Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes DOI
Stephen Blaskowski, Marie Roald, Paul M. Berube

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 18, 2024

Microbes respond to changes in their environment by adapting physiology through coordinated adjustments the expression levels of functionally related genes. To detect these shifts situ, we developed a sparse tensor decomposition method that derives gene co-expression patterns from inherently complex whole community RNA-sequencing data. Application metatranscriptomes abundant marine cyanobacteria Prochlorococcus and Synechococcus identified responses scarcity two essential nutrients, nitrogen iron, including increased transporter expression, restructured photosynthesis carbon metabolism, mitigation oxidative stress. Further, profiles clusters suggest both populations experience simultaneous iron stresses transition zone between North Pacific oceanic gyres. The results demonstrate power our approach infer organism environmental pressures, hypothesize functions uncharacterized genes, extrapolate ramifications for biogeochemical cycles changing ecosystem. Teaser New analytical reveals may help cope with stressors.

Language: Английский

Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes DOI Creative Commons
Stephen Blaskowski, Marie Roald, Paul M. Berube

et al.

Science Advances, Journal Year: 2025, Volume and Issue: 11(14)

Published: April 4, 2025

Microbes respond to changes in their environment by adapting physiology through coordinated adjustments the expression levels of functionally related genes. To detect these shifts situ, we developed a sparse tensor decomposition method that derives gene co-expression patterns from inherently complex whole community RNA sequencing data. Application metatranscriptomes abundant marine cyanobacteria Prochlorococcus and Synechococcus identified responses scarcity two essential nutrients, nitrogen iron, including increased transporter expression, restructured photosynthesis carbon metabolism, mitigation oxidative stress. Further, profiles clusters suggest both populations experience simultaneous iron stresses transition zone between North Pacific oceanic gyres. The results demonstrate power our approach infer organism environmental pressures, hypothesize functions uncharacterized genes, extrapolate ramifications for biogeochemical cycles changing ecosystem.

Language: Английский

Citations

0
Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes DOI
Stephen Blaskowski, Marie Roald, Paul M. Berube

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 18, 2024

Microbes respond to changes in their environment by adapting physiology through coordinated adjustments the expression levels of functionally related genes. To detect these shifts situ, we developed a sparse tensor decomposition method that derives gene co-expression patterns from inherently complex whole community RNA-sequencing data. Application metatranscriptomes abundant marine cyanobacteria Prochlorococcus and Synechococcus identified responses scarcity two essential nutrients, nitrogen iron, including increased transporter expression, restructured photosynthesis carbon metabolism, mitigation oxidative stress. Further, profiles clusters suggest both populations experience simultaneous iron stresses transition zone between North Pacific oceanic gyres. The results demonstrate power our approach infer organism environmental pressures, hypothesize functions uncharacterized genes, extrapolate ramifications for biogeochemical cycles changing ecosystem. Teaser New analytical reveals may help cope with stressors.

Language: Английский

Citations

0