ena-STUDY-CIIMAR - Interdisciplinary Centre of Marine and Environmental Research-05-07-2018-18:25:27:391-1901
Development of an autonomous biosampler to capture in situ aquatic microbiomes
The importance of planktonic microbial communities is well acknowledged, since they are fundamental for several natural processes of aquatic ecosystems. Microorganisms naturally control the flux of nutrients, and also degrade and recycle anthropogenic organic and inorganic contaminants. Nevertheless, climate change effects and/or  the runoff of nutrients/pollutants can affect the equilibrium of natural microbial communities influencing the occurrence of microbial pathogens and/or microbial toxin producers, which can imbalance the natural ecosystem functioning and compromise ecosystem environmental status. Therefore, it is essential to improve microbial plankton monitoring to better understand how these communities respond to environmental shifts. However, monitoring marine microbial communities involves sampling procedures highly cost and time consumer difficulting the obtaining of samples and data. In this context we developed and validated an in situ autonomous biosampler (IS-ABS) able to collect/concentrate in situ planktonic communities of different size fractions (targeting prokaryotes and unicellular eukaryotes) for posterior genomic, metagenomic, and/or transcriptomic analysis at a home laboratory. The IS-ABS field prototype is a small size and compactness system able to operate up to 150 m depth. Water is pumped by a micropump (TCS MG2000), through an hydraulic circuit that allow in situ filtration of environmental water through one or more Sterivex filters placed in a filter cartridge. The IS-ABS also includes an application to program sampling definitions, allowing pre-setting configuration of the sampling. The efficiency of the IS-ABS was tested with traditional laboratory filtration standardized protocols, and results showed that there were no differences in terms of DNA recovery and prokaryotic (16S rDNA) and eukaryotic (18S rDNA) community diversity obtained by the IS-ABS. The IS-ABS automates the process of collecting environmental DNA and is expected to dramatically increase the biological surveillance capabilities by allowing its integration in water observation systems and by promoting the use of highly sensitive genomic approaches for the detection of the diversity and functions of whole or specific microbial communities.
The importance of planktonic microbial communities is well acknowledged, since they are fundamental for several natural processes of aquatic ecosystems. Microorganisms naturally control the flux of nutrients, and also degrade and recycle anthropogenic organic and inorganic contaminants. Nevertheless, climate change effects and/or  the runoff of nutrients/pollutants can affect the equilibrium of natural microbial communities influencing the occurrence of microbial pathogens and/or microbial toxin producers, which can imbalance the natural ecosystem functioning and compromise ecosystem environmental status. Therefore, it is essential to improve microbial plankton monitoring to better understand how these communities respond to environmental shifts. However, monitoring marine microbial communities involves sampling procedures highly cost and time consumer difficulting the obtaining of samples and data. In this context we developed and validated an in situ autonomous biosampler (IS-ABS) able to collect/concentrate in situ planktonic communities of different size fractions (targeting prokaryotes and unicellular eukaryotes) for posterior genomic, metagenomic, and/or transcriptomic analysis at a home laboratory. The IS-ABS field prototype is a small size and compactness system able to operate up to 150 m depth. Water is pumped by a micropump (TCS MG2000), through an hydraulic circuit that allow in situ filtration of environmental water through one or more Sterivex filters placed in a filter cartridge. The IS-ABS also includes an application to program sampling definitions, allowing pre-setting configuration of the sampling. The efficiency of the IS-ABS was tested with traditional laboratory filtration standardized protocols, and results showed that there were no differences in terms of DNA recovery and prokaryotic (16S rDNA) and eukaryotic (18S rDNA) community diversity obtained by the IS-ABS. The IS-ABS automates the process of collecting environmental DNA and is expected to dramatically increase the biological surveillance capabilities by allowing its integration in water observation systems and by promoting the use of highly sensitive genomic approaches for the detection of the diversity and functions of whole or specific microbial communities.