaliana seedlings and antagonistic activity over phytopathogenic fungus Fusarium sp., besides studying their lytic ability when confronted with cellulose, pectin, or chitin as carbon sources. Such strains were classified into Curtobacterium, Plantibacter, Bacillus, Brevibacterium, Carnobacterium, Staphylococcus, Erwinia, Serratia, Exiguobacterium and Yersinia genera. Every single strain revealed at least one of the evaluated characteristics. Yersinia sp. strain PsH3-014(14D) and Bacillus sp. strain Hay2-01H(7) stand out from the other strains due to their capacity to promote plant growth in A. thaliana seedlings as well as antagonist activity against of Fusarium sp.; moreover, PsH3-014(14D) also degrades pectin and chitin, while Hay2-01H(7) degrades cellulose and pectin. In contrast, Carnobacterium gallinarum strain Chi2-3Ri was detrimental for the development of Arabidopsis seedlings but it can degrade cellulose. Erwinia sp. strain Hay2-1H was the only strain capable to degrade all three biopolymers tested (cellulose, pectin, and chitin). Further research could be directed towards the isolation and characterization of key enzymes produced by the referred strains, as well as further exploration of other metabolic capacities.

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Real-time PCR for quantification in soil of glycoside hydrolase family 6 cellulase genes

Cited by 14 publications

References 23 publications

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Environmental filtering drives bacterial community structure and function in a subalpine area of northern China

Characterization of bacteria with plant growth promotion and antagonistic activity associated to rhizosphere and phyllosphere of Platanus mexicana and Persea shiedeana trees natural hosts of ambrosial beetle

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