scholarly journals Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3347 ◽  
Author(s):  
Olivier Laroche ◽  
Susanna A. Wood ◽  
Louis A. Tremblay ◽  
Gavin Lear ◽  
Joanne I. Ellis ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Beta Diversity ◽  
Benthic Communities ◽  
Oil Production ◽  
Environmental Dna ◽  
Ribosomal Rna Gene ◽  
Alpha And Beta Diversity ◽  
Physico Chemical ◽  
Production Platform ◽  
Shared Otus

Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil production activity. Overall, the data appeared more robust when trimmed by shared OTUs, showing a greater effect of the platform on alpha- and beta-diversity. Trimming by shared OTUs likely removes taxa derived from legacy DNA and technical artefacts introduced through reverse transcriptase, polymerase-chain-reaction and sequencing. Findings from our scoping study suggest that metabarcoding-based biomonitoring surveys should, if funds, time and expertise allow, be assessed using both eDNA and eRNA products.

scholarly journals Hydrographic fronts shape productivity, nitrogen fixation, and microbial community composition in the South Indian Ocean and the Southern Ocean

2021 ◽  
Author(s):  
Cora Hörstmann ◽  
Eric J. Raes ◽  
Pier Luigi Buttigieg ◽  
Claire Lo Monaco ◽  
Uwe John ◽  
...  
Keyword(s):  
Microbial Community ◽  
Indian Ocean ◽  
Southern Ocean ◽  
Microbial Diversity ◽  
N2 Fixation ◽  
Beta Diversity ◽  
South Indian Ocean ◽  
Alpha And Beta Diversity ◽  
South Indian ◽  
Physico Chemical

Abstract. Biogeochemical cycling of carbon (C) and nitrogen (N) in the ocean depends on both the composition and activity of underlying biological communities and on abiotic factors. The Southern Ocean is encircled by a series of strong currents and fronts, providing a barrier to microbial dispersion into adjacent oligotrophic gyres. Our study region straddles the boundary between the nutrient-rich Southern Ocean and the adjacent oligotrophic gyre of the South Indian Ocean, providing an ideal region to study changes in microbial productivity. Here, we measured the impact of C- and N- uptake on microbial community diversity, contextualized by hydrographic factors and local physico-chemical conditions across the Southern Ocean and South Indian Ocean. We observed that contrasting physico-chemical characteristics led to unique microbial diversity patterns, with significant correlations between microbial alpha diversity and primary productivity (PP). However, we detected no link between specific PP (PP normalized by chlorophyll a concentration) and microbial alpha and beta diversity. Prokaryotic alpha and beta diversity were correlated with biological N2 fixation, itself a prokaryotic process, and we detected measurable N2 fixation to 60° S. While regional water masses have distinct microbial genetic fingerprints in both the eukaryotic and prokaryotic fractions, PP and N2 fixation vary more gradually and regionally. This suggests that microbial phylogenetic diversity is more strongly bounded by physical oceanographic features, while microbial activity responds more to chemical factors. We conclude that concomitant assessments of microbial diversity and activity is central in understanding the dynamics and complex responses of microorganisms to a changing ocean environment.

scholarly journals Hydrographic fronts shape productivity, nitrogen fixation, and microbial community composition in the southern Indian Ocean and the Southern Ocean

2021 ◽  
Vol 18 (12) ◽  
pp. 3733-3749
Author(s):  
Cora Hörstmann ◽  
Eric J. Raes ◽  
Pier Luigi Buttigieg ◽  
Claire Lo Monaco ◽  
Uwe John ◽  
...  
Keyword(s):  
Microbial Community ◽  
Indian Ocean ◽  
Southern Ocean ◽  
Microbial Diversity ◽  
N2 Fixation ◽  
Beta Diversity ◽  
Southern Indian Ocean ◽  
Alpha And Beta Diversity ◽  
Physico Chemical ◽  
The Impact

Abstract. Biogeochemical cycling of carbon (C) and nitrogen (N) in the ocean depends on both the composition and activity of underlying biological communities and on abiotic factors. The Southern Ocean is encircled by a series of strong currents and fronts, providing a barrier to microbial dispersion into adjacent oligotrophic gyres. Our study region straddles the boundary between the nutrient-rich Southern Ocean and the adjacent oligotrophic gyre of the southern Indian Ocean, providing an ideal region to study changes in microbial productivity. Here, we measured the impact of C and N uptake on microbial community diversity, contextualized by hydrographic factors and local physico-chemical conditions across the Southern Ocean and southern Indian Ocean. We observed that contrasting physico-chemical characteristics led to unique microbial diversity patterns, with significant correlations between microbial alpha diversity and primary productivity (PP). However, we detected no link between specific PP (PP normalized by chlorophyll-a concentration) and microbial alpha and beta diversity. Prokaryotic alpha and beta diversity were correlated with biological N2 fixation, which is itself a prokaryotic process, and we detected measurable N2 fixation to 60∘ S. While regional water masses have distinct microbial genetic fingerprints in both the eukaryotic and prokaryotic fractions, PP and N2 fixation vary more gradually and regionally. This suggests that microbial phylogenetic diversity is more strongly bounded by physical oceanographic features, while microbial activity responds more to chemical factors. We conclude that concomitant assessments of microbial diversity and activity are central to understanding the dynamics and complex responses of microorganisms to a changing ocean environment.

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