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Aerobic anoxygenic phototrophic (AAP) bacteria harvest light energy using bacteriochlorophyll-containing reaction centers to supplement their mostly heterotrophic metabolism. While their abundance and growth have been intensively studied in coastal environments, much less is known about their activity in oligotrophic open ocean regions. Therefore, we combined in situ sampling in the North Pacific Subtropical Gyre, north of O'ahu island, Hawaii, with two manipulation experiments. Infra-red epifluorescence microscopy documented that AAP bacteria represented approximately 2% of total bacteria in the euphotic zone with the maximum abundance in the upper 50 m. They conducted active photosynthetic electron transport with maximum rates up to 50 electrons per reaction center per second. The in situ decline of bacteriochlorophyll concentration over the daylight period, an estimate of loss rates due to predation, indicated that the AAP bacteria in the upper 50 m of the water column turned over at rates of 0.75¿0.90 d¿1. This corresponded well with the specific growth rate determined in dilution experiments where AAP bacteria grew at a rate 1.05 ± 0.09 d¿1. An amendment of inorganic nitrogen to obtain N:P = 32 resulted in a more than 10 times increase in AAP abundance over 6 days. The presented data document that AAP bacteria are an active part of the bacterioplankton community in the oligotrophic North Pacific Subtropical Gyre and that their growth was mostly controlled by nitrogen availability and grazing pressure.

Holothurians, as benthic invertebrates inhabiting marine ecosystems, have a crucial function in that they actively process organic detritus in the sediments. Previous works have provided evidence of the capability of holothurians to reduce nitrate and ammonium concentrations in aquaculture tanks. However, the mechanisms underlying this nitrogen decrease still need to be elucidated and might be related to bacterial symbionts in the holothurians. Here we characterize the community of bacterial symbionts in the biofilm and subcuticle of Holothuria tubulosa and explore the presence of nitrification and denitrification genes. To characterize these bacterial symbionts, we extracted DNA and amplified the V3-V4 hypervariable region of the 16S rRNA gene. We obtained a notable contribution of Bacteroidota, Alphaproteobacteria (mostly Rhodobacterales), and Gammaproteobacteria (mostly Pseudomonadales) both within the biofilm and subcuticle of H. tubulosa. Subsequently, we tested the presence of specific genes encoding enzymes involved in nitrification (i.e. archaeal amoA and bacterial amoA) and denitrification (i.e. nirS and nosZ). Our results confirm the presence of denitrification genes in the holothurian biofilms. These findings indicate that the holothurians house a diverse community of bacterial symbionts, which includes species with the potential for nitrogen removal. Therefore, holothurian holobionts may play a multifaceted ecological role, both processing organic detritus and reducing nitrogen levels in coastal areas. These roles could be extended to sustainable aquaculture, making them valuable ecosystem engineers with significant implications for ecosystem and aquaculture health.

Marine prokaryotes play crucial roles in ocean biogeochemical cycles, being their contribution strongly influenced by their growth rates. Hence, elucidating the variability and phylogenetic imprint of marine prokaryotes' growth rates are crucial for better determining the role of individual taxa in biogeochemical cycles. Here, we estimated prokaryotic growth rates at high phylogenetic resolution in manipulation experiments using water from the northwestern Mediterranean Sea. Experiments were run in the four seasons with different treatments that reduced growth limiting factors: predators, nutrient availability, viruses, and light. Single-amplicon sequence variants (ASVs)-based growth rates were calculated from changes in estimated absolute abundances using total prokaryotic abundance and the proportion of each individual ASV. The trends obtained for growth rates in the different experiments were consistent with other estimates based on total cell-counts, CARD-FISH subcommunity cell-counts or metagenomic-OTUs. Our calculations unveil a broad range of growth rates [0.3-10 d-1] with significant variability even within closely related ASVs. Likewise, the impact of growth limiting factors changed over the year for individual ASVs. High numbers of responsive ASVs were shared between winter and spring seasons, as well as throughout the year in the treatments with reduced nutrient limitation and viral pressure. The most responsive ASVs were rare in the in situ communities, comprising a large pool of taxa with the potential to rapidly respond to environmental changes. Essentially, our results highlight the lack of phylogenetic coherence in the range of growth rates observed, and differential responses to the various limiting factors, even for closely related taxa

The volcanic eruption that occurred in La Palma Island (Canary Islands, Spain) in 2021 resulted in molten lava flowing into the ocean and forming a delta in the coastline, besides the emission of large amounts of ashes being deposited in a vast area around the Canary Islands. In order to assess the effects of the eruption on seawater, two oceanographic cruises were carried out, one at the beginning of the eruption and a second one a month later. We used an oceanographic CTD rosette sampler for collecting seawater in different areas of La Palma coastline together with Unmanned Aerial Vehicles (UAVs) equipped with a sampling device to collect surface samples near the delta newly formed on the coastal fringe. We sequenced the 16S rRNA gene in order to assess the response of bacterioplankton to such natural disturbance. The results show that the abundance of Thiomicrospirales, Gammaproteobacteria capable of oxidizing poly-metal sulfides, increased significantly in UAV samples collected near the lava delta. Moreover, in stations where the largest physical-chemical anomalies were recorded with the CTD, sequence data showed drastic changes in the prokaryotic community structure; cyanobacterial abundance decreased while the ammonia-oxidizing archeon Nitrosopelagicus and the bacterial SAR324 clade, with potential sulfur-based chemolithoautotrophic lifestyle, dominated the communities. The combined used of shipboard operations and UAVs provided a unique opportunity to study the prokaryotic response to a massive lava input, an event that is rarely observed and sampled in real time.

La nostra relació amb l’oceà és més estreta del que ens pensem: l’oceà ens alimenta, absorbeix l’excés de gasos d’efecte d’hivernacle i de calor, captura carboni, i és també una font perenne d’inspiració artística. El consens sobre la importància de la seva conservació és indubtable. En aquesta taula rodona conversem amb dones pioneres que s’han endinsat en les profunditats oceàniques i que ens expliquen els resultats de les seves experiències submarines. L’oceanògrafa Cristina Romera dialoga amb l’apneista i fotògrafa japonesa Ai Futaki i amb la microbiòloga Isabel Ferrera, una de les poques persones que ha descendit a 2.600 metres de profunditat a bord de l’Alvin, el submarí que va descobrir les restes del Titanic. El diàleg ofereix, també, una radiografia de l’estat actual dels oceans

Underwater hydrothermal systems release nutrient-rich fluids that are favorable for microbial activity. This allows the growth of a plethora of microorganisms that can be found inhabiting hydrothermal plumes, metalliferous sediments, or forming dense microbial biofilms or mats on the surrounding of the vents. Most of the current knowledge on the microbiology associated with underwater volcanic activity comes from the study of deep-sea hydrothermal vents. However, much less is known about shallow underwater hydrothermal systems. The submarine volcanic eruption that took place near El Hierro (Canary Islands) in October 2011 and gave rise to the Tagoro volcano, located only 1.8 km from land and approximately 89 m below the sea surface, provided a rare occasion to study almost in real time the microbiology associated with an underwater eruptive process, from its birth to the current degassing state, allowing investigations of its effects on the surrounding pelagic and benthic communities. In this chapter, we summarize what is known 10 years after the formation of the Tagoro submarine volcano, and we discuss what questions should be pursued in order to foster our knowledge of the microbiology associated with this volcano and its surrounding waters

The shallow Tagoro submarine volcano monitoring represents a unique opportunity not only for improving our sparse understanding of submarine volcanic processes in specific scientific fields as physical and chemical oceanography or marine geology but also its interactions over the marine biology in one of the richest marine ecosystems in Europe. This chapter aims to summarize the most relevant physical–chemical, geological and biological changes that occurred in the marine ecosystem of El Hierro island, at the Marine Reserve Punta de La Restinga—El Mar de Las Calmas, due to the genesis of the new underwater volcano Tagoro (27º37′07″N–017º59′28″W) in October 2011. During the first six months of the eruption, extreme physical–chemical perturbations caused by this event, comprising thermal increase from up to + 18.8 °C, water acidification with a pH decrease of 2.9 units, deoxygenation to anoxic levels and extremely high metal enrichment among others, resulted in significant and dramatic alterations of the marine ecosystem. After March 2012, once the eruptive phase was finished, the new submarine volcano entered an active hydrothermal phase involving the release of heat with smaller but still significant and important thermal anomalies of up to + 2.55 °C around the craters, density decrease of − 1.43 kg m−3, pH decrease of − 1.25 units, and high concentrations of metals and inorganic nutrients similar to upwelling zones. These enrichments are still active up to date, producing clear signs of marine recovery not only in the benthonic strata but also in the whole water column compared with pre-eruptive data. Since its eruption ten years ago, an unprecedented monitoring effort has turned into the longest and most complete multidisciplinary time-series for the study of a shallow submarine volcano, with the realization of 31 oceanographic multidisciplinary expeditions that systematically measure more than 40 different physical–chemical and biological variables. All this info

Isolation of microorganisms is a useful approach to gathering knowledge about their genomic properties, physiology, and ecology, in addition to allowing the characterization of novel taxa. We performed an extensive isolation effort on samples from seawater manipulation experiments that were carried out during the four astronomical seasons in a coastal site of the northwest Mediterranean to evaluate the impact of grazing, viral mortality, resource competition reduction, and light presence/absence on bacterioplankton growth. Isolates were retrieved using two growth media, and their full 16S rRNA gene was sequenced to assess their identity and calculate their culturability across seasons and experimental conditions. A total of 1,643 isolates were obtained, mainly affiliated to the classes Gammaproteobacteria (44%), Alphaproteobacteria (26%), and Bacteroidia (17%). Isolates pertaining to class Gammaproteobacteria were the most abundant in all experiments, while Bacteroidia were preferentially enriched in the treatments with reduced grazing. Sixty-one isolates had a similarity below 97% to cultured taxa and are thus putatively novel. Comparison of isolate sequences with 16S rRNA gene amplicon sequences from the same samples showed that the percentage of reads corresponding to isolates was 21.4% within the whole data set, with dramatic increases in the summer virus-reduced (71%) and diluted (47%) treatments. In fact, we were able to isolate the top 10 abundant taxa in several experiments and from the whole data set. We also show that top-down and bottom-up controls differentially affect taxa in terms of culturability. Our results indicate that culturing marine bacteria using agar plates can be successful in certain ecological situations

Studies based on protein-coding genes are essential to describe the diversity within bacterial functional groups. In the case of aerobic anoxygenic phototrophic (AAP) bacteria, the pufM gene has been established as the genetic marker for this particular functional group, although available primers are known to have amplification biases. We review here the existing primers for pufM gene amplification, design new ones, and evaluate their phylogenetic coverage. We then use samples from contrasting marine environments to evaluate their performance. By comparing the taxonomic composition of communities retrieved with metagenomics and with different amplicon approaches, we show that the commonly used PCR primers are biased towards the Gammaproteobacteria phylum and some Alphaproteobacteria clades. The metagenomic approach, as well as the use of other combinations of the existing and newly designed primers, show that these groups are in fact less abundant than previously observed, and that a great proportion of pufM sequences are affiliated to uncultured representatives, particularly in the open ocean. Altogether, the framework developed here becomes a better alternative for future studies based on the pufM gene and, additionally, serves as a reference for primer evaluation of other functional genes

Microbes drive the biogeochemical cycles of marine ecosystems through their vast metabolic diversity. While we have a fairly good understanding of the spatial distribution of these metabolic processes in various ecosystems, less is known about their seasonal dynamics. We investigated the annual patterns of 21 biogeochemical relevant functions in an oligotrophic coastal ocean site by analysing the presence of key genes, analysing high-rank gene taxonomy and the dynamics of nucleotide variants. Most genes presented seasonality: photoheterotrophic processes were enriched during spring, phosphorous-related genes were dominant during summer, coinciding with potential phosphate limitation, and assimilatory nitrate reductases appeared mostly during summer and autumn, correlating negatively with nitrate availability. Additionally, we identified the main taxa driving each function at each season and described the role of underrecognized taxa such as Litoricolaceae in carbon fixation (rbcL), urea degradation (ureC), and CO oxidation (coxL). Finally, the seasonality of single variants of some families presented a decoupling between the taxonomic abundance patterns and the functional gene patterns, implying functional specialization of the different genera. Our study unveils the seasonality of key biogeochemical functions and the main taxonomic groups that harbour these relevant functions in a coastal ocean ecosystem

Marine prokaryotes play crucial roles in ocean’s biogeochemical cycles, being their contribution largely determined by their growth rates. To improve our understanding of microbial communities’ dynamics and structure, we estimated prokaryotic growth rates at high resolution, the amplicon sequence variant (ASV) level, using manipulation experiments in each of the four astronomical seasons with different treatments that reduced limiting growth factors such as predators, nutrient availability, viruses and light. Single-ASV-based growth rate calculations showed a continuous range of values, reaching almost 10 day-1. Mean growth rates per treatment increased as limiting factors were removed, and changed seasonally. Results revealed significant variability in growth rate distribution patterns even within closely related ASVs, and with no general taxonomic coherence observed after removal of each growth limiting factor. Reduction of these factors showed that most responsive ASVs were rare, and formed a pool of taxa with the potential to rapidly respond to environmental changes. In essence, our results highlight the significance of rare-responsive taxa often overlooked in whole-community studies and suggest high dynamism in marine microbial communities with a strong capacity to adapt to changing environments

Diversity of protists was researched in different coastal areas of the Mediterranean Sea by means of high throughput sequencing technologies based on the amplification of a specific region of the 18S rRNA gene. A total of 25 samples were obtained in the Mar Menor coastal lagoon (MMS) in 2016-2017 after the ecosystem suffered a so-called 'ecosystem disruptive algal bloom' which was attributed to nitrate pollution. Another set of samples (9) was harvested in 2018 at a coastal area of the northern Alboran Sea, which received urban wastewater (CS). The community structure in these two areas was compared with samples collected at stations of the Alboran Sea following a trophic gradient from coast to open sea (UP; 15 samples; OAS) located far from pollution sources. On average, Alveolata, Stramenopila and Rhizaria counted for more than 85% of the total sequence reads in the three areas although the contribution of the three groups was different. The relative abundance of Alveolata reads averaged 62% in OAS but increased notably in CS (80%) and MMS (70%). In contrast, both diversity and abundance of Rhizaria were reduced in CS (1.4% and 4.7% of reads and OTUs) and MMS (3% and 7%) compared to OAS (5.5% and 9.7%). The highest contribution of Stramenopila to total reads was obtained in OAS (20% compared to 8% and 13% in CS and MMS, respectively). a-diversity of autotrophs, dinoflagellates and heterotrophs decreased in the areas impacted by nutrient pollution. However, these was not a consistent variability pattern in b-diversity.

Presentación realizada para el IV Congreso Internacional Jóvenes Investigadores del Mar, celebrado entre el 6 al 9 de septiembre en Almería

Microplankton is an heterogeneous group of organisms ranging between 20 and 200 microns in size. Morphological characterization of its diversity is challenging as it includes Chromista, Protozoa, and Metazoa (adults and larvae). We characterized the composition of the microzooplankton community (heterotrophic and mixotrophic) collected with a CalVET net (50 µm mesh), in a coastal area affected by urban wastewater discharges in the N Alboran Sea (SW Mediterranean). We applied an integrative taxonomic approach, combining metabarcoding of the mtDNA cytochrome oxidase I (COI) and the V4 region of the 18S rRNA (18S) genes with morphological microscopic identification of organisms. Both methods showed differentiated coastal and offshore microzooplankton assemblages. The dominant taxa varied depending on the method used, with Dinophyceae accounting for 64-85% of the microscopy counts but Arthropoda representing up to 98% or the COI and 18S reads. When computing Protozoa and Metazoa relative abundances separately, both microscopy and metabarcoding revealed unicellular communities dominated by thecate Dinophyceae, followed by Ciliophora. Metazoa microscopy counts were dominated by eggs, followed by Copepoda nauplii in offshore waters, whilst by Appendicularia and Mollusca larvae in the shallow coastal stations. COI reads also corresponded mostly to Copepoda and Mollusca. However, 18S reads were dominated by Thecostraca and Copepoda. Despite the identification level differed among methods and taxa, the integrated approach revealed higher diversity than expected.

The aerobic anoxygenic phototrophic (AAP) bacteria are common in most marine environments but their global diversity and biogeography remain poorly characterized. Here, we analyzed AAP communities across 113 globally-distributed surface ocean stations sampled during the Malaspina Expedition in the tropical and subtropical ocean. By means of amplicon sequencing of the pufM gene, a genetic marker for this functional group, we show that AAP communities along the surface ocean were mainly composed of members of the Halieaceae (Gammaproteobacteria), which were adapted to a large range of environmental conditions, and of different clades of the Alphaproteobacteria, which seemed to dominate under particular circumstances, such as in the oligotrophic gyres. AAP taxa were spatially structured within each of the studied oceans, with communities from adjacent stations sharing more taxonomic similarities. AAP communities were composed of a large pool of rare members and several habitat specialists. When compared to the surface ocean prokaryotic and picoeukaryotic communities, it appears that AAP communities display an idiosyncratic global biogeographical pattern, dominated by selection processes and less influenced by dispersal limitation. Our study contributes to the understanding of how AAP communities are distributed in the horizontal dimension and the mechanisms underlying their distribution across the global surface ocean.

The surface ocean is inhabited by a great variety of microorganisms with diverse and versatile metabolisms. Understanding the ecology of marine microbes is of paramount importance since they are essential components of the marine ecosystem, performing key transformations in almost all biogeochemical cycles. A functional group that has attracted the attention of microbial ecologists in the last years is the aerobic anoxygenic phototrophic bacteria, also known as “AAPs”, which are among the few bacterial groups which can use both dissolved organic matter and harvest solar energy for their growth. Their discovery in the surface ocean several years ago, changed the classical conception of bacterioplankton being composed of photoautotrophic microorganisms as primary producers and of chemoheterotrophs as consumers, and forced to rethink the models of organic carbon cycles in the ocean. Since then, AAP bacteria have been studied in diverse marine ecosystems, and at different seasonal scales to understand their ecological role. In this study, we provide the first global assessment of AAP bacterial communities across the tropical and subtropical oceans, using samples collected by the Malaspina Circumnavigation Expedition. By using amplicon sequence variants of the pufM gene, the genetic marker for this functional group, we were able to inspect the composition of AAP communities at a fine scale and describe their diversity and biogeographic patterns. AAP communities in the surface ocean are mainly composed of members of the Halieaceae (Gammaproteobacteria) and different clades of the Alphaproteobacteria, and their distribution changes along gradients of salinity, temperature, and chlorophyll-a concentration. We show that AAP bacteria display their own spatial patterns that largely differ from the observed for the bulk bacterioplankton. Their communities are highly subjected to small changes in environmental conditions and as a result, are dominated by many rare bacteria and h

Ocean microbes constitute ~ 70% of the marine biomass, are responsible for ~ 50% of the Earth’s primary production and are crucial for global biogeochemical cycles. Marine microbiotas include core taxa that are usually key for ecosystem function. Despite their importance, core marine microbes are relatively unknown, which reflects the lack of consensus on how to identify them. So far, most core microbiotas have been defined based on species occurrence and abundance. Yet, species interactions are also important to identify core microbes, as communities include interacting species. Here, we investigate interconnected bacteria and small protists of the core pelagic microbiota populating a long-term marine-coastal observatory in the Mediterranean Sea over a decade.

The Mediterranean Sea is subjected to strong anthropogenic pressures that may be causing important ecosystem changes, particularly in coastal areas under high anthropogenic pressure. We characterized the composition of the microzooplankton community in a coastal area in the N Alboran Sea (SW Mediterranean) highly impacted by urban wastewater pollution. Two offshore outfalls release urban wastewater to the sea at a 40 m bottom depth, from a nearby town. We applied an integrative taxonomic approach, combining metabarcoding of the mitochondrial COI and the 18S rRNA genes with morphological microscopic identification of organisms, collected with a CalVET net (50 µm mesh). Hydrology was notably affected near the bottom at the vicinity of the submarine emissaries exit, presenting increased temperature and turbidity, and decreased salinity due to the urban freshwater discharge. Nutrient concentrations exceeded the Water Framework Directive limits; however, chlorophyll a concentrations were not very high, due to strong water column stratification. Microzooplankton communities (50-200 µm) were dominated by dinoflagellates (50-80% relative abundance), followed by copepods (copepodites and nauplii), eggs and cysts. We found significant differences in communities’ composition between the coastal shallow area and the offshore waters, driven by pollution and stratification.

Marine microbes play fundamental roles in nutrient cycling and climate regulation at a planetary scale. The field of marine microbial ecology has experienced major breakthroughs following the application of high-throughput sequencing and cultureindependent methodologies that have pushed the exploration of the marine microbiome to an unprecedented scale. This chapter overviews how the advances in gene- and genome-centric approaches as well as in culturing and single cell physiological methodologies in conjunction with global oceanographic circumnavigation expeditions and long-term time series are fueling our understanding of the biogeography, temporal dynamics, functional diversity, and evolutionary processes of microbial populations. We discuss how the joint effort of all those integrative approaches will help to boost our knowledge of the marine microbiome to reach a predictive understanding of how it is going to evolve in future scenarios.