Effects of sampling and storage procedures on 16S rDNA amplicon sequencing results of kelp microbiomes

Burgunter-Delamare, Bertille; Tanguy, Gwenn; Legeay, Erwan; Boyen, Catherine; Dittami, Simon M.

doi:10.1016/j.margen.2022.100944

Cited by 9 publications

(6 citation statements)

References 35 publications

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“…However, the overall community composition patterns remained comparable (Figure A4 ), and no major groups of organisms were excluded from the data set in either preservation protocol treatment. This is consistent with recent findings of Burgunter‐Delamare et al ( 2022 ). Interestingly, RNAlater‐treated samples appeared to be less impacted by DNA extraction bias in the case of eukaryotic communities, illustrated by the smaller 95% confidence interval in Figure 1a .…”

Section: Resultssupporting

confidence: 94%

“…The optimal preservation protocol for a given study depends on different factors like practicability under field conditions, perishability of the sample material, and expected storage time of the samples. It might, for example, not be possible to transport liquid nitrogen to remote sampling sites, on long field trips, or in small boats (Burgunter‐Delamare et al, 2022 ). In this case, prefilled tubes with RNAlater would be better suited.…”

Section: Resultsmentioning

confidence: 99%

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DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes

Bräuer

Bengtsson

2022

MicrobiologyOpen

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DNA extraction and preservation bias is a recurring topic in DNA sequencing‐based microbial ecology. The different methodologies can lead to distinct outcomes, which has been demonstrated especially in studies investigating prokaryotic community composition. Eukaryotic microbes are ubiquitous, diverse, and increasingly a subject of investigation in addition to bacteria and archaea. However, little is known about how the choice of DNA preservation and extraction methodology impacts perceived eukaryotic community composition. In this study, we compared the effect of two DNA preservation methods and six DNA extraction methods on the community profiles of both eukaryotes and prokaryotes in phototrophic biofilms on seagrass ( Zostera marina ) leaves from the Baltic Sea. We found that, whereas both DNA preservation and extraction method caused significant bias in perceived community composition for both eukaryotes and prokaryotes, extraction bias was more pronounced for eukaryotes than for prokaryotes. In particular, soft‐bodied and hard‐shelled eukaryotes like nematodes and diatoms, respectively, were differentially abundant depending on the extraction method. We conclude that careful consideration of DNA preservation and extraction methodology is crucial to achieving representative community profiles of eukaryotes in marine biofilms and likely all other habitats containing diverse eukaryotic microbial communities.

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Section: Resultssupporting

confidence: 94%

Section: Resultsmentioning

confidence: 99%

DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes

Bräuer

Bengtsson

2022

MicrobiologyOpen

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“…After 7 days of continuous oral administration, the faeces of mice in each group were collected and immediately frozen in liquid nitrogen before being transferred to a −80 °C refrigerator for 16S rDNA amplicons sequencing. 32…”

Section: Methodsmentioning

confidence: 99%

The effects of Lactobacillus reuteri microcapsules on radiation-induced brain injury by regulating the gut microenvironment

Zhang,

Hu,

Song

et al. 2023

Food Funct.

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“…Two parts of the blades were sampled: the basal meristem and the tip (Figure 1). A disc with Ø2cm was punched out for each part of the blade and placed in a 15 ml Falcon tube containing 5 ml of clean silica gel (2-6 mm; VWR), following the protocol developed in our laboratory (Burgunter-Delamare et al, 2022). Tubes were stored at room temperature for up to 15 days before DNA extraction.…”

Section: Biological Materials and Environmental Variablesmentioning

confidence: 99%

The Saccharina latissima microbiome: Effects of region, season, and physiology

et al. 2023

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IntroductionSaccharina latissima is a canopy-forming species of brown algae and, as such, is considered an ecosystem engineer. Several populations of this alga are exploited worldwide, and a decrease in the abundance of S. latissima at its southern distributional range limits has been observed. Despite its economic and ecological interest, only a few data are available on the composition of microbiota associated with S. latissima and its role in algal physiologyn.MethodsWe studied the whole bacterial community composition associated with S. latissima samples from three locations (Brittany, Helgoland, and Skagerrak) by 16S metabarcoding analyses at different scales: algal blade part, regions, season (at one site), and algal physiologic state.Results and DiscussionWe have shown that the difference in bacterial composition is driven by factors of decreasing importance: (i) the algal tissues (apex/meristem), (ii) the geographical area, (iii) the seasons (at the Roscoff site), and (iv) the algal host’s condition (healthy vs. symptoms). Overall, Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia dominated the general bacterial communities. Almost all individuals hosted bacteria of the genus Granulosicoccus, accounting for 12% of the total sequences, and eight additional core genera were identified. Our results also highlight a microbial signature characteristic for algae in poor health independent of the disease symptoms. Thus, our study provides a comprehensive overview of the S. latissima microbiome, forming a basis for understanding holobiont functioning.

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Effects of sampling and storage procedures on 16S rDNA amplicon sequencing results of kelp microbiomes

Cited by 9 publications

References 35 publications

DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes

DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes

The effects of Lactobacillus reuteri microcapsules on radiation-induced brain injury by regulating the gut microenvironment

The Saccharina latissima microbiome: Effects of region, season, and physiology

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