Lake Ecosystem Robustness and Resilience Inferred from a Climate-Stressed Protistan Plankton Network

Co‐occurrence is not evidence of ecological interactions

(2020) F. Guillaume Blanchet et al.   ECOLOGY LETTERS

Soil Microbiomes Under Climate Change and Implications for Carbon Cycling

(2020) Dan Naylor et al.   Annual Review of Environment and Resources

Does functional redundancy affect ecological stability and resilience? A review and meta‐analysis

(2020) Christopher R. Biggs et al.   Ecosphere

Aquatic food webs in deep temperate lakes: Key species establish through their autecological versatility

(2020) Zhishuai Qu et al.   MOLECULAR ECOLOGY

Time series are critical to understand microbial plankton diversity and ecology

(2019) David Moreira et al.   MOLECULAR ECOLOGY

Benthic Diatom Communities in an Alpine River Impacted by Waste Water Treatment Effluents as Revealed Using DNA Metabarcoding

(2019) Teofana Chonova et al.   Frontiers in Microbiology

Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants

(2019) Dominik Forster et al.   ENVIRONMENTAL MICROBIOLOGY

Use and abuse of correlation analyses in microbial ecology

(2019) Alex Carr et al.   ISME Journal

Microbial food webs in hypertrophic fishponds: Omnivorous ciliate taxa are major protistan bacterivores

(2019) Karel Šimek et al.   LIMNOLOGY AND OCEANOGRAPHY

Using co‐occurrence network topology in assessing ecological stress in benthic macroinvertebrate communities

(2019) Ariel Levi Simons et al.   Ecology and Evolution

Annual Protist Community Dynamics in a Freshwater Ecosystem Undergoing Contrasted Climatic Conditions: The Saint-Charles River (Canada)

(2019) Perrine Cruaud et al.   Frontiers in Microbiology

Species co-occurrence networks: Can they reveal trophic and non-trophic interactions in ecological communities?

(2018) Mara A. Freilich et al.   ECOLOGY

Grazing impact and prey selectivity of picoplanktonic cells by mixotrophic flagellates in oligotrophic lakes

(2018) Marina Gerea et al.   HYDROBIOLOGIA

Keystone taxa as drivers of microbiome structure and functioning

(2018) Samiran Banerjee et al.   NATURE REVIEWS MICROBIOLOGY

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience

(2018) Dinka Mandakovic et al.   Scientific Reports

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

(2018) Sina M. Adl et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Soil bacterial networks are less stable under drought than fungal networks

(2018) Franciska T. de Vries et al.   Nature Communications

Uptake of dimethylsulphoniopropionate (DMSP) by the diatom Thalassiosira weissflogii: a model to investigate the cellular function of DMSP

(2018) K. Petrou et al.   BIOGEOCHEMISTRY

Quantifying long-term recurrence in planktonic microbial eukaryotes

(2018) Caterina R. Giner et al.   MOLECULAR ECOLOGY

Microbial diversity and ecological networks as indicators of environmental quality

(2017) Battle Karimi et al.   Environmental Chemistry Letters

Diversity and succession of pelagic microorganism communities in a newly restored Illinois River floodplain lake

(2017) Michael J. Lemke et al.   HYDROBIOLOGIA

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters

(2017) David M Needham et al.   ISME Journal

Using null models to infer microbial co-occurrence networks

(2017) Nora Connor et al.   PLoS One

Articulation points in complex networks

(2017) Liang Tian et al.   Nature Communications

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Abrupt stop of deep water turnover with lake warming: Drastic consequences for algal primary producers

(2017) Yana Yankova et al.   Scientific Reports

Merging DNA metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems

(2016) Darren M. Evans et al.   FUNCTIONAL ECOLOGY

Prolongation, deepening and warming of the metalimnion change habitat conditions of the harmful filamentous cyanobacterium Planktothrix rubescens in a prealpine lake

(2016) Yana Yankova et al.   HYDROBIOLOGIA

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

Trade-off between taxon diversity and functional diversity in European lake ecosystems

(2016) Lars Grossmann et al.   MOLECULAR ECOLOGY

Universal resilience patterns in complex networks

(2016) Jianxi Gao et al.   NATURE

How Structured Is the Entangled Bank? The Surprisingly Simple Organization of Multiplex Ecological Networks Leads to Increased Persistence and Resilience

(2016) Sonia Kéfi et al.   PLOS BIOLOGY

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Resistant Microbial Cooccurrence Patterns Inferred by Network Topology

(2015) Sari Peura et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomics meets time series analysis: unraveling microbial community dynamics

(2015) Karoline Faust et al.   CURRENT OPINION IN MICROBIOLOGY

Bacterioplankton community resilience to ocean acidification: evidence from microbial network analysis

(2015) Yu Wang et al.   ICES JOURNAL OF MARINE SCIENCE

Marked seasonality and high spatial variability of protist communities in shallow freshwater systems

(2015) Marianne Simon et al.   ISME Journal

Marine microbial community dynamics and their ecological interpretation

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

Network of Interactions Between Ciliates and Phytoplankton During Spring

(2015) Thomas Posch et al.   Frontiers in Microbiology

Cross-biome comparison of microbial association networks

(2015) Karoline Faust et al.   Frontiers in Microbiology

Swarm v2: highly-scalable and high-resolution amplicon clustering

(2015) Frédéric Mahé et al.   PeerJ

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

(2014) Francisco Dini-Andreote et al.   ISME Journal

Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems

(2014) Delphine Lallias et al.   ISME Journal

Parasite Fitness Traits Under Environmental Variation: Disentangling the Roles of a Chytrid’s Immediate Host and External Environment

(2014) Silke Van den Wyngaert et al.   MICROBIAL ECOLOGY

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Long-term changes in hypoxia and soluble reactive phosphorus in the hypolimnion of a large temperate lake: consequences of a climate regime shift

(2013) Ryan P. North et al.   GLOBAL CHANGE BIOLOGY

Beyond the Plankton Ecology Group (PEG) Model: Mechanisms Driving Plankton Succession

(2012) Ulrich Sommer et al.   Annual Review of Ecology Evolution and Systematics

Impacts of climate warming on the long-term dynamics of key fish species in 24 European lakes

(2012) Erik Jeppesen et al.   HYDROBIOLOGIA

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

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

Global insights into water resources, climate change and governance

(2012) R. Quentin Grafton et al.   Nature Climate Change

Harmful filamentous cyanobacteria favoured by reduced water turnover with lake warming

(2012) Thomas Posch et al.   Nature Climate Change

Phytoplankton Chytridiomycosis: Fungal Parasites of Phytoplankton and Their Imprints on the Food Web Dynamics

(2012) Télesphore Sime-Ngando   Frontiers in Microbiology

Fundamentals of Microbial Community Resistance and Resilience

(2012) Ashley Shade et al.   Frontiers in Microbiology

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Using species co-occurrence networks to assess the impacts of climate change

(2011) Miguel B. Araújo et al.   ECOGRAPHY

Rapid successions affect microbial N-acetyl-glucosamine uptake patterns during a lacustrine spring phytoplankton bloom

(2011) Ester M. Eckert et al.   ENVIRONMENTAL MICROBIOLOGY

Chytrid infections and diatom spring blooms: paradoxical effects of climate warming on fungal epidemics in lakes

(2011) BAS W. IBELINGS et al.   FRESHWATER BIOLOGY

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

Quantitative dominance of seasonally persistent filamentous cyanobacteria (Planktothrix rubescens) in the microbial assemblages of a temperate lake

(2010) Silke Van den Wyngaert et al.   LIMNOLOGY AND OCEANOGRAPHY

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

(2010) VIOLA NOLTE et al.   MOLECULAR ECOLOGY

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Conservation of species interaction networks

(2009) Jason M. Tylianakis et al.   BIOLOGICAL CONSERVATION

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Resistance, resilience, and redundancy in microbial communities

(2008) S. D. Allison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA