Pervasive effect of bottom trawling on benthic biodiversity unravelled by metabarcoding across the Tree of Life
- 1University of Montpellier, Ifremer, CNRS, IRD, MARine Biodiversity Exploitation and Conservation (MARBEC), Sete, France
Abstract
Bottom trawling is the most widespread human disturbance on the seafloor, known to affect seabed structure and benthic biota. Yet, its impact on benthic communities remains documented mainly for taxa identifiable through morphology, leaving microscopic benthic communities largely overlooked. The Gulf of Lion continental shelf has been trawled for decades by French and Spanish fleets, to the point that encountering untrawled reference areas became elusive. Here, we examined prokaryote, protist and Animalia benthic communities at eight stations, using eDNA metabarcoding of core sediment samples, with five primer-pairs. Benthic communities were cross-referenced with contrasted trawling impacts, integrated across three periods: over one month, three years or ten years preceding the sampling. The community composition was primarily structured by ecological habitats, yet, trawling pressure showed association with prokaryotes and Animalia diversity. Diversity was higher at sites trawled more intensively in the preceding month, whereas long-term trawling was associated with a significant erosion of Animalia alpha diversity. Unexpectedly, communities did not display consistent vertical structure and the relative contributions of trawling and hydrodynamic reworking remain unresolved due to the absence of untrawled sites. Overall, our results show that trawling effects extend to prokaryotic compartments rarely considered in impact assessments, providing a proof of concept for eDNA-based assessment, and underline a pervasive long-term effect on Animalia communities. This study also highlights the importance of the timescale used to quantify fishing pressure and underscores the complexity of impact assessment when monitoring begins too late to establish a clear baseline, particularly when no reference site remains.
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BibTeX
@misc{beaulieu2026pervasive,
title = {{Pervasive effect of bottom trawling on benthic biodiversity unravelled by metabarcoding across the Tree of Life}},
author = {C. Beaulieu and S. Vaz and T. Henault and C. Labrune and C. Barras and M. Schweizer and J. Rzeznik-Orignac and G. Maillet and A. Pruski and N. Henry and S. Arnaud-Haond},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.05.756630},
url = {https://www.biorxiv.org/content/10.64898/2026.10.05.756630v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - Pervasive effect of bottom trawling on benthic biodiversity unravelled by metabarcoding across the Tree of Life
AU - C. Beaulieu
AU - S. Vaz
AU - T. Henault
AU - C. Labrune
AU - C. Barras
AU - M. Schweizer
AU - J. Rzeznik-Orignac
AU - G. Maillet
AU - A. Pruski
AU - N. Henry
AU - S. Arnaud-Haond
PY - 2026
DA - 2026/10/05
PB - bioRxiv
DO - 10.64898/2026.10.05.756630
UR - https://www.biorxiv.org/content/10.64898/2026.10.05.756630v1
AB - Bottom trawling is the most widespread human disturbance on the seafloor, known to affect seabed structure and benthic biota. Yet, its impact on benthic communities remains documented mainly for taxa identifiable through morphology, leaving microscopic benthic communities largely overlooked. The Gulf of Lion continental shelf has been trawled for decades by French and Spanish fleets, to the point that encountering untrawled reference areas became elusive. Here, we examined prokaryote, protist and Animalia benthic communities at eight stations, using eDNA metabarcoding of core sediment samples, with five primer-pairs. Benthic communities were cross-referenced with contrasted trawling impacts, integrated across three periods: over one month, three years or ten years preceding the sampling. The community composition was primarily structured by ecological habitats, yet, trawling pressure showed association with prokaryotes and Animalia diversity. Diversity was higher at sites trawled more intensively in the preceding month, whereas long-term trawling was associated with a significant erosion of Animalia alpha diversity. Unexpectedly, communities did not display consistent vertical structure and the relative contributions of trawling and hydrodynamic reworking remain unresolved due to the absence of untrawled sites. Overall, our results show that trawling effects extend to prokaryotic compartments rarely considered in impact assessments, providing a proof of concept for eDNA-based assessment, and underline a pervasive long-term effect on Animalia communities. This study also highlights the importance of the timescale used to quantify fishing pressure and underscores the complexity of impact assessment when monitoring begins too late to establish a clear baseline, particularly when no reference site remains.
ER -