Effects of Nori Aquaculture on the Marine Flora of Cobscook Bay and Selected Sites Within the Gulf of Maine

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Theme Area: 
Coastal Ecosystem and Public Health
Sustainable Aquaculture


Arthur Mathieson UNH - Jackson Estuarine Lab Principal Investigator
Christopher Neefus UNH - Department of Biological Sciences Co-Principal Investigator
Anita Klein UNH - Department of Biological Sciences Principal Investigator
Donald Cheney Northeastern University - Marine Science Center Co-Principal Investigator

Students Involved:

Andrew West UNH - Graduate Program in Genetics
Brian Teasdale UNH - Department of Biological Sciences
Aaron Wallace UNH - Department of Molecular, Cellular & Biomedical Sciences
Katherine Watson Northeastern University
Danielle Friel Cain UNH - Graduate Program in Genetics

To assess the impact of the fledgling nori aquaculture industry on the marine flora of Cobscook Bay and selected sites within the Gulf of Maine by:

1) Examining dispersal and persistence of Porphyra yezoensis at sites adjacent to current and new cultivation sites

2) Developing genetic profiles for the U-51 strain that has been cultivated during the past seven years within Cobscook Bay, as well as additional strains of P. yezoensis proposed for use by Coastal Plantations Inc. (CPI) in their expanded aquaculture program

3) Establishing baseline information regarding the distribution and abundance of indigenous Porphyra species within the Cobscook Bay cultivation and nursery areas, and at proposed sites (e.g., the Bagaduce River near Castine, Maine)


1) Intensive monthly surveys will be made in order to assess the seasonal and spatial abundance patterns of Porphyra yezoensis and indigenous species surrounding diverse nori aquaculture sites within the Gulf of Maine

2) Molecular methods based upon PCR-amplification of species-specific alleles will be used to positively type (identify) species

3) Amplified Fragment Length of Polymorphisms (AFLP) will be used to develop genotype profiles for the various cultivars of P. yezoensis, as well as to examine the occurrence of indigenous Porphyra species at each aquaculture site. Molecular methods are expected to be more accurate than traditional morphological/reproductive features because of the plant's extreme phenotypic plasticity and infrequent occurrence of critical reproductive stages. They are also amenable to the high through-put required for this type of ecological survey.


1) To provide regulatory agencies and the aquaculture industry with a significant basis for making decisions about the introduction of aquaculture strains/species in relation to the management of coastal resources

2) To establish a scientific basis for measuring the impact of mariculture of economically important seaweeds on native species and the marine environment

In the early 1990s Coastal Plantations International (CPI) began to commercially farm nori in Cobscook Bay, Maine. The company received permits from local, state, federal and international agencies to grow two cultivars of the Japanese species Porphyra yezoensis strains U51 and H25. Since both Porphyra yezoensis cultivars are nonindigenous to Cobscook Bay, there was widespread concern among marine ecologists as to whether Porphyra yezoensis, an introduced species, could 1) over winter in Cobscook Bay and 2) become invasive.
As part of this project, we established molecular methods to identify native Northwest Atlantic Porphyra species, and uncovered two cryptic species of Porphyra. We also described the distribution and floristic patterns of native Porphyra species.
Porphyra samples were collected from intertidal transects and artificial substrata constructed of Japanese nori netting for over two years. Porphyra plants were identified to species using morphological characteristics, as well as DNA markers. The Rubisco large subunit (rbcL) and rRNA genes were used to distinguish putative P. yezoensis plants from native species. The results of both the intertidal iransect studies conducted by the UNH team (Mathieson and Klein) and the nori-netting studies conducted by the Northeastern University team (Watson and Cheney) led to the same conclusion—that Porphyra yezoensis could only recruit in the Coastal Plantations farm sites during the summer and autumn seasons and could not over-winter in significant numbers. There was no evidence that P. yezoensis could establish a permanent population in Cobscook Bay. No plants of Porphyra yezoensis were found in transects or on nori netting in the vicinity of the farm sites six months after Coastal Plantations ceased farming nori in Cobscook Bay in 1998. Thus, our investigations show that the permitting process for the introduction of this particular exotic species worked and that P. yezoensis does not appear to pose a threat where it was being farmed.
Andrew West's studies in New Hampshire documented the occurrence of two "cryptic" taxa recorded for northern Maine and the Canadian Maritime Provinces. Overall, the detailed ecological and molecular studies supported by this project have shown the value of conducting a detailed bio-monitoring investigation on an introduced marine species, and have fostered a better understanding of the "native" Porphyra species found in the western Atlantic.
During the current NOAA project, we have resolved a number additional cryptic species, all of which are morphologically similar to P. leucosticta. Importantly, we have evidence that the Porphyra yezoensis, which was cultivated by CPI, is closely related genetically to the Northwest Atlantic Porphyra.
Correct identification of vegetative Porphyra thalli based solely on morphology is still problematic. In original methodology we had proposed to use allelic specific Polymerase Chain Reaction (AS-PCR) as a molecular screen to distinguish between native Northwest Atlantic Porphyras. AS-PCR turned out to be an unnecessarily complicated way to sort out the >eight different taxa now known to be native in the Gulf of Maine. Instead, because of the relatively high level of sequence divergence in the rbcLgene between the native Porphyras, it was possible to design a molecular screen using PCR amplification with Bangia specific rbcLprimers, and diagnostic restriction digests. Using molecular screens to aid morphological studies, we have been able to improve the morphology, ecology and phenalogy of native species of Porphyras.


Available from the National Sea Grant Library (use NHU number to search) or NH Sea Grant

Journal Article

  • West, A., A. Mathieson, A. Klein, C. Neefus and T. Bray (2005). Molecular ecological studies of New England species of "Porphyra" (Rhodophyta, Bangiales). Nova Hedwigia 80(1-2):1-24.
  • Kunimoto, M., H. Kito, Y. Yamamoto, D. Cheney, Y. Kaminishi and Y. Mizukami (1999). Discrimination of "Porphyra" species based on small subunit ribosomal RNA gene sequence. Journal of Applied Phycology 11:203-209.
  • Mathieson, A., E. Hehre, C. Dawes and C. Neefus (2008). An historical comparison of seaweed populations from Casco Bay, Maine. Rhodora 110(941):1-102, Winter 2008.
  • Neefus, C., A. Mathieson, A. Klein, B. Teasdale, T. Bray and C. Yarish (2002). "Porphyra birdiae sp. nov." (Bangiales, Rhodophyta): A new species from the northwest Atlantic. Algae 17(4):203-216.
  • Klein, A., A. Mathieson, C. Neefus, D. Cain, H. Taylor, B. Teasdale, A. West, E. Hehre, J. Brodie, C. Yarish and A. Wallace (2003). Identification of Northwestern Atlantic "Porphyra" (Bangiaceae, Bangiales) based on sequence variation in nuclear SSU and plastic rbcL genes. Phycologia 42(2):109-122.
  • Teasdale, B., A. West, H. Taylor and A. Klein (2002). A simple restriction fragment length polymorphism (RFLP) assay to discriminate common "Porphyra" (Bangiophyceae, Rhodophyta) taxa from the Northwest Atlantic. Journal of Applied Phycology 14(4):293-298.


  • Cain, D. (2000). Genetic characterization and phylogenetic analysis of native western North Atlantic "Porphyra" using the 18S ribosomal gene. Master's Thesis, University of New Hampshire.
  • West, A. (2001). Molecular and ecological studies of New Hampshire species of "Porphyra" (Rhodophyta, Bangiales). Master's Thesis, University of New Hampshire.
  • Teasdale, B. (2004). An investigation of genetic variation within Northwest Atlantic "Porphyra" (Bangiales, Rhodophyta) with specific phylogeographic analysis of the common, rocky intertidal species, "Porphyra umbilicalis." Doctoral dissertation, University of New Hampshire.
  • Wallace, A. (2005). The taxonomic and systematic relationships of several salt marsh "Fucus" taxa (Heterokontophyta, Phaeophyceae) within the Gulf of Maine and Ireland examined using microsatellite markers. Doctoral Dissertation, University of New Hampshire.


  • Watson, K., D. Cheney and I. Levine (1999). Biomonitoring of an aquacultured introduced seaweed, "Porphyra yezonensis" (Rhodophyta, Bangiophycidae) in Cobscook Bay, Maine, USA. In: Marine Bioinvasions: Proceedings of the First National Conference, J. Pederson, ed., 1999, pp. 260-264.