Plan 9: Research Barnegat Bay— Benthic Invertebrate Community Monitoring & Year 3 Indicator Development for the Barnegat Bay-Little Egg Harbor Estuary - Barnegat Bay Diatom Nutrient Inference Model Hard Clams as Indicators of Suspended Assessment of Particulates in Barnegat Bay Stinging Sea Nettles Assessment of Fishes & Crabs Responses to (Jellyfishes) in Barnegat Bay Human Alteration of Barnegat Bay Baseline Characterization of Phytoplankton and Harmful Algal Blooms Baseline Characterization of Zooplankton in Barnegat Bay Dr. Paul Bologna, Montclair University Project Manager: Joe Bilinski, Division of Science, Research and Environmental Health Multi-Trophic Level Modeling of Barnegat Bay Tidal Freshwater & Thomas Belton, Barnegat Bay Research Coordinator Salt Marsh Wetland Studies of Changing Dr. Gary Buchanan, Director—Division of Science, Ecological Function & Research & Environmental Health Adaptation Strategies Bob Martin, Commissioner, NJDEP Chris Christie, Governor Ecological Evaluation of Sedge Island Marine Conservation Zone February 2016 Impacts of Invasive Sea Nettles (Chrysaora quinquecirrha) and Ctenophores on Planktonic Community Structure and Bloom Prediction of Sea Nettles Using Molecular Techniques Final Project Report Submitted to New Jersey Department of Environmental Protection by Paul Bologna, John Gaynor, Robert Meredith Department of Biology Montclair State University QAQC Director: Kevin Olsen Department of Chemistry and Biochemistry Montclair State University Research Support, Data Entry, QAQC Procedures, and Presentation Support by Christie Castellano, Dena Restaino, Idali Rios, Alex Sorrano, Alan Buob, George Shchegolev, Maria Carvalho, Ivonne Lozano, Zachary Fetske, Nashali Ferrara, Isabel Pastor 1 Acknowledgements We would like to acknowledge the support of the New Jersey Department of Environmental Protection for funding of this project and the Administrative staff of Montclair State University who provided technical assistance in pre- and post-grant awards procedures. We would like to thank numerous students who assisted in field and laboratory activities. Specifically we want to acknowledge the contributions of Dena Restaino and Christie Castellano who provided enormous support for completion of all facets of the research. Lastly, we would like to acknowledge and thank our QAQC officer Kevin Olsen. His support and oversight regarding water quality was invaluable. 2 Table of Contents Page Executive Summary 11 Project Introduction 13 Overall Project Objectives 15 Study Area 15 2012 Project Objectives 18 2012 Project Methodology 19 2013 Project Objectives 25 2013 Project Methodology 25 2014 Project Objectives 30 2014 Project Methodology 30 Results and Discussion 2012 Research Objectives 33 2013 Research Objectives 51 2014 Research Objectives 81 Conclusions and Recommendations 116 New Jersey DEP Management Options 117 Results Dissemination 119 Bibliography 121 Appendices Appendix A. CTAB/NaCl DNA Extraction Protocol 124 Appendix B. Dissemination of Results: Presentation Abstracts 126 Electronic Supplementals Provided to NJDEP 2012 QAPP 2013 QAPP 2014 QAPP Water Quality Data Lift Net Data Plankton Tow Data Molecular Analysis Data NextGen Sequencing Data for C. quinquecirrha Diet Analysis BLAST/MEGAN Search Summary 3 List of Tables Page 1 Names and Coordinates for the 20 Barnegat Bay, NJ Research Sites 16 2 Research Sampling Event Collection Dates for 2012 18 3 Set up of qPCR Reactions 21 4 Total yield and quality of DNA extracted for molecular diet analysis in 28 2013 5 Temperatures recorded for each sampling event at the 16 sampling sites 33 in 2012 6 Salinity measurements for the eight sampling events in 2012 33 7 Dissolved oxygen measurements for the eight sampling events in 2012 34 8 Average densities of taxa exhibiting significant differences among sites 37 from plankton tows collected in 2012 9 Peracarida correlation analysis from samples collected in 2012 40 10 Contributing taxa defining the planktonic community associated with 40 plankton tow samples based upon SIMPER Analysis for 2012 11 Results from the AUTOREG analysis between C. quinquecirrha 48 juveniles collected during a sampling event and adults collected two- weeks later 12 Results from the AUTOREG analysis between C. quinquecirrha ephyra 48 collected during a sampling event and juveniles collected two-weeks later 13 Results from the AUTOREG analysis between C. quinquecirrha 48 molecular DNA on the 500 µm filter collected during a sampling event and juveniles collected in plankton nets two-weeks later 14 Results from the AUTOREG analysis between C. quinquecirrha adult 49 distribution and molecular DNA on the 100 µm filter collected during a sampling event representing sexual reproduction 15 Density and prevalence of organisms settling on experimental settlement 49 platforms collected in 2012 16 Monthly sampling dates for bay-wide and lagoon sampling events in 51 2013 17 Bay-wide Water quality data for 2013 collected during sampling events 51 18 Lagoon Water quality data for 2013 collected during sampling events 52 19 Average densities of gelatinous zooplankton taxa exhibiting significant 60 differences in density among sites in 2013. 20 Significant Correlations among taxa collected from Plankton Tow 61 samples in 2013 21 Contributing taxa defining the planktonic community associated with 65 plankton tow samples based upon SIMPER Analysis for bay-wide collections in 2013 4 List of Tables (Continued) Page 22 Contributing taxa defining the planktonic community associated with 69 plankton tow samples collected in the lagoon sites based upon SIMPER Analysis in 2013 23 Results from the ANOSIM statistical test for Pair wise comparisons 71 between lagoon sites for plankton community structure for samples collected in 2013 24 Average density or percent cover of settling solitary organisms or 73 colonial taxa encountered on settling plates deployed in 2013 25 Number of contigs assigned by MEGAN from samples collected in 2013 78 26 C. quinquecirrha prey items identified in both the gut lavage and 80 tentacle picks 27 Monthly sampling dates for bay-wide and lagoon sampling events in 81 2014 28 Bay-wide Water quality data for 2014 collected during sampling events 81 29 Lagoon Water quality data for 2014 collected during sampling events 82 30 Contributing taxa defining the planktonic community associated with 89 plankton tow samples collected in the bay-wide surveys based upon SIMPER Analysis for 2014 31 Contributing taxa defining the planktonic community associated with 94 plankton tow samples collected in the lagoon sites during 2014 based upon SIMPER Analysis 32 Results from the ANOSIM statistical test for pair wise comparisons 96 between lagoon sites for plankton community structure from 2014 33 Identified prey items from dissected C. quinquecirrha collected in 2014 100 34 C. quinquecirrha prey items identified through sequencing in the 103 combined gut lavage and tentacle pick build from 2014. 35 Contributing taxa defining the planktonic community associated with 109 plankton tow samples collected among years based upon SIMPER Analysis 36 Comparison of C. quinquecirrha prey items identified in the combined 114 gut lavage and tentacle pick builds for 2013-2014. 5 List of Figures Page 1 Sampling stations in Barnegat Bay, NJ 16 2 qPCR amplification plot of C. quinquecirrha DNA 22 3 Standard Curve developed for qPCR analysis 22 4 Melting curve developed for qPCR analysis 23 5 Spatial and temporal distribution of adult Chrysaora quinquecirrha in Barnegat 35 Bay collected from lift nets during the summer of 2012 6 Spatial and temporal distribution of adult Mnemiopsis leidyi in Barnegat Bay 36 collected from lift nets during the summer of 2012 7 Density of juvenile C. quinquecirrha collected in plankton tows in 2012 38 8 Density of C. quinquecirrha ephyra collected in plankton tows in 2012 38 9 Crab larvae density among sites collected from plankton nets in 2012 39 10 Relative abundance of sea nettle DNA on 500 µm filters in water samples from 45 2012 11 Relative abundance of sea nettle DNA on 100 µm filters in water samples from 46 2012 12 Relative abundance of sea nettle DNA on 0.45 µm filters in water samples from 47 2012 13 Molecular Assessment of DNA concentrations (16S rDNA) collected on the 53 500µm filters from monthly bay-wide sampling events in 2013. 14 Molecular Assessment of DNA concentrations (16S rDNA) collected on the 54 100µm filters from monthly bay-wide sampling events in 2013. 15 Molecular Assessment of DNA concentrations (16S rDNA) collected on the 55 500µm filters from monthly lagoon sampling events in 2013 16 Molecular Assessment of DNA concentrations (16S rDNA) collected on the 56 100µm filters from monthly lagoon sampling events. in 2013 17 Distribution of Chrysaora quinquecirrha and Mnemiopsis leidyi collected 57 during bay-wide lift net sampling events in 2013 18 Distribution of Chrysaora quinquecirrha and Mnemiopsis leidyi collected 58 during lagoon lift net sampling events in 2013 19 Distribution of Chrysaora quinquecirrha and Mnemiopsis leidyi collected 58 during bay-wide plankton net sampling events in 2013 20 Distribution of Chrysaora quinquecirrha and Mnemiopsis leidyi collected 59 during lagoon plankton net sampling events in 2013 21 Density of calanoid copepods among sites and dates of collection in 2013 for 61 bay-wide samples. 22 Density of calanoid copepods among sites and dates of collection in 2013 for 64 lagoon samples. 23 MDS plot of planktonic community structure from bay-wide samples plotted 68