Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential

Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes

(2021) L. Armbrecht et al.   Scientific Reports

Environmental palaeogenomic reconstruction of an Ice Age algal population

(2021) Youri Lammers et al.   Communications Biology

A method for achieving complete microbial genomes and improving bins from metagenomics data

(2021) Lauren M. Lui et al.   PLoS Computational Biology

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

(2021) Donovan H Parks et al.   NUCLEIC ACIDS RESEARCH

Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico

(2021) Bárbara Moguel et al.   Scientific Reports

PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly

(2021) Maxime Borry et al.   PeerJ

Deciphering the molecular signal from past and alive bacterial communities in aquatic sedimentary archives

(2021) John K. Pearman et al.   Molecular Ecology Resources

An optimized method for the extraction of ancient eukaryote DNA from marine sediments

(2020) Linda Armbrecht et al.   Molecular Ecology Resources

Blooms of Toxic Cyanobacterium Nodularia spumigena in Norwegian Fjords During Holocene Warm Periods

(2020) Robert Konkel et al.   Toxins

PIA: More Accurate Taxonomic Assignment of Metagenomic Data Demonstrated on sedaDNA From the North Sea

(2020) Becky Cribdon et al.   Frontiers in Ecology and Evolution

The Potential of Sedimentary Ancient DNA to Reconstruct Past Ocean Ecosystems

(2020) Linda Armbrecht et al.   OCEANOGRAPHY

Assessing the response of micro-eukaryotic diversity to the Great Acceleration using lake sedimentary DNA

(2020) François Keck et al.   Nature Communications

Aerobic microbial life persists in oxic marine sediment as old as 101.5 million years

(2020) Yuki Morono et al.   Nature Communications

Atribacteria Reproducing over Millions of Years in the Atlantic Abyssal Subseafloor

(2020) Aurèle Vuillemin et al.   mBio

Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea

(2019) Kuldeep D. More et al.   Geobiology

Fluid inclusions from the deep Dead Sea sediment provide new insights on Holocene extreme microbial life

(2019) C. Thomas et al.   QUATERNARY SCIENCE REVIEWS

Scientists’ warning to humanity: microorganisms and climate change

(2019) Ricardo Cavicchioli et al.   NATURE REVIEWS MICROBIOLOGY

Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation

(2019) Linda H. Armbrecht et al.   EARTH-SCIENCE REVIEWS

Linking metagenomics to aquatic microbial ecology and biogeochemical cycles

(2019) Hans‐Peter Grossart et al.   LIMNOLOGY AND OCEANOGRAPHY

A 43 kyr record of protist communities and their response to oxygen minimum zone variability in the Northeastern Arabian Sea

(2018) Kuldeep D. More et al.   EARTH AND PLANETARY SCIENCE LETTERS

Earth BioGenome Project: Sequencing life for the future of life

(2018) Harris A. Lewin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Survival of the fewest: Microbial dormancy and maintenance in marine sediments through deep time

(2018) James A. Bradley et al.   Geobiology

Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline

(2018) Nicolás Rascovan et al.   CELL

Tracking a century of changes in microbial eukaryotic diversity in lakes driven by nutrient enrichment and climate warming

(2017) Eric Capo et al.   ENVIRONMENTAL MICROBIOLOGY

DNA-based methods in paleolimnology: new opportunities for investigating long-term dynamics of lacustrine biodiversity

(2017) Isabelle Domaizon et al.   JOURNAL OF PALEOLIMNOLOGY

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus

(2017) Laura S. Weyrich et al.   NATURE

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

GenBank

(2017) Dennis A Benson et al.   NUCLEIC ACIDS RESEARCH

Microbial community assembly and evolution in subseafloor sediment

(2017) Piotr Starnawski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neandertal and Denisovan DNA from Pleistocene sediments

(2017) Viviane Slon et al.   SCIENCE

Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti, Indonesia

(2017) Aurèle Vuillemin et al.   Frontiers in Microbiology

Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems

(2017) Joanne B. Emerson et al.   Microbiome

Homogenization of lake cyanobacterial communities over a century of climate change and eutrophication

(2017) Marie-Eve Monchamp et al.   Nature Ecology & Evolution

Climate oscillations reflected within the microbiome of Arabian Sea sediments

(2017) William D. Orsi et al.   Scientific Reports

Sedimentary DNA Reveals Cyanobacterial Community Diversity over 200 Years in Two Perialpine Lakes

(2016) Marie-Eve Monchamp et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Propidium monoazide treatment to distinguish between live and dead methanogens in pure cultures and environmental samples

(2016) Janine Heise et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Postglacial viability and colonization in North America’s ice-free corridor

(2016) Mikkel W. Pedersen et al.   NATURE

Marine microbial community dynamics and their ecological interpretation

(2015) Jed A. Fuhrman et al.   NATURE REVIEWS MICROBIOLOGY

The Red Queen Race between Parasitic Chytrids and Their Host, Planktothrix: A Test Using a Time Series Reconstructed from Sediment DNA

(2015) Marcia Kyle et al.   PLoS One

A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome

(2014) C. Warinner et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

(2013) Hákon Jónsson et al.   BIOINFORMATICS

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

(2013) J. Dabney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of the plankton paleome in the Black Sea from the Deglacial to Anthropocene

(2013) M. J. L. Coolen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Global distribution of microbial abundance and biomass in subseafloor sediment

(2012) J. Kallmeyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep subseafloor microbial cells on physiological standby

(2011) B. B. Jorgensen   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS