Is Planktonic Diversity Well Recorded in Sedimentary DNA? Toward the Reconstruction of Past Protistan Diversity

A spatiotemporal investigation of varved sediments highlights the dynamics of hypolimnetic hypoxia in a large hard-water lake over the last 150 years

(2016) Jean-Philippe Jenny et al.   LIMNOLOGY AND OCEANOGRAPHY

Multi-scale phylogenetic heterogeneity of archaea, bacteria, methanogens and methanotrophs in lake sediments

(2015) Elodie Billard et al.   HYDROBIOLOGIA

Evidence for an active rare biosphere within freshwater protists community

(2015) Didier Debroas et al.   MOLECULAR ECOLOGY

Preservation potential of ancient plankton DNA in Pleistocene marine sediments

(2015) A. C. BOERE et al.   Geobiology

Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments

(2014) Aurélie Chambouvet et al.   BMC MICROBIOLOGY

Patterns of Rare and Abundant Marine Microbial Eukaryotes

(2014) Ramiro Logares et al.   CURRENT BIOLOGY

Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams

(2014) Linda Wilhelm et al.   ENVIRONMENTAL MICROBIOLOGY

Effects of nutrients and warming onPlanktothrixdynamics and diversity: a palaeolimnological view based on sedimentary DNA and RNA

(2014) Olga Savichtcheva et al.   FRESHWATER BIOLOGY

Placing Environmental Next-Generation Sequencing Amplicons from Microbial Eukaryotes into a Phylogenetic Context

(2014) Micah Dunthorn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Alkenone distribution in Lake Van sediment over the last 270 ka: influence of temperature and haptophyte species composition

(2014) Marie-Ève Randlett et al.   QUATERNARY SCIENCE REVIEWS

Geographic distance and ecosystem size determine the distribution of smallest protists in lacustrine ecosystems

(2013) Cécile Lepère et al.   FEMS MICROBIOLOGY ECOLOGY

Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists

(2013) Cheryl-Emiliane T Chow et al.   ISME Journal

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

(2013) Steven J Blazewicz et al.   ISME Journal

A meta-analysis of changes in bacterial and archaeal communities with time

(2013) Ashley Shade et al.   ISME Journal

High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences

(2013) Kevin L Vergin et al.   ISME Journal

Trophic history of French sub-alpine lakes over the last ~150 years: phosphorus reconstruction and assessment of taphonomic biases

(2013) Vincent Berthon et al.   JOURNAL OF LIMNOLOGY

Late Holocene changes in cyanobacterial community structure in maritime Antarctic lakes

(2013) Rafael Fernandez-Carazo et al.   JOURNAL OF PALEOLIMNOLOGY

Deep Sequencing of Subseafloor Eukaryotic rRNA Reveals Active Fungi across Marine Subsurface Provinces

(2013) William Orsi et al.   PLoS One

Phylogenetic Affiliation of SSU rRNA Genes Generated by Massively Parallel Sequencing: New Insights into the Freshwater Protist Diversity

(2013) Najwa Taib et al.   PLoS One

Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters

(2013) M. Hugoni 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

Short-term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes

(2012) Jean-François Mangot et al.   ENVIRONMENTAL MICROBIOLOGY

Viability of Alexandrium tamarense cysts in the sediment of Funka Bay, Hokkaido, Japan: Over a hundred year survival times for cysts

(2012) Akira Miyazono et al.   HARMFUL ALGAE

Hidden diversity in diatoms of Kenyan Lake Naivasha: a genetic approach detects temporal variation

(2012) KATHLEEN R. STOOF-LEICHSENRING et al.   MOLECULAR ECOLOGY

CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

(2012) Jan Pawlowski et al.   PLOS BIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Effects of production, sedimentation and taphonomic processes on the composition and size structure of sedimenting cladoceran remains in a large deep subalpine lake: paleo-ecological implications

(2011) Benjamin Alric et al.   HYDROBIOLOGIA

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records

(2011) Arjan C. Boere et al.   ORGANIC GEOCHEMISTRY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Marine subsurface eukaryotes: the fungal majority

(2010) Virginia P. Edgcomb et al.   ENVIRONMENTAL MICROBIOLOGY

PANGEA: pipeline for analysis of next generation amplicons

(2010) Adriana Giongo et al.   ISME Journal

Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments

(2010) C. CORINALDESI et al.   MOLECULAR ECOLOGY

Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity

(2010) VIOLA NOLTE et al.   MOLECULAR ECOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Community Structure and Dynamics of Small Eukaryotes Targeted by New Oligonucleotide Probes: New Insight into the Lacustrine Microbial Food Web

(2009) J.-F. Mangot et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Vertical distribution of metabolically active eukaryotes in the water column and sediments of the Black Sea

(2009) Marco J.L. Coolen et al.   FEMS MICROBIOLOGY ECOLOGY

Late-Holocene succession of dinoflagellates in an Antarctic fjord using a multi-proxy approach: paleoenvironmental genomics, lipid biomarkers and palynomorphs

(2009) A. C. BOERE et al.   Geobiology

Late-Holocene summer temperature reconstruction from chironomid assemblages of Lake Anterne, northern French Alps

(2009) Laurent Millet et al.   HOLOCENE

Sedimentological and geochemical records of past trophic state and hypolimnetic anoxia in large, hard-water Lake Bourget, French Alps

(2009) Charline Giguet-Covex et al.   JOURNAL OF PALEOLIMNOLOGY

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

(2009) Linda A. Amaral-Zettler et al.   PLoS One

Unexpected Importance of Potential Parasites in the Composition of the Freshwater Small-Eukaryote Community

(2008) C. Lepere et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Sources for sedimentary bacteriohopanepolyols as revealed by 16S rDNA stratigraphy

(2008) Marco J. L. Coolen et al.   ENVIRONMENTAL MICROBIOLOGY

Protists are microbes too: a perspective

(2008) David A Caron et al.   ISME Journal

Damage and degradation rates of extracellular DNA in marine sediments: implications for the preservation of gene sequences

(2008) C. CORINALDESI et al.   MOLECULAR ECOLOGY