Integrating viral metagenomics into an ecological framework

P Sommers, A Chatterjee, A Varsani… - Annual review of …, 2021 - annualreviews.org
Viral metagenomics has expanded our knowledge of the ecology of uncultured viruses,
within both environmental (eg, terrestrial and aquatic) and host-associated (eg, plants and …

Prospects for multi-omics in the microbial ecology of water engineering

EA McDaniel, SA Wahl, S Ishii, A Pinto, R Ziels… - Water Research, 2021 - Elsevier
Advances in high-throughput sequencing technologies and bioinformatics approaches over
almost the last three decades have substantially increased our ability to explore …

[HTML][HTML] A critical perspective on interpreting amplicon sequencing data in soil ecological research

LV Alteio, J Séneca, A Canarini, R Angel… - Soil Biology and …, 2021 - Elsevier
Microbial community analysis via marker gene amplicon sequencing has become a routine
method in the field of soil research. In this perspective, we discuss technical challenges and …

Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments

MM Lynes, V Krukenberg, ZJ Jay, AJ Kohtz… - ISME …, 2023 - academic.oup.com
Metagenomic studies on geothermal environments have been central in recent discoveries
on the diversity of archaeal methane and alkane metabolism. Here, we investigated …

Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane

LJ McKay, HJ Smith, EP Barnhart… - The ISME …, 2022 - academic.oup.com
Microbial metabolisms and interactions that facilitate subsurface conversions of recalcitrant
carbon to methane are poorly understood. We deployed an in situ enrichment device in a …

Earthworm stocking density regulates microbial community structure and fatty acid profiles during vermicomposting of lignocellulosic waste: unraveling the microbe …

J Devi, R Pegu, H Mondal, R Roy… - Bioresource …, 2023 - Elsevier
Earthworm-induced microbial enrichment is the key to success in vermitechnology, yet the
influence of initial earthworm stocking density on microbial community profiles in vermibeds …

Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment

ES Frates, RL Spietz, MR Silverstein, P Girguis… - Frontiers in …, 2023 - frontiersin.org
Salt marshes are dynamic, highly productive ecosystems positioned at the interface between
terrestrial and marine systems. They are exposed to large quantities of both natural and …

High potential for biomass-degrading enzymes revealed by hot spring metagenomics

NJ Reichart, RM Bowers, T Woyke… - Frontiers in …, 2021 - frontiersin.org
Enzyme stability and activity at elevated temperatures are important aspects in
biotechnological industries, such as the conversion of plant biomass into biofuels. In order to …

Opportunities in optical and electrical single-cell technologies to study microbial ecosystems

F Mermans, V Mattelin, R Van den Eeckhoudt… - Frontiers in …, 2023 - frontiersin.org
New techniques are revolutionizing single-cell research, allowing us to study microbes at
unprecedented scales and in unparalleled depth. This review highlights the state-of-the-art …

Tracking de novo protein synthesis in the activated sludge microbiome using BONCAT-FACS

Z Du, SF Behrens - Water Research, 2021 - Elsevier
In order to ensure stable performance of engineered biotechnologies that rely on mixed
microbial community systems, it is important to identify process-specific microbial traits and …