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Harmful algae blooms (HABs) cause acute effects on marine ecosystems due to their production of endogenous toxins or their enormous biomass, leading to significant impacts on local economies and public health. Although HAB monitoring has been intensively performed at spatiotemporal scales in coastal areas of the world over the last decades, procedures have not yet been standardized. HAB monitoring procedures are complicated and consist of many methodologies, including physical, chemical, and biological water sample measurements. Each monitoring program currently uses different combinations of methodologies depending on site specific purposes, and many prior programs refer to the procedures in quotations. HAB monitoring programs in Chile have adopted the traditional microscopic and toxin analyses but not molecular biology and bacterial assemblage approaches. Here we select and optimize the HAB monitoring methodologies suitable for Chilean geography, emphasizing on metabarcoding analyses accompanied by the classical tools with considerations including cost, materials and instrument availability, and easiness and efficiency of performance. We present results from a pilot study using the standardized stepwise protocols, demonstrating feasibility and plausibility for sampling and analysis for the HAB monitoring. Such specific instructions in the standardized protocol are critical obtaining quality data under various research environments involving multiple stations, different analysts, various time-points, and long HAB monitoring duration.

Freshwater discharge affects the biogeochemistry of river-influenced nearshore environments by contributing with carbon and nutrients. An increase in human activities in river basins may alter the natural riverine nutrients and carbon export to coastal ecosystems. Along a wide latitudinal range (32°55′S–40°10′S), this study explores the role of climate and land use in determining the nutrient and carbon concentrations in the river mouth and fluxes to adjacent coastal areas. Between winter 2011 and fall 2012, we collected monthly samples in five river mouths in central southern Chile and at rocky shore sites affected by river plumes. Basins were characterized by different land uses and meteorological conditions along this latitudinal range. Water samples were collected for pH measurements, nutrients, dissolved organic and inorganic carbon, particulate organic carbon, and isotopic signatures (δ13C). Our results show a north-south gradient in concentrations of nutrients and carbon. The highest concentrations were observed in the Maipo basin, which presents the highest percentage of urban-industrial activities. Nutrients and carbon contributions, in most cases, were lowest in the southern Valdivia basin, which has the least human intervention and a greater percentage of vegetation. The Biobio River had the highest nutrient and carbon fluxes, in most cases, due to its high river discharge. Our results show the influence of river plume effects on carbon and nitrogen concentrations in river-influenced rocky shore sites. Moreover, our study suggests that land use might influence some parameters of carbonate system in rivers and river-influenced rocky shore environments. River-influenced rocky shore environments may exhibit suppression in aragonite saturation state with implications for calcifiers inhabiting these marine environments.