16S and 18S rRNA Gene Metabarcoding Provide Congruent Information on the Responses of Sediment Communities to Eutrophication

Jesse P Harrison,Tom Jilbert,Panagiota-Myrsini Chronopoulou,Karoliina A Koho,Iines S Salonen

doi:10.3389/fmars.2021.708716

Abstract

Metabarcoding analyses of bacterial and eukaryotic communities have been proposed as efficient tools for environmental impact assessment. It has been unclear, however, to which extent these analyses can provide similar or differing information on the ecological status of the environment. Here, we used 16S and 18S rRNA gene metabarcoding to compare eutrophication-induced shifts in sediment bacterial and eukaryotic community structure in relation to a range of porewater, sediment and bottom-water geochemical variables, using data obtained from six stations near a former rainbow trout farm in the Archipelago Sea (Baltic Sea). Shifts in the structure of both community types were correlated with a shared set of variables, including porewater ammonium concentrations and the sediment depth-integrated oxygen consumption rate. Distance-based redundancy analyses showed that variables typically employed in impact assessments, such as bottom water nutrient concentrations, explained less of the variance in community structure than alternative variables (e.g., porewater NH4+ inventories and sediment depth-integrated O2 consumption rates) selected due to their low collinearity (up to 40 vs. 58% of the variance explained, respectively). In monitoring surveys where analyses of both bacterial and eukaryotic communities may be impossible, either 16S or 18S rRNA gene metabarcoding can serve as reliable indicators of wider ecological impacts of eutrophication.

Highlights

Assessing the ecological integrity of benthic habitats is crucial to marine ecosystem management (Fernandes et al, 2001), with seafloor monitoring efforts having traditionally relied on morphological inventories of macrofauna (≥0.5 mm size fraction) and associated indices (Lejzerowicz et al, 2015; Pawlowski et al, 2016)
Sediment bacterial community structure differed between sampling stations, as demonstrated by metabarcoding analysis of a total of 30 microbial communities (1-way global PERMANOVA using Aitchison distances: pseudoF5,24 = 6.559, p < 0.001) (Figure 3A)
Comparing OTU relative abundances showed sediments from all sites to be dominated by 16S rRNA gene sequences from the phylum Proteobacteria, followed by Bacteroidetes (Figure 4A; for class-level relative abundances, see Supplementary Figure 4)

Summary

Introduction

Assessing the ecological integrity of benthic habitats is crucial to marine ecosystem management (Fernandes et al, 2001), with seafloor monitoring efforts having traditionally relied on morphological inventories of macrofauna (≥0.5 mm size fraction) and associated indices (Lejzerowicz et al, 2015; Pawlowski et al, 2016) While producing such inventories requires considerable time, taxonomic expertise and finances, environmental DNA (eDNA) metabarcoding. The use of metabarcoding as a monitoring tool has been explored with reference to localized disturbances caused by dredging (Zhang et al, 2017) and off-shore drilling (Lanzén et al, 2016; Laroche et al, 2017; Frontalini et al, 2020) These studies have shown that bacterial and eukaryotic metabarcoding analyses can serve as sensitive methods to detect anthropogenic impacts on sediment habitats, including both short-term responses and longterm effects on community resilience and stability. A recent cross-laboratory comparison of eDNA metabarcoding results produced using a standardized protocol has demonstrated a high degree of reproducibility between individual metabarcoding data sets, which is essential to the successful deployment of eDNA-based monitoring methods (Dully et al, 2021)

Methods

Results

Conclusion