Microbial interactions within multiple-strain biological control agents impact soil-borne plant disease

B Niu, W Wang, Z Yuan, RR Sederoff… - Frontiers in …, 2020 - frontiersin.org
Major losses of crop yield and quality caused by soil-borne plant diseases have long
threatened the ecology and economy of agriculture and forestry. Biological control using …

Benchmarking metagenomics tools for taxonomic classification

HY Simon, KJ Siddle, DJ Park, PC Sabeti - Cell, 2019 - cell.com
Metagenomic sequencing is revolutionizing the detection and characterization of microbial
species, and a wide variety of software tools are available to perform taxonomic …

Reduction of microbial diversity in grassland soil is driven by long-term climate warming

L Wu, Y Zhang, X Guo, D Ning, X Zhou, J Feng… - Nature …, 2022 - nature.com
Anthropogenic climate change threatens ecosystem functioning. Soil biodiversity is essential
for maintaining the health of terrestrial systems, but how climate change affects the richness …

High-throughput microbial culturomics using automation and machine learning

Y Huang, RU Sheth, S Zhao, LA Cohen… - Nature …, 2023 - nature.com
Pure bacterial cultures remain essential for detailed experimental and mechanistic studies in
microbiome research, and traditional methods to isolate individual bacteria from complex …

Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir

Y Mo, F Peng, X Gao, P Xiao, R Logares, E Jeppesen… - Microbiome, 2021 - Springer
Background Freshwater salinization may result in significant changes of microbial
community composition and diversity, with implications for ecosystem processes and …

[HTML][HTML] Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites

D Bogaert, GJ Van Beveren, EM de Koff, PL Parga… - Cell Host & Microbe, 2023 - cell.com
Early-life microbiota seeding and subsequent development is crucial to future health.
Cesarean-section (CS) birth, as opposed to vaginal delivery, affects early mother-to-infant …

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

JS Johnson, DJ Spakowicz, BY Hong… - Nature …, 2019 - nature.com
The 16S rRNA gene has been a mainstay of sequence-based bacterial analysis for
decades. However, high-throughput sequencing of the full gene has only recently become a …

Primer, pipelines, parameters: issues in 16S rRNA gene sequencing

I Abellan-Schneyder, MS Matchado, S Reitmeier… - Msphere, 2021 - Am Soc Microbiol
Short-amplicon 16S rRNA gene sequencing is currently the method of choice for studies
investigating microbiomes. However, comparative studies on differences in procedures are …

Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher …

D Vu, M Groenewald, M De Vries… - Studies in …, 2019 - ingentaconnect.com
Species identification lies at the heart of biodiversity studies that has in recent years
favoured DNA-based approaches. Microbial Biological Resource Centres are a rich source …

The global-scale distributions of soil protists and their contributions to belowground systems

AM Oliverio, S Geisen, M Delgado-Baquerizo… - Science …, 2020 - science.org
Protists are ubiquitous in soil, where they are key contributors to nutrient cycling and energy
transfer. However, protists have received far less attention than other components of the soil …