A DNA‐based method for identification of krill species and its application to analysing the diet of marine vertebrate predators

Jarman, Simon; Gales, Nicholas J.; Tierney, Megan; Gill, Peter C.; Elliott, Nicholas

doi:10.1046/j.1365-294x.2002.01641.x

Cited by 112 publications

(104 citation statements)

References 45 publications

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“…In most cases, these studies build on one of two techniques: specific PCR primers designed to reveal predation on one or a few specific prey taxa, or the amplification of DNA using universal or group-specific primers as followed by sequencing of the amplicon. Diet studies of these types have been applied extensively to marine taxa ranging from higher trophic levels (e.g., Deagle et al 2005;Dunn et al 2010;Méheust et al 2015) through marine birds (e.g., Deagle et al 2007;Bowser et al 2013) and fish (e.g., Moran et al 2016) to different invertebrates and lower trophic levels (e.g., Jarman et al 2002;Nejstgaard et al 2003;Blankenship and Yayanos 2005;Leal et al 2014b;Olsen et al 2014;Hu et al 2015;reviewed in Calado and Leal 2015). DNA-based approaches have also yielded breakthrough dietary analyses in complex freshwater systems (e.g., Corse et al 2010;Carreon-Martinez et al 2011;Bartley et al 2015).…”

Section: Clarifying the Links Of Aquatic Food Websmentioning

confidence: 99%

The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

Roslin

Majaneva

2016

Genome

104

103

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By depicting who eats whom, food webs offer descriptions of how groupings in nature (typically species or populations) are linked to each other. For asking questions on how food webs are built and work, we need descriptions of food webs at different levels of resolution. DNA techniques provide opportunities for highly resolved webs. In this paper, we offer an exposé of how DNA-based techniques, and DNA barcodes in particular, have recently been used to construct food web structure in both terrestrial and aquatic systems. We highlight how such techniques can be applied to simultaneously improve the taxonomic resolution of the nodes of the web (i.e., the species), and the links between them (i.e., who eats whom). We end by proposing how DNA barcodes and DNA information may allow new approaches to the construction of larger interaction webs, and overcome some hurdles to achieving adequate sample size. Most importantly, we propose that the joint adoption and development of these techniques may serve to unite approaches to food web studies in aquatic and terrestrial systems-revealing the extent to which food webs in these environments are structured similarly to or differently from each other, and how they are linked by dispersal.Key words: DNA barcodes, food webs, species delimitation, species identification, trophic links, ecological networks.Résumé : En brossant le tableau de qui mange qui, les réseaux trophiques livrent une description des liens qui unissent des groupes d'espèces ou de populations. Afin de déterminer comment ces réseaux sont constitués et comment ils fonctionnent, il nous faut une description de ces réseaux à différents niveaux de résolution. Les techniques de l'ADN permettent de produire des réseaux trophiques de grande résolution. Dans ce travail, les auteurs décrivent comment les techniques fondées sur l'ADN, en particulier les codes à barres de l'ADN, ont récemment été employées pour étudier la structure des réseaux trophiques chez des systèmes tant terrestres qu'aquatiques. Les auteurs soulignent comment ces techniques peuvent servir à simultanément améliorer la résolution taxonomique des noeuds d'un réseau (i.e. les espèces) ainsi que les relations entre eux (qui mange qui). Les auteurs terminent en proposant des moyens via lesquels les codes à barres et l'information tirée de l'ADN rendent possible de nouvelles approches en vue de la construction de plus grands réseaux d'interaction et permettent de surmonter des difficultés rencontrées dans l'acquisition d'échantillons de taille suffisante. Surtout, les auteurs proposent que l'adoption et le développement conjoints de ces techniques peut contribuer à unifier les approches employées dans l'étude des réseaux trophiques au sein des systèmes aquatiques et terrestres. Cela permettra de révéler l'étendue de la similarité ou de la dissimilarité dans la façon dont sont structurés les réseaux dans ces différents environnements et comment ils sont liés par la dispersion. [Traduit par la Rédaction]

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Section: Clarifying the Links Of Aquatic Food Websmentioning

confidence: 99%

The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

Roslin

Majaneva

2016

Genome

104

103

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“…Environmental richness was high (2-fold higher than diet samples), with an average of 32% (n = 3, SD = 4.6) of the phylotypes detected being found in dietary components. The use of a primer set targeting all eukaryotes, the approach applied in this study, differs from most studies employing PCR-based diet analyses, which often utilize highly specific primers designed to identify single species (Jarman et al 2002, Symondson 2002, Nejstgaard et al 2003, or group-specific primers (Höss et al 1992, Jarman et al 2004). The use of primers targeting all eukaryotes allowed us to (1) develop an approach inclusive of all potential prey, (2) develop a comparatively broad picture of the diversity in Euphausia superba's diet, and (3) avoid additional potential for PCR bias (see below) by conducting a single round of PCR.…”

Section: Discussionmentioning

confidence: 99%

Molecular approach (PCR-DGGE) to diet analysis in young Antarctic krill Euphausia superba

Martín¹,

Ross²,

Quetin³

et al. 2006

Mar. Ecol. Prog. Ser.

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Antarctic krill Euphausia superba Dana comprise a key component of the Southern Ocean food web, yet despite decades of research, questions concerning the regional, seasonal and ontogenetic differences in their diet remain. All current methods used to characterize krill diet have limitations for identifying the full complement of the diet. Using DNA as a marker molecule, our goal in this study has been to evaluate the efficacy of a PCR-DGGE (denaturing gradient gel electrophoresis) approach targeting the 18S rDNA gene to discriminate among diet constituents in gut and fecal pellet samples from young Antarctic krill relative to their feeding environment -the seawater and sea ice microbial community. We conducted 2 laboratory-based feeding experiments with known food items and 3 field samplings of both the krill and their feeding environment. Sequenced PCR-DGGE phylotypes from laboratory trials clearly distinguished diatom and copepod prey, while in situ feeding analyses revealed that a broad diversity of taxa were ingested, including diatoms (Bacillariophyta, the most prevalent group detected), dinoflagellates, cryptomonads, prasinophytes, ciliates, cercozoans, choanoflagellates, turbellarians and (possibly) sponge larvae. Band image analyses allowed environmental and diet phylotypes to be matched. On average, 32% of those from the environment were present in the diet; conversely, of the phylotypes detected in the diet, an average of 59% were in common with the environment. Changes in environmental phylotypes among sampling dates were reflected by similar changes in the krill diet as potential prey diversity (richness) decreased during a phytoplankton bloom.KEY WORDS: Antarctic krill · Euphausia superba · Diet · DGGE · 18S rDNA · Sea ice microbial community · Omnivory Resale or republication not permitted without written consent of the publisherMar Ecol Prog Ser 319: [155][156][157][158][159][160][161][162][163][164][165] 2006 undigested hard parts such as copepod mandibles, diatom frustules, or tintinnid loricae (Hopkins & Torres 1989), gut fluorescence detects only algal pigments (Ross et al. 2004), and monoclonal antibodies target specific species of interest (Haberman et al. 2002). Biomarker methods analyzing fatty acid and stable isotope composition of krill have been found to target a wider variety of diet components, but are limited in the taxonomic resolution they provide (Frazer 1996, Alonzo et al. 2003. PCR-based molecular methods for detecting DNA offer promising new avenues for diet analysis (Symondson 2002), and are currently being used in marine systems (Jarman et al. 2002, Nejstgaard et al. 2003. A distinct advantage of using a molecule such as DNA to detect diet diversity is that all potential prey items have DNA, and thus detection of a dietary item will depend more on sensitivity to the molecular signal than on such group-specific biases as those mentioned above. Although a number of studies have utilized some form of DNA detection of prey in predator diets (e.g. Zaidi et al. 1999, R...

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“…Where a herbivore grazes a cultivated pasture, usually containing only a limited number of pasture species, the diet is relatively simple. The more the sources of DNA in any sample the greater the difficulty in isolating individual sources of DNA (Jarman et al, 2002).…”

Section: Pcr Amplification Of Kangaroo Faecesmentioning

confidence: 99%

“…The exquisite sensitivity and specificity afforded by PCR are particularly useful under conditions where the target is present at low copy number and in a potentially non-permissive matrix (Saiki et al, 1985;Zhao et al, 2002). Recently, faecal DNA amplification has been used for the evaluation of diets in sea lions (Deagle et al, 2005) and of marine vertebrate predators (Jarman et al, 2002). In this study, faecal DNA was used as a means of determining dietary components of kangaroos grazing on the southern rangelands of Western Australia.…”

Section: Introductionmentioning

confidence: 99%

Using faecal DNA to determine consumption by kangaroos of plants considered palatable to sheep

Krebs

McCafferty

et al. 2010

Animal

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Disagreement exists within the scientific community with regards to the level of competition for feed between sheep and kangaroos in the Australian rangelands. The greatest challenge to solving this debate is finding effective means of determining the composition of the diets of these potential grazing competitors. An option is to adopt a non-invasive approach that combines faecal collection and molecular techniques that focus on faecal DNA as the primary source of dietary information. As proof-of-concept, we show that a DNA reference data bank on plant species can be established. This DNA reference data bank was then used as a library to identify plant species in kangaroo faeces collected in the southern rangelands of Western Australia. To enhance the method development and to begin the investigation of competitive grazing between sheep and kangaroos, 16 plant species known to be palatable to sheep were initially targeted for collection. To ensure that only plant sequences were studied, PCR amplification was performed using a universal primer pair previously shown to be specific to the chloroplast transfer RNA leucine (trnL) UAA gene intron. Overall, genus-specific, single and differently sized amplicons were reliably and reproducibly generated; enabling the differentiation of reference plants by PCR product length heterogeneity. However, there were a few plants that could not be clearly differentiated on the basis of size alone. This prompted the adoption of a post-PCR step that enabled further differentiation according to base sequence variation. Restriction endonucleases make sequence-specific cleavages on DNA to produce discrete and reproducible fragments having unique sizes and base compositions. Their availability, affordability and simplicity-of-use put restriction enzyme sequence (RES) profiling as a logical post-PCR step for confirming plant species identity. We demonstrate that PCR-RES profiling of plant and faecal matter is useful for the identification of plants included in the diet of kangaroos. The limitations, potential and the opportunities created for researchers interested in investigating the diet of competing herbivores in the rangelands are discussed.

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A DNA‐based method for identification of krill species and its application to analysing the diet of marine vertebrate predators

Cited by 112 publications

References 45 publications

The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

Molecular approach (PCR-DGGE) to diet analysis in young Antarctic krill Euphausia superba

Using faecal DNA to determine consumption by kangaroos of plants considered palatable to sheep

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