1 Department of Biological Sciences, Queensborough Community College, City University of New York, Bayside, New York, USA

2 Department of Biological Sciences, Kingsborough Community College, City University of New York, Brooklyn, New York, USA

3 Department of Biology, Georgia State University, Atlanta, Georgia, USA


Plumb Beach, Brooklyn, New York in USA is an important horseshoe crab breeding and nursery ground that has experienced substantial anthropogenic influence, including pollution, erosion and subsequent restoration. Since little is known about the relationship between sediment microbial communities and juvenile horseshoe crab survival, next generation sequencing was used to characterize and compare the sediment microbiome of three distinct areas of Plumb Beach:- a tidal creek with abundant juveniles, East Beach with moderate number of juveniles, and West Beach- a highly disturbed area where juvenile crabs are rarely seen. The microbiome of juvenile crab intestinal content (both dissected gut content and fecal flush content) from the tidal creek site was also examined. The results showed that in our 2017 survey, the overall dominant sediment orders at all beach sites were Vibrionales (30%), Flavobacteriales (22%) and Alteromonadales (21%). Although alpha diversity was similar among the three beach sites, Bray-Curtis distances assessed by Permanova revealed significant differences in Beta diversity, with a unique microbial assemblage found in the tidal creek. Both crab gut and fecal flush samples did not sequence well, showing low species diversity and very high variability. This study is the first to use next generation sequencing to characterize Plumb Beach sediment microbes and the first attempt to examine the gut microbiome of juvenile horseshoe crabs. This information will contribute to understanding the relationships between sediment microbial assemblages and juvenile crab populations within this important urban habitat.

Graphical Abstract

Sediment microbiomes associated with critical habitat of the Juvenile American Horseshoe Crab; Limulus polyphemus


  • The study is the first to use a metagenomics approach to examine microbial assemblages in the sediments at Plumb Beach (Jamaica Bay, NY)- an important habitat for juvenile horseshoe crabs whose numbers have been in decline in recent years;
  • The results show that distinct beach areas share several taxa in common but also have their own unique assemblages. Vibrionales, Flavobacteriales and Alteromonadales were the most common orders found among all sediments;
  • Samples taken from juvenile horseshoe crab digestive tracts (fecal samples and dissected gut contents) yielded low sequence numbers and high variability;
  • Knowledge of the sediment microbiome at Plumb Beach will increase understanding of environmental conditions suitable for juvenile horseshoe crabs that could inform future conservation, restoration and reintroduction activities.


Main Subjects

Bolyen, E., Rideout, J.R.; Dillon, M.R.; Bokulich, N.A.; Abnet, C.C.; Al-Ghalith, G.A.; Alexander, H.; Alm, E.J.; Arumugam, M.; Asnicar, F.; Bai, Y.; Bisanz, J.E.; Bittinger, K.; Brejnrod, A.; Brislawn, C.J.; Brown, C.T.; Callahan, B.J.; Caraballo-Rodríguez, A.M.; Chase, J.; Cope, E.K.; Da Silva, R.; Diener, C.; Dorrestein, P.C.; Douglas, G.M.; Durall, D.M.; Duvallet, C.; Edwardson, C.F.; Ernst, M.; Estaki, M.; Fouquier, J.; Gauglitz, J.M.; Gibbons, S.M.; Gibson, D.L.; Gonzalez, A.; Gorlick, K.; Guo, J.; Hillmann, B.; Holmes, S.; Holste, H.; Huttenhower, C.; Huttley, G.A.; Janssen, S.; Jarmusch, A.K.; Jiang, L.; Kaehler, B.D.; Kang, K.B.; Keefe, C.R.; Keim, P.; Kelley, S.T.; Knights, D.; Koester, I.; Kosciolek, T.; Kreps, J.; Langille, M.G.I.; Lee, J.; Ley, R.; Liu, Y.X.; Loftfield, E.; Lozupone, C.; Maher, M.; Marotz, C.; Martin, B.D.; McDonald, D.; McIver, L.J.; Melnik, A.V.; Metcalf, J.L.; Morgan, S.C.; Morton, J.T.; Naimey, A.T.; Navas-Molina, J.A.; Nothias, L.F.; Orchanian, S.B.; Pearson, T.; Peoples, S.L.; Petras, D.; Preuss, M.L.; Pruesse, E.; Rasmussen, L.B.; Rivers, A.; Robeson, M.S.; Rosenthal, P.; Segata, N.; Shaffer, M.; Shiffer, A.; Sinha, R.; Song, S.J.; Spear, J.R.; Swafford, A,D.; Thompson, L.R.; Torres, P.J.; Trinh, P.; Tripathi, A.; Turnbaugh, P.J.; Ul-Hasan, S.; van der Hooft, J.J.J.; Vargas, F.; Vázquez-Baeza, Y.; Vogtmann, E.; von Hippel, M.; Walters, W.; Wan, Y.; Wang, M.; Warren, J.; Weber, K.C.; Williamson, C.H.D.; Willis, A.D.; Xu, Z.Z.; Zaneveld, J.R.; Zhang, Y.; Zhu, Q.; Knight, R.; and Caporaso, J.G., (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37: 852–857.9 (6 pages). 
Colon C. P.; Botton M.; Funch P.; Hoffgaard E.; Mandeep K., Mansfield K., (in press) Population Dynamics, Growth, Diet and Survival of Juvenile American Horseshoe Crabs (Limulus polyphemus) at Plumb Beach Brooklyn New York. In Tanacredi, J. (ed) Springer Research and Considerations in the Global Efforts to Conserve and Protect the Four Species of Horseshoe Crabs. Springer.

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