Diet Assessment of the Atlantic Sea Nettle Chrysaora Quinquecirrha in Barnegat Bay, New Jersey, Using Next-Generation Sequencing Robert W
Total Page：16
File Type：pdf, Size：1020Kb
Montclair State University Montclair State University Digital Commons Department of Biology Faculty Scholarship and Department of Biology Creative Works 10-27-2016 Diet assessment of the Atlantic Sea Nettle Chrysaora quinquecirrha in Barnegat Bay, New Jersey, using next-generation sequencing Robert W. Meredith Montclair State University, [email protected] John J. Gaynor Montclair State University, [email protected] Paul AX Bologna Montclair State University, [email protected] Follow this and additional works at: https://digitalcommons.montclair.edu/biology-facpubs Part of the Biodiversity Commons, Bioinformatics Commons, Genomics Commons, Marine Biology Commons, and the Terrestrial and Aquatic Ecology Commons MSU Digital Commons Citation Meredith, Robert W.; Gaynor, John J.; and Bologna, Paul AX, "Diet assessment of the Atlantic Sea Nettle hrC ysaora quinquecirrha in Barnegat Bay, New Jersey, using next-generation sequencing" (2016). Department of Biology Faculty Scholarship and Creative Works. 5. https://digitalcommons.montclair.edu/biology-facpubs/5 This Article is brought to you for free and open access by the Department of Biology at Montclair State University Digital Commons. It has been accepted for inclusion in Department of Biology Faculty Scholarship and Creative Works by an authorized administrator of Montclair State University Digital Commons. For more information, please contact [email protected]. Molecular Ecology (2016) doi: 10.1111/mec.13918 Diet assessment of the Atlantic Sea Nettle Chrysaora quinquecirrha in Barnegat Bay, New Jersey, using next- generation sequencing ROBERT W. MEREDITH, JOHN J. GAYNOR and PAUL A. X. BOLOGNA Department of Biology, Montclair State University, Montclair, NJ 07043, USA Abstract Next-generation sequencing (NGS) methodologies have proven useful in deciphering the food items of generalist predators, but have yet to be applied to gelatinous animal gut and tentacle content. NGS can potentially supplement traditional methods of visual identification. Chrysaora quinquecirrha (Atlantic sea nettle) has progressively become more abundant in Mid-Atlantic United States’ estuaries including Barnegat Bay (New Jersey), potentially having detrimental effects on both marine organisms and human enterprises. Full characterization of this predator’s diet is essential for a comprehensive understanding of its impact on the food web and its management. Here, we tested the efficacy of NGS for prey item determination in the Atlantic sea nettle. We implemented a NGS ‘shotgun’ approach to randomly sequence DNA frag- ments isolated from gut lavages and gastric pouch/tentacle picks of eight and 84 sea nettles, respectively. These results were verified by visual identification and co-occur- ring plankton tows. Over 550 000 contigs were assembled from ~110 million paired-end reads. Of these, 100 contigs were confidently assigned to 23 different taxa, including soft-bodied organisms previously undocumented as prey species, including copepods, fish, ctenophores, anemones, amphipods, barnacles, shrimp, polychaete worms, flukes, flatworms, echinoderms, gastropods, bivalves and hemichordates. Our results not only indicate that a ‘shotgun’ NGS approach can supplement visual identi- fication methods, but targeted enrichment of a specific amplicon/gene is not a prerequi- site for identifying Atlantic sea nettle prey items. Keywords: Chrysaora quinquecirrha, gut content, jellyfish diet, next-generation sequencing Received 14 June 2015; revision received 22 October 2016; accepted 27 October 2016 research dedicated to determining their effect on marine Introduction ecosystems as related to commercially important species Jellyfish blooms in recent years have become conspicu- (e.g. fish). The apparent proliferation of massive jelly- ous components of worldwide marine ecosystems, par- fish blooms along with range extensions has been asso- ticularly during productive summer months, often to ciated with anthropogenic stresses such as overfishing, the detriment of both marine organisms and human eutrophication, climate change, translocation and habi- enterprises (Mills 2001; Brodeur et al. 2002, 2008; Purcell tat modification (Richardson et al. 2009; Purcell 2012; 2012). Jellyfish are opportunistic, voracious predators of Condon et al. 2013). However, the current data are zooplankton and ichthyoplankton (fish larvae and eggs) inconclusive in regard to whether jellyfish are actually (Purcell 1997; Brodeur et al. 2008) and have the poten- globally increasing (Gibbons & Richardson 2013). For tial to alter planktonic food webs. As a consequence, example, both Brotz et al. (2012) and Duarte et al. (2013) recent decades have seen a dramatic increase in suggest near-global increasing trends, while Condon et al. (2012) found no evidence. Most recently, Condon Correspondence: Robert W. Meredith, Fax: (973) 655-7047; et al. (2013) suggested jellyfish populations appear to ~ E-mail: [email protected] follow decadal oscillations ( 20 years) with no © 2016 John Wiley & Sons Ltd 2 R. W. MEREDITH ET AL. significant increase over the last 140 years. However, more efficient and thorough investigation into potential Condon et al. (2013) also suggest a significant, but weak prey items is possible. increase since the 1970s. Clearly, there is no consensus Molecular techniques are potentially far more appeal- and much of the confusion centres around the lack of ing for prey item identification than standard visual long-term data sets (Condon et al. 2012; Gibbons & identification methods (Pompanon et al. 2012). For Richardson 2013). example, larval forms of many marine species remain Trophic relationships of most gelatinous animals (ani- undescribed or are not easily identifiable to the species mals belonging to Cnidaria or Ctenophora) are poorly level. Prey DNA sequence data can be readily identified known (Purcell et al. 2007; Purcell 2012). As a conse- to the species level when searched against reference quence, it is unclear as to what role most jellyfish play databases (e.g. National Center for Biotechnology Infor- in benthic and pelagic food webs (Condon et al. 2012). mation) if present in the database, while visual identifi- Additionally, most gelatinous species are assumed to be cation often requires an expert in morphology and pelagic generalist/opportunists. Full characterizations years of training. Additionally, visual identifications are of gelatinous animal diets are essential for a compre- often of low resolution (e.g. family level or above), hensive understanding of their impacts on the food time-consuming and, more significantly, require prey web and their management (Purcell 1997, 2009; Pauly items to be intact and/or in the very early stages of et al. 2009). digestion prior to the destruction of physical The Atlantic Sea nettle (Chrysaora quinquecirrha) is nat- characteristics. urally distributed along the coast of the western Atlan- Visual identification can prove to be problematic tic Ocean (Morandini & Marques 2010). In recent years, when predators have potentially high digestive clear- sea nettles have become progressively more abundant ance rates, as is the case with C. quinquecirrha in Mid-Atlantic State estuaries, suggesting these coastal (3.5 Æ 1.1 h for copepods; Purcell 1992) or prey does ecosystems are possibly experiencing fundamental not possess structural components (e.g. ctenophores). shifts in planktonic trophic web structure (Purcell et al. NGS methods should be able to detect prey items well 2007). For example, the warming waters of the Chesa- after visual identification becomes impossible and thou- peake Bay (USA) have resulted in a C. quinquecirrha sands of sequences can be identified within a day. Here, population ‘explosion’ that has had devastating ecologi- we test the efficacy of utilizing NGS technologies in the cal and economic effects (Cargo & King 1990; Delano identification of C. quinquecirrha prey items in Barnegat 2006; Purcell et al. 2007). Further to the north, the shal- Bay to start to unravel predator–prey interactions. We low estuary Barnegat Bay (Ocean County, New Jersey, successfully demonstrate that a ‘shotgun’ approach to USA) is likewise experiencing a population ‘explosion’ sequencing gelatinous prey items found in the gut and/ of C. quinquecirrha. Barnegat Bay is a highly eutrophic or on tentacles can supplement visual identification brackish water system with nutrients arriving in the methods and is potentially equally as effective as other bay via run-off and atmospheric inputs (Kennish et al. NGS methods that use targeted enrichment of a specific 2007). Prior to the mid-1990s, C. quinquecirrha was virtu- gene (e.g. COI). ally unknown from the bay, but this sea nettle now appears to be a permanent resident (Crum et al. 2014). Methods Gelatinous prey identification has historically involved either direct observation or the collection of Gastric lavage adults, the excision and preservation of the gastric pouches and tentacles and then visual inspection of We sampled eight adult jellyfish from three Barnegat contents under a microscope in the laboratory. Molecu- Bay localities (two from Forked River West, three from lar techniques have recently been devised and utilize Toms River West, and three from Silver Bay East) using Sanger sequencing or next-generation sequencing nets, ladles and/or buckets on 30 July 2013 (NGS). DNA can be extracted from the gut contents of (Appendix S1, Supporting information). Depths ranged the predator and then sequenced. The DNA sequences from the