Next-generation physiology approaches to study microbiome function at single cell level

R Hatzenpichler, V Krukenberg, RL Spietz… - Nature Reviews …, 2020 - nature.com
The function of cells in their native habitat often cannot be reliably predicted from genomic
data or from physiology studies of isolates. Traditional experimental approaches to study the …

Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats

R Liu, X Wei, W Song, L Wang, J Cao, J Wu, T Thomas… - Microbiome, 2022 - Springer
Background The deep sea harbors the majority of the microbial biomass in the ocean and is
a key site for organic matter (OM) remineralization and storage in the biosphere. Microbial …

Aged plastic leaching of dissolved organic matter is two orders of magnitude higher than virgin plastic leading to a strong uplift in marine microbial activity

C Romera-Castillo, S Birnstiel… - Frontiers in Marine …, 2022 - frontiersin.org
Plastic debris reaching the ocean is exponentially increasing in parallel with plastic
production. Once into seawater, plastic starts to leach organic compounds that are …

The potential for redox-active metabolites to enhance or unlock anaerobic survival metabolisms in aerobes

JA Ciemniecki, DK Newman - Journal of bacteriology, 2020 - journals.asm.org
Classifying microorganisms as “obligate” aerobes has colloquially implied death without air,
leading to the erroneous assumption that, without oxygen, they are unable to survive …

[HTML][HTML] Structure and activity of marine bacterial communities responding to plastic leachates

S Birnstiel, M Sebastián, C Romera-Castillo - Science of The Total …, 2022 - Elsevier
Plastic in the ocean releases organic compounds that are able to enter the marine dissolved
organic carbon pool and be utilized by heterotrophic bacteria. However, no information is …

Metaproteomic analysis decodes trophic interactions of microorganisms in the dark ocean

Z Zhao, C Amano, T Reinthaler, F Baltar… - Nature …, 2024 - nature.com
Proteins in the open ocean represent a significant source of organic matter, and their profiles
reflect the metabolic activities of marine microorganisms. Here, by analyzing metaproteomic …

Metabolic implications of using BioOrthogonal Non-Canonical Amino Acid Tagging (BONCAT) for tracking protein synthesis

KF Steward, B Eilers, B Tripet, A Fuchs… - Frontiers in …, 2020 - frontiersin.org
BioOrthogonal Non-Canonical Amino acid Tagging (BONCAT) is a powerful tool for tracking
protein synthesis on the level of single cells within communities and whole organisms. A …

Major imprint of surface plankton on deep ocean prokaryotic structure and activity

C Ruiz‐González, M Mestre, M Estrada… - Molecular …, 2020 - Wiley Online Library
Deep ocean microbial communities rely on the organic carbon produced in the sunlit ocean,
yet it remains unknown whether surface processes determine the assembly and function of …

Water aging and the quality of organic carbon sources drive niche partitioning of the active bathypelagic prokaryotic microbiome

M Sebastián, P Sánchez, G Salazar… - Limnology and …, 2024 - Wiley Online Library
Due to the scarcity of organic matter (OM) sources in the bathypelagic (1000–4000 m depth),
prokaryotic metabolism is believed to be concentrated on particles originating from the …

Hydrothermal plumes as hotspots for deep-ocean heterotrophic microbial biomass production

C Cathalot, EG Roussel, A Perhirin, V Creff… - Nature …, 2021 - nature.com
Carbon budgets of hydrothermal plumes result from the balance between carbon sinks
through plume chemoautotrophic processes and carbon release via microbial respiration …