Thesis Proposal Draft – Do Not Steal

Here, McCollum Proposal is a .pdf of the actual proposal I gave to the department. This may be more interesting to you than 10 pages of unedited text. Please don’t steal it, either. (Apologies for the jumbled animations, ask and I can explain things if you have questions…)

The effects of settlement time and location on the survival of the early life history stages of Macrocystis pyrifera in the Point Loma kelp forest


Giant kelp forests span the southwestern coast of North America and occur in rocky, wave-swept nearshore habitats throughout temperate waters of the northern and southern hemisphere. The iconic foundational species of many kelp forests is the giant kelp Macrocystis pyrifera. M. pyrifera is characteristic of most brown macroalgal species (Phaeophyceae) in that it is attached to the substrate by a holdfast comprised of haptera, root-like structures that anchor the plant to the rocky seafloor but unlike roots, do not provide nutrients to the plant. Directly above the holdfast is the growing portion of the plant known as the meristem. The meristem sends up flexible stipes, which grow toward the surface and branch out to leaf-like fronds. The fronds, also referred to as blades, are where the majority of photosynthesis occurs. When sexually mature, a bundle of sporophylls form just above the holdfast. These sporophylls, which occur as small, feather-shaped blades, contain the reproductive material of M. pyrifera in an area known as the sori. The bulk of the biomass of a M. pyrifera plant occurs at the surface where the fronds form a dense canopy, obscuring light to the water column and benthic habitat below (Reed et al., 2011)(Fig. 1.). The stipes and canopy provide a food source and structural habitat for many fishes and invertebrates that live within the kelp forest (O’Conner and Anderson, 2010), and also sequester a great deal of atmospheric carbon dioxide (Wilmers et al. 2012).

The holdfasts of M. pyrifera outcompete many other benthic organisms for substrate space (Dayton and Tegner, 1984, Dayton et al., 1984). However, once reaching the surface, the M. pyrifera canopy blocks out sunlight that many other understory kelps and algae require for photosynthesis. The competition for space in a kelp forest community is three-dimensional; organisms need benthic space for attachment but also need access to sunlight from an unobscured water column. A number of opportunistic kelp species may live below the M. pyrifera canopy, such as the arborescent Pterygophora californica and Eisenia arborea, and the prostrate Laminaria farlowii, Cystoseira osmundacea, and Dictyoneurum californicum, but they are limited in their dispersal abilities by the availability of light and appropriate habitat substratum (Clark et al., 2004; Dayton et al., 1984, 1985). Beneath the understory kelp exists a complex mosaic of seasonal brown algae, such as Desmarestia ligulata, the articulated coralline algae Calliarthron tuberculosum and Bossiella californica, and many species of foliose Rhodophyceae (red algae) that grow both epiphytically on the coralline species and individually on the substrate, in addition to a host of sessile invertebrates such as sponges and tunicates. Many of these understory species have been found to be light adapted, in that they increase in abundance as a response to an increase in light (Clark et al. 2004). M. pyrifera however, is able to persist as a competitively dominant speciesby growing faster than its competitors, and once established, blocking access to sunlight which limits the growth of other kelps (Dayton et al., 1984).

Like most of the Laminariales (kelp), M. pyrifera has a bipartite life history. The adult plant takes the form of a continuously reproductive, but asexual sporophyte. Biflagellate, planktonic, haploid zoospores are expelled from the sori of the sporophylls and settle to the substratum in a pre-recruitment stage. Once settled, the microscopic zoospores germinate into male and female gametophytes. Upon receiving a chemical cue from the female gametophyte, the male gametophyte releases biflagellate sperm, also referred to as antherzooids, which must travel within a one millimeter range to find and fertilize the female gametophytes’ egg (Reed 1990b). Following syngamy, the now diploid embryonic sporophyte undergoes cell division and begins the process of growing towards the surface (Dayton et al. 1984). The embryonic sporophyte takes approximately 45 days to reach a size that is visible to the naked eye, if growth conditions are adequate. However, over this growing process, the sporophyte and its cohort undergo a process of self-thinning, by which density-dependent mortality continuously reduces the population until the presence of an individual no longer negatively affects the closest neighbor of its cohort (Schmitt et al. 1986, 1987, Li et al. 2000).

Figure 1. Macrocystis pyrifera life cycle sketch by Wheeler J North, from

Figure 1. Macrocystis pyrifera life cycle sketch by Wheeler J North, from

Many field-based studies on the life-history of macroalgae, focus on the visible size classes of sporophytes (Sundene 1962, Dayton 1973, Paine 1979, 1988, Chapman 1984, Dayton et al. 1984, Harris et al. 1984, Reed and Foster 1984, Dean et al. 1989, Dayton et al. 1992). Quantification of gametophyte or embryonic sporophyte density is nearly impossible as the zoospores are released by the millions. However, great progress has been made in determining the ecology of the early life-history stages of M.pyrifera in laboratory settings. Several previous studies have determined the light, temperature and nutrient conditions needed for gametophyte and early sporophyte survival (Anderson and North 1969, Luning and Neushul 1978, Luning 1980, Reed et al. 1991, Kinlan et al. 2003, Carney and Edwards 2010). Due to their small size, relatively few studies have observed the effects of physical and biological factors on the early life-history stages of M. pyrifera in the field. The few exceptions are Deysher and Dean (1986), Reed et al. (1988), Reed (1990), and Ladah and Zertuche-Gonzalez (2007). In these studies, gametophytes or early sporophytes were seeded at known densities, and outplanted into the field where their survival under natural or ambient conditions was quantified. However, many of these studies were short-lived and unable to track the survival of individuals to larger size classes. According to Dayton et al. (1984), natural survival in the field is variable during the early life-history stages. Of the 1543 M. pyrifera recruits that were mapped at first appearance to the naked eye and tracked over 9 months (until they reached the surface), only 300 survived to the 5 cm size class. Surprisingly, of those that reached 5 cm, 259 also survived to reach a size of 1-2 m. The 1-2 m young adults also went through a bottleneck and of the 259 only 35 survived to reach the surface.

The study I propose aims to examine the survival of the early life-history stages of M. pyrifera when outplanted at 3 size classes (embryonic sporophytes, 5-10 mm sporophytes, and 3-5 cm sporophytes). These sizes encompass the ranges examined by Deysher and Dean (1986), Reed et al. (1988), Reed (1990), and Ladah and Zertuche-Gonzalez (2007), and Dayton et al. (1984) with the intention of identifying 1) if there is a size refuge for juvenile M.pyrifera where density-dependent mortality is lessened, 2) the limiting life-history stage for juvenile M.pyrifera, and 3) if the patterns of natural survival observed by Dayton et al. (1984) persist with individuals recruited in the laboratory and outplanted in the field. Additionally, recruitment and survival of M. pyrifera has been observed to be seasonally variable with changes in temperature and nutrient availability. However, M. pyrifera is continuously reproductive once reaching sexual maturity and recruitment of individuals may occur throughout the year corresponding with the occurrence of “recruitment windows”, when conditions match the temperature and light requirements for gametogenesis (temperatures below 16.3 °C and irradiation levels above 0.4 E · m-2 · day-1) (Deysher and Dean 1986a). Therefore, outplants of the 3 size classes will occur on a 3-month cycle to examine for differences in survival related to the time of recruitment.

Study site

The Point Loma kelp forest, just offshore of San Diego, CA is the longest continuous kelp forest in the United States. and one of the most studied kelp forest communities in the world. The first known study of kelp at Point Loma occurred in 1857 (North 1971). It was in this kelp forest where organized scientific diving was pioneered by Scripps Institute of Oceanography researchers in the 1950’s, and the area has been a site of constant scientific inquiry for the last 60 years. This kelp forest is characterized by an abundance of bedrock forming the substratum, interspersed with patches of sand and cobble, with the added vertical complexity of an occasional boulder. This area is popular with both commercial and recreational lobstermen, and the area specifically known as New Hope Rock which is in the general vicinity where this research is taking place, is also a site frequented by dive tourists. Research sites (3) were selected at random in the central portion of the kelp forest and are located at N 32 40’57.8” x W 117 15’52.5”, N 32 41’04.6 x W 117 16’00.1”, and N 32 41’10.7 x W 117 16’01.0”, respectively, each separated by at least 180 m (Fig. 2.). The sites occur at a depth of 10-14 m and cover an area of 50 m2.

Figure 2. Location of the 3 research sites, labeled BMc1, BMc2, and BMc3, in relation to Point Loma and the mouth of San Diego Bay via Google Earth.

Figure 2. Location of the 3 research sites, labeled BMc1, BMc2, and BMc3, in relation to Point Loma and the mouth of San Diego Bay via Google Earth.


Sporophylls were collected from adult M.pyrifera plants in the Point Loma kelp forest on January 31st, 2013. 10-20 sporophylls were collected from approximately 10 plants by a class of new scientific divers to assure randomness and increase the genetic diversity of the gametophytes produced. Sporophylls were placed in a cooler of seawater and transported back to San Diego State University’s Coastal and Marine Institute Laboratory. At the laboratory, sporophylls with large visible sori were rinsed in fresh seawater and placed between layers of paper towels moistened with seawater and placed in the dark for 3 hrs at 10 °C. Spore release was induced by rehydrating the sporophylls in 12 °C seawater under ambient laboratory lighting. The spore suspension concentration of this stock solution was determined using a hemocytometer. These methods are similar to the spore release methods of Reed et al. (1991). This solution was added to a 80L tray of seawater so that spore densities in the tray were approximately 100 spores per mm2. Inside the tray were 54 – 12 cm segments of polypropylene rope weighed down by 1 stainless steel hex nut on each end. Also in the tray were 20 clean glass slides. The tray was stored in a temperature-controlled room at 12 °C under artificial lighting with an output of ~20mmols • m-2• s-1 of light on a 12:12 hr light/dark photoperiod. After 72 hrs, 2 slides were removed from the tray and density of settled gametophytes was quantified per field of view using a microscope at 40x. This process was repeated 4 times on each of the two slides to give an average settlement density.

Sporophytes at the medium and larger size classes will be collected using a paint scraper from the Point Loma kelp forest, with care taken to maintain the integrity of their holdfasts. 300 individuals of each size class will be collected, positively identified, and added to the tray of gametophytes. Every other day, 2 slides were removed from the tray and checked for the presence of embryonic sporophytes. Once syngamy has occurred in 90% of the individuals observed on the slides, the rope segments will be prepared for outplanting. At this time, the medium and large sized individuals will be separated and braided into 54 new 12 cm polypropylene rope segments, respectively. This process involves twisting the rope so that the fibers stretch open, placing the holdfast between the fibers, and twisting the rope closed to its original position. 4 individuals will be braided into the center 8 cm of each rope segment. At this time, hex nuts will be removed from the ends of the smallest size classes’ rope segments, and a cement nail and stainless steel washer will be added to the ends of all 162 rope segment, and a color-coded and numbered tag will be attached to each segment. 18 rope segments of the smallest size class will be placed in a 3.75 L ziplock bag filled with seawater. This bag of the smallest size class of sporophytes will be added to a 7.5 L ziplock bag filled with seawater, also containing 18 rope segments of the medium size class and 18 segments of the large size class. This process will be repeated until all of the rope segments are bagged as described.

Each of the 3 research sites have been surveyed along 4 – 25 m transects for benthic diversity and adult M. pyrifera abundance. Additionally, the substratum has been surveyed for the presence or absence of understory algae. 3 of the 4 transects at each site will be selected at random for the outplanting experiments. 2 random 1 m2 plots will be selected along each of the 3 transects. Plots will be rejected and replaced if they contain less than 90% bedrock. 1 of the 2 plots on each transect will be cleared of all organisms to the bedrock, with the exception of encrusting algae. The other plot will be left intact, as a control. In each of the 2 plots, 3 rope segments of each size class will be attached to the bedrock by hammering in the cement nails and securing them with ZSPAR marine epoxy. This process will be repeated on 3 of 4 transects at all 3 sites over a 3 day period. The growth and survival on each rope segment will be monitored weekly. Light and temperature meters have been deployed at each site and will be continuously monitoring these parameters throughout the experiment. After 3 months, a new set of sporophylls will be collected as before, and the process will begin again using 2 new plots at each of the 3 transects at all 3 sites.

Expected Results

Survival will be monitored as the presence or absence of individuals in each of the medium and larger size classes. Survival in the smallest size class will be quantified as a count of visible individuals on each sampling date. Total rates of survival for all size classes will be compared assuming normal distribution and homoscedascity. Data will be transformed as needed to meet these assumptions. Data from the cleared plots will be analyzed separately from the control plots to look at the effects of space competition and shading on growth and survival. Assuming no difference between sites, each of the 9 transects will be considered replicates. I expect that survival will be lowest in the smallest size classes overall, due to the process of self-thinning. However, sporophytes in the middle and large size classes will most likely show reduced growth and survival in the control plots with an undisturbed understory community.

Estimated Budget   

The bulk of the expense for this research project will come from boat fuel. At current fuel prices each round trip outing cost approximately $20.  Assuming this experiment will continue for 3 – 3 month cycles, with 1 day of diving per week, boat fuel alone should cost over $600. The majority of laboratory supplies, glassware, microscope, hemocytometer, seawater, ZSPAR, coolers and aquaria have been provided for use by CMIL and Dr. Edwards. Additional funds of approximately $300 will be needed for hardware including the polypropylene rope, a paint scraper, cement nails, washers, ziplock bags and numbered tags.


Despite our vast knowledge on the ecology of adult Macrocystis pyrifera, there exists a gap in our understanding when it comes to how the early life-history stages survive and grow in the field. New technologies such as underwater microscopy may be beneficial in the near future, however current models are cumbersome and logistically difficult to deal with in the periodic swell experienced while diving in the Point Loma kelp forest. Outplanting early life-history stages that have been grown and monitored in the laboratory, or collected in the field and positively identified in the laboratory, will allow us to quantify growth rates and survival at different sizes and in different habitats. By monitoring our outplants weekly, we will be able to determine at what size or age juvenile M. pyrifera escapes the effects of density-dependent mortality when influenced by the physical forces and biotic factors present in the kelp forest. Including the embryonic sporophyte size class in this study will allow us to examine if, as observed by Dayton et al. (1984), juvenile M.pyrifera experience a survival bottleneck before reaching 5 cm. Leaving our original outsplants out in the field while adding new juveniles every 3 months, will give us the opportunity to track individuals until they reach the surface. This study follows up on a legacy of kelp forest ecology in the Point Loma kelp forest. In a time of future climate uncertainty, and with predictions of more frequent, more intense storms (Reed et al. 2011) knowing the ecology of the entire life-history of Macrocystis pyrifera will be critical to mitigating the consequences of climate change and applying effective management in this important and valuable ecosystem.


Anderson, E. K. & North, W. J. 1969. Light requirements of juvenile and microscopic stages of giant kelp, Macrocystis. Proc. Int. Seaweed Symp. 6:3–15.

Carney, L.T., and M. S. Edwards. 2010. Role of nutrient fluctuations and delayed development in gametophyte reproduction by Macrocystis pyrifera (Phaeophyceae) in southern California. J. Phycol. 46:987-996.

Chapman, A. R. 0. 1984. Reproduction, recruitment and mortality in two species of Laminaria in southwest Nova Scotia. Journal of Experimental Marine Biology and Ecology 78:99-109.

Clark, R.P., Edwards, M.S., Foster, M.S. 2004. Effects of shade from multiple kelp canopies on an understory algal assemblage. Mar Ecol Prog Ser. Vol 267:107-119.

Dayton, P. K. 1973. Dispersion, dispersal and persistence of the annual intertidal algal Postelsia palmaeformis. Ecology 54:433-438.

Dayton, P.K. 1985. Ecology of kelp communities. Annual Review of Ecology and Systematics: 16, 215– 245.

Dayton, P. K., and M. J. Tegner. 1984. Catastrophic storms, El Nino, and patch stability in a southern California kelp community. Science 224:283-285.

Dayton, P.K., Currie, V., Gerrodette, T., Keller, B.K., Rosenthal, R., Ven Tresca, D. 1984. Patch Dynamics and Stability of Some California Kelp Communities. Ecol. Mono. Vol. 54:254-289.

Dayton, P.K., Tegner, M.J., Parnell, P. E., Edwards, P.B. 1992. Temporal and spatial patterns of disturbance and recovery in a kelp forest community. Ecol. Mono. Vol. 62:421–445.

Dean, T.A., Thies, K., Lagos, S.L. 1989. Survival of juvenile giant kelp: the effects of demographic factors, competitors, and grazers. Ecology. 70(2): 483-495.

Deysher, L., and T. A. Dean. 1986. In situ recruitment of the giant kelp, Macrocystis pyrifera: effects of physical factors. Journal of Experimental Marine Biology and Ecology 103:41-63.

Harris, L. G., A. W. Ebeling, D. R. Laur, and R. J. Rowley. 1984. Community recovery after storm damage: a case of facilitation in primary succession. Science 224:1336-1338.

Kinlan, B.P., Graham, M.H., Sala, E., Dayton, P.K. 2003. Arrested development of giant kelp (Macrocystis pyrifera, Phaeophycea) embryonic sporophytes: a mechanism for delayed recruitment in perennial kelps? J. Phycol. 39:47-57.

Ladah, L. B. & Zertuche-Gonza´lez, J. A. 2007. Survival of microscopic stages of a perennial kelp (Macrocystis pyrifera) from the center and the southern extreme of its range in the Northern Hemisphere after exposure to simulated El Nin˜o stress. Mar. Biol. 152:677–86.

Li, B., H. Wu, G. Zou. 2000. Self-thinning rule: a causal interpretation from ecological theory. Ecological Modelling. 132:167-173.

Luning, K., 1980. Critical levels of light and temperature regulating the gametogenesis of three Laminaria species (Phaeophyceae). J. Phycol., Vol. 16, pp. l-15.

Luning, K. & Neushul, M. 1978. Light and temperature demands for growth and reproduction of laminarian gametophytes in southern and central California. Mar. Biol. 45:297–309.

North, W.J., editor. 1971. The biology of giant kelp beds (Macrocystis) in California. Beihefte zur Nova Hedwigia. 32:1-600.

O’Conner, K.C., Anderson, T.W. 2010. Consequences of habitat disturbance and recovery to recruitment and the abundance of kelp forest fishes. J. Exp. Mar. Bio. Eco. 386:1-10

Paine, R. T. 1979. Disaster, catastrophe, and local persistence of the sea palm, Postelsia palmaeformis. Science 205: 685-687.

Paine, R. T. 1988. Habitat suitability and local population persistence of the sea palm Postelsia palmaeformis. Ecology 69:1787-1794.

Reed, D. C. 1990. The effects of variable settlement and early competition on patterns of kelp recruitment. Ecology 71: 776–87.

Reed, D. C., and M. S. Foster. 1984. The effects of canopy shading on algal recruitment and growth in a giant kelp (Macrocystis pyrifera) forest. Ecology 65:937-948.

Reed, D.C., Laur, D.R., Ebeling, A.W. 1988. Variation in algal dispersal and recruitment: the importance of episodic events. Ecological Monographs. 58(4):321-335.

Reed, D. C., Neushul, M. & Ebeling, A. W. 1991. Role of settlement density on gametophyte growth and reproduction in the kelps Pterygophora californica and Macrocystis pyrifera (Phaeophyceae). J. Phycol. 27:361–6.

Reed, D.C., Rassweiler, A., Carr, M.H., Cavanaugh, K.C., Malone, D.P., Siegel, D.A. 2011. Wave Disturbance overwhelms top-down and bottom-up control of primary production in California kelp forests. Ecology. Vol. 92, No. 11: 2108-2116.

Schmitt, J., D. W. Ehrhardt, and M. Cheo. 1986. Light-dependent dominance and suppression in experimental radish populations. Ecology 67:1502-1507.

Schmitt, J., J. Eccleston, and D. W. Ehrhardt. 1987. Dominance and suppression, size-dependent growth and self-thinning in a natural Impatiens capensis population. Journal of Ecology 75:651-665.

Sundene, 0. 1962. The implications of transplant and culture experiments on the growth and distribution of Alaria esculenta. Nytt Magasin Botanikk 9:155-174.

Christopher C Wilmers, James A Estes, Matthew Edwards, Kristin L Laidre, and Brenda Konar. 2012. Do trophic cascades affect the storage and flux of atmospheric carbon? An analysis of sea otters and kelp forests. Frontiers in Ecology and the Environment 10: 409–415.


One comment on “Thesis Proposal Draft – Do Not Steal

  1. Pingback: Proposal Fest « Micromacrocystis

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s