Assessing the impact of the threatened crucian carp (Carassius carassius) on pond invertebrate diversity - a comparison of conventional and molecular tools

Abstract

Fishes stocked for recreation and angling can damage freshwater habitats and negatively impact biodiversity. The pond-associated crucian carp (Carassius carassius) is rare across Europe and stocked for conservation management in England, but impacts on pond biota are understudied. Freshwater invertebrates contribute substantially to aquatic biodiversity, encompassing many rare and endemic species, but small size and high abundance complicates their assessment. Practitioners have employed sweep-netting and kick-net sampling with microscopy, but specimen size/quality and experience can bias identification. DNA and eDNA metabarcoding offer alternative means of invertebrate assessment. We compared invertebrate diversity in ponds (N = 18) with and without crucian carp using sweep-netting and microscopy, DNA metabarcoding, and eDNA metabarcoding. Five 2-L water samples and 4-minute sweep-net samples were collected at each pond. Inventories produced by morphotaxonomic identification of netted samples, DNA metabarcoding of bulk tissue samples, and eDNA metabarcoding of water samples were compared. Alpha diversity was greatest with DNA or eDNA metabarcoding, depending on whether standard or unbiased methods were considered. DNA metabarcoding reflected morphotaxonomic identification, whereas eDNA metabarcoding produced markedly different communities. Therefore, these complementary tools should be combined for comprehensive invertebrate assessment. Crucian carp presence minimally reduced alpha diversity in ponds, but positively influenced beta diversity through taxon turnover (i.e. ponds with crucian carp contained different invertebrates to fishless ponds). The crucian carp appears to be non-impactful, supporting continued conservation management in England. Our results show that molecular tools can enhance freshwater invertebrate assessment and facilitate development of more accurate and ecologically effective pond management strategies.

Environmental DNA for biomonitoring

“…Gleason et al ( 2021 ) show that bulk DNA metabarcoding more accurately represents the local stream macroinvertebrate community, with water eDNA data being overwhelmed by non‐metazoan sequences. The same difference was observed when comparing bulk DNA to water eDNA and morphological inventories of pond macroinvertebrates (Harper et al, 2021 ). However, the authors consider both approaches as complementary and suggest that they should be combined for comprehensive assessment of the invertebrate community.…”

Estuarine molecular bycatch as a landscape-wide biomonitoring tool

“…Since the inception of eDNA-based biodiversity assessment, there has been an emphasis on comparing detection performance with well-established biomonitoring approaches that use capture, visual or acoustic identification (Jerde et al 2011; Foote et al 2012; Thomsen et al 2012; Yamamoto et al 2016). The popularity of eDNA-based analysis today owes much to the realisation that, in many important contexts, the new tool offered significant advantages over conventional sampling methods, either through sheer improvement of detection efficacy (Boussarie et al 2018; McElroy et al 2020), through the discovery of its unique complementarity (Aglieri et al 2020; Harper et al 2020), or by simply being less resource-intensive (Bálint et al 2018; Aglieri et al 2020). On the other hand, little effort has gone into evaluating the intrinsically serendipitous nature of high-throughput sequencing, which, irrespective of the metabarcoding markers chosen, consistently yields substantial amounts of non-target sequences.…”

“…Aquatic environments have been the main beneficiaries of this ‘eDNA revolution’, largely owing to the utility of eDNA-based methods for exploring inherently poorly accessible realms, and the relative ease of collecting water, within which DNA naturally disperses, thus facilitating species detection. The utility of the methods ranges from the relatively straightforward recovery of rare (Boussarie et al 2018) and invasive (Imamura et al 2020) species, to more sophisticated inference on habitat gradients (Sigsgaard et al 2019), productivity dynamics (Kelly et al 2016; Djurhuus et al 2020) and ecosystem structure (Aglieri et al 2020; Harper et al 2020). It is now possible consider aquatic eDNA as a useful tool for tackling some of the most pressing biodiversity conservation challenges in a swift, affordable and standardised way, particularly given growing interest in the generation and curation of reference DNA sequence databases.…”

Editorial 2022

“…An important step in implementing new molecular tools is validation of the data, which is the focus of the second group of papers within the special issue. In the case of eDNA, validation involves comparing eDNA approaches to traditional methods of biodiversity monitoring, including bulk DNA metabarcoding (Antich et al, 2021; Gleason et al, 2021; Harper et al, 2021; van de Loos & Nijland, 2021; Suter et al, 2021) and macrofauna surveys (Drinkwater et al, 2021; He et al, 2021; Lopes et al, 2020). Additional papers within this section examine the impacts of marker selection (Ficetola et al, 2021; Martins et al, 2021; Meyer et al, 2021), methods of soil preservation (Guerrieri et al, 2021), and optimization of data analysis (Mächler et al, 2021).…”