Camila Fernandez

Camila Fernandez
Observatoire Océanologique de Banyuls · Laboratoire Oceanographie Microbienne

About

96
Publications
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Publications

Publications (96)
Article
Full-text available
In this study, we used stable isotopes of oxygen (δ¹⁸O), deuterium (δD), and dissolved inorganic carbon (δ¹³CDIC) in combination with temperature, salinity, oxygen, and nutrient concentrations to characterize the coastal (71°–78°W) and an oceanic (82°–98°W) water masses (SAAW—Subantarctic Surface Water; STW—Subtropical Water; ESSW—Equatorial Subsur...
Article
Full-text available
Chile is the second largest global producer of farmed salmon. The growth of salmon production has not been free of environmental challenges, such as the increasing use of pesticides to control the parasitic load of the sea lice Caligus rogercresseyi. The lack of the specificity of pesticides can potentially affect non-target organisms, as well as t...
Article
Full-text available
Aquaculture releases organic matter to the water column through excretion, fecal pellets, and uneaten food, but also by the continuous release of fish epithelium mucus. The effect of the latter on natural bacterial assemblages was determined using ammonium amended experiments at Puyuhuapi fjord in Chilean Patagonia. Mucus was added to seawater comi...
Article
The landscapes of high-altitude wetland ecosystems are characterized by different kinds of aquatic sites, including ponds holding conspicuous microbial life. Here, we examined a representative pond of the wetland landscape for dynamics of greenhouse gases, and their association with other relevant biogeochemical conditions including diel shifts of...
Chapter
Salar de Huasco is a high-altitude (3800 m a.s.l.) polyextreme aquatic environment located in the Chilean Altiplano. This chapter highlights over 15 years of microbial ecology research conducted in this fascinating system covering microbial diversity, microbial adaptation to extreme conditions, and the role of microbes in biogeochemical cycles, inc...
Article
We studied the input of ammonium coming from the dissolution of food pellets commonly used in salmon farming as well as its potential for mineralization via ammonification and ammonium oxidation by natural bacterioplankton communities. Through experiments in central and southern Chile, we evaluated the potential for photo‐ and bio‐ammonification of...
Book
Full-text available
Únicamente tenemos un solo océano, cubre el 72 % de la superficie terrestre y es esencial para la humanidad. El océano ha permitido que la Tierra sea un planeta habitable y los beneficios que nos brinda en nuestro día a día son numerosos. Sin duda, su rol en el ámbito socioeconómico, climático y ambiental, incluso en zonas alejadas del mar, lo hace...
Article
Full-text available
The high production levels of the Chilean salmon farming industry have resulted in the emergence of several diseases that affect all stages of development of cultured species. The parasitic copepod Caligus rogercresseyi is considered a potential vector of pathologies, and different chemical compounds such as pyrethroids and organophosphates have be...
Article
Full-text available
Zooplankton play a key role in the regeneration of nitrogen and phosphorus in the ocean through grazing and metabolism. This study investigates the role of the organic and inorganic nitrogen and phosphorus compounds released by copepods on biogeochemical processes and on the microbial community composition during the OUTPACE cruise (18 February–3 A...
Article
Full-text available
Composition, carbon and nitrogen uptake, and gene transcription of microbial mat communities in Porcelana neutral hot spring (Northern Chilean Patagonia) were analyzed using metagenomics, metatranscriptomics and isotopically labeled carbon (H13CO3) and nitrogen (15NH4Cl and K15NO3) assimilation rates. The microbial mat community included 31 phyla,...
Data
Total transcripts (cDNA) assigned to phototrophic processes. (a) Transcripts associated with photosystems PSI (psaA gene) and PSII (psbA gene) in oxygenic photosynthesis. (b) Transcripts (pufM, fmoA, pscA and bchC genes) associated with anoxygenic photosynthesis. Each bar represents a different temperature and daily period. Transcripts were normali...
Data
Diurnal carbon and nitrogen assimilation rates recorded at 58 and 48°C in Porcelana microbial mats. Nitrogen fixation data from Alcamán et al. (2015). The black bars represent the C or N assimilation rates in the dark.
Data
Process and pathways analyzed with principal genes associated and encoding protein. All this was used as diagnostic for phototrophy, autotrophy, and nitrogen cycle transformations.
Data
Taxonomic assignment of Chloroflexi by metagenomic (DNA; white bars) and metatranscriptomic reads (cDNA day: gray bars; cDNA night: black bars) at the Order (a) and genus (b) levels at the three temperatures studied.
Data
Total transcripts (cDNA) associated with the autotrophic carbon fixation pathways. CC, Calvin–Benson–Basham cycle (rbcL gene); 3HP, 3-hydroxypropionate bi-cycle (mcr gene); HH, hydroxypropionate-hydroxybutyrate cycle (atoB gene). Transcripts were normalized by RPKM.
Data
Total transcripts (cDNA) associated with specific carbon fixation pathways. (a) 3-Hydroxypropionate bi-cycle (mcr, prpE, and mcl genes) and (b) hydroxypropionate-hydroxybutyrate atoB, crt, abfD, sucD genes) cycle. Transcripts were normalized by RPKM.
Data
Results of high throughput sequencing: raw reads, quality reads, percentage of reads corresponding to ribosomal RNA, non-ribosomal genes, non-redundant (NR) hits and percentage of the latter that could be taxonomically assigned. Numbers of sequences are shown in millions.
Data
Taxonomic assignment of Cyanobacteria by metagenomic (DNA; white bars) and metatranscriptomic reads (cDNA day: gray bars; cDNA night: black bars) at the three temperatures studied. (a) Proportion of cyanobacterial reads in different Orders. (b) Proportion of Stigonematales reads in different genera.
Data
Total reads assigned to Proteobacteria by 16S rRNA sequences recovered from metagenomes. Rhodospirillales (alphaproteobacteria) and Burkholderiales (betaproteobacteria) were the most abundant orders at the lowest temperature. Note that the vertical scale is logarithmic.
Data
Total transcripts (cDNA) assigned to nitrogen cycle pathways: ammonia transporter (amt gene), nitrate assimilation (narB gene), ammonia assimilation (glnA gene), ammonia oxidation (amoA gene), N2 fixation (nifH gene), DNRA (nrfA gene), and denitrification (nosZ gene). Transcripts were normalized by RPKM.
Data
Total percentage of Bacteria and Archaea phyla present in the entire temperature gradient of Porcelana hot spring at noon and night (N) periods.
Data
Best hits and % similarity in the SILVA database of the most relevant organisms found in Porcelana mat.
Article
Chromophoric dissolved organic matter (CDOM) is a biologically active component of dissolved organic matter that influences the optical properties of aquatic environments, thereby playing an important role in the photochemical and photobiology processes occurring in the euphotic layer. Three cruises were carried out at three contrasting oceanograph...
Article
Full-text available
Northern Chile harbors different bioclimatic zones including hyper-arid and arid ecosystems and hotspots of microbial life, such as high altitude wetlands, which may contribute differentially to greenhouse gases (GHG) such as carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O). In this study, we explored ground level GHG distribution and th...
Article
Full-text available
High altitude wetland holds freshwater springs, evaporitic ponds and lagoon with variable salinity and nutrients, potentially influencing the ecology of nitrifying communities. In this study, nitrifying microorganisms in Salar de Huasco (Chile) were surveyed to determine bacterial and archaeal contribution to ammonium (AO), nitrite oxidation (NO),...
Article
Full-text available
Zooplankton play a key role in the regeneration of nitrogen and phosphorus in the ocean through grazing and metabolism. This study investigates the role of the organic and inorganic nitrogen and phosphorus compounds released by copepods on biogeochemical processes and on the microbial community composition during the OUTPACE cruise (18 February–3 A...
Article
Aquaculture has become an important component of Chilean economy, especially in the southern region, where salmon farming is an active industry. However, high density in salmon cages can increase stress and susceptibility to parasitic outbreaks of the copepod Caligus rogercresseyi. The pesticides used against sea lice can have potential effects on...
Article
Full-text available
Copepods are important suppliers of bioreactive compounds for marine bacteria through fecal pellet production, sloppy feeding, and the excretion of dissolved compounds. However, the interaction between copepods and bacteria in the marine environment is poorly understood. We determined the nitrogen and phosphorus compounds excreted by copepods fed w...
Article
The role of zooplankton in microbial nitrogen turnover in marine environments is poorly understood. Here, we present results from two experiments designed to determine the excretion rate of ammonium and dissolved organic nitrogen (DON) by dominant copepods, Acartia tonsa and Paracalanus cf indicus, fed with two natural sized-fractioned diets (20–15...
Article
Full-text available
We report the seasonal and single-diurnal variability of potentially active members of the prokaryote community in coastal surface waters off central Chile and the relationship between nitrifiers and solar radiation by combining 16S cDNA-based pyrosequencing, RT-qPCR of specific gene markers for nitrifiers (amoA, for general AOA, AOA-A, AOA-B, Nitr...
Article
Full-text available
Heterotrophic bacterial communities in marine environments are exposed to a heterogeneous mixture of dissolved organic compounds with different bioreactivity that may control both their activity and composition. The coastal environment is an example of a mixing area where recalcitrant allochthonous organic matter from rivers can encounter labile or...
Article
Full-text available
Although the Southern Ocean is considered a high-nutrient, low-chlorophyll (HNLC) area, massive and recurrent blooms are observed over and downstream of the Kerguelen Plateau. This mosaic of blooms is triggered by a higher iron supply resulting from the interaction between the Antarctic Circumpolar Current and the local bathymetry. Net primary prod...
Article
Nitrification, the microbially mediated oxidation of ammonium into nitrate, is generally expected to be low in the Southern Ocean mixed layer. This paradigm assumes that nitrate is mainly provided through vertical mixing and assimilated during the vegetative season, supporting the concept that nitrate uptake is equivalent to the new primary product...
Article
Full-text available
Cyanobacteria from Subsection V (Stigonematales) are important components of microbial mats in non-acidic terrestrial hot springs. Despite their diazotrophic nature (N2 fixers), their impact on the nitrogen cycle in such extreme ecosystems remains unknown. Here, we surveyed the identity and activity of diazotrophic cyanobacteria in the neutral hot...
Article
Although N2 fixation could represent a supplementary source of bioavailable nitrogen in coastal upwelling areas and underlying oxygen minimum zones (OMZs), the limited data available prevent assessing its variability and biogeochemical significance. Here we report the most extensive N2 fixation data set gathered to date in the upwelling area off ce...
Article
Full-text available
This paper presents whole water column data for nitrate N, O isotopic composition for the Kerguelen Plateau area and the basin extending east of Heard Island, aiming at understanding the N-cycling in this naturally iron fertilized area that is characterized by large recurrent phy-toplankton blooms. The KEOPS 2 expedition (October– November 2011) to...
Article
Full-text available
The concentrations of greenhouse gases (GHGs), such as nitrous oxide (N2O) and methane (CH4), were measured in the Kerguelen Plateau region (KPR). The KPR is affected by an annual microalgal bloom caused by natural iron fertilization, and this may stimulate the microbes involved in GHG cycling. This study was carried out during the KEOPS 2 cruise d...
Article
Full-text available
N2 fixation rates were measured during the KEOPS2 cruise in the HNLC area of Southern Ocean and in naturally iron-fertilized waters (Kerguelen Island 49.25° S, 69.58° E) using the 15N isotopic technique. We detected N2 fixation within the mixed layer at all stations, from the surface to 140 m depth. The data shows high variability with rates rangin...
Article
Full-text available
Although the Southern Ocean is considered a High Nutrient Low Chlorophyll area (HNLC), massive and recurrent blooms are observed over and downstream the Kerguelen Plateau. This mosaic of blooms is triggered by a higher iron supply resulting from the interaction between the Antarctic Circumpolar Current and the local bathymetry. Net primary producti...
Article
Full-text available
This paper presents whole water column data for nitrate N, O isotopic composition for the Kerguelen Plateau area and the basin extending east of the island, aiming at understanding the N-cycling in this naturally iron fertilized area that is characterized by large re-current phytoplankton blooms. The KEOPS 2 expedition (October–November 2011) took...
Article
Full-text available
The concentrations of greenhouse gases (GHGs) like nitrous oxide (N2O) and methane (CH4) were measured in the Kerguelen Plateau Region (KPR), an area with annual microalgal bloom caused by natural Fe fertilization, which may stimulate microbes involved in GHG cycling. This study was carried out during the KEOPS 2 cruise during the austral spring of...
Article
Full-text available
We investigated the production of ammonium by the photodegradation of dissolved organic matter (DOM) in the coastal upwelling system off central Chile (36°S). The mean penetration of solar radiation (Z1%) between April 2011 and February 2012 was 9.4 m, 4.4 m and 3.2 m for Photosynthetically Active Radiation (PAR; 400-700 nm), UV-A (320-400 nm) and...
Article
Full-text available
We analyzed the coupling between bacterioplankton and phytoplankton in Laguna de Rocha through an experimental approach. A freshwater zone of high turbidity and macrophytes growth and a brackish zone of higher light penetration and lower macrophytes biomass characterize this coastal lagoon. It has been shown that dissolved inorganic nitrogen, espec...
Article
Full-text available
Aerobic nitrite oxidation in marine environments plays a key role in the nitrification process. Marine bacteria involved in this nitrate-producing process have however been seldom studied compared with the ammonia-oxidizing community. Here, we report for the first time the community structure of aerobic nitrite-oxidizing bacteria (NOB) in the seaso...
Article
Full-text available
Despite the importance of nitrous oxide (N2O) in the global radiative balance and atmospheric ozone chemistry, its sources and sinks within the Earth's system are still poorly understood. In the ocean, N2O is produced by microbiological processes such as nitrification and partial denitrification, which account for about a third of global emissions....
Data
Isotopic and Isotopomeric determination (DOCX)
Data
Experimental setup used with in natural and cyanobacteria cultured samples to asses assimilative N2O fixation. (DOCX)
Data
ΔN2O inventories (µmol·m−2) and estimated net N2O production (µmol·m−2·d−1) in surface waters at selected stations along N2O air-sea exchange (µmol·m−2·d−1) and N2O consumption rates by fixation. In some station, denitrification and N2 fixation rates (both based on published data) are available in order to compare with other N2O consuming processes...
Data
Oceanic N2O undersaturation (saturation %) and air-sea flux (µmol m−2 d−1) reported in surface and subsurface/intermediate waters around the global ocean. Depths of hypoxic/suboxic waters are indicted (DOCX)
Article
Mesoscale features are recurrently found in the Coastal Transition Zone (CTZ) off central-southern Chile (∼35–40°S), a region characterized by seasonal wind-driven coastal upwelling. In this study, oceanographic data from two consecutive cruises carried out during the upwelling season (January 2009) were combined with satellite time series data in...
Article
Full-text available
The main processes involved in nitrogen cycling (as NO3- and NH4+ assimilation and their regeneration) were studied using N-tracer experiments in the coastal upwelling system off central Chile (36 degrees S). The study area shows seasonal surface fertilization and the development of subsurface hypoxia in austral spring and summer. The rates of NO3-...
Article
Full-text available
The semi-enclosed nature of the Mediterranean Sea, together with its smaller inertia due to the relative short residence time of its water masses, make it highly reactive to external forcings, in particular variations of water, energy and matter fluxes at the interfaces. This region, which has been identified as a “hotspot” for climate change, is t...
Article
Nitrogen excretion by zooplankton was studied in the coastal upwelling area off Concepción (36° S) in central/southern Chile. Experiments were performed using numerically dominant copepods of the mesozooplankton community during two contrasting periods (winter and spring 2009). The experimental setup was aimed at characterizing the organic and inor...
Data
Time course experiments of nitrogen fixation rates carried out in the upwelling system off central Chile (36°S) in 2008. Data shows (A) an accumulation of %15N in all samples over time and (B) A relatively constant trend in particulate nitrogen (PN) during the same experiments. Samples were obtained at 5 m (Times Series 1), 80 m (Time Series 2), 15...
Data
Distribution of the different OTUs found at each station and depth during the Galathea-3 cruise. (DOC)
Data