Quantification of marine benthic communities with metabarcoding

Klunder, Lise; Bleijswijk, Judith van; Schaars, Loran Kleine; Veer, Henk W. van der; Luttikhuizen, Pieternella C.; Bijleveld, Allert I.

doi:10.1111/1755-0998.13536

Cited by 11 publications

(6 citation statements)

References 65 publications

(99 reference statements)

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“…Sorting bulk samples by specimen biomass or body size could improve taxa detection using DNA metabarcoding (Elbrecht et al, 2017). However, we chose the current method as it makes less susceptible to contamination, and the purpose of the study was not to detect small and rare taxa in the bulk samples, which were also discussed by Elbrecht et al and other researchers (Aylagas et al, 2016; Klunder et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

Monitoring insect biodiversity and comparison of sampling strategies using metabarcoding: A case study in the Yanshan Mountains, China

Lei

Wang

et al. 2023

Ecology and Evolution

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Insects are the richest and most diverse group of animals and yet there remains a lack, not only of systematic research into their distribution across some key regions of the planet, but of standardized sampling strategies for their study. The Yanshan Mountains, being the boundary range between the Inner Mongolian Plateau and the North China Plain, present an indispensable piece of the insect biodiversity puzzle: both requiring systematic study and offering opportunities for the development of standardized methodologies. This is the first use of DNA metabarcoding to survey the insect biodiversity of the Yanshan Mountains. The study focuses on differences of community composition among samples collected via different methods and from different habitat types. In total, 74 bulk samples were collected from five habitat types (scrubland, woodland, wetland, farmland and grassland) using three collection methods (sweep netting, Malaise traps and light traps). After DNA extraction, PCR amplification, sequencing and diversity analysis were performed, a total of 7427 Operational Taxonomic Units (OTUs) at ≥97% sequence similarity level were delimited, of which 7083 OTUs were identified as belonging to Insecta. Orthoptera, Diptera, Coleoptera and Hemiptera were found to be the dominant orders according to community composition analysis. Nonmetric multidimensional scaling (NMDS) analysis based on Bray–Curtis distances revealed highly divergent estimates of insect community composition among samples differentiated by the collection method (R = .524802, p = .001), but nonsignificant difference among samples differentiated according to habitat (R = .051102, p = .078). The study therefore appears to indicate that the concurrent use of varied collection methods is essential to the accurate monitoring of insect biodiversity.

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Section: Discussionmentioning

confidence: 99%

Monitoring insect biodiversity and comparison of sampling strategies using metabarcoding: A case study in the Yanshan Mountains, China

Lei

Wang

et al. 2023

Ecology and Evolution

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“…Metagenomic methods are increasingly being applied in marine ecosystem monitoring to provide deeper insights into communities of microbial organisms (Pawlowski et (Klunder et al, 2022). These methods are e cient, cost-effective, and offer a much higher level of taxonomic resolution compared to other approaches.…”

Section: Discussionmentioning

confidence: 99%

Mock samples resolve biases in diversity estimates and quantitative interpretation of zooplankton metabarcoding data

Ershova

Wangensteen

Falkenhaug

2023

Preprint

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Metabarcoding is a rapidly developing tool in marine zooplankton ecology, although most zooplankton surveys continue to rely on visual identification for monitoring purposes. We attempted to resolve some of the biases associated with metabarcoding by sequencing a 313 b.p. fragment of the COI gene in 34 “mock” samples from the North Sea which were pre-sorted to species level, with biomass and abundance estimates obtained for each species and taxonomic group. The samples were preserved either in 97% ethanol or dried for 24 hours in a drying oven at 65° C (the routine way of preserving samples for dry weight measurements). The visual identification yielded a total of 59 unique holoplanktonic and 16 meroplanktonic species/taxa. Metabarcoding identified 86 holoplanktonic and 124 meroplanktonic species/taxa, which included all but 3 of the species identified visually as well as numerous species of hard-to-identify crustaceans, hydrozoan jellyfish and larvae of benthic animals. On a sample-to-sample basis, typically 90–95% of visually registered species were recovered, but the number of false positives was also high. We demonstrate robust correlations of relative sequence abundances to relative biomass for most taxonomic groups and develop conversion factors for different taxa to account for sequencing biases. We then combine the adjusted sequencing data with a single bulk biomass measurement for the entire sample to produce a quantitative parameter akin to species biomass. When examined with multivariate statistics, this parameter, which we call BWSR (Biomass weighed sequence reads) showed very similar trends to species biomass and comparable patterns to species abundance, highlighting the potential of metabarcoding not only for biodiversity estimation and mapping of presence/absence of species, but also for quantitative assessment of zooplankton communities.

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“…Research on effects of climate change would also benefit from methodological diversity. For example, more extensive use of biochemical and genetic methods, such as biomarkers (Turja et al, 2014(Turja et al, , 2015Villnäs et al, 2019), stable isotopes (Voss et al, 2000;Gorokhova et al, 2005;Morkune et al, 2016;Lienart et al, 2021), compound-specific isotope analyses (Ek et al, 2018;Weber et al, 2021) or metabarcoding (Leray and Knowlton, 2015;Bucklin et al, 2016;Klunder et al, 2022), as well as development of remote sensing methods (Huber et al, 2021), could yield novel information on stress levels experienced by organisms and environmental niches preferred by species. Such information would allow validation of the biogeochemical models under different environmental and climate scenarios.…”

Section: Knowledge Gapsmentioning

confidence: 99%

Global climate change and the Baltic Sea ecosystem: direct and indirect effects on species, communities and ecosystem functioning

Viitasalo

Bonsdorff

2022

Earth Syst. Dynam.

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Abstract. Climate change has multiple effects on Baltic Sea species, communities and ecosystem functioning through changes in physical and biogeochemical environmental characteristics of the sea. Associated indirect and secondary effects on species interactions, trophic dynamics and ecosystem function are expected to be significant. We review studies investigating species-, population- and ecosystem-level effects of abiotic factors that may change due to global climate change, such as temperature, salinity, oxygen, pH, nutrient levels, and the more indirect biogeochemical and food web processes, primarily based on peer-reviewed literature published since 2010. For phytoplankton, clear symptoms of climate change, such as prolongation of the growing season, are evident and can be explained by the warming, but otherwise climate effects vary from species to species and area to area. Several modelling studies project a decrease of phytoplankton bloom in spring and an increase in cyanobacteria blooms in summer. The associated increase in N:P ratio may contribute to maintaining the “vicious circle of eutrophication”. However, uncertainties remain because some field studies claim that cyanobacteria have not increased and some experimental studies show that responses of cyanobacteria to temperature, salinity and pH vary from species to species. An increase of riverine dissolved organic matter (DOM) may also decrease primary production, but the relative importance of this process in different sea areas is not well known. Bacteria growth is favoured by increasing temperature and DOM, but complex effects in the microbial food web are probable. Warming of seawater in spring also speeds up zooplankton growth and shortens the time lag between phytoplankton and zooplankton peaks, which may lead to decreasing of phytoplankton in spring. In summer, a shift towards smaller-sized zooplankton and a decline of marine copepod species has been projected. In deep benthic communities, continued eutrophication promotes high sedimentation and maintains good food conditions for zoobenthos. If nutrient abatement proceeds, improving oxygen conditions will first increase zoobenthos biomass, but the subsequent decrease of sedimenting matter will disrupt the pelagic–benthic coupling and lead to a decreased zoobenthos biomass. In the shallower photic systems, heatwaves may produce eutrophication-like effects, e.g. overgrowth of bladderwrack by epiphytes, due to a trophic cascade. If salinity also declines, marine species such as bladderwrack, eelgrass and blue mussel may decline. Freshwater vascular plants will be favoured but they cannot replace macroalgae on rocky substrates. Consequently invertebrates and fish benefiting from macroalgal belts may also suffer. Climate-induced changes in the environment also favour establishment of non-indigenous species, potentially affecting food web dynamics in the Baltic Sea. As for fish, salinity decline and continuing of hypoxia is projected to keep cod stocks low, whereas the increasing temperature has been projected to favour sprat and certain coastal fish. Regime shifts and cascading effects have been observed in both pelagic and benthic systems as a result of several climatic and environmental effects acting synergistically. Knowledge gaps include uncertainties in projecting the future salinity level, as well as stratification and potential rate of internal loading, under different climate forcings. This weakens our ability to project how pelagic productivity, fish populations and macroalgal communities may change in the future. The 3D ecosystem models, food web models and 2D species distribution models would benefit from integration, but progress is slowed down by scale problems and inability of models to consider the complex interactions between species. Experimental work should be better integrated into empirical and modelling studies of food web dynamics to get a more comprehensive view of the responses of the pelagic and benthic systems to climate change, from bacteria to fish. In addition, to better understand the effects of climate change on the biodiversity of the Baltic Sea, more emphasis should be placed on studies of shallow photic environments. The fate of the Baltic Sea ecosystem will depend on various intertwined environmental factors and on development of the society. Climate change will probably delay the effects of nutrient abatement and tend to keep the ecosystem in its “novel” state. However, several modelling studies conclude that nutrient reductions will be a stronger driver for ecosystem functioning of the Baltic Sea than climate change. Such studies highlight the importance of studying the Baltic Sea as an interlinked socio-ecological system.

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Quantification of marine benthic communities with metabarcoding

Cited by 11 publications

References 65 publications

Monitoring insect biodiversity and comparison of sampling strategies using metabarcoding: A case study in the Yanshan Mountains, China

Monitoring insect biodiversity and comparison of sampling strategies using metabarcoding: A case study in the Yanshan Mountains, China

Mock samples resolve biases in diversity estimates and quantitative interpretation of zooplankton metabarcoding data

Global climate change and the Baltic Sea ecosystem: direct and indirect effects on species, communities and ecosystem functioning

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