Microvolume DNA extraction methods for microscale amplicon and metagenomic studies

Bramucci, AR; Focardi, A; Rinke, C; Hugenholtz, P; Tyson, GW; Seymour, JR; Raina, J-B

Microvolume DNA extraction methods for microscale amplicon and metagenomic studies

Bramucci, AR Focardi, A

Rinke, C Hugenholtz, P Tyson, GW Seymour, JR Raina, J-B

Permalink

Publisher:: Nature Publishing Group
Publication Type:: Journal Article
Citation:: ISME Communications, 2021, 1, (1), pp. 1-5
Issue Date:: 2021-12-17

Open Access

Copyright Clearance Process

Recently Added
In Progress
Open Access

This item is open access.

Adobe PDF

Download full textAdobe PDF (804.38 kB)

View on publisher's site

View statistics

Full metadata record

Field	Value	Language
dc.contributor.author	Bramucci, AR
dc.contributor.author	Focardi, A https://orcid.org/0000-0002-0340-4225
dc.contributor.author	Rinke, C
dc.contributor.author	Hugenholtz, P
dc.contributor.author	Tyson, GW
dc.contributor.author	Seymour, JR
dc.contributor.author	Raina, J-B
dc.date.accessioned	2022-02-03T05:01:29Z
dc.date.available	2022-02-03T05:01:29Z
dc.date.issued	2021-12-17
dc.identifier.citation	ISME Communications, 2021, 1, (1), pp. 1-5
dc.identifier.issn	2730-6151
dc.identifier.issn	2730-6151
dc.identifier.uri	http://hdl.handle.net/10453/154174
dc.description.abstract	Investigating the composition and metabolic capacity of aquatic microbial assemblages usually requires the filtration of multi-litre samples, which are up to 1 million-fold larger than the microenvironments within which microbes are predicted to be spatially organised. To determine if community profiles can be reliably generated from microlitre volumes, we sampled seawater at a coastal and an oceanic site, filtered and homogenised them, and extracted DNA from bulk samples (2 L) and microvolumes (100, 10 and 1 μL) using two new approaches. These microvolume DNA extraction methods involve either physical or chemical lysis (through pH/thermal shock and lytic enzymes/surfactants, respectively), directly followed by the capture of DNA on magnetic beads. Downstream analysis of extracted DNA using both amplicon sequencing and metagenomics, revealed strong correlation with standard large volume approaches, demonstrating the fidelity of taxonomic and functional profiles of microbial communities in as little as 1 μL of seawater. This volume is six orders of magnitude smaller than most standard operating procedures for marine metagenomics, which will allow precise sampling of the heterogenous landscape that microbes inhabit.
dc.language	en
dc.publisher	Nature Publishing Group
dc.relation	http://purl.org/au-research/grants/arc/DP180100838
dc.relation	http://purl.org/au-research/grants/arc/DP200100919
dc.relation.ispartof	ISME Communications
dc.relation.isbasedon	10.1038/s43705-021-00079-z
dc.rights	info:eu-repo/semantics/openAccess
dc.title	Microvolume DNA extraction methods for microscale amplicon and metagenomic studies
dc.type	Journal Article
utslib.citation.volume	1
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - C3 - Climate Change Cluster
utslib.copyright.status	open_access	*
pubs.consider-herdc	false
dc.date.updated	2022-02-03T05:01:28Z
pubs.issue	1
pubs.publication-status	Published
pubs.volume	1
utslib.citation.issue	1

Abstract:

Investigating the composition and metabolic capacity of aquatic microbial assemblages usually requires the filtration of multi-litre samples, which are up to 1 million-fold larger than the microenvironments within which microbes are predicted to be spatially organised. To determine if community profiles can be reliably generated from microlitre volumes, we sampled seawater at a coastal and an oceanic site, filtered and homogenised them, and extracted DNA from bulk samples (2 L) and microvolumes (100, 10 and 1 μL) using two new approaches. These microvolume DNA extraction methods involve either physical or chemical lysis (through pH/thermal shock and lytic enzymes/surfactants, respectively), directly followed by the capture of DNA on magnetic beads. Downstream analysis of extracted DNA using both amplicon sequencing and metagenomics, revealed strong correlation with standard large volume approaches, demonstrating the fidelity of taxonomic and functional profiles of microbial communities in as little as 1 μL of seawater. This volume is six orders of magnitude smaller than most standard operating procedures for marine metagenomics, which will allow precise sampling of the heterogenous landscape that microbes inhabit.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/154174