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Oysters are an important component of many coastal ecosystems and a lucrative economic resource for many coastal communities. Oysters are ecosystem engineers that build on one another to provide critical habitat for fishes and invertebrates. Oyster reefs protect shorelines from the impacts of severe storms, improve water through filtration, and sequester carbon. However, despite their ecological value, oyster populations have declined precipitously over the last 130 years, decreasing by an estimated 85%.
Despite the importance of oysters, there are many shortcomings in current oyster reef biodiversity assessment methods––methods that would enable coastal managers to restore and conserve remaining oyster reefs. For instance, current assessment methods are time-intensive, costly, dependent on weather conditions, and destructive to existing habitat. With these shortcomings in mind, our team worked on developing novel methods that leverage remote, less invasive technologies such as passive acoustics and aerial imagery to produce robust, rapid, and cost-effective assessments of oyster reef health and biodiversity. Specifically, our team used Autonomous Reef Monitoring Structures (ARMS), unoccupied aerial vehicles (UAVs), and passive acoustic monitoring to assess the health and biodiversity of three oyster reefs in the Rachel Carson Reserve off the coast of Beaufort, North Carolina.
Autonomous Reef Monitoring Structures (ARMS) & Traditional Quadrat Surveys: ARMS are stacks of 9 PVC plates that are arranged to mimic the structural complexity of a reef and used by scientists as a standardized way to measure marine biodiversity. ARMS are deployed on a reef and left for months to years. Over time, invertebrates settle and grow on the structures, creating a micro-community representative of the area around them. The ARMS are then collected and every organism is accounted for using visual and genetic techniques to estimate local biodiversity. Researchers have primarily used ARMS to study coral reef biodiversity, but they may also be useful on temperate oyster reefs to quantify reef-associated diversity. However, before they can be implemented as a widespread tool they need to be compared to more extractive, conventional methods. Thus we also surveyed each reef using random quadrats (i.e. excavating a few representative chunks from each reef and counting all of the organisms in each chunk). These data allow us to both (1) compare whether ARMS are a viable non-destructive alternative to traditional quadrat surveys and (2) examine how the different diversity metrics relate to sound and UAV-based metrics. Check out the video below to see one of our ARMS in turbid, North Carolina waters and the photo below to see what a quadrat looks like.
Unoccupied Aerial Vehicles (UAVs): Using two-dimensional, georeferenced UAV imagery, we created 3-D renderings of oyster reefs through a process called Structure from Motion, in which we used the software package Pix4D to identify unique pixel clusters across multiple images, examine the relative positions of these unique pixel clusters, and output an orthomosaic of each reef.
Passive Acoustic Monitoring: We deployed a hydrophone on three different oyster reefs - one recently constructed reef, one reef that was constructed over a decade ago, and a natural reef. We quantified different qualities of the recorded soundscape, such as the intensity and frequency distribution of the sound. By comparing the soundscapes to 1) the biological communities measured by using quadrats and ARMS and 2) the habitat structure measured using UAVs, we can develop passive acoustic monitoring proxies to assess reef health and biodiversity.
Social survey: Our team also conducted a social survey in order to assess managers’ impressions of these innovative monitoring methodologies. Through outreach, we were able to talk with 9 managers across a handful of organizations. Broadly, though these managers were excited about the prospect of incorporating innovative, remote technologies into their restoration and conservation efforts, many of them also flagged two central limitations: time and money. In fact, many of these managers don’t conduct regular and rigorous evaluations of their reefs because many of their grants don’t provide funding for this longevity of attention. For those managers who did have regular monitoring regimes, many of them relied on volunteers to do this work. That being said, many of these managers also had dependable partners at a range of academic institutions and surmised whether there weren’t opportunities to incorporate these efforts by way of university partners.
Between Hurricane Dorian and COVID-19, our team learned to be adaptive--we would be remiss not to acknowledge the impact of both Hurricane Dorian and COVID-19 on our team’s plans. In the Fall, our team had intended to begin passive sampling. However, because of Hurricane Dorian in September 2019, we had to pull up the ARMS we had deployed in April 2019 and start again from scratch. In the face of this unforeseen event, we (1) started a new side project looking at how thermal buffering is related to reef diversity and whether remotely-sensed thermal metrics are good proxies for reef temperatures and (2) pushed back our project timeline by ~5 months. This altered timeline meant that our big ARMS recovery field trip was pushed to April 2020 and was ultimately cancelled when the COVID-19 outbreak began. The outbreak also prevented us from finishing our diversity processing in the lab and transitioned all of our meetings online. That said, we are optimistic that with an extended timeline we will still be able to finish most of the work.
Oysters can promote diversity by lessening the physical stress of living in an intertidal environment. As the tide comes in and goes out, organisms living in the intertidal zone are subject to extreme salinity, moisture, and temperature swings. By creating structure to retain water and provide shade, oysters help improve living conditions for reef-associated organisms. One important control on many organisms globally--and one that’s predicted to change in the future--is temperature. We still do not know how reef-associated organisms are influenced by temperature on the whole or how changes in temperature will alter reef communities.
To look at whether reef temperature and the thermal buffering capacity of a reef influences community composition, we took two types of temperature measurements on three reefs around Pivers Island, NC. To quantify surface temperature, we flew three UAV flights over the reefs with a thermal camera and to quantify internal temperatures, we deployed twenty-three temperature loggers inside the reefs at different tidal elevations. At each reef we also excavated two reef quadrats--one high on the reef crest and one low on the reef towards the low water line--to quantify the community composition in each reef. We then related heat metrics to biological metrics to examine potential relationships between temperature and the species assemblage at a given reef.
For our initial oyster reef biodiversity assessment, we selected three sites off of Piver’s Island in Beaufort, North Carolina (Figure 1). These sites, identified in the map below, were all shoreline oyster reefs which became exposed at low tide. The NOAA site was a reef in a small, disturbed salt marsh. The Bridge and Mound sites were situated near each other, but were far enough apart to be considered separate reefs. Despite the proximity of Bridge and Mound, we found that the Bridge and NOAA sites were more similar in oyster size and reef structure than Bridge and Mound, indicating that proximity, in this case, did not necessarily dictate reef community.
The Mound site was particularly interesting. Mound was most exposed at low tides and experienced the largest temperature range daily when compared to the Bridge and NOAA sites. We found that the Mound reef had the largest number of dead oysters, live oysters, and clumps of live oysters. While it has the most structure and sheer number of oysters, the mean live oyster length was nearly half of what we observed in the other two reefs. This could indicate that experiencing a larger temperature range and additional environmental stress may prevent oysters from surviving to reach adult length. Even though the oysters were small, they seem to have provided the largest amount of structure for invertebrates. We found that the Mound site had a high species richness but a low Shannon-Weaver index value. This, combined with the fact that the reef had the highest number of individual invertebrates, leads us to believe that Mound, with its larger oyster density and structure, can act as a habitat for more invertebrates but those invertebrates are not spread evenly across the reef. This could be because of the thermal stress that the peak of the reef experiences.
UAV thermal snapshots fail to capture both the temperature average and the temperature range of oyster reefs
We were interested in whether UAV-based temperature measurements captured over three flights on a single day could capture the general differences in temperature regimes among reefs. If so, UAV-based surveying could be an effective way to examine heat stress across oyster reefs. However, we found that UAV-based thermal metrics did not appear to be correlated with temperature measurements taken directly in the reef with temperature loggers over a longer time period (Figure 2).
Temperature range appeared to be the most important variable for predicting the biological community of a reef
We found that extreme temperatures (e.g. large temperature ranges) were negatively associated with reef diversity and average oyster length (Figure 3). Reef diversity is a combination of both how many different types of organisms were found at a site and how evenly distributed they are (e.g. if most of the organisms belong to one or two taxonomic groups vs. similar abundances across taxonomic groups). Looking more closely at these two components, it appears that diversity differences were largely due to increased evenness at sites with lower temperature ranges. Given that the intertidal environment of these reefs is already stressful, it is likely that more intense temperature fluctuations limit the number of species that can live on a reef and may prevent oysters from reaching large sizes. In support of this theory, we also found that quadrats taken at low reef elevations (i.e. those closer to the low water line that experience the lowest temperature swings) had higher species richness than those at high reef elevations (Figure 4).
Although more research with larger sample sizes is needed to flesh out these preliminary results, if temperature variation is limiting reef community development, future reefs may be less diverse with smaller oysters. As climate change intensifies, temperature variation is projected to increase, which could stunt the oysters themselves, as well as the community of reef-associate species.
We deployed hydrophones - autonomous underwater microphones (Figure 5)- to assess the biological communities and habitat structures at oyster reefs. Oyster reefs are some of the loudest underwater ecosystems, filled with the crackle of snapping shrimp and the humming of fishes. Snapping shrimp produce sounds mostly in the higher frequencies (>2000 Hz), whereas fishes and geological sound dominate the lower frequencies (<2000 Hz). We predicted that richer and more diverse biological communities would produce louder sounds. In bioacoustics, we call the loudness of a recording the sound pressure level. Furthermore, we predicted that areas with diverse biological soundscapes would have greater temporal variation of acoustic intensity - a factor we can measure using the acoustic complexity index. Finally, areas with denser biological communities might produce more sound in the higher frequencies, as invertebrate sounds begin to dominate geological sounds. The frequency that contains the most acoustic power in a recording is called the peak frequency.
We deployed hydrophones on three oyster reefs to determine how they varied acoustically. Our three reefs ranged from a recently constructed reef (CCA), an older constructed reef (1L5), and a natural reef (Nat2). By comparing the soundscape on a reef to 1) the biological community and 2) the habitat structure, we can develop acoustic metrics that remotely and rapidly assess the habitat health, biodiversity, and restoration success on oyster reefs. Watch the video below to hear one of the reefs and see how we summarize those sounds using pressure, frequency, and power.
SPL
CCA was the quietest reef with a mean full spectrum SPL of 108.1 dB. Nat2 was the loudest reef (mean 117.5 dB). 1L5 was between the other two reefs (mean 115.8 dB) but closer to Nat2 (Figure 6). SPL measures how loud a recording is, with higher SPL representing louder soundscapes. This is consistent with our predictions. If 1L5 had a decade to recruit and develop a rich biological community, then it should have a similar sound intensity compared to the natural reef, Nat2. Because CCA is the newest and presumably least developed reef, it may have fewer sound-producing animals and thus a quieter soundscape.
To determine whether the difference in SPL resulted from invertebrates, fishes, or geological noise, we filtered the sound and calculated the SPL for high frequencies where invertebrates dominate (>2000 Hz) and low frequencies where fishes and geological noise dominates (<2000 Hz) (Figures 7a and 7b). This analysis revealed that 1L5 had the highest high frequency SPL (mean 106.9 dB), followed by Nat 2 (mean 103.9 dB) and CCA (mean 99.3). There was little variation between sites in low frequency SPL. From this, we concluded that 1L5, the older constructed site, had the most invertebrate activity. Nat 2, the natural site had a similar level of invertebrate activity while CCA, the newly constructed site, had the least.
ACI
We also calculated the acoustic complexity index (ACI) for each site, which measures the variability in intensity of a sound recording. CCA had the highest ACI, reaching 28.9, while 1L5 and Nat2 were much lower, with ACIs of 9.6 and 7 respectively (Figure 8). Having a lower ACI indicates that these reefs are consistently loud, with little variability in intensity. This is most likely from the constant bombardment of snapping shrimp snaps at Nat2 and 1L5. CCA, on the other hand, exhibits more variation in intensity, possibly due to fewer snapping shrimp snaps with quiet intervals between snaps.
Peak Frequency
CCA had the lowest peak frequency at 558.8 Hz, while 1L5 had the highest at 2395.0 Hz, and Nat2 was measured to be 1464.3 Hz (Figure 9). This suggests that the soundscape at CCA - the site with the lowest peak frequency - is dominated by geological sounds, such as waves, whereas the soundscape at 1L5 and Nat2 are dominated by invertebrates like snapping shrimp which produce high frequency sounds.
Based on our findings, a thermal image snapshot of a reef does not appear to be a robust proxy for the thermal regime of an oyster reef. The data collected from thermal imagery did not match the data from the temperature loggers and we placed more weight on the data from temperature loggers because the loggers were deployed for a month while the drone imagery could only account for a brief instant in time.
While our findings from our three study reefs show clear trends in the relationship between thermal stability and biodiversity, future studies with larger sample sizes are needed to validate these preliminary findings. Additionally, increasing the taxonomic resolution of surveys might change the results we found. Purely visual identification presents a challenge when attempting to classify invertebrates at the species level. A promising alternative is DNA metabarcoding, which would provide clear, high resolution identification of the invertebrates present in our samples. Future studies leveraging these techniques could provide further insight to what we found here.
We will continue to deepen our analysis, looking at metrics such as the total number of snapping shrimp snaps per minute and the acoustic entropy. Once pandemic restrictions are lifted and we have biodiversity estimates and information about the habitat structure, we will also develop models where we can determine which acoustic variables are most predictive of the biological communities and habitat structure.
