Spatial and temporal dynamics of a freshwater eukaryotic plankton community revealed via 18S rRNA gene metabarcoding

Abstract

DNA metabarcoding is a sophisticated molecular tool that can enhance biological surveys of freshwater plankton communities by providing broader taxonomic coverage and, for certain groups, higher taxonomic resolution compared to morphological methods. We conducted 18S rRNA gene metabarcoding analyses on 214 water samples collected over a four-month period from multiple sites within a freshwater reservoir. We detected 1,314 unique operational taxonomic units that included various metazoans, protists, chlorophytes, and fungi. Alpha diversity differed among sites, suggesting local habitat variation linked to differing species responses. Strong temporal variation was detected at both daily and monthly scales. Diversity and relative abundance patterns for several protist groups (including dinoflagellates, ciliates, and cryptophytes) differed from arthropods (e.g., cladocerans and copepods), a traditional focus of plankton surveys. This suggests that the protists respond to different environmental dimensions and may therefore provide additional information regarding ecosystem status. Comparison of the sequence-based population survey data to conventional-based data revealed similar trends for taxa that were ranked among the most abundant in both approaches, although some groups were missing in each data set. These results highlight the potential benefit of supplementing conventional biological survey approaches with metabarcoding to obtain a more comprehensive understanding of freshwater plankton community structure and dynamics.

Diverse microbial communities hosted by the model carnivorous pitcher plant Sarracenia purpurea: analysis of both bacterial and eukaryotic composition across distinct host plant populations

“…Shannon bacterial diversity in both populations (2.72–8.15) were generally higher than the values (2.17–2.47) for S. purpurea based on T-RFLP analysis (Peterson et al, 2008) and other inquiline communities based on DGGE (Ponnusamy et al, 2008), but more similar to values using Illumina sequencing reported in S. purpurea (Paisie, Miller & Mason, 2014; Bittleston et al, 2018) and the pitcher plant Darlingtonia californica (Sarraceniaceae) (Armitage, 2017). Shannon diversity of bacteria in these small volume pitchers was within the ranges reported for freshwater habitats (Wang et al, 2012; Banerji et al, 2018). Higher Chao1 richness in both populations (5,083–22,188) than previous reports for S. purpurea (∼200–500) (Paisie, Miller & Mason, 2014), suggests good sequence coverage, high diversity and representation of relatively rare bacterial taxa.…”

Protocols for Monitoring Harmful Algal Blooms for Sustainable Aquaculture and Coastal Fisheries in Chile

“…However, due to its qualitative application, the metabarcoding analysis still needs to be coupled with microscopic analysis. One should also keep in mind that metabarcoding technology is costly and requires labor-intensive sample workups that could increase errors even with trained analysts [ 20 ]. Our metabarcoding analysis method can currently determine algal taxonomy to genus levels based on the genetic sequences.…”

“…To this end, we adopt metabarcoding analysis to understand the microbe assemblages and their importance in the marine environment in Chile. The metabarcoding analysis is a powerful tool for its ability to detect massive taxonomic information in a sample, even with a low abundance of target organisms [ 20 , 21 , 22 ].…”

A Review and Perspective of eDNA Application to Eutrophication and HAB Control in Freshwater and Marine Ecosystems

“…Molecular genetic assessment based on DNA sequences could help researchers to obtain more information quickly and economically. DNA metabarcoding was used to investigate the spatial and temporal dynamics of planktonic organisms, such as fungi and green algae [28].…”

“…Many studies have reported that eDNA has been used in the investigation of freshwater and marine ecosystems. As suggested by Banerji et al, DNA metabarcoding supplements conventional biological methods to obtain more comprehensive profiles of freshwater plankton community structure and distribution [28]. The rapid monitoring of changes in biodiversity using eDNA holds great promise for monitoring the changes expected as a result of climate change, especially in large lake ecosystems [29].…”