Biology subjects

Cochero, J.

Publications and source records attributed to Cochero, J..

3 recordsLinked to original sources

bioRxiv2021

DiaThor: R package for computing diatom metrics and biotic indices

O_LIDiatoms are widely used to detect changes in water quality due to their specific sensibility to a variety of environmental conditions. Among the different diatom-based tools to measure water quality, the biotic indices, ecological and morphological traits are the most commonly used. C_LIO_LIDiaThor, contains 18 functions that provide morphological data of the samples (number and shape of chloroplasts, total biovolume), ecological data (species richness, evenness, diversity, size classes, ecological guilds, ecological preferences) and biotic indices (Descy Index, EPID Index, Indice Diatomique Artois-Picardie, Swiss Diatom Index, Pampean Diatom Index, ILM index, Specific Pollution sensitivity Index, Lobo Index, Sladecek index, SPEARherbicides index and the Trophic index). A web application (in Shiny) was also developed to provide access to the package for those users not familiar with the R environment. C_LIO_LIThe structure of the package, how it functions and the structure of the input and output data are explained. To demonstrate the most common use of DiaThor, an example of the package performance is also provided. C_LIO_LIThe DiaThor package aims to contribute to the water quality assessment based on diatom assemblages, while also providing researchers with an open platform to suggest new statistics and functionalities to be integrated into future builds. C_LI

ecology↗

bioRxiv2020

Epipelic biofilms respond early to the impacts of urbanization in lowland streams

Multiple structural and functional endpoints of stream biofilms are employed by water quality monitoring programs to detect both direct and indirect environmental impacts. Since multiple co-occurring stressors influence biofilm development, active biomonitoring (translocation experiments) could provide a useful monitoring tool that reflects the overall water quality of the urbanized sites. The aim of this research was to study the short-term responses of epipelic biofilms caused by their translocation to more polluted reaches in lowland urban streams. Fluvial sediment was translocated in three streams that run through urban areas following an urbanization gradient. The epipelic biofilms in the sediment were sampled to identify any fast occurring changes in their algal and bacterial biomasses, in their respiration and oxygen consumption. The results show that structural changes in the biofilm, such as an increased bacterial density and chlorophyll-a concentration, were measurable after two days of exposure to sites with impaired water quality. These immediate changes in the structure of the biofilm indicate that they are sensitive endpoints that can be employed in fast and inexpensive biomonitoring programs in urbanized streams.

ecology↗

bioRxiv2019

OPTIMOS PRIME: An R package for autoecological (optima and tolerance range) data calculation

O_LICalculation of autoecological data, such as optima and tolerance ranges to environmental variables, can be useful to establish the distribution and abundance of the species. These calculations, although mathematically not complex, can be prone to error when using a large database.\nC_LIO_LIWe present an R package (\"optimos.prime\") that uses species abundance data and environmental data to calculate the optimum value and tolerance range of each species to each environmental factor, by weighted average. Additionally, the package can create caterpillar plots to show the results.\nC_LIO_LIUsing sample data from a phytoplankton database, we exemplify the use of the R package and its functions. A stand-alone version for Windows is also provided, and source code and documents are freely available on GitHub to encourage collaborative work.\nC_LI

ecology↗