Emergent properties of microbial activity in heterogeneous soil microenvironments: different research approaches are slowly converging, yet major challenges remain

PC Baveye, W Otten, A Kravchenko… - Frontiers in …, 2018 - frontiersin.org
Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data
showing that the bulk, macroscopic parameters (eg, granulometry, pH, soil organic matter …

Beyond microbial diversity for predicting soil functions: A mini review

P Nannipieri, J Ascher-Jenull, MT Ceccherini… - Pedosphere, 2020 - Elsevier
Since the advent of sequencing technologies, the determination of microbial diversity to
predict microbial functions, which are the major determinants of soil functions, has become a …

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

P Carini, PJ Marsden, JW Leff, EE Morgan… - Nature …, 2016 - nature.com
Extracellular DNA from dead microorganisms can persist in soil for weeks to years 1–3.
Although it is implicitly assumed that the microbial DNA recovered from soil predominantly …

[PDF][PDF] Assessment of fecal DNA extraction protocols for metagenomic studies

F Yang, J Sun, H Luo, H Ren, H Zhou, Y Lin… - …, 2020 - academic.oup.com
Background Shotgun metagenomic sequencing has improved our understanding of the
human gut microbiota. Various DNA extraction methods have been compared to find …

Impacts of DNA extraction and PCR on DNA metabarcoding estimates of soil biodiversity

A Dopheide, D Xie, TR Buckley… - Methods in Ecology …, 2019 - Wiley Online Library
Soils are ubiquitous and important components of terrestrial ecosystems, richly populated
with diverse organisms with important ecological roles. DNA metabarcoding is a promising …

Architecture of soil microaggregates: Advanced methodologies to explore properties and functions

W Amelung, N Tang, N Siebers… - Journal of Plant …, 2024 - Wiley Online Library
The functions of soils are intimately linked to their three‐dimensional pore space and the
associated biogeochemical interfaces, mirrored in the complex structure that developed …

Extracellular DNA in environmental samples: Occurrence, extraction, quantification, and impact on microbial biodiversity assessment

S Bairoliya, J Koh Zhi Xiang, B Cao - Applied and Environmental …, 2022 - Am Soc Microbiol
Environmental DNA, ie, DNA extracted directly from environmental samples, has been used
to understand microbial communities in the environment and to monitor contemporary …

Quantification of nitrogen cycle functional genes from viable archaea and bacteria in paddy soil

A Manfredini, E Malusà, F Pinzari… - Journal of Applied …, 2023 - academic.oup.com
Aims One of the main challenges of culture-independent soil microbiology is distinguishing
the microbial community's viable fraction from dead matter. Propidium monoazide (PMA) …

The seagrass holobiont: what we know and what we still need to disclose for its possible use as an ecological indicator

C Conte, A Rotini, L Manfra, MM D'Andrea, G Winters… - Water, 2021 - mdpi.com
Microbes and seagrass establish symbiotic relationships constituting a functional unit called
the holobiont that reacts as a whole to environmental changes. Recent studies have shown …

The use of extracellular DNA as a proxy for specific microbial activity

M Nagler, SM Podmirseg, GW Griffith, H Insam… - Applied Microbiology …, 2018 - Springer
The ubiquity and relevance of extracellular DNA (exDNA) are well-known and increasingly
gaining importance in many fields of application such as medicine and environmental …