The objective of this project is to develop a protocol for fast and reliable monitoring of water quality in lentic systems. These include major river stretches, natural lakes, coastal brackish lagoons and reservoirs across several river basins in Spain. Among them are lagoons in Andalusia, as well as lagoons and reservoirs in the Segura, Miño and Guadiana basins. The project also covers transitional waters in Andalusia and Galicia.

This implies a broader geographical scope than the one covered by the project itself. The project is titled “Research and development of protocols using metabarcoding techniques for defining and adapting biological water-quality indices based on diatoms and benthic crustaceans.” A project awarded to Eurofins Cavendish, S.L., it is being carried out across a wider range of water-body types.

To achieve this, we will rely on diversity indices developed using organisms that function as ecological indicators of environmental quality. This approach has practical advantages: directly documenting ecosystem changes in relation to human activity would be costly and highly time-consuming.

Several biomonitoring protocols have been developed and incorporated into Spanish legislation. However, they are not fully suitable for lentic ecosystems because of the limitations associated with studying these organisms. In fact, phytoplankton, macroinvertebrates, aquatic flora and fish fauna form the basis for developing environmental-quality indices. The challenge is tat they are not consistently present across all water-body types, or (2) their sensivity to disturbances is debatable.

In addition, sampling processes are often tedious. Therefore, this project aims to develop new biological indices based on organisms that are not currently used as bioindicators, despite being sensitive to various alterations in these environments.

Identifying the different species is time-consuming, and the accuracy of the results depends largely on the taxonomic skills of the observer. Therefore, using them as ecological indicators requires a method that is faster and more precise than visually counting organisms under a microscope. This would allow the composition of the communities to be documented more effectively.

In this project, with the aim of developing a quality index based on Arcellinida, a novel environmental-quality monitoring protocol based on metabarcoding will be applied. This protocol consists of inferring the composition of environmental communities by sequencing a PCR amplicon of an appropriate DNA marker obtained from environmental DNA extracted from a sample taken in the study area. This marker —specific to this group of organisms— is currently being developed at the Royal Botanical Garden of Madrid.

The application of this approach to environmental monitoring has been enabled by the development of new high-throughput sequencing (HTS) technologies, such as Illumina MiSeq.

This technology delivers thousands to millions of sequence reads, enabling the simultaneous processing of hundreds of samples and the identification of organisms at species level, thereby increasing the sensivity of environmental-quality analyses.

In parallel, implementing new data-analysis methods based on supervised machine learning wil further increase the accuracy of environmental-quality assessment. The advantages of this protocol are numerous: it allows the rapid screening of the diversity of several hundred samples at once.

The implementation of the metabarcoding technique will overcome the drawbacks of conventional studies of biological communities; lentic-water sediment samples are easy to obtain, and the method does not require highly specialised personnel.

It should be noted that the use of this novel molecular methodology is a tool —rather than an end in itself— for obtaining a taxonomic list that will serve as the basis for developing the proposed biological index. In this respect, it shares this tool with the “Project on the adaptation of biological indices”, although its objective differs significantly.