Sediment Metagenomes as Time Capsules of Lake Microbiomes

ABSTRACT The reconstruction of ecological time series from lake sediment archives can retrace the environmental impact of human activities. Molecular genetic approaches in paleolimnology have provided unprecedented access to DNA time series, which record evidence of the microbial ecologies that unde...

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Autores principales:	Rebecca E. Garner, Irene Gregory-Eaves, David A. Walsh
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	paleolimnology shotgun sequencing metagenomics DNA preservation paleogenomics bacterioplankton Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/f4709089ca2045b28a8ea6100e2a0e10
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spelling	oai:doaj.org-article:f4709089ca2045b28a8ea6100e2a0e102021-11-15T15:31:13ZSediment Metagenomes as Time Capsules of Lake Microbiomes10.1128/mSphere.00512-202379-5042https://doaj.org/article/f4709089ca2045b28a8ea6100e2a0e102020-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00512-20https://doaj.org/toc/2379-5042ABSTRACT The reconstruction of ecological time series from lake sediment archives can retrace the environmental impact of human activities. Molecular genetic approaches in paleolimnology have provided unprecedented access to DNA time series, which record evidence of the microbial ecologies that underlaid historical lake ecosystems. Such studies often rely on single-gene surveys, and consequently, the full diversity of preserved microorganisms remains unexplored. In this study, we probed the diversity archived in contemporary and preindustrial sediments by comparative shotgun metagenomic analysis of surface water and sediment samples from three eastern Canadian lakes. In a strategy that was aimed at disentangling historical DNA from the indigenous sediment background, microbial preservation signals were captured by mapping sequence similarities between sediment metagenome reads and reference surface water metagenome assemblies. We detected preserved Cyanobacteria, diverse bacterioplankton, microeukaryotes, and viruses in sediment metagenomes. Among the preserved microorganisms were important groups never before reported in paleolimnological reconstructions, including bacteriophages (Caudovirales) and ubiquitous freshwater Betaproteobacteria (Polynucleobacter and Limnohabitans). In contrast, ultramicroscopic Actinobacteria (“Candidatus Nanopelagicales”) and Alphaproteobacteria (Pelagibacterales) were apparently not well preserved in sediment metagenomes even though they were numerically dominant in surface water metagenomes. Overall, our study explored a novel application of whole-metagenome shotgun sequencing for discovering the DNA remains of a broad diversity of microorganisms preserved in lake sediments. The recovery of diverse microbial time series supports the taxonomic expansion of microbiome reconstructions and the development of novel microbial paleoindicators. IMPORTANCE Lakes are critical freshwater resources under mounting pressure from climate change and other anthropogenic stressors. The reconstruction of ecological time series from sediment archives with paleolimnological techniques has been shown to be an effective means of understanding how humans are modifying lake ecosystems over extended timescales. In this study, we combined shotgun DNA sequencing with a novel comparative analysis of surface water and sediment metagenomes to expose the diversity of microorganisms preserved in lake sediments. The detection of DNA from a broad diversity of preserved microbes serves to more fully reconstruct historical microbiomes and describe preimpact lake conditions.Rebecca E. GarnerIrene Gregory-EavesDavid A. WalshAmerican Society for Microbiologyarticlepaleolimnologyshotgun sequencingmetagenomicsDNA preservationpaleogenomicsbacterioplanktonMicrobiologyQR1-502ENmSphere, Vol 5, Iss 6 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	paleolimnology shotgun sequencing metagenomics DNA preservation paleogenomics bacterioplankton Microbiology QR1-502
spellingShingle	paleolimnology shotgun sequencing metagenomics DNA preservation paleogenomics bacterioplankton Microbiology QR1-502 Rebecca E. Garner Irene Gregory-Eaves David A. Walsh Sediment Metagenomes as Time Capsules of Lake Microbiomes
description	ABSTRACT The reconstruction of ecological time series from lake sediment archives can retrace the environmental impact of human activities. Molecular genetic approaches in paleolimnology have provided unprecedented access to DNA time series, which record evidence of the microbial ecologies that underlaid historical lake ecosystems. Such studies often rely on single-gene surveys, and consequently, the full diversity of preserved microorganisms remains unexplored. In this study, we probed the diversity archived in contemporary and preindustrial sediments by comparative shotgun metagenomic analysis of surface water and sediment samples from three eastern Canadian lakes. In a strategy that was aimed at disentangling historical DNA from the indigenous sediment background, microbial preservation signals were captured by mapping sequence similarities between sediment metagenome reads and reference surface water metagenome assemblies. We detected preserved Cyanobacteria, diverse bacterioplankton, microeukaryotes, and viruses in sediment metagenomes. Among the preserved microorganisms were important groups never before reported in paleolimnological reconstructions, including bacteriophages (Caudovirales) and ubiquitous freshwater Betaproteobacteria (Polynucleobacter and Limnohabitans). In contrast, ultramicroscopic Actinobacteria (“Candidatus Nanopelagicales”) and Alphaproteobacteria (Pelagibacterales) were apparently not well preserved in sediment metagenomes even though they were numerically dominant in surface water metagenomes. Overall, our study explored a novel application of whole-metagenome shotgun sequencing for discovering the DNA remains of a broad diversity of microorganisms preserved in lake sediments. The recovery of diverse microbial time series supports the taxonomic expansion of microbiome reconstructions and the development of novel microbial paleoindicators. IMPORTANCE Lakes are critical freshwater resources under mounting pressure from climate change and other anthropogenic stressors. The reconstruction of ecological time series from sediment archives with paleolimnological techniques has been shown to be an effective means of understanding how humans are modifying lake ecosystems over extended timescales. In this study, we combined shotgun DNA sequencing with a novel comparative analysis of surface water and sediment metagenomes to expose the diversity of microorganisms preserved in lake sediments. The detection of DNA from a broad diversity of preserved microbes serves to more fully reconstruct historical microbiomes and describe preimpact lake conditions.
format	article
author	Rebecca E. Garner Irene Gregory-Eaves David A. Walsh
author_facet	Rebecca E. Garner Irene Gregory-Eaves David A. Walsh
author_sort	Rebecca E. Garner
title	Sediment Metagenomes as Time Capsules of Lake Microbiomes
title_short	Sediment Metagenomes as Time Capsules of Lake Microbiomes
title_full	Sediment Metagenomes as Time Capsules of Lake Microbiomes
title_fullStr	Sediment Metagenomes as Time Capsules of Lake Microbiomes
title_full_unstemmed	Sediment Metagenomes as Time Capsules of Lake Microbiomes
title_sort	sediment metagenomes as time capsules of lake microbiomes
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/f4709089ca2045b28a8ea6100e2a0e10
work_keys_str_mv	AT rebeccaegarner sedimentmetagenomesastimecapsulesoflakemicrobiomes AT irenegregoryeaves sedimentmetagenomesastimecapsulesoflakemicrobiomes AT davidawalsh sedimentmetagenomesastimecapsulesoflakemicrobiomes
_version_	1718427863090200576

Sediment Metagenomes as Time Capsules of Lake Microbiomes

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