Federico Baltar | Amano Lab | Hokkaido University

The contribution of pelagic fungi to ocean biomass

Tue, 01 Jul 2025 00:00:00 +0000

Anaplerotic processes are key contributors to dark carbon fixation in the ocean

Wed, 25 Sep 2024 00:00:00 +0000

Abstract Anaplerotic carbon fixation is ubiquitous in heterotrophic organisms including those inhabiting the ocean1. Despite its prevalence, the drivers of this process and its significance in ocean carbon cycling remain poorly understood2,3. Here we combined global ocean metatranscriptomic analysis, laboratory experiments on a bacterial model strain, and microautoradiography combined with catalyzed reporter deposition fluorescence in situ hybridization (MICRO-CARD-FISH) on marine microbial communities, to uncover the global prevalence of anaplerotic processes in oceanic dark dissolved inorganic carbon (DIC) fixation. Metatranscriptomic analysis revealed high expression levels of key anaplerotic genes, especially in mesopelagic waters, comparable to those of photo- and chemolithoautotrophic DIC fixation genes. Alteromonas emerged as the main contributor to anaplerotic DIC fixation gene expression, highlighting its role in DIC assimilation in the global ocean. Laboratory incubations with a marine Alteromonas representative confirmed their capability to fix DIC, which varied with organic matter availability and temperature. MICRO-CARD-FISH on oceanic samples revealed that Alteromonas contributed 0–40% (14 ± 16%, mean ± s.d.) to the dark DIC fixation in the pelagic ocean. Considering that Alteromonas is an obligate heterotroph lacking chemoautotrophic DIC fixation genes, its contribution to DIC fixation should be attributed to anaplerotic processes. Based on these results, we estimated a contribution of anaplerotic processes to dark DIC fixation of 0–0.5 C Pg y-1 in the global dark ocean. Yet, since Alteromonas is not the only taxon performing anaplerotic DIC fixation, our results represent a baseline conservative estimate. Collectively, our findings place anaplerotic DIC fixation as a relevant processes in the oceanic carbon cycling.

Metaproteomic analysis decodes trophic interactions of microorganisms in the dark ocean

Tue, 30 Jul 2024 00:00:00 +0000

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 samples collected from the Pacific, Atlantic and Southern Ocean, we reveal size-fractionated patterns of the structure and function of the marine microbiota protein pool in the water column, particularly in the dark ocean (>200 m). Zooplankton proteins contributed three times more than algal proteins to the deep-sea community metaproteome. Gammaproteobacteria exhibited high metabolic activity in the deep-sea, contributing up to 30% of bacterial proteins. Close virus-host interactions of this taxon might explain the dominance of gammaproteobacterial proteins in the dissolved fraction. A high urease expression in nitrifiers suggested links between their dark carbon fixation and zooplankton urea production. In summary, our results uncover the taxonomic contribution of the microbiota to the oceanic protein pool, revealing protein fluxes from particles to the dissolved organic matter pool.

A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean

Mon, 24 Apr 2023 00:00:00 +0000

Autofluorescence Is a Common Trait in Different Oceanic Fungi

Sun, 29 Aug 2021 00:00:00 +0000

Natural autofluorescence is a widespread phenomenon observed in different types of tissues and organisms. Depending on the origin of the autofluorescence, its intensity can provide insights on the physiological state of an organism. Fungal autofluorescence has been reported in terrestrial and human-derived fungal samples. Yet, despite the recently reported ubiquitous presence and importance of marine fungi in the ocean, the autofluorescence of pelagic fungi has never been examined. Here, we investigated the existence and intensity of autofluorescence in five different pelagic fungal isolates. Preliminary experiments of fungal autofluorescence at different growth stages and nutrient conditions were conducted, reflecting contrasting physiological states of the fungi. In addition, we analysed the effect of natural autofluorescence on co-staining with DAPI. We found that all the marine pelagic fungi that were studied exhibited autofluorescence. The intensity of fungal autofluorescence changed depending on the species and the excitation wavelength used. Furthermore, fungal autofluorescence varied depending on the growth stage and on the concentration of available nutrients. Collectively, our results indicate that marine fungi can be auto-fluorescent, although its intensity depends on the species and growth condition. Hence, oceanic fungal autofluorescence should be considered in future studies when fungal samples are stained with fluorescent probes (i.e., fluorescence in situ hybridization) since this could lead to misinterpretation of results.