Biology subjects

Irigoien, X.

Publications and source records attributed to Irigoien, X..

5 recordsLinked to original sources

bioRxiv2026

The potential role of viruses controlling phytoplankton community size structure

The size structure of phytoplankton communities plays a key role in the fate of carbon fixed by photosynthesis. Whether phytoplankton cells sink, enter the microbial loop, or are consumed by larger organisms is generally determined by their size. Grazing has been advanced as a factor determining size structure, but sources of mortality other than grazing, such as viruses also are recognized to be important. Based on the observation that cell size and genome size are related in phytoplankton, we hypothesize that viruses can also play a role in shaping the size structure of the phytoplankton community. Because cell size is related to genome size, we suggest that phytoplankton species with larger genomes will have a more developed immune system to defend against viral infection. As a first step to test this hypothesis, we screened the published transcriptomes of 125 phytoplankton species for expressed viral and immune-response related genes. We found a significant negative correlation between host-cell size and viral-gene diversity, and a positive correlation between host-cell size and the number of immune-response related genes. Our hypothesis supported by preliminary findings opens new pathways to explore whether we should consider viruses as an additional evolutionary driver for larger phytoplankton size, along with grazing and nutrients.

ecology↗

bioRxiv2024

What determines the vertical structuring of pelagic ecosystems in the global ocean?

Offshore pelagic ecosystems are composed of vertically and functionally distinct epipelagic, migrant and resident mesopelagic communities. While this vertical structure plays a key role in carbon sequestration and in supporting important fisheries, there is still no consensus on the respective contribution of the environmental factors (light, oxygen) and processes controlling it at both global and regional scale. Here we combine mechanistic modelling and acoustic observations from the worldwide Malaspina scientific campaign to show that, while underwater light intensity is the primary factor controlling the vertical distribution and migration of pelagic organisms globally, oxygen plays a critical role in limiting the depth of migratory communities and the abundance of mesopelagic communities in Oxygen Minimum Zones. Furthermore, we show that a faithful reproduction of acoustic observations in some regions of the global ocean (southern Indian Ocean, western Pacific) cannot be achieved without separating migratory and resident mesopelagic communities into deep and shallow groups. By proposing a unified mechanistic model and an archetypical ecosystem structure constrained by comprehensive acoustic observations, this study provides a consistent understanding of the vertical structure and function of global pelagic ecosystems and paves the way for more reliable estimates of their climate-induced variability and change.

ecology↗

bioRxiv2021

Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep-sea fishes

The deep-sea remains among the most unknown ecosystems on Earth despite its relevant role in carbon sequestration and increasing threat due to interest by fishing and mining industries. This, together with the recent discovery that the upper layer of this ecosystem (mesopelagic zone) harbors about 90% of the fish biomass on Earth, claims for a deeper understanding of the deep-sea so that the foundations for a sustainable use of its resources can be established. The analysis of environmental DNA (eDNA) collected from the water column emerges as an alternative to traditional methods to acquire this elusive information, but its application to the deep ocean is still incipient. Here, we have amplified and sequenced the fish eDNA contained in vertical profile samples (from surface to 2000 m depth) collected during day and night-time throughout the Bay of Biscay. We found that eDNA-derived deep-sea fish richness and abundance follow a day-night pattern that is consistent with the diel migratory behavior of many mesopelagic species, and that eDNA can reveal species-specific distribution and movement through the water column. These results highlight the potential of eDNA-based studies to improve our knowledge on the species inhabiting the dark ocean before this still pristine ecosystem is exploited.

ecology↗

bioRxiv2019

Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area

Current methods for monitoring marine fish diversity mostly rely on trawling surveys, which are invasive, costly and time-consuming. Moreover, these methods are selective, targeting a subset of species at the time, and can be inaccessible to certain areas. Here, we explore the potential of environmental DNA (eDNA), the DNA present in the water column as part of shed cells, tissues or mucus, to provide comprehensive information about fish diversity in a large marine area. Further, eDNA results were compared to the fish diversity obtained in pelagic trawls. A total of 44 5L-water samples were collected onboard a wide-scale oceanographic survey covering about 120,000 square kilometres in Northeast Atlantic Ocean. A short region of the 12S rRNA gene was amplified and sequenced through metabarcoding generating almost 3.5 million quality-filtered reads. Trawl and eDNA samples resulted in the same most abundant species (European anchovy, European pilchard, Atlantic mackerel and blue whiting), but eDNA metabarcoding resulted in more detected fish and elasmobranch species (116) than trawling (16). Although an overall correlation between fish biomass and number of reads was observed, some species deviated from the common trend, which could be explained by inherent biases of each of the methods. Species distribution patterns inferred from eDNA metabarcoding data coincided with current ecological knowledge of the species, suggesting that eDNA has the potential to draw sound ecological conclusions that can contribute to fish surveillance programs. Our results support eDNA metabarcoding for broad scale marine fish diversity monitoring in the context of Directives such as the Common Fisheries Policy or the Marine Strategy Framework Directive.

ecology↗

bioRxiv2019

Dissolved organic matter and heterotrophic prokaryotes diel patterns reveal enhanced growth at the mesopelagic fish layer during daytime

Contrary to epipelagic waters, where biogeochemical processes closely follow the light and dark periods, little is known about diel cycles in the oceans mesopelagic realm. Here, we monitored the dynamics of dissolved organic matter (DOM) and planktonic heterotrophic prokaryotes every 2 h for one day at 0 and 550 m (a depth occupied by vertically migrating fish during light hours) in oligotrophic waters of the central Red Sea. We additionally performed predator-free seawater incubations of samples collected from the same site both at midnight and at noon. Comparable in situ variability in microbial biomass and dissolved organic carbon concentration suggests a diel supply of fresh DOM in both layers. The presence of fish in the mesopelagic zone during daytime promoted a sustained, longer growth of larger prokaryotic cells. The specific growth rates were consistently higher in the noon experiments from both depths (surface: 0.34 vs. 0.18 d-1, mesopelagic: 0.16 vs. 0.09 d-1). Heterotrophic bacteria and archaea in the mesopelagic fish layer were also more efficient at converting DOM into new biomass. These results suggest that the oceans twilight zone receives a consistent diurnal supply of labile DOM from diel vertical migrating fishes, enabling an unexpectedly active community of heterotrophic prokaryotes.

ecology↗