Gomes, H. | Search bioRxiv

bioRxiv2025

Phytoplankton community structure and photophysiological strategies in the oligotrophic Indian Ocean spawning ground of Southern Bluefin Tuna

The Argo Basin, a persistently oligotrophic seascape downstream of the Indonesian Throughflow (ITF), is the only known spawning ground of Southern Bluefin Tuna (Thunnus maccoyii). Its surface waters are capped by the warm, low saline, nitrate-depleted Pacific Ocean outflow, that leads to intense water-column stratification and chronic nutrient scarcity. During the BLOOFINZ campaign (R/V Roger Revelle, January-March 2022), we combined high-resolution underway surveys with Lagrangian experiments to examine hydrography, nutrient stoichiometry, and phytoplankton photophysiology across the basin. This study was motivated by the need to: 1) identify the phytoplankton communities capable of persisting in this nutrient-impoverished region, and 2) uncover the unique photophysiological traits that underpin their survival and growth, particularly under acute nitrate limitation. Nutrient fields revealed strongly negative N*, positive Si*, and elevated Si:P ratios, indicating a system of acute nitrate scarcity but with residual phosphate and latent silicate availability. Phytoplankton communities were dominated by the cyanobacteria, Prochlorococcus, whose survival strategies included small functional absorption cross section of PSII ({sigma}PSII), enhanced PSII connectivity (p), highly elastic and reversible diel photophysiology that balanced high-light stress and nitrogen scarcity. Longer turnover times especially {tau}2 ({micro}s; PSII-PSI electron transport) seen in the region around 115{degrees} and 120{degrees}E and at 15{degrees}S, and during Cycles 3 and 4 are indicative of populations that were being stressed by Fe limitation as well. Our inference of Prochlorococcus is supported by complimentary measurements of flow cytometry, phytoplankton pigment composition and microscopy all of which confirmed the dominance of Prochlorococcus in these nutrient impoverished waters. Our observations further indicate that mesoscale eddies generated by ITF-SICC (South Indian Counter Current) interactions, can episodically shoal the nutricline, triggering transient pulses of larger eukaryotes. Collectively, these results demonstrate how acute nitrate depletion, compounded by Fe stress, structures a microbial community finely tuned to oligotrophy and capable of sustaining a short food chain involving appendicularians that directly support larval tuna. The Argo Basin therefore exemplifies how circulation-nutrient coupling shapes microbial communities and ecosystem function within a globally significant spawning habitat. Highlights1) Chronic nitrate limitation, with strongly negative N* and persistent N:P imbalance defines the Argo Basin while phosphate and silicate remain in relative excess. 2) Picocyanobacteria especially Prochlorococcus dominate the ecosystem, sustaining productivity under extreme oligotrophy through photophysiological strategies of reduced {sigma}PSII, enhanced PSII connectivity, and diel recovery from light stress. 3) Mesoscale eddies at the ITF-SICC front provide episodic relief, shoaling the nutricline and fueling transient pulses of larger phytoplankton that episodically reshape phytoplankton community structure and biomass 4) This oligotrophic-frontal seascape supports a short, efficient food web, enabling transfer of picophytoplankton to Southern Bluefin Tuna larvae via mainly appendicularians.

ecology↗

bioRxiv2023

Characterization and Phylogenetic Insights into the First Viral Major Vault Proteins (MVPs), Identified in Bacteriophages from the Human Gut.

The Major Vault Protein (MVP) is the principal component of the enigmatic vault complex, dome-shaped cytoplasmic ribonucleoproteins found in eukaryotes. Although vaults have been associated with several minor functions, including amino acid storage and cargo transport, their overall function remains to be fully understood. While MVPs are widely distributed among most higher eukaryotes and have homologs in prokaryotes, no similar protein have been reported in viral species until now. In this study, we explored the NCBI viral protein database for MVP homologs and identified two putative MVPs from distinct tailed bacteriophage isolates from the Class Caudoviricetes, ctOa11 and ctRi15, of human gut metagenomic samples. Further in silico analysis were conducted to describe and characterize these unprecedent phage proteins. Phylogenetic topologies indicate that viral MVPs are closely related to bacterial MVP homologs. Tridimensional protein models of viral MVPs were generated to perform protein structure comparisons with eukaryotic and prokaryotic MVPs, indicating a significant similarity to bacterial proteins. For the functional significance of MVPs in phage infectivity, we suggest that they may have an unknown metabolic role enhancing phage fitness. While this work provides new insights into the genetic phage diversity and phylogenetic distribution of MVPs, complementary functional studies are necessary to fully elucidate their function in viral and bacterial species.

genomics↗

bioRxiv2018

Robust Algorithms for Capturing Population Dynamics and Transport in Oceanic Variables along Drifter Trajectories using Linear Dynamical Systems with Latent Variables

The blooms of Noctiluca in the Gulf of Oman and the Arabian Sea have been intensifying in recent years posing a threat to regional fisheries and the long-term health of an ecosystem supporting a coastal population of nearly 120 million people. We present the results of a microscopic data analysis to investigate the onset and patterns of the Noctiluca (mixotrophic dinoflagellate Noctiluca scintillans) blooms, which form annually during the winter monsoon in the Gulf of Oman and in the Arabian Sea. Our approach combines methods in physical and biological oceanography with machine learning techniques. In particular, we present a robust algorithm, the variable-length Linear Dynamic Systems (vLDS) model, that extracts the causal factors and latent dynamics at the microscopic population-level along each individual drifter trajectory, and demonstrate its effectiveness by using it to test and confirm previously benchmarked macroscopic scientific hypotheses. The test results provide microscopic statistical evidence to support and recheck the macroscopic physical and biological Oceanography hypotheses on the Noctiluca blooms; it also helps identify complementary microscopic dynamics that might not be visible or discoverable at the macroscopic scale. The vLDS model also exhibits a generalization capability (inherited from a machine learning methodology) to investigate important causal factors and hidden dynamics associated with ocean biogeochemical processes and phenomena at the population-level.

ecology↗