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Title: Long- and short-term soil storage methods other than freezing can be useful for DNA-based microbial community analysis

Journal Article · · Soil Biology and Biochemistry

Sponsoring Organization:
USDOE
OSTI ID:
2287700
Journal Information:
Soil Biology and Biochemistry, Journal Name: Soil Biology and Biochemistry Vol. 191 Journal Issue: C; ISSN 0038-0717
Publisher:
ElsevierCopyright Statement
Country of Publication:
United Kingdom
Language:
English

References (68)

Arbuscular Mycorrhizal Tree Communities Have Greater Soil Fungal Diversity and Relative Abundances of Saprotrophs and Pathogens than Ectomycorrhizal Tree Communities journal January 2022
Best practices in metabarcoding of fungi: From experimental design to results journal April 2022
Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing journal October 2016
Impact of short-term storage temperature on determination of microbial community composition and abundance in aerated forest soil and anoxic pond sediment samples journal December 2014
Time in a bottle: Use of soil archives for understanding long‐term soil change journal February 2022
Plant-soil feedback: experimental approaches, statistical analyses and ecological interpretations: Design and analysis of feedback experiments journal July 2010
Variation in hyphal production rather than turnover regulates standing fungal biomass in temperate hardwood forests journal February 2021
Variation Partitioning of Species data Matrices: Estimation and Comparison of Fractions journal October 2006
Phosphorus cycling in deciduous forest soil differs between stands dominated by ecto‐ and arbuscular mycorrhizal trees journal October 2015
Rare taxa maintain the stability of crop mycobiomes and ecosystem functions journal October 2020
Effects of air-drying and freezing on phosphorus fractions in soils with different organic matter contents journal May 2011
Patient propagules: Do soil archives preserve the legacy of fungal and prokaryotic communities? journal August 2020
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications journal October 2018
ITS alchemy: On the use of ITS as a DNA marker in fungal ecology journal October 2023
Barcoded NS31/AML2 Primers for Sequencing of Arbuscular Mycorrhizal Communities in Environmental Samples journal August 2017
Considerations in the storage of soil samples for enzyme activity analysis journal November 2012
Impact of sequencing depth on the characterization of the microbiome and resistome journal April 2018
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy journal June 2007
Tree mycorrhizal type predicts within-site variability in the storage and distribution of soil organic matter journal April 2018
Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review journal January 2013
Comparison of temperature effects on soil respiration and bacterial and fungal growth rates journal March 2005
Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples journal November 2021
Emerging biological archives can reveal ecological and climatic change in Antarctica journal September 2022
Soil inoculation method determines the strength of plant–soil interactions journal December 2012
Soil Drying and Rewetting, or Freezing and Thawing, Affects Soil Solution Composition journal March 1992
Long-term seasonal and interannual variability of marine aerobic anoxygenic photoheterotrophic bacteria journal March 2019
The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota) journal June 2010
Coupling of plant and mycorrhizal fungal diversity: its occurrence, relevance, and possible implications under global change journal January 2022
Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies journal February 2014
Patterns of Species Diversity journal November 1965
The mycorrhizal-associated nutrient economy: a new framework for predicting carbon-nutrient couplings in temperate forests journal April 2013
Predicting Plant-Soil Feedback in the Field: Meta-Analysis Reveals That Competition and Environmental Stress Differentially Influence PSF journal June 2020
Heterogeneity in arbuscular mycorrhizal fungal communities may contribute to inconsistent plant-soil feedback in a Neotropical forest journal August 2018
hillR: taxonomic, functional, and phylogenetic diversity and similarity through Hill Numbers journal November 2018
The microbial rare biosphere: current concepts, methods and ecological principles journal November 2020
Soil bacterial networks are less stable under drought than fungal networks journal August 2018
Core microbiota drive functional stability of soil microbiome in reforestation ecosystems journal December 2021
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies journal August 2012
Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples: Influence of short-term storage conditions on microbiota journal March 2010
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools journal November 2012
Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing journal July 2012
Defining and quantifying the core microbiome: Challenges and prospects journal December 2021
Climate-driven convergent evolution in riparian ecosystems on sky islands journal February 2023
Concatenation of paired-end reads improves taxonomic classification of amplicons for profiling microbial communities journal October 2021
Rapid shifts in plant distribution with recent climate change journal August 2008
Global projections of the soil microbiome in the Anthropocene journal February 2021
Dominant role of abundant rather than rare bacterial taxa in maintaining agro-soil microbiomes under environmental disturbances journal November 2019
Effect of soil sample preservation, compared to the effect of other environmental variables, on bacterial and eukaryotic diversity journal March 2009
The chosen few—variations in common and rare soil bacteria across biomes journal May 2021
Sample storage for soil enzyme activity and bacterial community profiles journal April 2010
Teasing apart plant community responses to N enrichment: the roles of resource limitation, competition and soil microbes journal August 2016
The subzero microbiome: microbial activity in frozen and thawing soils journal April 2016
Sample storage conditions alter colonisation structures of arbuscular mycorrhizal fungi and, particularly, fine root endophyte journal April 2016
Partitioning Diversity into Independent Alpha and beta Components journal October 2007
Air-drying and long time preservation of soil do not significantly impact microbial community composition and structure journal June 2021
The preservation of microbial DNA in archived soils of various genetic types journal March 2017
Evolutionary ecology of plant-microbe interactions: soil microbial structure alters selection on plant traits journal June 2011
Decay rates of leaf litters from arbuscular mycorrhizal trees are more sensitive to soil effects than litters from ectomycorrhizal trees journal October 2015
Forest tree growth is linked to mycorrhizal fungal composition and function across Europe journal January 2022
Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results journal March 2020
Diversity and Evenness: A Unifying Notation and Its Consequences journal March 1973
A meta-analysis of context-dependency in plant response to inoculation with mycorrhizal fungi journal March 2010
Divergence of species responses to climate change journal May 2017
Identifying ecological and evolutionary research targets and risks in climate change studies to break barriers to broad inference journal December 2023
Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples journal July 2013
Soil microbiomes and climate change journal October 2019
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 journal December 2014
Coming up short: Identifying substrate and geographic biases in fungal sequence databases journal December 2018