Clara Ruiz-González

Institut de Ciències del Mar · Marine biology and oceanography

Heterotrophic bacterioplankton are main consumers of dissolved organic matter (OM) in aquatic ecosystems, including the sunlit upper layers of the ocean and freshwater bodies. Their well-known sensitivity to ultraviolet radiation (UVR), together with some recently discovered mechanisms bacteria have evolved to benefit from photosynthetically availa...

Aim The need to go beyond taxonomy to understand patterns in microbial function has led to an increased use of trait‐based approaches, yet we know little about how microbial functional traits vary across large‐scale environmental gradients in natural ecosystems. Here, we apply a trait‐based approach to explore the large‐scale variability in the tra...

Bacteria inhabiting boreal freshwaters are part of metacommunities where local assemblages are often linked by the flow of water in the landscape, yet the resulting spatial structure and the boundaries of the network metacommunity have never been explored. Here, we reconstruct the spatial structure of the bacterial metacommunity in a complex boreal...

Deep ocean microbial communities rely on the organic carbon produced in the sunlit ocean, yet it remains unknown whether surface processes determine the assembly and function of bathypelagic prokaryotes to a larger extent than deep‐sea physico‐chemical conditions. Here, we explored whether variations in surface phytoplankton assemblages across Atla...

Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, the microbial dimension of SGD remains poorly understood. SGD can influence marine microbial communities through supplying chemical compounds and microorganisms, and in turn, microbes at the land-ocean transition zone determine the chemistry of the groundwater...

The ocean’s mercury (Hg) content has tripled due to anthropogenic activities, and although the dark ocean (>200 m) has become an important Hg reservoir, concentrations of the toxic and bioaccumulative methylmercury (MeHg) are low and therefore very difficult to measure. As a consequence, the current understanding of the Hg cycle in the deep ocean i...

The osmotrophic uptake of dissolved organic compounds in the ocean is considered to be dominated by heterotrophic prokaryotes, whereas the role of planktonic eukaryotes is still unclear. We explored the capacity of natural eukaryotic plankton communities to incorporate the synthetic amino acid L-homopropargylglycine (HPG, analogue of methionine) us...

Estuaries are among the most productive ecosystems in the world and are highly dynamic due to the interaction of freshwater and seawater, which results in strong spatial gradients in physico-chemical conditions. Bacterioplankton play a central role in these systems, driving the fluxes of carbon and energy, and being central for contaminant removal...

Coastal aquifers are characterized by their unique land-sea interaction and the main difficulty in studying these systems is the complexity of their biogeochemical cycles. Important processes in the "mixing zone" of coastal systems are associated with the ecosystem's diversity, and supply and exchange of chemical compounds. This coastal body known...

Antarctic polynyas are highly productive open water areas surrounded by ice where extensive phytoplankton blooms occur, but little is known about how these surface blooms influence carbon fluxes and prokaryotic communities from deeper waters. By sequencing the 16S rRNA gene, we explored the vertical connectivity of the prokaryotic assemblages assoc...

Subterranean estuaries are biogeochemically active coastal sites resulting from the underground mixing of fresh aquifer groundwater and seawater. In these systems, microbial activity can largely transform the chemical elements that may reach the sea through submarine groundwater discharge (SGD), but little is known about the microorganisms thriving...

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 amplico...

The role of the Arctic Ocean ecosystem in climate regulation may depend on the responses of marine microorganisms to environmental change. We applied genome-resolved metagenomics to 41 Arctic seawater samples, collected at various depths in different seasons during the Tara Oceans Polar Circle expedition, to evaluate the ecology, metabolic potentia...

Review article as part of the 2020 Award Pius Font i Quer de Ciències de la Vida by the Institut d'Estudis Catalans (IEC).-- 42 pages, 8 figures

In parts of the Baltic Sea, the phytoplankton spring bloom communities, commonly dominated by diatoms, are shifting toward the co‐occurrence of diatoms and dinoflagellates. Although phytoplankton are known to shape the composition and function of associated bacterioplankton communities, the potential bacterial responses to such a decrease of diatom...

Microbes associated with sinking marine particles play key roles in carbon sequestration in the ocean. The sampling of particle-attached microorganisms is often done with sediment traps or by filtration of water collected with oceanographic bottles, both involving a certain time lapse between collection and processing of samples that may result in...

Methane-oxidizing bacteria (MOB) present in the water column mitigate methane (CH4) emissions from hydropower complexes to the atmosphere. By creating a discontinuity in rivers, dams cause large environmental variations, including in CH4 and oxygen concentrations, between upstream, reservoir, and downstream segments. Although highest freshwater met...

The Arctic Ocean is a key player in the regulation of climate and at the same time is under increasing pressure as a result of climate change. Predicting the future of this ecosystem requires understanding of the responses of Arctic microorganisms to environmental change, as they are the main drivers of global biogeochemical cycles. However, little...

Prokaryotes play a fundamental role in decomposing organic matter in the ocean, but little is known about how microbial metabolic capabilities vary at the global ocean scale and what are the drivers causing this variation. We aimed at obtaining the first global exploration of the functional capabilities of prokaryotes in the ocean, with emphasis on...

Oceans connect all life and affect climate worldwide, and interestingly, the ocean’s smallest residents have a huge role in this process. The ocean microbiota modulates global biogeochemical cycles, which influences energy balance in the atmosphere. Unfortunately, the underlying factors structuring the ocean microbiota are unclear, and better under...

Background: The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have large-scale consequences. Yet, the underlying ecological mechanisms structuring it are unclear. Here, we investigate how fundamental ecological mechanisms (selection, dispersal and ecological drift) shape the smallest members of the tro...

Aerobic anoxygenic phototrophic (AAP) bacteria are a phylogenetically diverse and ubiquitous group of prokaryotes that use organic matter but can harvest light using bacteriochlorophyll a. Although the factors regulating AAP ecology have long been investigated through field surveys, the few available experimental studies have considered AAP as a gr...

Background The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have largescale consequences. Yet, the underlying ecological mechanisms structuring it are unclear. Here we investigate how fundamental ecological mechanisms ( selection , dispersal and ecological drift ) shape the smallest members of the tro...

Lake methane (CH4) emissions are largely controlled by aerobic methane‐oxidizing bacteria (MOB) which mostly belong to the classes Alpha‐ and Gammaproteobacteria (Alpha‐ and Gamma‐MOB). Despite the known metabolic and ecological differences between the two MOB groups, their main environmental drivers and their relative contribution to CH4 oxidation...

Background The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have largescale consequences. Yet, the underlaying ecological mechanisms structuring it are unclear. Here we investigate how fundamental ecological mechanisms (selection, dispersal and ecological drift) shape the smallest members of the tropi...

Estuaries are among the most productive ecosystems in the world. They are considered as changing environments because the interaction of freshwater and seawater leads to the formation of specific conditions strongly influenced by a combination of physical, chemical and biological drivers. Nicoya´s gulf is a tropical estuary located in the Pacific c...

Aerobic methanotrophic bacteria (methanotrophs) use methane as a source of carbon and energy, thereby mitigating net methane emissions from natural sources. Methanotrophs represent a widespread and phylogenetically complex guild, yet the biogeography of this functional group and the factors that explain the taxonomic structure of the methanotrophic...

Experiments with bacteria in culture have shown that they often display “feast and famine” strategies that allow them to respond with fast growth upon pulses in resource availability, and enter a growth-arrest state when resources are limiting. Although feast responses have been observed in natural communities upon enrichment, it is unknown whether...

Microbial taxa range from being ubiquitous and abundant across space to extremely rare and endemic, depending on their ecophysiology and on different processes acting locally or regionally. However, little is known about how cosmopolitan or rare taxa combine to constitute communities and whether environmental variations promote changes in their rel...

In the Baltic Sea, climate change has caused shifts in the phytoplankton spring bloom communities with co-occurrence of diatoms and dinoflagellates. Such changes likely affect the composition and function of associated bacterioplankton, key members of the carbon cycling, although the actual effects are unknown. To understand how changes in phytopla...

In the Baltic Sea, climate change has caused shifts in the phytoplankton spring bloom communities with co-occurrence of diatoms and dinoflagellates. Such changes likely affect the composition and function of associated bacterioplankton, key members of the carbon cycling, although the actual effects are unknown. To understand how changes in phytopla...

In the Baltic Sea, climate change has caused shifts in the phytoplankton spring bloom communities with co-occurrence of diatoms and dinoflagellates. Such changes likely affect the composition and function of associated bacterioplankton, key members of the carbon cycling, although the actual effects are unknown. To understand how changes in phytopla...

In the Baltic Sea, climate change has caused shifts in the phytoplankton spring bloom communities with co-occurrence of diatoms and dinoflagellates. Such changes likely affect the composition and function of associated bacterioplankton, key members of the carbon cycling, although the actual effects are unknown. To understand how changes in phytopla...

The smallest members of the sunlit-ocean microbiome (prokaryotes and picoeukaryotes) participate in a plethora of ecosystem functions with planetary-scale effects. Understanding the processes determining the spatial turnover of this assemblage can help us better comprehend the links between microbiome species composition and ecosystem function. Eco...

The sinking of organic particles formed in the photic layer is a main vector of carbon export into the deep ocean. Although sinking particles are heavily colonized by microbes, so far it has not been explored whether this process plays a role in transferring prokaryotic diversity from surface to deep oceanic layers. Using Illumina sequencing of the...

Freshwater bacterioplankton communities are influenced by the inputs of material and bacteria from the surrounding landscape, yet few studies have investigated how different terrestrial inputs affect bacterioplankton. We examined whether the addition of soils collected under various tree species combinations differentially influences lake bacterial...

Freshwater bacterioplankton communities are influenced by the transport of bacteria from the surrounding terrestrial environments. It has been shown that, although most of these dispersed bacteria gradually disappear along the hydrologic continuum, some can thrive in aquatic systems and become dominant, leading to a gradual succession of communitie...

Seed banks are believed to contribute to compositional changes within and across microbial assemblages, but the application of this concept to natural communities remains challenging. Here we describe the core seed bank of a bacterial metacommunity from a boreal watershed, using the spatial distribution of bacterial operational taxonomic units (OTU...

One of the major contemporary challenges in microbial ecology has been to discriminate the reactive core from the random, unreactive components of bacterial communities. In previous work we used the spatial abundance distributions of bacterioplankton across boreal lakes of Québec to group taxa into four distinct categories that reflect either hydro...

Streams are typically supersaturated in carbon dioxide (CO2) and methane (CH4), and are recognized as important components of regional carbon (C) emissions in northern landscapes. Whereas there is consensus that in most of the systems the CO2 emitted by streams represents C fixed in the terrestrial ecosystem, the pathways delivering this C to strea...

Aquatic bacterial communities harbour thousands of coexisting taxa. To meet the challenge of discriminating between a ‘core’ and a sporadically occurring ‘random’ component of these communities, we explored the spatial abundance distribution of individual bacterioplankton taxa across 198 boreal lakes and their associated fluvial networks (188 river...

Disentangling the mechanisms shaping bacterioplankton communities across freshwater ecosystems requires considering a hydrologic dimension that can influence both dispersal and local sorting, but how the environment and hydrology interact to shape the biogeography of freshwater bacterioplankton over large spatial scales remains unexplored. Using Il...

Disentangling the mechanisms shaping bacterioplankton communities across freshwater ecosystems requires considering a hydrologic dimension that can influence both dispersal and local sorting, but how the environment and hydrology interact to shape the biogeography of freshwater bacterioplankton over large spatial scales remains unexplored. Using Il...

Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophs that despite their low abundances have been hypothesized to play an ecologically and biogeochemically important role in aquatic systems. Characterizing this role requires a better understanding of the in situ dynamics and activity of AAP bacteria. Here we provide the first assessm...

Deductions about the ecology of high taxonomic bacterial ranks (i.e., phylum, class, order) are often based on their abundance patterns, yet few studies have quantified how accurately variations in abundance of these bacterial groups represent the dynamics of the taxa within them. Using 454-pyrosequencing of the 16S rRNA gene, we investigated wheth...

A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straight forward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to...

Catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) is a powerful approach to quantify bacterial taxa. In this study, we compare the performance of the widely used Bacteroidetes CF319a probe with the new CF968 probe. In silico analyses and tests with isolates demonstrate that CF319a hybridizes with non-Bacteroidetes sequenc...

Microbial plankton experience short-term fluctuations in total solar irradiance and in its spectral composition as they are vertically moved by turbulence in the oceanic upper mixed layer (UML). The fact that the light exposure is not static but dynamic may have important consequences for biogeochemical processes and ocean–atmosphere fluxes. Howeve...

[1] Dimethylsulfide (DMS) is a biogenic gas with potential climatic effects, and its marine emission depends on the interplay between microbial activity and physical forcing in the oceanic upper mixed layer. We investigated the diel cycling patterns of DMS and its precursor dimethylsulfoniopropionate (DMSP) in four experiments (28 to 48 h long) per...

Microbial plankton experience fluctuations in total solar irradiance and in its spectral composition as they are vertically moved by turbulence in the oceanic upper mixed layer (UML). The fact that the light exposure is not static but dynamic may have important consequences for biogeochemical processes and ocean-atmosphere fluxes. However, most bio...

We investigated the short-term effects of variable solar irradiance and spectrum on the gross biological production of dimethylsulfide (DMS), a trace gas with potential climatic effects, in eight experiments performed at different times of the year in a northwest Mediterranean coastal site. Experimentally determined net community DMS production, DM...

Microbial plankton experience short-term fluctua-tions in total solar irradiance and in its spectral composition as they are vertically moved by turbulence in the oceanic up-per mixed layer (UML). The fact that the light exposure is not static but dynamic may have important consequences for bio-geochemical processes and ocean–atmosphere fluxes. How...

Large rivers are commonly regulated by damming, yet the effects of such disruption have seldom been studied on prokaryotic communities. We describe the effects of the three large reservoirs of the Ebro river (NE Iberian Peninsula) on bacterioplankton assemblages by comparing several sites located before and after the impoundments on three occasions...

The sensitivity of coastal marine bacterioplankton to natural photosynthetically active radiation (PAR, 400–700 nm) and ultraviolet radiation (UVR, 280– 400 nm) was evaluated in five experiments over a seasonal cycle in the Blanes Bay, NW Mediterranean Sea. Exposure to natural solar radiation generally inhibited bulk bacterial activities or damaged...

Even though the uptake and assimilation of organic compounds by phytoplankton has been long recognized, very little is still known about its potential ecological role in natural marine communities and whether it varies depending on the light regimes the algae experience. We combined measurements of size-fractionated assimilation of trace additions...

The effect of photosynthetically available radiation (PAR; 400-700 nm) and ultraviolet radiation (UVR; 280-400 nm) on marine bacterial heterotrophic activity was assessed monthly throughout a seasonal cycle in Blanes Bay (northwestern Mediterranean Sea). Seawater samples amended with H-3-leucine were exposed to solar radiation under three radiation...

The regulation of large rivers to meet human requirements (e.g. hydroelectricity production, flood prevention, recreation activities) alters the longitudinal distribution of plankton communities and may affect their capacity to use nutrients and organic matter. Here we analyzed phosphorus (P) availability and use by phytoplankton and bacterioplankt...

Bacterial community activity and structure are thought to be directly or indirectly related to phytoplankton development and, in particular, to the phytoplankton species dominating specific algal blooms. To test this hypothesis, we performed a mesocosm experiment designed to generate blooms of different types of phytoplankton through the additions...

Two diel cycle studies were conducted to determine the effect of day–night light changes on winter bacterial activity in the coastal Mediterranean (Blanes Bay Microbial Observatory). Bacterial abundances, bacterial heterotrophic activity, and flagellate grazing counts were determined at 4-h intervals during two 3-d periods separated by 2 d. Twice a...

There is a large body of evidence supporting a major role of heterotrophic bacteria in dimethylsulphoniopropionate (DMSP) utilisation as a source of reduced sulphur. However, a role for phototrophic microorganisms has been only recently described and little is known about their contribution to DMSP consumption and the potential modulating effects o...

The influence of solar ultraviolet radiation and photosynthetically active radiation (PAR) on summertime marine bacterial uptake and assimilation of sulfur from radiolabeled dimethlysulfoniopropionate (35S-DMSP) was studied at four Arctic and two Antarctic stations. Incubations with 3H-leucine were also conducted for comparative purposes as a measu...