A bacterial index to estimate lake trophic level: National scale validation

A step towards the validation of bacteria biotic indices using DNA metabarcoding for benthic monitoring

(2021) Eva Aylagas et al.   Molecular Ecology Resources

Investigating variability in microbial community composition in replicate environmental DNA samples down lake sediment cores

(2021) John K. Pearman et al.   PLoS One

Widespread deoxygenation of temperate lakes

(2021) Stephen F. Jane et al.   NATURE

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

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

Reference and current Trophic Level Index of New Zealand lakes: benchmarks to inform lake management and assessment

(2020) Jonathan M. Abell et al.   NEW ZEALAND JOURNAL OF MARINE AND FRESHWATER RESEARCH

Local factors drive bacterial and microeukaryotic community composition in lake surface sediment collected across an altitudinal gradient

(2020) John K Pearman et al.   FEMS MICROBIOLOGY ECOLOGY

Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes

(2020) Larissa Frühe et al.   MOLECULAR ECOLOGY

Ecosystems monitoring powered by environmental genomics: a review of current strategies with an implementation roadmap

(2020) Tristan Cordier et al.   MOLECULAR ECOLOGY

A large-scale assessment of lakes reveals a pervasive signal of land use on bacterial communities

(2020) S. A. Kraemer et al.   ISME Journal

The application of stressor–response relationships in the management of lake eutrophication

(2020) Marc Schallenberg   Inland Waters

Monitoring the ecological status of rivers with diatom eDNA metabarcoding: a comparison of taxonomic markers and analytical approaches for the inference of a molecular diatom index

(2020) Laure Apothéloz‐Perret‐Gentil et al.   MOLECULAR ECOLOGY

Modeling the ecological status response of rivers to multiple stressors using machine learning: A comparison of environmental DNA metabarcoding and morphological data

(2020) Juntao Fan et al.   WATER RESEARCH

Ground-truthing of a fish-based environmental DNA metabarcoding method for assessing the quality of lakes

(2019) Jianlong Li et al.   JOURNAL OF APPLIED ECOLOGY

Bacterial community and eutrophic index analysis of the East Lake

(2019) Bin Ji et al.   ENVIRONMENTAL POLLUTION

Under the radar: long-term perspectives on ecological changes in lakes

(2019) John P. Smol   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Quantifying the Extent of Anthropogenic Eutrophication of Lakes at a National Scale in New Zealand

(2019) Jonathan M. Abell et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Patterns and assembly processes of planktonic and sedimentary bacterial community differ along a trophic gradient in freshwater lakes

(2019) Jin Zeng et al.   ECOLOGICAL INDICATORS

Neonicotinoids disrupt aquatic food webs and decrease fishery yields

(2019) Masumi Yamamuro et al.   SCIENCE

Sediment bacterial communities associated with environmental factors in Intermittently Closed and Open Lakes and Lagoons (ICOLLs)

(2019) Giulia Filippini et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Diatom metabarcoding applied to large scale monitoring networks: Optimization of bioinformatics strategies using Mothur software

(2019) Sinziana F. Rivera et al.   ECOLOGICAL INDICATORS

eDNA metabarcoding in zooplankton improves the ecological status assessment of aquatic ecosystems

(2019) Jianghua Yang et al.   ENVIRONMENT INTERNATIONAL

Heterogeneity of epiphytic diatoms in shallow lakes: Implications for lake monitoring

(2019) Luisa Riato et al.   ECOLOGICAL INDICATORS

Development and preliminary validation of a multi-trophic metabarcoding biotic index for monitoring benthic organic enrichment

(2018) Nigel Keeley et al.   ECOLOGICAL INDICATORS

The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems

(2018) Jan Pawlowski et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive

(2018) Daniel Hering et al.   WATER RESEARCH

Metabarcoding of lake benthic diatoms: from structure assemblages to ecological assessment

(2017) S. F. Rivera et al.   HYDROBIOLOGIA

Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle

(2017) K. Dimitri Kits et al.   NATURE

Contaminants of emerging concern in tributaries to the Laurentian Great Lakes: II. Biological consequences of exposure

(2017) Linnea M. Thomas et al.   PLoS One

Characterization of sediment bacterial communities in plain lakes with different trophic statuses

(2017) Wei Huang et al.   MicrobiologyOpen

Recovery of lakes and coastal marine ecosystems from eutrophication: A global meta-analysis

(2016) Michelle L. McCrackin et al.   LIMNOLOGY AND OCEANOGRAPHY

First evaluation of foraminiferal metabarcoding for monitoring environmental impact from an offshore oil drilling site

(2016) Olivier Laroche et al.   MARINE ENVIRONMENTAL RESEARCH

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Water quality in New Zealand rivers: current state and trends

(2016) ST Larned et al.   NEW ZEALAND JOURNAL OF MARINE AND FRESHWATER RESEARCH

Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity

(2015) Philip Francis Thomsen et al.   BIOLOGICAL CONSERVATION

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

(2015) Eric Capo et al.   MICROBIAL ECOLOGY

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems

(2015) Franck Lejzerowicz et al.   Scientific Reports

Long livestock farming history and human landscape shaping revealed by lake sediment DNA

(2014) Charline Giguet-Covex et al.   Nature Communications

Eutrophication reverses whole-lake carbon budgets

(2014) Felipe Pacheco et al.   Inland Waters

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Looking forward through the past: identification of 50 priority research questions in palaeoecology

(2013) Alistair W. R. Seddon et al.   JOURNAL OF ECOLOGY

Relationships between land use and nitrogen and phosphorus in New Zealand lakes

(2013) Jonathan M. Abell et al.   MARINE AND FRESHWATER RESEARCH

Marine monitoring during an economic crisis: The cure is worse than the disease

(2013) Ángel Borja et al.   MARINE POLLUTION BULLETIN

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Catchment land use and trophic state impacts on phytoplankton composition: a case study from the Rotorua lakes’ district, New Zealand

(2012) Wendy J. Paul et al.   HYDROBIOLOGIA

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

The dilemma of controlling cultural eutrophication of lakes

(2012) D. W. Schindler   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Lakes as sentinels of climate change

(2011) Rita Adrian et al.   LIMNOLOGY AND OCEANOGRAPHY

Lakes and reservoirs as regulators of carbon cycling and climate

(2011) Lars J. Tranvik et al.   LIMNOLOGY AND OCEANOGRAPHY

Cogs in the endless machine: Lakes, climate change and nutrient cycles: A review

(2011) Brian Moss   SCIENCE OF THE TOTAL ENVIRONMENT

Associations between species and groups of sites: indices and statistical inference

(2009) Miquel De Cáceres et al.   ECOLOGY

Lakes and streams as sentinels of environmental change in terrestrial and atmospheric processes

(2008) Craig E Williamson et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Sediment and nutrient accumulation rates in sediments of twelve New Zealand lakes: influence of lake morphology, catchment characteristics and trophic state

(2008) Dennis Trolle et al.   MARINE AND FRESHWATER RESEARCH

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE