Quantitative microbial metatranscriptomics

Transcriptional Mechanisms of Thermal Acclimation in Prochlorococcus

Low temperature limits the growth and the distribution of the key oceanic primary producer Prochlorococcus, which does not proliferate above a latitude of ca. 40°. Yet, the molecular basis of thermal acclimation in this cyanobacterium remains unexplored. We analyzed the transcriptional response of the Prochlorococcus marinus strain MIT9301 in long-term acclimations and in natural Prochlorococcus populations along a temperature range enabling its growth (17 to 30°C). MIT9301 upregulated mechanisms of the global stress response at the temperature minimum (17°C) but maintained the expression levels of genes involved in essential metabolic pathways (e.g., ATP synthesis and carbon fixation) along the whole thermal niche. Notably, the declining growth of MIT9301 from the optimum to the minimum temperature was coincident with a transcriptional suppression of the photosynthetic apparatus and a dampening of its circadian expression patterns, indicating a loss in their regulatory capacity under cold conditions. Under warm conditions, the cellular transcript inventory of MIT9301 was strongly streamlined, which may also induce regulatory imbalances due to stochasticity in gene expression. The daytime transcriptional suppression of photosynthetic genes at low temperature was also observed in metatranscriptomic reads mapping to MIT9301 across the global ocean, implying that this molecular mechanism may be associated with the restricted distribution of Prochlorococcus to temperate zones. IMPORTANCE Prochlorococcus is a major marine primary producer with a global impact on atmospheric CO₂ fixation. This cyanobacterium is widely distributed across the temperate ocean, but virtually absent at latitudes above 40° for yet unknown reasons. Temperature has been suggested as a major limiting factor, but the exact mechanisms behind Prochlorococcus thermal growth restriction remain unexplored. This study brings us closer to understanding how Prochlorococcus functions under challenging temperature conditions, by focusing on its transcriptional response after long-term acclimation from its optimum to its thermal thresholds. Our results show that the drop in Prochlorococcus growth rate under cold conditions was paralleled by a transcriptional suppression of the photosynthetic machinery during daytime and a loss in the organism's regulatory capacity to maintain circadian expression patterns. Notably, warm temperature induced a marked shrinkage of the organism's cellular transcript inventory, which may also induce regulatory imbalances in the future functioning of this cyanobacterium.

"Circadian misalignment and the gut microbiome. A bidirectional relationship triggering inflammation and metabolic disorders"- a literature review

Over the last decade, emerging studies have related the gut microbiome and gut dysbiosis to sleep and sleep disorders. For example, intermittent hypoxia associated with obstructive sleep apnea was shown to reproducibly alter the gut microbiome. Circadian rhythm disorders (CRD) (eg, shift work disorders, delayed sleep phase syndrome, and advanced sleep phase syndrome) constitute another group of conditions that might be influenced by gut dysbiosis. Indeed, both central and peripheral clocks can affect and be affected by gut microbiota and their metabolites. In addition, the tight rhythmic regulation of almost all metabolic pathways involved in the anabolism and catabolism of carbohydrates, protein, and lipids in addition to detoxification processes that take place in specific cells could be ultimately linked to changes in the microbiota. Since there are no studies to date examining the impact of gut dysbiosis on delayed sleep phase and advanced sleep phase syndrome, and considering the ever-increasing number of people engaging in shift work, more accurate and informed delineation of the association between gut dysbiosis and shift work can provide guidance and opportunities for new avenues of treating circadian rhythm disorders and preventing the metabolic complications of shiftwork via restoration of gut dysbiosis. In this review, the potential bidirectional relationships between gut dysbiosis and circadian rhythm misalignment, their impact on different metabolic pathways, and the potential development of metabolic and systemic disorders, especially in shift work models are critically assessed.

New Technologies for Studying Biofilms

Bacteria have traditionally been studied as single-cell organisms. In laboratory settings, aerobic bacteria are usually cultured in aerated flasks, where the cells are considered essentially homogenous. However, in many natural environments, bacteria and other microorganisms grow in mixed communities, often associated with surfaces. Biofilms are comprised of surface-associated microorganisms, their extracellular matrix material, and environmental chemicals that have adsorbed to the bacteria or their matrix material. While this definition of a biofilm is fairly simple, biofilms are complex and dynamic. Our understanding of the activities of individual biofilm cells and whole biofilm systems has developed rapidly, due in part to advances in molecular, analytical, and imaging tools and the miniaturization of tools designed to characterize biofilms at the enzyme level, cellular level, and systems level.