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 …

Growth rates of microbes in the oceans

DL Kirchman - Annual review of marine science, 2016 - annualreviews.org
A microbe's growth rate helps to set its ecological success and its contribution to food web
dynamics and biogeochemical processes. Growth rates at the community level are …

The mammalian midbody and midbody remnant are assembly sites for RNA and localized translation

S Park, R Dahn, E Kurt, A Presle, K VanDenHeuvel… - Developmental cell, 2023 - cell.com
Long ignored as a vestigial remnant of cytokinesis, the mammalian midbody (MB) is
released post-abscission inside large extracellular vesicles called MB remnants (MBRs) …

Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum

X Mayali, TJ Samo, JA Kimbrel, MM Morris… - Nature …, 2023 - nature.com
Bacterial remineralization of algal organic matter fuels algal growth but is rarely quantified.
Consequently, we cannot currently predict whether some bacterial taxa may provide more …

Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria

S Smriga, VI Fernandez, JG Mitchell… - Proceedings of the …, 2016 - National Acad Sciences
The microenvironment surrounding individual phytoplankton cells is often rich in dissolved
organic matter (DOM), which can attract bacteria by chemotaxis. These “phycospheres” may …

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal− bacterial consortia

R Hatzenpichler, SA Connon… - Proceedings of the …, 2016 - National Acad Sciences
To understand the biogeochemical roles of microorganisms in the environment, it is
important to determine when and under which conditions they are metabolically active …

Temporal patterns of rarity provide a more complete view of microbial diversity

A Shade, JA Gilbert - Trends in microbiology, 2015 - cell.com
Recently, conditionally rare taxa (CRTs)–those taxa that are typically in very low abundance
but occasionally achieve prevalence–were shown to contribute to patterns of microbial …

Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment

NJ Reichart, ZJ Jay, V Krukenberg, AE Parker… - The ISME …, 2020 - academic.oup.com
Metagenomic studies have revolutionized our understanding of the metabolic potential of
uncultured microorganisms in various ecosystems. However, many of these genomic …

Vertically distinct microbial communities in the Mariana and Kermadec trenches

LM Peoples, S Donaldson, O Osuntokun, Q Xia… - Plos one, 2018 - journals.plos.org
Hadal trenches, oceanic locations deeper than 6,000 m, are thought to have distinct
microbial communities compared to those at shallower depths due to high hydrostatic …

Bacterial degradation of ctenophore Mnemiopsis leidyi organic matter

E Fadeev, JH Hennenfeind, C Amano, Z Zhao, K Klun… - Msystems, 2024 - Am Soc Microbiol
Blooms of gelatinous zooplankton, an important source of protein-rich biomass in coastal
waters, often collapse rapidly, releasing large amounts of labile detrital organic matter (OM) …