Big Ideas

San Francisco Bay Subtidal Habitat Goals Project

I recently learned about the San Francisco Subtidal Habitat Goals Project, a self-stated “Collaborative, Interagency Approach to Protect the Hidden Bay.” The organization is a collaboration between a variety of local and federal agencies and local conservation groups, and is committed to “setting science-based goals for maintaining a healthy, productive, and resilient ecosystem.”

Figure 3-1 from the most recent report from SF Bay Subtidal Habitat Goals Project, illustrating the types of subtidal habitats and processes that are common in subtidal urban environments

Quite a feat for an organization that works on urbanized subtidal environments – the ultimate unknown when it comes to modern marine ecology. I’m most impressed!

I’m particularly impressed because of their open and informed recognition that managing urban subtidal ecosystems is critical despite the limitations of our current understanding. In their own words: “Although a tremendous amount of scientific information is available from research and monitoring in the bay, little of it is useful in making decisions about specific proposals for development or restoration as it relates to subtidal habitat. Part of the reason for this shortfall is that subtidal habitats are usually invisible in the bay’s turbid waters, and most sampling methods cannot provide detailed information about the location and condition of the various habitats. Equally important is the need to learn more about the functions of these habitats, how they respond to environmental change, and how to protect and enhance them.”

I bring up this recent discovery because the organization put out a 200+ page report that is more comprehensive, contemplative, and contemporary in the context of current theoretical ecology than any I’ve ever seen from a governmental/non-profit collaboration of any kind, let alone one focused on urban subtidal ecosystems! In their report, highlighted science goals include identifying the ecosystem services that urban subtidal habitats support, understanding how artificial structures affect estuarine ecosystems, and characterizing the interactions between different urban subtidal habitat types. This is novel stuff! Someone involved is quite up to date on the cutting edge of ecology, and is applying it where it matters.

Not only are the research needs they highlight completely on point, they represent essential areas of study if climate change adaptation efforts are to be planned and implemented in a way that maintains and/or enhances the services that subtidal ecosystems provide to urban populations. Unless we understand how the modifications we make to marine habitats influence fishing, crabbing, the filtering and processing of water-borne pollutants, and various other benefits we receive from subtidal ecosystems, we may lose these benefits as we amour and prepare our shorelines for rising seas.

Figure 6-3 from San Francisco Bay Subtidal Habitat Goals Project’s 2010 report – an impressive flow chart of the relevant effects and considerations when managing urban artificial structures

Indeed, urban subtidal ecosystems globally are understudied and poorly understood.  But the Bay Area has surprised me by being well ahead of the curve. Whether it’s their impressive benthic maps or their honest statements of the limitations of current knowledge, I’m quite glad to know that my hometown is in good hands with the San Francisco Bay Subtidal Habitat Goals Project. Stay tuned to all their endeavors here. And read their full report from 2010 here.


Big Ideas

Urbanization and evolution

Galapagos finches, drawn by John Gould (1804-1881)

Galapagos finches, drawn by John Gould (1804-1881)

Urbanization may affect many aspects of marine ecosystems, but as ecologists we often ignore the potential evolutionary consequences of urban development. Several years ago now, there was a great study on just this by Andrew Hendry and colleagues in Proceedings of the Royal Society. They studied the most famous of model species for evolution: Darwin’s finches (the ground finch, genus Geospiza).

Specifically, Hendry et al. were studying two morphs (right) of the Medium Ground Finch (Geospiza fortis) on the island of Santa Cruz in Galapagos. The two morphs had different beaks sizes (used for eating different foods), different songs, and tended to mate preferentially within their morph (ie – with other birds that looked like them).

Two finch morphs (Photo by A.P. Hendry, 2014)

By documenting the differences between these two morphs, Hendry and colleagues expected they were in the process of observing a speciation event. But then something strange happened: in areas on the island where there were lots of humans, the morphological differences between the two morphs diminished. In particular, the “bimodal” (distinct large and small) beak sizes of the two morphs fused and beak size became widely variable in more urban locations. Why would this happen? Human activities had made a wider variety of food sources available to the finches (see photo of finch on cereal box). The little birds indulged in the anthropogenic cornucopia urbanization offered, and human food of all shapes and sizes was sure to satiate regardless of one’s beak morphology. Selection against intermediate beak size was thus eliminated, allowing birds of all beak sizes to thrive in urban areas. As Hendry describes it, humans were causing “reverse speciation”.

Galapagos finch on a cereal box (Photo by A.P. Hendry, 2014)

Galapagos finch on a cereal box (Photo by A.P. Hendry, 2014)

This is old news really, as it was published almost a decade ago. Two things have led me to post about it now: (1) I recently came across this blog post by Hendry on eco-evo, which I highly suggest, and (2) Hendry’s findings were featured in Episode 3 of Galapagos, which was made available on YouTube earlier this month. (The episode in its entirety is worth making an evening of! But skip forward to 36:08 if you just want to hear about urban finches).

To my knowledge, there have yet to be any comparable examples documented in the marine environment. Other human activities are known to influence evolutionary traits in marine organisms. For instance, fishing can lead to an earlier age or smaller size at which marine fish become reproductive. But evolutionary consequences from marine urbanization specifically are poorly understood.

With time and further study, we hope to know more!

Big Ideas, Recent Research


Figure 1 from Loke et al. (2014) - A screenshot from CASU.

Figure 1 from Loke et al. (2014) – A screenshot from CASU.

Here’s a neat tool that could be of use to urban planners and restoration ecologists – CASU, the “Complexity for Artificial Substrates” program. CASU is open source software developed by Lynette Loke at the National University of Singapore and colleagues in Singapore, the Netherlands, Brazil, and the United Kingdom. The program allows users to design and visualize artificial substrates for urban waterfronts that are more complex than traditional, uniform surfaces we currently see on most bulkheads and seawalls. Since substrate complexity is tied to biodiversity of intertidal ecosystems, more complex substrates like those generated by CASU may serve as “ecological enhancements” for urban waterfronts.

Loke and colleagues originally developed CASU as part of a project aimed at increasing biodiversity on seawalls in Singapore using molded concrete tiles. By manipulating the topographic complexity of the tiles and deploying them in the field, they wanted to test whether more complex tile designs would increase the diversity of intertidal organisms. The problem is that you can define complexity in number of different ways. What specific aspects of habitat complexity actually affect intertidal diversity most and which are most important to include in your design?

CASU allows the user to modify 5 variables that affect complexity: (1) the number of object types, (2) relative abundance of object types, (3) density of objects, (4) variability and range in the objects’ dimensions, and (5) their spatial arrangement. In the case of their molded tiles, these 5 variables altered the arrangement and configuration of depressions in the tiles’ exposed surface (which are the “objects” that alter habitat complexity in their study).

Loke and colleagues describe CASU in further detail in a recent article in PLoS One. Indeed, after deploying their tiles in the field for 13 months, they did find that tiles with more complex surfaces supported greater diversity of intertidal organisms. Their subsequent work teasing apart which components of complexity are most influential for intertidal diversity on Singapore’s seawalls appears to be in press at the moment, so stay tuned for that. In the meantime though, you can download CASU using the links at the bottom of this page.

Figure 2 from Loke et al. (2014) - their caption reads: "3D models (AutoCAD drawings) of tiles with a single structural component (square-pits) at two levels of complexity generated via CASU. (A) ‘simple tile’ and (B) ‘complex tile’. (C) a fabricated 40×40×6 cm^3 concrete tile mounted onto a seawall (photograph taken one month after deployment)."

Figure 2 from Loke et al. (2014) – their caption reads: “3D models (AutoCAD drawings) of tiles with a single structural component (square-pits) at two levels of complexity generated via CASU. (A) ‘simple tile’ and (B) ‘complex tile’. (C) a fabricated 40×40×6 cm^3 concrete tile mounted onto a seawall (photograph taken one month after deployment).”


Big Ideas, Ecosystem Services, Recent Research

Engineering for the greater ecological good

Photo of eagle statue at Redondo Beach, WA

Invertebrate-encrusted eagle statue with a Metridium anemone growing on its wing

As coastal cities become increasingly urbanized, the surrounding waters are littered with a plethora of artificial structures. An “artificial structure” can be anything from seawalls and breakwaters to an abandoned garden statue, like this eagle (right) in South Seattle, which ended it’s long terrestrial journey at the bottom of the ocean. Though colonized by a colorful variety of organisms, artificial structures are rarely added to underwater landscapes with clear, coordinated, and ecologically-oriented goals in mind. The undersides of coastal cities can therefore become ecosystems of happenstance, a chaotic patchwork of opportunistic marine species that may or may not promote the conservation agenda of urban residents or the ecosystems services upon which urban residents rely.

But does it have to be this way? This was the question posed by Dr. Katherine Dafforn and colleagues in a recent publication in Frontiers in Ecology and the Environment (link). Using a series of case studies, they explore how artificial structures might instead be designed, or engineered, to meet specific ecological goals. For instance, to combat pollution, artificial structures could be “seeded” with seaweeds that absorb contaminants, and bivalves that filter organic pollutants. If we want to promote local biota, we could design artificial structures to mimic natural conditions, and restore natural coastal barriers, like wetlands and other shoreline features. (Here’s one such example documented by other UW biologists at the Olympic Sculpture Park in downtown Seattle. The video below shows the kelp forest ecosystem that formed at the site after old artificial structures were rebuilt with more natural materials.)

Though ecological engineering is not a new idea, Dafforn et al. are among the first to emphasize how the approach could help us realize the “multifunctional potential” of artificial structures in urban marine environments. Indeed, anyone who spends time observing marine life in cities is aware of the diversity of life these structures support and the benefits they could offer, both ecologically, and for people, if developed intentionally and with clear objectives in mind. As Dafforn and colleagues explain, these objectives do not need to be singular, as a multifaceted coastal management plan that incorporates a variety of ecological engineering projects and techniques could provide many benefits simultaneously. Perhaps it’s not too grandiose to conjecture that forward-thinking design initiatives could even realign the trajectories of humans and marine ecosystems in coastal cities so that they converge onto a single, more sustainable path forward.


Photo banner from the website
Big Ideas

Blue Urbanism

Recently, while browsing in a small bookstore in my hometown of San Francisco, I came across this new fantastic read: Blue Urbanism: Exploring Connections Between Cities and Oceans, by Timothy Beatley. Upon reading even just the dedication at the beginning (“Dedicated to all of the marine life we don’t (usually) see and the many individuals in cities who work tirelessly to understand and protect it”), I knew I was hooked.

Cover of Blue Urbanism, by Timothy Beatley

(c) Island Press, 2014

In a Places Journal essay (available here), Beatley notes, “Blue urbanism — an emerging set of ideas and perspectives — would mean that cities would seriously evaluate and carefully regulate their effects on marine environments; and city planners are potentially on the front lines of this new movement.” Because cities have jurisdiction over nearshore environments, he argues, they also have the power to actively manage these environments and mitigate the effect of city development on marine ecosystems. This may be done through a suite of management tools, including reducing pollution and “urban detritus” (such as plastic wastes), changing regulatory guidelines for ports and shipping, and curbing greenhouse gas emissions. Even simply incorporating maps of “ocean sprawl” into city planning may allow for considerable progress.

But Beatley’s exploration goes well beyond regulatory tools, eventually developing a completely new vision for how we interact with urban marine environments. If you’re a sci-fi fan, an urban dweller, a lover of marine habitats, or all of the above, I suspect you’ll find this vision to be an appealing one. Floating cities, underwater buildings, soft urban edges, and public spaces that integrate the shoreline are just a few of the ideas Beatley considers…. Did you know there’s already a restaurant in the Maldives where you can dine 5m below the sea’s surface (link)? And a luxury resort in Fiji where you vacation (for the cost of an entire college education) entirely underwater, at 12m depth, in the bottom of a tropical lagoon (link)?

These of course are venues most of us will never have access to, and who knows the extent of their environmental impact, but they stimulate consideration of a novel concept that I think is helpful: Perhaps we, as part of coastal food webs and marine ecosystems, could live our lives in a way that is intentionally and visibly integrated with the marine environment. Whether we’re purposeful about it or not, we are actively shaping and recreating urban marine landscapes. Why not do this in a way that promotes sustainability, helps marine ecosystems thrive, and enriches our own awareness and sense of well being?

Blue Urbansim, by Timothy Beatley. Check it out!



Photograph of ocean and riprap at dusk
Big Ideas, Ecosystem Services, Recent Research

Climate change and the proliferation of shoreline armoring

Louise Firth and colleagues recently published this article in Environmental Science Processes & Impacts: Climate change and adaptational impacts in coastal systems: the case of sea defences. It provides a brief exploration of shoreline armoring in the face of climate change. The general idea is this: as sea levels rise, coastal cities and developments are requiring increases in coastal defense structures (breakwaters, riprap, etc). These structures carry negative and potentially positive impacts for marine ecosystems. Why not construct them with these impacts in mind?

Photo of coastline with riprap and seawall

(c) Nigel Chadwick

“There is no doubt,” Firth and colleagues state in their paper, “that [armoring structures] modify the natural environment and can have deleterious impacts…” They cite research that has demonstrated how armoring structures act as stepping stones for species undergoing range expansions and how they have facilitated biological invasions. However, they may have potentially beneficial impacts as well, by supporting species of conservation importance and increasing habitat heterogeneity, as Firth et al. (2013) note.

So what does this mean for the construction of coastal defense structures? If the objective is to enhance intertidal biodiversity, Firth et al. (2013) provide these guidelines:

  • ”Build structure lower in the intertidal zone.”  Areas that are submerged for longer tend to support a greater number of species. Would this alter habitat that would otherwise be unaltered? That’s a discussion for another day I suppose.
  • Avoid smooth rocky material“, as these types of surfaces tend to be to be colonized by fewer species.  Specifically, they suggest a mixture of hard and soft rock to create greater surface roughness.
  • Create rock pools,” which should provide refuges for some species at low tide and support greater diversity.
  • Create pits” and crevices.  These provide hiding places and habitat heterogeneity.
  • Deploy precast habitat enhancement units.” Firth et al. (2013) note that a variety of such units are currently being tested around the world at the moment.  More on this soon in future posts!



Photos of marine life growing on seawall
Big Ideas

Living Seawalls for the Intertidal

It’s a bit old at this point, but I recently came across this article in Conservation Magazine on “How to Build a Living Seawall”.  It gives a good summary of work done by colleagues at the University of Washington and the University of Sydney on different seawall configurations that support greater intertidal biodiversity.  More updates as these findings are incorporated into the construction of a new seawall in Seattle…