Changes in soil microbial communities in post mine ecological restoration: Implications for monitoring using high throughput DNA sequencing

Invertebrate DNA metabarcoding reveals changes in communities across mine site restoration chronosequences

(2019) Kristen Fernandes et al.   RESTORATION ECOLOGY

International principles and standards for the practice of ecological restoration. Second edition

(2019) George D. Gann et al.   RESTORATION ECOLOGY

High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration

(2018) DongFeng Yan et al.   BIOLOGICAL CONSERVATION

Effects of heavy metal concentrations on biological activity of soil micro-organisms

(2018) M. Šmejkalová et al.   PLANT SOIL AND ENVIRONMENT

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

(2018) Rolf Henrik Nilsson et al.   NUCLEIC ACIDS RESEARCH

How Soil Biota Drive Ecosystem Stability

(2018) Gaowen Yang et al.   TRENDS IN PLANT SCIENCE

Impact of no tillage vs. conventional tillage on the soil bacterial community structure in a winter wheat cropping succession in northern China

(2017) Wenyi Dong et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Using metagenomics to show the efficacy of forest restoration in the New Jersey Pine Barrens

(2017) William D. Eaton et al.   GENOME

Revegetation rewilds the soil bacterial microbiome of an old field

(2017) Nicholas J. C. Gellie et al.   MOLECULAR ECOLOGY

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Microbial Functional Capacity Is Preserved Within Engineered Soil Formulations Used In Mine Site Restoration

(2017) Deepak Kumaresan et al.   Scientific Reports

Restoration of tropical peat soils: The application of soil microbiology for monitoring the success of the restoration process

(2016) Yuana Nurulita et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Tillage effects on soil microbial biomass, SOM mineralization and enzyme activity in a semi-arid Calcixerepts

(2016) Vida Kabiri et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Spatial scale drives patterns in soil bacterial diversity

(2016) Sarah L. O'Brien et al.   ENVIRONMENTAL MICROBIOLOGY

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

(2016) Nhu H. Nguyen et al.   Fungal Ecology

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

A framework for the practical science necessary to restore sustainable, resilient, and biodiverse ecosystems

(2016) Ben P. Miller et al.   RESTORATION ECOLOGY

Soil quality indicators to assess functionality of restored soils in degraded semiarid ecosystems

(2016) Miriam Muñoz-Rojas et al.   RESTORATION ECOLOGY

obitools: aunix-inspired software package for DNA metabarcoding

(2015) Frédéric Boyer et al.   Molecular Ecology Resources

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

(2015) Jonathan W. Leff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Soil microbial community variation correlates most strongly with plant species identity, followed by soil chemistry, spatial location and plant genus

(2015) J. H. Burns et al.   AoB Plants

From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows

(2015) Dáithí C. Murray et al.   PLoS One

Temporal variability in soil microbial communities across land-use types

(2013) Christian L Lauber et al.   ISME Journal

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

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

Hurdles and Opportunities for Landscape-Scale Restoration

(2013) M. H. M. Menz et al.   SCIENCE

Cross-Site Soil Microbial Communities under Tillage Regimes: Fungistasis and Microbial Biomarkers

(2012) Timo P. Sipilä et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

(2012) Katarina Ihrmark et al.   FEMS MICROBIOLOGY ECOLOGY

METAGENassist: a comprehensive web server for comparative metagenomics

(2012) D. Arndt et al.   NUCLEIC ACIDS RESEARCH

Increasing Soil Water Retention with Native-Sourced Mulch Improves Seedling Establishment in Postmine Mediterranean Sandy Soils

(2012) Stephen M. Benigno et al.   RESTORATION ECOLOGY

Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration

(2011) Natasha C. Banning et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The ecological coherence of high bacterial taxonomic ranks

(2010) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Miquel De Cáceres et al.   ECOLOGY

Bacterial communities are more dependent on soil type than fertilizer type, but the reverse is true for fungal communities

(2009) Chika Suzuki et al.   SOIL SCIENCE AND PLANT NUTRITION

Soil CO2 respiration: Comparison of chemical titration, CO2 IRGA analysis and the Solvita gel system

(2008) R.L. Haney et al.   RENEWABLE AGRICULTURE AND FOOD SYSTEMS

Recovery of soil organic matter, organic matter turnover and nitrogen cycling in a post-mining forest rehabilitation chronosequence

(2008) N.C. Banning et al.   SOIL BIOLOGY & BIOCHEMISTRY

Ectomycorrhizal fungal communities of rehabilitated bauxite mines and adjacent, natural jarrah forest in Western Australia

(2007) M. Glen et al.   FOREST ECOLOGY AND MANAGEMENT