Silvia Pajares

Understanding the microbial processes involved in ammonium loss in highly productive marine systems is crucial for reconstructing the global nitrogen cycle. This study is the first to examine the anaerobic ammonium oxidation coupled with dissimilatory Fe(III) reduction (Feammox) and the abundance of iron-reducing bacteria (IRB) in a seagrass-dominated coastal lagoon exposed to two contrasting upwelling conditions. Potential Feammox rates varied from 6.0 to 39.2 mg N · m^-2 · d^-1 and were positively correlated with the abundance of IRB (Acidomicrobiaceae A6 spp. and Geobacteraceae spp.), suggesting that IRB mediated the Feammox process. The limited impact of near-mouth productivity conditions on Feammox activity and IRB was largely inherent to sediment type (eelgrass or adjacent bare bottom) and station-specific, depending on the degree of confinement relative to the nearby ocean. The partial least squares structural equation modeling approach revealed that dissimilatory Fe(III) reduction exerted a direct effect on potential Feammox rates, while upwelling conditions indirectly influenced the process through sediment characteristics. The contribution of Feammox to total ammonium loss exceeded 60% and increased with the distance from the mouth of the lagoon. A minimum of 3.7 ± 0.5 mg N · m^-2 · d^-1 was catalyzed by electron acceptors besides Fe(III), highlighting the co-occurrence of alternative chemoautotrophic pathways in ammonium removal. Furthermore, an average loss of 38.4 ± 6.7 t N · y^-1 was attributed to the anaerobic ammonium oxidation processes, accounting for 5.1 ± 1.6% of the annual oceanic N transported into the lagoon. These findings extend our current understanding of N and Fe cycles in coastal environments linked to eastern boundary upwelling systems.

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are abundant in the global ocean, playing a crucial role in marine nitrogen cycling through nitrification. Despite extensive studies using the ammonia monooxygenase α-subunit (amoA) gene, our understanding of their distribution patterns in marine habitats remains limited. This study offers the first integrative framework to assess the diversity and biogeography of ammonia-oxidizing communities across different marine habitats, based on a meta-analysis and phylogenetic examination of archaeal and bacterial amoA sequences from public databases. Most sequences were retrieved from estuarine sediments and coastal waters, while habitats such as pelagic open ocean, OMZ, deep sea, hydrothermal vents, and benthic organisms are underexplored. AOA exhibited higher phylogenetic diversity than AOB, with many unclassified AOA-amoA sequences likely representing novel clades. The dominant AOA clades were Ca. Nitrosopelagicus, Nitrosoarchaeum, and Nitrosopumilus, while Nitrosospira was the predominant clade among AOB. AOA show greater ecological versatility, thriving in nutrient-poor and low-oxygen environments, whereas AOB are more prevalent in nutrient-rich estuarine habitats. Further research is needed to better understand the ecological roles of novel AOA clades and the contributions of AOB in less-explored marine habitats.

The ecology of eukaryotic picoplankton in oxygen minimum zones (OMZs) is crucial to understand global primary production, trophic dynamics and plankton diversity. This study analyses picoeukaryotic diversity and distribution patterns along the water column at two locations (slope and oceanic) in the tropical Mexican Pacific OMZ using metabarcoding and flow cytometry. Well-known groups of Chlorophytes (Mamiellophyceae) and Ochrophytes (Chrysophyceae, Dictyochophyceae, Pelagophyceae) occurred in high relative abundances, whereas less-known groups such as Chloropicophyceae and Prasinodermophyta were found in lower abundances. Picoeukaryotic diversity was higher at the lower end of the oxycline (10 μM O2) than at the surface and subsurface layers. Differential distributions of picoeukaryotes were also detected along the water column, with almost exclusive communities at each depth. Mamiellophyceae dominated the surface and subsurface layers, whereas Syndiniales (parasitic dinoflagellates), Radiolaria, Ochrophyta, and Sagenista (MArine STramenopiles -MAST groups-) were prevalent at the oxycline. Post-upwelling oceanographic conditions possibly contributed to shape the differences in community composition and distribution. These findings highlight that oxygen concentration is a key factor driving microbial distribution and that oxyclines provide specialized niches that promote high picoplankton diversity and multiple trophic strategies including autotrophy, mixotrophy, heterotrophy and parasitism.

Coastal lagoons are dynamic transitional ecosystems shaped by complex hydrodynamic and biogeochemical processes. Their sediments host diverse microbial communities essential for nutrient cycling, organic matter sequestration, and pollutant degradation. However, the taxonomic and functional profiles of these communities remain poorly understood, especially in pristine systems. Here, shotgun metagenomics was used to investigate microbial diversity and functional potential in a seagrass-dominated coastal lagoon on the Mexican Pacific coast, influenced by seasonal upwelling and with minimal anthropogenic impact. Despite pronounced physicochemical gradients and oceanographic variability, these sediments harbored a diverse and taxonomically conserved microbial community. 60% of genera and 38% of species (with relative abundance >0.1%) were consistently shared across sites and the two upwelling seasons, with Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Flavobacteria, and Actinobacteria as dominant taxa. Genes associated with nitrogen and sulfur metabolic pathways were consistently detected, suggesting the presence of a conserved functional core supporting key biogeochemical processes. In contrast, genes related to antibiotic resistance and virulence factors exhibited more heterogeneous distributions. Among measured physicochemical variables, only nitrate and ferric iron significantly influenced microbial community structure and its functional repertoire, suggesting that additional factors likely contribute to the broader distribution of these communities. These findings reveal a high degree of taxonomic and functional stability of microbial communities in a minimally impacted lagoon, providing a valuable baseline for understanding microbial dynamics in coastal sediments primarily shaped by oceanographic processes.

La desnitrificación es la principal vía por la cual el nitrógeno fijado se pierde en los sistemas marinos y consiste en la respiración secuencial de nitrato a nitrógeno molecular a través de diversos microorganismos heterótrofos. Ya que los sedimentos estuarinos representan un nicho importante para la desnitrificación, este estudio evaluó la distribución y actividad potencial de bacterias desnitrificantes aerobias aisladas de sedimentos a 2 profundidades y en 2 hábitats (con pastos de Zostera marina y sin pastos) a lo largo de un transecto en la Bahía de San Quintín (México), así como su relación con diferentes parámetros ambientales. Se aislaron 1,611 bacterias, de las cuales 85.1% contuvieron alguno de los genes desnitrificantes (nirK, nirS o nosZ). Su distribución fue heterogénea en la bahía y estuvo influenciada principalmente por la textura, el pH, el carbono orgánico total y el nitrógeno total de los sedimentos, encontrándose una mayor abundancia de bacterias desnitrificantes en los sedimentos superficiales (66.2%). Los aislados desnitrificantes se clasificaron en 23 especies pertenecientes a γ-Proteobacteria (82.4% de los aislados), α Proteobacteria (7.9%), Bacilli (5.7%) y Actinobacteria (4%). Se comprobó la actividad desnitrificante en condiciones aerobias en 7 especies de bacterias portadoras de genes desnitrificantes: Paracoccus marcusii, Planococcus maritimus, Planococcus rifietoensis, Pseudomonas songnenensis, Psychrobacter alimentarius, Psychrobacter celer y Psychrobacter piscatorii. Los resultados sugieren que estos sedimentos presentan una elevada abundancia de bacterias cultivables con genes nirK, nirS o nosZ; sin embargo, en la mayoría no se pudo comprobar la actividad desnitrificante en condiciones aerobias, posiblemente debido a la inactividad de estos genes o de aquellos involucrados en la reducción de nitrato (nas, nar o nap). Este estudio representa el primer paso hacia el entendimiento de la ecología de los microorganismos involucrados en la desnitrificación aerobia en la Bahía de San Quintín y en las lagunas costeras en general.

The unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN‐A) is a key diazotroph in the global ocean owing to its high N ₂ fixation rates and wide distribution in marine environments. Nevertheless, little is known about UCYN‐A in oxygen‐deficient zones (ODZs), which may be optimal environments for marine diazotrophy. Therefore, the distribution and diversity of UCYN‐A were studied in two consecutive years under contrasting phases (La Niña vs. El Niño) of El Niño Southern Oscillation (ENSO) along a transect in the ODZ of the Mexican Pacific upwelling system. Of the three UCYN‐A sublineages found, UCYN‐A1 and UCYN‐A3 were barely detected, whereas UCYN‐A2 was dominant in all the stations and showed a wide distribution in both ENSO phases. The presence of UCYN‐A was associated with well‐oxygenated waters, but it was also found for the first time under suboxic conditions (<20 μM) at the bottom of a shallow coastal station, within the oxygen‐poor and nutrient‐rich Subsurface Subtropical water mass. This study contributes to the understanding of UCYN‐A distribution under different oceanographic conditions associated with ENSO phases in upwelling systems, especially because of the current climate change and increasing deoxygenation in many areas of the world's oceans.

Dissolved oxygen regulates microbial distribution and nitrogen cycling and, therefore, ocean productivity and Earth's climate. To date, the assembly of microbial communities in relation to oceanographic changes due to El Niño Southern Oscillation (ENSO) remains poorly understood in oxygen minimum zones (OMZ). The Mexican Pacific upwelling system supports high productivity and a permanent OMZ. Here, the spatiotemporal distribution of the prokaryotic community and nitrogen‐cycling genes was investigated along a repeated transect subjected to varying oceanographic conditions associated with La Niña in 2018 and El Niño in 2019. The community was more diverse during La Niña and in the aphotic OMZ, dominated by the Subtropical Subsurface water mass, where the highest abundances of nitrogen‐cycling genes were found. The largest proportion of the Gulf of California water mass during El Niño provided warmer, more oxygenated, and nutrient‐poor waters towards the coast, leading to a significant increase of Synechococcus in the euphotic layer compared with the opposite conditions during La Niña. These findings suggest that prokaryotic assemblages and nitrogen genes are linked to local physicochemical conditions (e.g. light, oxygen, nutrients), but also to oceanographic fluctuations associated with ENSO phases, indicating the crucial role of climate variability in microbial community dynamics in this OMZ.

Mesoscale eddies in oxygen minimum zones profoundly affect the structure and productivity of marine planktonic communities and alter key biogeochemical cycles. The influence of a mesoscale cyclonic eddy on the spatial distribution of bacterioplankton was investigated in a semi-enclosed, oxygen-depleted basin in the Gulf of California, Mexico. Most of the bacterial taxa showed a strong vertical distribution from oxygen-rich surface waters to anoxic bottom waters, but also a horizontal distribution pattern in the upper ocean associated with the eddy presence. Synechococcocales, Flavobacteriales, SAR86, and Actinomarinales were abundant in the euphotic zone within the Gulf of California water mass, whereas SAR324, SAR406, SAR202, SUP05, Arctic97B-4, and Thioglobaceae dominated the bottom layer of this basin within the Subtropical Subsurface water mass. In contrast, bacterial taxa with a preference for mesopelagic waters (Thiomicrospirales, SAR324, SAR202, HOC36, UBA10353 marine group, and Nitrospinales) dominated surface waters of the eddy center where common surface taxa (Synechococcus, SAR86, and Actinomarinales) were scarce. These changes in community composition led to a distinct diversity of bacterioplankton between the center and edges of the eddy within the euphotic zone. These results show the strong role of oxygen and water masses in controlling the vertical distribution of bacterioplankton, whereas the eddy more strongly modifies the bacterial assemblage in the upper ocean.