First insights into the prokaryotic community structure of Lake Cote, Costa Rica: Influence on nutrient cycling.

Prokaryotic diversity in lakes has been studied for many years mainly focusing on community structure and how the bacterial assemblages are driven by physicochemical conditions such as temperature, oxygen, and nutrients. However, little is known about how the composition and function of the prokaryotic community changes upon lake stratification. To elucidate this, we studied Lake Cote in Costa Rica determining prokaryotic diversity and community structure in conjunction with physicochemistry along vertical gradients during stratification and mixing periods. Of the parameters measured, ammonium, oxygen, and temperature, in that order, were the main determinants driving the variability in the prokaryotic community structure of the lake. Distinct stratification of Lake Cote occurred (March 2018) and the community diversity was compared to a period of complete mixing (March 2019). The microbial community analysis indicated that stratification significantly altered the bacterial composition in the epi-meta- and hypolimnion. During stratification, the Deltaproteobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, and Euryarchaeota were dominant in the hypolimnion yet largely absent in surface layers. Among these taxa, strict or facultative anaerobic bacteria were likely contributing to the lake nitrogen biogeochemical cycling, consistent with measurements of inorganic nitrogen measurements and microbial functional abundance predictions. In general, during both sampling events, a higher abundance of Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and Cyanobacteria was found in the oxygenated layers. Lake Cote had a unique bacterial diversity, with 80% of Amplicon Sequence Variant (ASV) recovered similar to unclassified/uncultured strains and exhibits archetypal shallow lake physicochemical but not microbial fluctuations worthy of further investigation. This study provides an example of lake hydrodynamics impacts to microbial community and their function in Central American lakes with implications for other shallow, upland, and oligotrophic lake systems.

Anaerobic methane oxidation in a coastal oxygen minimum zone: spatial and temporal dynamics.

Coastal waters are a major source of marine methane to the atmosphere. Particularly high concentrations of this potent greenhouse gas are found in anoxic waters, but it remains unclear if and to what extent anaerobic methanotrophs mitigate the methane flux. Here we investigate the long-term dynamics in methanotrophic activity and the methanotroph community in the coastal oxygen minimum zone (OMZ) of Golfo Dulce, Costa Rica, combining biogeochemical analyses, experimental incubations and 16S rRNA gene sequencing over 3 consecutive years. Our results demonstrate a stable redox zonation across the years with high concentrations of methane (up to 1.7 µmol L-1 ) in anoxic bottom waters. However, we also measured high activities of anaerobic methane oxidation in the OMZ core (rate constant, k, averaging 30 yr-1 in 2018 and 8 yr-1 in 2019-2020). The OPU3 and Deep Sea-1 clades of the Methylococcales were implicated as conveyors of the activity, peaking in relative abundance 5-25 m below the oxic-anoxic interface and in the deep anoxic water respectively. Although their genetic capacity for anaerobic methane oxidation remains unexplored, their sustained high relative abundance indicates an adaptation of these clades to the anoxic, methane-rich OMZ environment, allowing them to play major roles in mitigating methane fluxes.

Marine litter on sandy beaches with different human uses and waste management along the Gulf of Nicoya, Costa Rica.

This study was a baseline with quantitative data of marine litter along the Gulf of Nicoya, Costa Rica. The objective of the study was to quantify marine litter and its association with human activities in this estuarine gulf. A total of fourteen sandy beaches were cataloged by the degree of urbanization, tourism intensity, beach cleaning programs, and tributary rivers as possible drivers of marine litter presence. The items of the marine litter were separated and weighted by type. Analysis by the clean coastal index (CCI) and multivariate statistics were applied to find spatial patterns in marine litter in the gulf. On beaches with the highest touristic activity, cigarette butts and straws were the main components. Locations with river plume influence, less frequent cleanup, or waste cans showed more bottles, plastic parts, and sanitary waste than beaches in other conditions. A beach in a fisherman town had recently utilized plastic bags, household goods, and boat parts in the marine litter. A wildlife refuge beach showed only small plastic and coffee foam cup fragments that came with currents from other points in the estuary. River basin management, solid waste disposal programs, and environmental education to avoid single-use items combined with correct waste disposal are needed to reduce marine litter in tropical countries focused on ecological tourism.

A fjord-like tropical ecosystem, Pacific coast of Costa Rica: overview of research in Golfo Dulce / Un ecosistema tropical similar a un fiordo, costa del Pacífico de Costa Rica: panorama de la investigación en el Golfo Dulce

Abstract Introduction: Coastal ecosystems worldwide are under the influence of local, regional and global stressors, such as pollution, eutrophication and climate change. Golfo Dulce is a relatively pristine and accessible deep tropical ecosystem that provides opportunities for comparative and collaborative research. Objective: To summarize published reports on past research conducted in this ecosystem, identify topics for further study, and suggest new research issues. Methods: A search was made on the web for reports based on research conducted in Golfo Dulce and published in scientific journals. Reports focusing on environmental parameters and on the biota were included. Results: A total of 123 studies that include data from Golfo Dulce are cited. The four topics more frequently addressed were reports based on the results of the R/V Victor Hensen expedition (1993-1994) and follow-up work on microbiology, studies on water parameters, research on vertebrates, and zooplankton studies. The reports focusing on vertical profiles of oxygen and temperature are discussed in detail, followed by those on the biota. Conclusions: Golfo Dulce has low oxygen concentrations below 50 m and is frequently anoxic at the 200 m deep basin with occasional formation of H2S. However, the ecosystem contains a relatively high diversity of identified organisms, from bacteria to whales. Of particular relevance for future studies are multidisciplinary surveys aiming at obtaining data on primary productivity, the diversity and biomass of the main groups of planktonic, demersal and benthic organisms, and the frequency and magnitude of the influx of deep offshore waters over the sill into the basin. These data, as well as the information gathered in the past, are essential for updating the trophic model developed more than 25 years ago and in support of new predictive models on the functioning of the ecosystem.

Resumen Introducción: Los ecosistemas costeros alrededor del mundo están bajo la influencia de tensores locales, regionales y globales, como la contaminación, la eutroficación y el cambio climático. El Golfo Dulce es un profundo ecosistema tropical relativamente inalterado y accesible, que provee oportunidades para la investigación comparativa y colaborativa. Objetivo: Resumir los informes publicados sobre investigaciones pasadas realizadas en el ecosistema, identificar tópicos para estudios futuros y sugerir nuevas áreas de investigación. Métodos: Se hizo una búsqueda en la red de informes basados en investigaciones hechas en Golfo Dulce y publicadas en revistas científicas. Fueron incluidos aquellos informes sobre parámetros ambientales y la biota. Resultados: Un total de 123 estudios que incluyen datos sobre Golfo Dulce son citados. Los cuatro tópicos citados con más frecuencia fueron: Los resultados de la expedición del R/V Victor Hensen (1993-1994) y estudios de seguimiento sobre microbiología, informes sobre parámetros acuáticos, investigaciones sobre vertebrados y estudios sobre zooplancton. Los informes sobre perfiles de oxígeno y temperatura son presentados con mayor detalle, seguidos por aquellos sobre la biota. Conclusiones: Golfo Dulce tiene bajas concentraciones de oxígeno por debajo de 50 m y es usualmente anóxico a 200 m en el fondo, con formación ocasional de H2S. Sin embargo, el ecosistema contiene una diversidad de organismos identificados relativamente alta, desde bacterias hasta ballenas. De relevancia particular para futuros estudios es, entre otros, la conducción, de muestreos multidisciplinarios orientados a obtener datos sobre productividad primaria, la diversidad y biomasa de los principales grupos de organismos planctónicos, demersales y bénticos, así como la frecuencia y magnitud del flujo de agua oceánica hacia el interior. Estos datos, así como los obtenidos en el pasado, son esenciales para actualizar el modelo trófico desarrollado hace más de 25 años, o en apoyo de nuevos modelos predictivos de funcionamiento del ecosistema.

Water column dissolved silica concentration limits microphytobenthic primary production in intertidal sediments.

Primary production of microphytobenthos (MPB) contributes significantly to the total production in shallow coastal environments. MPB is a diverse community in which diatoms are usually the main microalgal group. Diatoms require N, P, and other nutrients as with other autotrophs, but in addition require silicate to create their outer cell wall. Therefore, dissolved silica (DSi) might be a potential limiting factor for benthic primary production in areas with reduced freshwater input. To test this hypothesis, a microcosm experiment was conducted using intact sediment cores collected from an intertidal mudflat in the Bay of Cádiz and supplied with increasing concentrations of DSi (0, 5, 10, 25, and 45 µmol · L-1 ). After 7 d of enrichment, we determined chlorophyll a and c (Chl a, c) contents, metabolic rates (Net [Pn ] and Areal Gross [PgA ] Production and Light [RL ] and Dark [RD ] Respiration), as well as fluxes of inorganic nutrients across the sediment-water interface. Chl a and c contents increased significantly with respect to the initial conditions but no differences between treatments were found. Both Pn and PgA showed a saturating-like pattern with silicate concentration, reaching maximum rates at a DSi concentration of 45 µmol · L-1 . The addition of DSi also resulted in an increase of DSi and ammonium uptake by the sediment, which was significantly higher in light than in darkness. Our results clearly show that water column DSi concentrations have a direct impact on benthic primary production, also controlling other related processes such as inorganic nutrient fluxes.

NC10 bacteria in marine oxygen minimum zones.

Bacteria of the NC10 phylum link anaerobic methane oxidation to nitrite denitrification through a unique O2-producing intra-aerobic methanotrophy pathway. A niche for NC10 in the pelagic ocean has not been confirmed. We show that NC10 bacteria are present and transcriptionally active in oceanic oxygen minimum zones (OMZs) off northern Mexico and Costa Rica. NC10 16S rRNA genes were detected at all sites, peaking in abundance in the anoxic zone with elevated nitrite and methane concentrations. Phylogenetic analysis of particulate methane monooxygenase genes further confirmed the presence of NC10. rRNA and mRNA transcripts assignable to NC10 peaked within the OMZ and included genes of the putative nitrite-dependent intra-aerobic pathway, with high representation of transcripts containing the unique motif structure of the nitric oxide (NO) reductase of NC10 bacteria, hypothesized to participate in O2-producing NO dismutation. These findings confirm pelagic OMZs as a niche for NC10, suggesting a role for this group in OMZ nitrogen, methane and oxygen cycling.

Productividad primaria en el Humedal Nacional Térraba-Sierpe, Costa Rica / Primary productivity in the National Térraba-Sierpe Wetland, Costa Rica

Resumen Se determinó la productividad primaria (PP) del fitoplancton en un amplio sector del Humedal Nacional Térraba Sierpe (HNTS) de Costa Rica, durante la estación lluviosa del año 2008 y en la estación seca del año 2009. Seis sitios se ubicaron en las áreas norte y central del humedal, donde por lo general ocurre la mayor influencia del aporte de caudal del Río Grande de Térraba. Se realizaron adicionalmente determinaciones de otros parámetros ambientales, asociados con la productividad primaria, como profundidad de penetración del disco de Secchi, la concentración de sólidos en suspensión, la concentración de clorofila a, la salinidad, la temperatura, la concentración del oxígeno disuelto en el agua, la concentración de nutrimentos inorgánicos disueltos (amonio, nitrito, fósforo disuelto, silicato), la conductividad eléctrica específica y se llevó a cabo un estudio basado en el análisis de componentes principales. La PP en el HNTS fue en general baja, con un valor máximo de 8.16gC/m2·d de PPN, el cual se registró en la estación seca, en marzo del 2009, en Isla Loros. Los sitios de mayor influencia del río (Samu y El Caite en la estación lluviosa), fueron los que tuvieron valores más bajos, mientras que los sitios con mayor influencia marina fueron los que presentaron los valores más altos de este estudio, cuyo promedio y desviación estándar fue de 0.79±0.50gC/m2.d (n=12), y la mediana fue 0.80gC/m2.d. Esta diferencia se debe principalmente al elevado aporte de agua dulce y de sólidos en suspensión del Río Grande de Térraba que limita el desarrollo del fitoplancton marino en el humedal. Es importante que se establezca y mantenga un programa de monitoreo de los parámetros medidos en este estudio, con al menos dos muestreos por año, uno en la época seca y otro en la época lluviosa, siguiendo el gradiente de salinidad desde el río hasta el mar al menos en dos direcciones.

Abstract Phytoplankton primary production (PP) was determined in a broad sector of the Térraba-Sierpe National Wetland, Costa Rica, from September to November 2008 in the rainy season and from January to March 2009 in the dry season. Six sampling stations were located at the Northern and Central zone of the wetland, according to the main expected flux of Río Grande de Térraba. Additionally other environmental parameters such as Secchi disk depth, suspended solid matter concentration, chlorophyll-a concentration, salinity, temperature, dissolved oxygen concentration, dissolved inorganic nutrients concentrations (phosphate, nitrate, ammonium and silicate), specific conductivity were also measured and a principal components analysis was performed. The PP in the Terraba-Sierpe National Wetland (HNTS by its Spanish name) was generally low, with a maximum value of 8.16gC/m2·d of Net Primary Productivity (NPP), which was recorded in the dry season, in March 2009, at Loros island. Sites that had a greater riverine influence showed lower PP values, while sites with greater marine influence presented higher PP values. These latter had an average and standard deviation of 0.79±0.50gC/m2·d (n=12). This difference is the result of the high input of freshwater and suspended solids from the Río Grande de Térraba which limits the development of marine phytoplankton in the wetland. Rev. Biol. Trop. 63 (Suppl. 1): 9-28. Epub 2015 April 01.

Hidrocarburos de petróleo, disueltos y dispersos, en cuatro ambientes costeros de Costa Rica / Oil pollution status expressed as the fraction of dissolved and dispersed petroleum hydrocarbons

Entre los años 2000 a 2002 se recolectaron y se analizaron 130 muestras de agua de mar en las costas de Costa Rica, para determinarles la concentración de hidrocarburos de petróleo disueltos y dispersos (HPDD), referida a equivalentes de criseno en hexano, y expresada como µg·L-1. Se utilizó la técnica analítica de fluorescencia molecular. 42 muestras correspondieron al Caribe (Moín) y 81 al Pacífico (Bahía Culebra, Golfo de Nicoya, Golfo Dulce y en una ocasión se tomaron muestras a lo largo del Estero de Puntarenas). En la zona costera de Moín el promedio de la concentración de HPDD fue 0.10 µg·L-1, con una desviación estándar de ± 0.18 µg·L-1, en un ámbito desde concentraciones no detectables por el método, (nd), hasta 0.65 µg·L-1. En el Pacífico las concentraciones para todo el período del estudio, estuvieron entre nd y 0.37 µg·L-1. En la Bahía Culebra no se detectaron HPDD en ninguna de las muestras (n = 12); en el Golfo de Nicoya el promedio y la desviación estándar fueron 0.04 µg·L-1 ± 0.09 µg·L-1 (n = 51), en un ámbito desde nd hasta 0.33 µg·L-1. En el Golfo Dulce el promedio y la desviación estándar fueron 0.05 µg·L-1 ± 0.11 µg·L-1 (n = 18), en el ámbito desde nd a 0.37 µg·L-1. Durante las fechas en que se llevó a cabo el muestreo, no se encontró una situación de contaminación por petróleo en los ecosistemas costeros estudiados, puesto que las concentraciones de HPDD no rebasaron el límite de 10 µg·L-1 referido a equivalentes de criseno, considerado típico de áreas oceánicas contaminadas. En Bahía Culebra fue la primera vez que se hizo el estudio de la contaminación por petróleo y se comprobó que en las fechas de muestreo la zona estuvo libre de esta contaminación. El promedio y la desviación estándar en el Estero de Puntarenas fueron 1.21 µg·L-1 ± 2.10 µg·L-1 (n = 7), en un ámbito de 0.17 a 5.91 µg·L-1. Estos resultados evidenciaron una situación de contaminación moderada y la naturaleza estuarina de este cuerpo de agua costera, que distribuye irregularmente los HPDD descargados en ella

Four coastal ecosystems with contrasting characteristics were sampled in Costa Rica (2000 – 2002). Oil pollution status, expressed as the fraction of dissolved/dispersed petroleum hydrocarbons related to chrysene equivalents, was determined by the molecular fluorescence analytical technique. A total of 130 water samples were taken, from the Caribbean (Moín Bay), and from the Pacific (Bahía Culebra, Gulf of Nicoya and Dulce Gulf). On one occasion, seven samples along the Puntarenas estuary were also analysed. In Moín the mean and standard deviation were 0.10 µg·L-1 ± 0.18 µg·L-1, ranging from non detectable (nd) to 0.65 µg·L-1. For the Pacific ecosystems the total range was from nd to 0.37 µg·L-1. In Bahía Culebra no fluorescence signals were obtained. In the Gulf of Nicoya the mean and standard deviation were 0.04 µg·L-1 ± 0.09 µg·L-1, from nd to 0.33 µg·L-1. Values in Dulce Gulf were 0.05 µg·L-1 ± 0.11 µg·L-1, from nd to 0.37 µg·L-1. Along the Puntarenas estuary the range was 0.17 to 5.91 µg·L-1, with a mean of 1.21 µg·L-1 and a standard deviation of ± 2.10 µg·L-1. The four coastal ecosystems had concentrations below the 10 µg·L-1 limit for polluted oceanic areas. The Puntarenas estuary reflects the influence of antropogenic activities from and around the City of Puntarenas. These levels are considered low for inshore waters

[Oil pollution status expressed as the fraction of dissolved and dispersed petroleum hydrocarbons]. / Hidrocarburos de petróleo, disueltos y dispersos, en cuatro ambientes costeros de Costa Rica.

Four coastal ecosystems with contrasting characteristics were sampled in Costa Rica (2000-2002). Oil pollution status, expressed as the fraction of dissolved/dispersed petroleum hydrocarbons related to chrysene equivalents, was determined by the molecular fluorescence analytical technique. A total of 130 water samples were taken, from the Caribbean (Moín Bay), and from the Pacific (Bahía Culebra, Gulf of Nicoya and Dulce Gulf). On one occasion, seven samples along the Puntarenas estuary were also analysed. In Moín the mean and standard deviation were 0.10 microg x L(-1) +/- 0.18 micro x L(-1), ranging from non detectable (nd) to 0.65 microg x L(-1). For the Pacific ecosystems the total range was from nd to 0.37 microg x L(-1). In Bahia Culebra no fluorescence signals were obtained. In the Gulf of Nicoya the mean and standard deviation were 0.04 microg x L(-1) +/- 0.09 microg x L(-1), from nd to 0.33 microg x L(-1). Values in Dulce Gulf were 0.05 microg x L(-1) +/- 0.11 microg x L(-1), from nd to 0.37 microg x L(-1). Along the Puntarenas estuary the range was 0.17 to 5.91 microg x L(-1), with a mean of 1.21 microg x L(-1) and a standard deviation of +/- 2.10 microg x L(-1). The four coastal ecosystems had concentrations below the 10 microg x L(-1) limit for polluted oceanic areas. The Puntarenas estuary reflects the influence of antropogenic activities from and around the City of Puntarenas. These levels are considered low for inshore waters.