Watershed‐scale liming reveals the short‐ and long‐term effects of pH on the forest soil microbiome and carbon cycling

Microbial community shifts correspond with suppression of decomposition 25 years after liming of acidic forest soils

(2022) Bhavya Sridhar et al.   GLOBAL CHANGE BIOLOGY

A group of ectomycorrhizal fungi restricts organic matter accumulation in boreal forest

(2021) Björn D. Lindahl et al.   ECOLOGY LETTERS

Community Organization and Metagenomics of Bacterial Assemblages Across Local Scale pH Gradients in Northern Forest Soils

(2020) Joseph B. Yavitt et al.   MICROBIAL ECOLOGY

Microbial Community Succession and Response to Environmental Variables During Cow Manure and Corn Straw Composting

(2019) Qingxin Meng et al.   Frontiers in Microbiology

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Testing the dependence of microbial growth and carbon use efficiency on nitrogen availability, pH, and organic matter quality

(2019) Alex Silva-Sánchez et al.   SOIL BIOLOGY & BIOCHEMISTRY

Using metagenomics to reveal landscape scale patterns of denitrifiers in a montane forest ecosystem

(2019) C. Armanda Roco et al.   SOIL BIOLOGY & BIOCHEMISTRY

Beyond clay: towards an improved set of variables for predicting soil organic matter content

(2018) Craig Rasmussen et al.   BIOGEOCHEMISTRY

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Novel bacterial lineages associated with boreal moss species

(2018) Hannah Holland-Moritz et al.   ENVIRONMENTAL MICROBIOLOGY

Interactions among plants, bacteria, and fungi reduce extracellular enzyme activities under long-term N fertilization

(2018) Joseph E. Carrara et al.   GLOBAL CHANGE BIOLOGY

Soil pH mediates the balance between stochastic and deterministic assembly of bacteria

(2018) Binu M. Tripathi et al.   ISME Journal

Decomposer food web in a deciduous forest shows high share of generalist microorganisms and importance of microbial biomass recycling

(2018) Ruben López-Mondéjar et al.   ISME Journal

Comparison of Actinomycete Community Composition on the Surface and Inside of Japanese Black Pine (Pinus thunbergii) Tree Roots Colonized by the Ectomycorrhizal Fungus Cenococcum geophilum

(2018) Shoyo Sakoda et al.   MICROBIAL ECOLOGY

A global atlas of the dominant bacteria found in soil

(2018) Manuel Delgado-Baquerizo et al.   SCIENCE

Following the terrestrial tracks of Caulobacter - redefining the ecology of a reputed aquatic oligotroph

(2018) Roland C. Wilhelm   ISME Journal

Land use driven change in soil pH affects microbial carbon cycling processes

(2018) Ashish A. Malik et al.   Nature Communications

Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from the Firmicutes phylum

(2018) Craig R. Anderson et al.   PeerJ

Assessing fungal contributions to cellulose degradation in soil by using high-throughput stable isotope probing

(2018) Chantal Koechli et al.   SOIL BIOLOGY & BIOCHEMISTRY

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Using community trait-distributions to assign microbial responses to pH changes and Cd in forest soils treated with wood ash

(2017) Carla Cruz-Paredes et al.   SOIL BIOLOGY & BIOCHEMISTRY

Swine manure and quicklime have different impacts on chemical properties and composition of bacterial communities of an acidic soil

(2016) Weibing Xun et al.   APPLIED SOIL ECOLOGY

The shift of the microbial community in activated sludge with calcium treatment and its implication to sludge settleability

(2016) Chengchen Ye et al.   BIORESOURCE TECHNOLOGY

Fine root biomass declined in response to restoration of soil calcium in a northern hardwood forest

(2016) Timothy J. Fahey et al.   CANADIAN JOURNAL OF FOREST RESEARCH

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 new look at liming as an approach to accelerate recovery from acidic deposition effects

(2016) Gregory B. Lawrence et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum

(2016) Martina Peter et al.   Nature Communications

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Water hardness influences Flavobacterium columnare pathogenesis in channel catfish

(2015) David L. Straus et al.   AQUACULTURE

Calcium precipitate induced aerobic granulation

(2015) Chunli Wan et al.   BIORESOURCE TECHNOLOGY

Distribution and isolation of strains belonging to the order Solirubrobacterales

(2015) Tamae Seki et al.   JOURNAL OF ANTIBIOTICS

The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity

(2015) Anastasia Bragina et al.   MOLECULAR ECOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

Evaluating the effects of liming and wood-ash treatment on forest ecosystems through systematic meta-analysis

(2014) Carolyn Reid et al.   CANADIAN JOURNAL OF FOREST RESEARCH

Soil pH Determines Microbial Diversity and Composition in the Park Grass Experiment

(2014) Kateryna Zhalnina et al.   MICROBIAL ECOLOGY

Soil Chemical Dynamics after Calcium Silicate Addition to a Northern Hardwood Forest

(2014) Chris E. Johnson et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

Host-associated bacterial taxa from Chlorobi, Chloroflexi, GN02, Synergistetes, SR1, TM7, and WPS-2 Phyla/candidate divisions

(2014) Anuj Camanocha et al.   Journal of Oral Microbiology

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

The Paint Pots, Kootenay National Park, Canada — a natural acid spring analogue for Mars

(2013) Stephen E. Grasby et al.   CANADIAN JOURNAL OF EARTH SCIENCES

Forest liming increases forest floor carbon and nitrogen stocks in a mixed hardwood forest

(2013) April M. Melvin et al.   ECOLOGICAL APPLICATIONS

Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm

(2013) Andrea K. Bartram et al.   FEMS MICROBIOLOGY ECOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

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

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

Fungal community on decomposing leaf litter undergoes rapid successional changes

(2012) Jana Voříšková et al.   ISME Journal

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial control over carbon cycling in soil

(2012) Joshua P. Schimel et al.   Frontiers in Microbiology

Soil bacterial communities of a calcium-supplemented and a reference watershed at the Hubbard Brook Experimental Forest (HBEF), New Hampshire, USA

(2011) Ganapathi Sridevi et al.   FEMS MICROBIOLOGY ECOLOGY

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Soil bacterial and fungal communities across a pH gradient in an arable soil

(2010) Johannes Rousk et al.   ISME Journal

The genus Actinoallomurus and some of its metabolites

(2010) Roberta Pozzi et al.   JOURNAL OF ANTIBIOTICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

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

Forest liming durably impact the communities of ectomycorrhizas and fungal epigeous fruiting bodies

(2009) François Rineau et al.   ANNALS OF FOREST SCIENCE

Contrasting Soil pH Effects on Fungal and Bacterial Growth Suggest Functional Redundancy in Carbon Mineralization

(2009) J. Rousk et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

(2009) Miquel De Cáceres et al.   ECOLOGY

Belowground ectomycorrhizal fungal communities respond to liming in three southern Swedish coniferous forest stands

(2009) Rasmus Kjøller et al.   FOREST ECOLOGY AND MANAGEMENT

Transfer of Actinomadura spadix Nonomura and Ohara 1971 to Actinoallomurus spadix gen. nov., comb. nov., and description of Actinoallomurus amamiensis sp. nov., Actinoallomurus caesius sp. nov., Actinoallomurus coprocola sp. nov., Actinoallomurus fulvus sp. nov., Actinoallomurus iriomotensis sp. nov., Actinoallomurus luridus sp. nov., Actinoallomurus purpureus sp. nov. and Actinoallomurus yoronensis sp. nov.

(2009) T. Tamura et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Does forest liming impact the enzymatic profiles of ectomycorrhizal communities through specialized fungal symbionts?

(2009) François Rineau et al.   MYCORRHIZA

Soil carbon stocks in experimental mesocosms are dependent on the rate of labile carbon, nitrogen and phosphorus inputs to soils

(2008) M. A. Bradford et al.   FUNCTIONAL ECOLOGY

Germination and infectivity of ectomycorrhizal fungal spores in relation to their ecological traits during primary succession

(2008) Takahide A. Ishida et al.   NEW PHYTOLOGIST