The present study extended DNA fingerprinting analysis, which has been successfully applied in individual- and population-level research, to ecological investigation of plankton community. As we all know, the planktonic organisms play important roles in functioning of aquatic ecosystems and also in biogeochemical cycles. Therefore, researchers started to investigate their distribution, spatiotemporal dynamics and their potential relationships with environments since the very start of marine research expeditions. Traditional plankton investigations primarily focus on the composition and dynamics based on the morphospecies. However, morphological identification has historically been a difficult task due to the paucity of readily observable characters of taxonomic value. Additionally, only the planktonic organisms with certain size can be collected by the commonly used plankton nets, and many small organisms (e.g. bacterioplankton) were generally excluded in traditional plankton investigations. But these ignored microorganisms are usually very important in maintaining the balance of aquatic ecosystem. Here, the whole plankton community (including bacterioplankton, phytoplankton and zooplankton) were studied with metagenome-based fingerprinting methods.
This study characterized the biodiversity and dynamics of plankton community in target aquatic ecosystems, from species composition to metagenomic DNA fingerprints, to study the relationships between planktonic organisms and also between plankton community and environment. Firstly, the feasibility of applying DNA fingerprinting analysis to plankton community was explored and proved targeted the plankton communities from Donghu Lake. Then, RAPD and PCR-DGGE fingerprinting were applied to study the relationship between DNA polymorphisms and species composition of plankton communities in different ecosystems. Because community composition is dictated to a large degree by environmental factors, it is also a natural extension of this relationship between DNA fingerprints of plankton community and environmental conditions.
Studies in the Donghu Lake, Dongting Lake and the Three-Gorges Reservoir suggested that DNA fingerprints of plankton communities were generally correlated with species composition, as well as with physiochemical factors. Spatiotemporal heterogeneity of plankton communities in Donghu Lake indicated that factors strongly correlated with the distribution of plankton community were seasonally different. But the concentrations of total nitrogen (TN) and total phosphorus (TP) were generally the main factors related to the PCR-DGGE fingerprints of plankton communities. Additionally, environments that exhibit similar trophic level but different concentrations of heavy metals could be differentiated by the PCR-DGGE fingerprinting patterns. During ecological restoration in artificial simulation systems, plankton community succession (except the target cyanobacterial cells) was not significantly affected by the cyanobacteria removal process using chitosan-modified soils. TP was the most important environmental predictor of PCR-DGGE fingerprints of plankton community in the particular artificial niche. Additionally, the present study also explored DNA fingerprinting and sequencing for analyzing intestinal contents of filter-feeding fishes (silver carp and bighead carp), particular functional gene (nifH) and particular planktonic group (cyanobacteria). All these results suggested that metagenome-based fingerprinting analysis was promising tool for ecological investigation of plankton community. In fingerprinting analysis, multiple samples can be analyzed simultaneously with a standardized set of procedures, which making it practical to perform comparative analyses. It is reasonable to believe that metagenome-based study of plankton community will be an exciting direction for ecological study.