Abstract
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 compromise ecosystem environmental status. Therefore, improved microbial plankton monitoring is essential to better understand how these communities respond to environmental shifts. The study of marine microbial communities typically involves highly cost and time-consuming sampling procedures, which can limit the frequency of sampling and data availability. 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 compact system able to operate up to 150 m depth. Water is pumped by a micropump (TCS MG2000) through a hydraulic circuit that allows in situ filtration of environmental water in 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 against traditional laboratory filtration standardized protocols. Results showed a good performance in terms of DNA recovery, as well as prokaryotic (16S rDNA) and eukaryotic (18S rDNA) community diversity analysis, using either methodologies. The IS-ABS automates the process of collecting environmental DNA, and is suitable for integration in water observation systems, what will contribute to substantially increase biological surveillances. Also, the use of highly sensitive genomic approaches allows a further study of the diversity and functions of whole or specific microbial communities.
Highlights
Life in aquatic environments, including marine and freshwater ecosystems is dominated by a vast diversity and abundance of microorganisms
All the components of in situ autonomous biosampler (IS-ABS) were housed in a 150 mm diameter and 500 mm length aluminum pressure housing allowing for operation up to 150 m depth (Fig 9)
Environmental DNA has been proposed as a new bio-monitoring tool [40], best practice protocols and cost effective techniques are still under development [41]
Summary
Life in aquatic environments, including marine and freshwater ecosystems is dominated by a vast diversity and abundance of microorganisms. The whole marine microbial communities including phyto and zooplankton, bacteria, archaea, unicellular eukaryotes, protozoans and fungi are estimated to account for more than 90% of the total oceanic biomass. The activities of complex marine microbial communities are fundamental for the survival of all marine life [1,2]. Imbalances in plankton microbial communities, usually caused by environmental shifts can compromise water quality and all associated uses [6]. There is a great interest and need to study planktonic microbial communities on relevant temporal and spatial scales, to characterize their diversity and functional dynamics using the currently available highly sensitive genomic approaches
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