Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion

Methodological advances to study the diversity of soil protists and their functioning in soil food webs

(2018) Stefan Geisen et al.   APPLIED SOIL ECOLOGY

The need for standardisation: Exemplified by a description of the diversity, community structure and ecological indices of soil nematodes

(2018) B.S. Griffiths et al.   ECOLOGICAL INDICATORS

Soil protistology rebooted: 30 fundamental questions to start with

(2017) Stefan Geisen et al.   SOIL BIOLOGY & BIOCHEMISTRY

Possible mechanisms underlying abundance and diversity responses of nematode communities to plant diversity

(2017) Roeland Cortois et al.   Ecosphere

Belowground Plant–Herbivore Interactions Vary among Climate-Driven Range-Expanding Plant Species with Different Degrees of Novel Chemistry

(2017) Rutger A. Wilschut et al.   Frontiers in Plant Science

Organic farming practices result in compositional shifts in nematode communities that exceed crop-related changes

(2016) Casper W. Quist et al.   APPLIED SOIL ECOLOGY

Selecting cost effective and policy-relevant biological indicators for European monitoring of soil biodiversity and ecosystem function

(2016) B.S. Griffiths et al.   ECOLOGICAL INDICATORS

Thorough high-throughput sequencing analyses unravels huge diversities of soil parasitic protists

(2016) Stefan Geisen   ENVIRONMENTAL MICROBIOLOGY

A new primer set for DNA metabarcoding of soil Metazoa

(2016) E. Capra et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Do tropical rain forest soils have greater nematode diversity than High Arctic tundra? A metagenetic comparison of Malaysia and Svalbard

(2016) Dorsaf Kerfahi et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Interspecific differences in nematode control between range-expanding plant species and their congeneric natives

(2016) R.A. Wilschut et al.   SOIL BIOLOGY & BIOCHEMISTRY

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Top-down control of root-feeding nematodes in range-expanding and congeneric native plant species

(2015) Maria Viketoft et al.   BASIC AND APPLIED ECOLOGY

Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa

(2015) S. Geisen et al.   MOLECULAR ECOLOGY

A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual

(2015) Sebastian Eves-van den Akker et al.   MOLECULAR ECOLOGY

Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology

(2015) James I. Prosser   NATURE REVIEWS MICROBIOLOGY

Plant-feeding nematodes in coastal sand dunes: occurrence, host specificity and effects on plant growth

(2015) E. P. Brinkman et al.   PLANT AND SOIL

Determination of the optimal soil sample size to accurately characterise nematode communities in soil

(2015) Lea Wiesel et al.   SOIL BIOLOGY & BIOCHEMISTRY

Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages

(2015) Carola Gómez-Rodríguez et al.   Methods in Ecology and Evolution

High-throughput sequencing of nematode communities from total soil DNA extractions

(2015) Rumakanta Sapkota et al.   BMC ECOLOGY

Discrimination of Plant-Parasitic Nematodes from Complex Soil Communities Using Ecometagenetics

(2014) Dorota L. Porazinska et al.   PHYTOPATHOLOGY

Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia

(2014) Luisa W. Hugerth et al.   PLoS One

Plant invasions from a belowground nematocentric perspective

(2014) Dorota L. Porazinska et al.   SOIL BIOLOGY & BIOCHEMISTRY

High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure

(2013) B. J. Darby et al.   MOLECULAR ECOLOGY

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

Climate Change, Aboveground-Belowground Interactions, and Species' Range Shifts

(2012) Wim H. Van der Putten   Annual Review of Ecology Evolution and Systematics

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

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

Transgenic Potatoes for Potato Cyst Nematode Control Can Replace Pesticide Use without Impact on Soil Quality

(2012) Jayne Green et al.   PLoS One

SSU Ribosomal DNA-Based Monitoring of Nematode Assemblages Reveals Distinct Seasonal Fluctuations within Evolutionary Heterogeneous Feeding Guilds

(2012) Mariëtte T. W. Vervoort et al.   PLoS One

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

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 native and exotic range-expanding plant species on taxonomic and functional composition of nematodes in the soil food web

(2011) Elly Morriën et al.   OIKOS

A novel molecular approach for rapid assessment of soil nematode assemblages - variation, validation and potential applications

(2011) Suzanne Donn et al.   Methods in Ecology and Evolution

Ecology of Plant and Free-Living Nematodes in Natural and Agricultural Soil

(2010) Deborah A. Neher   Annual Review of Phytopathology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions

(2010) Anke Behnke et al.   ENVIRONMENTAL MICROBIOLOGY

A comparison of molecular methods for monitoring soil nematodes and their use as biological indicators

(2010) X.Y. Chen et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Ecometagenetics confirm high tropical rainforest nematode diversity

(2010) DOROTA L. PORAZINSKA et al.   MOLECULAR ECOLOGY

Selecting biological indicators for monitoring soils: A framework for balancing scientific and technical opinion to assist policy development

(2009) Karl Ritz et al.   ECOLOGICAL INDICATORS

Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure

(2009) DOROTA L. PORAZINSKA et al.   Molecular Ecology Resources

Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity

(2009) DOROTA L. PORAZINSKA et al.   Molecular Ecology Resources

Helkesimastix marina n. sp. (Cercozoa: Sainouroidea superfam. n.) a Gliding Zooflagellate of Novel Ultrastructure and Unusual Ciliary Behaviour

(2009) Thomas Cavalier-Smith et al.   PROTIST

Alien species in a warmer world: risks and opportunities

(2009) Gian-Reto Walther et al.   TRENDS IN ECOLOGY & EVOLUTION

Successful range-expanding plants experience less above-ground and below-ground enemy impact

(2008) Tim Engelkes et al.   NATURE