Revealing Biodiversity on Rocky Reefs using Natural Soundscapes

Post Provided by SYDNEY HARRIS

The Biodiversity Struggle

Typical rocky reef habitat in northeast New Zealand, characterized by encrusting red algae and Kelp forest. ©Sydney Harris

Typical rocky reef habitat in north east New Zealand, characterized by encrusting red algae and Kelp forest. ©Sydney Harris

By now we’re all familiar with the global biodiversity crisis: increasing numbers of species extinct or at risk of extinction; widespread habitat loss and a seemingly endless set of political, logistical and financial obstacles hampering swift action for conservation. The international Convention on Biological Diversity (CBD) has set twenty global diversity targets, many of which require participating nations to conduct accurate and efficient monitoring to assess their progress and inform policy decisions. Governing bodies and organizations worldwide have agreed that immediate, efficient action is essential to preserving our planet’s increasingly threatened ecosystems.

But how? Diversity measurement techniques are a tricky business. Accurately recording diversity can be time-consuming, labor-intensive, expensive, invasive and highly susceptible to human error. Often these methods involve the employment of trained specialists to individually identify hundreds or even thousands of species, a process that can take many months to complete.

Marine habitats are particularly difficult to access because of the physical limitations of humans underwater, and are often flawed due to the influence of our presence on marine organisms. However, the oceans contain many of the world’s most diverse systems, and, despite the limitations of current methods, the need to monitor marine diversity is a top priority for the global conservation movement.

An Answer in Acoustics

Hydrophone mounted on a weight, ready for deployment in the field. ©Rosalyn Putland

Hydrophone mounted on a weight, ready for deployment in the field. ©Rosalyn Putland

“Ecoacoustics,” or “Soundscape Ecology,” is an emerging field in which ecologists study entire soundscapes over various spatial and temporal scales to tackle all sorts of ecological monitoring challenges, including biodiversity measurement. Generally, a soundscape is defined as ‘the collection of sounds that emanate from landscapes,’ composed of:

  • biological sounds, such as animals vocalizing (biophony)
  • physical sounds, such as wind and rain (geophony)
  • anthropogenic noises, such as those from shipping (anthrophony)

Passive acoustic monitoring (PAM) of soundscapes can provide clues that help ecologists distinguish between healthy and deteriorating environments. Although PAM has been employed around the world for decades, it was only quite recently that ecoacousticians were able to develop acoustic diversity indices for measuring biodiversity using sound. These ecoacoustic indices can act as proxies for species assemblage diversity measures, and have proven quite effective in terrestrial environments.

What are the advantages of acoustic biodiversity measurement? It’s faster and cheaper, for one thing. It’s also much less invasive of the habitat we’re ultimately trying to monitor and protect. Finally, it eliminates visual sampling bias. PAM allows nature to do what nature does best and simply pays attention to the results.

Diving Deeper: Investigating the use of Ecoacoustic Indices Underwater

Ecologists have been exploring and fine-tuning terrestrial ecoacoustic indices with promising results. But what about those harder-to-reach marine habitats that are so critical to global environmental health? PAM in the marine environment is a long-standing practice for ecologists interested in mammals, but has been picking up momentum with a broadened scope over the past few decades. It makes sense to study acoustics in marine environments because sound is integral to the life histories of so many organisms in the ocean. Following this line of thought, searching for indicators of diversity in marine soundscapes seems a logical next step.

Our work has investigated the application of acoustic diversity indices to coastal rocky reefs. These are excellent places to tune in to – almost everything in this biological community has something to say. From snapping shrimp to sea urchins to schooling fish, a veritable uproar of hunting, feeding, navigation, mating and territory-defending calls occurs day and night, rising to an impressive din each dusk that is known as the “evening chorus.” It’s the perfect place to scan the soundscape for diversity clues. We compared direct, in situ reef fish species assemblage diversity measures from rocky reefs with ecoacoustic indices calculated from field recordings at the same locations.

Acoustic recordings were collected in north-eastern New Zealand during the summer new moon – when reef species are most acoustically active. Then, three ecoacoustic indices originally developed for terrestrial use – the Acoustic Complexity Index (ACI), Acoustic Entropy Index (H), and Acoustic Richness Index (AR) – were compared to three “traditional” species assemblage diversity measures: Shannon’s Diversity Index (H’), Pielou’s Evenness (J’), and estimated species richness (S).

Standardize, Standardize, Standardize

Since new methods are most helpful if they’re standardized, we developed and tested criteria for successful ecoacoustic indices, ultimately recommending the following requirements:

  • Positive correlations between species diversity and ecoacoustic indices in relevant frequency ranges – if an acoustic index doesn’t reflect results you would obtain using alternative methods within the particular habitat you want to monitor, it’s not a helpful proxy.
  • Robustness to changes in spectral resolution (essentially the ‘level of detail’ in the spectra from each recording) – not everyone can (or necessarily should) record at very high spectral resolution. You need indices that work in a wide range of conditions and that aren’t influenced by changes to resolution in the processing stage.
  • Robustness to the presence of natural noise interference (i.e. wind) – the ocean is a noisy place. There’s no getting around this. Indices that don’t need extensive post-processing to eliminate the effects of this noise are highly desirable.
  • Robustness to the presence of anthropogenic noise – unfortunately there’s no circumventing this one either. People are taking over the acoustic space in the sea. In this study, over 50% of the sound files we collected were drowned out by vessel noises, even in marine reserves (more on that in the future). Measuring biodiversity using PAM needs to be feasible despite the presence of anthropogenic noise interference.

It Works! (And We Know Why)

Two of the ecoacoustic indices we tested proved effective as proxies for diversity measures. Specifically, the Acoustic Complexity Index (ACI) worked well as an indicator of species evenness (J’) and Shannon’s Index (H’), and Acoustic Entropy (H) reliably predicted species richness (S) and H’ above a threshold spectral resolution of ~140 Hz. While these results were exciting, they weren’t entirely unexpected.

Ecoacoustic indices were designed on the underlying principle that the soundscape, like everything else in nature, is a resource for which organisms must compete. Different species occupy soundscapes (either intentionally or unintentionally, by vocalizing, foraging, navigating, etc.) in distinct ‘acoustic niches‘ so as not to overlap with one another. This ensures that many acoustic functions can occur simultaneously in diverse habitats without interference. On a rocky reef, for example, sea urchins dominate the mid-frequency range while fishes tend to vocalize at lower frequencies. All the while, marine mammals are communicating at the high-frequency end of the spectrum. In this way the whole system fits together.

Spectrogram from a New Zealand reef showing urchin sounds in the mid-frequency range and lower-frequency fish vocalizations. Color represents intensity. ©Craig Radford

Spectrogram from a New Zealand reef showing urchin sounds in the mid-frequency range and lower-frequency fish vocalizations. Color represents intensity. ©Craig Radford

Applying this concept to ecoacoustic indices, one would predict that the soundscape will be more acoustically diverse if the sound-producing community is more biologically diverse. (Since not every single species produces sound, even if you account for unintentional sound-producing behavior, this prediction assumes that diversity of the overall community will increase with the diversity of its acoustically active component.) And it seems, for rocky reefs, that the logic holds.

What’s Next?

This is only the beginning, but it’s a promising one. Monitoring critical habitats, marine reserves, threatened areas and anywhere in between to track biodiversity loss and recovery will become increasingly feasible with the development and spread of affordable hydrophone technology. All of the software used to process these field recordings and calculate the ecoacoustic indices is free and open-source, and once it has been established that a given index is appropriate for a specific area, visual surveys and further special techniques will no longer be required. In this time of accelerated global diversity loss, PAM may be the best way to obtain efficient, non-invasive marine diversity measures.

Of course, many questions remain unanswered: are there other, more effective ecoacoustic indices out there? Do they work in all marine environments – the tropics, for instance, or deep-sea hydrothermal vents? Would these results be similar for invertebrate diversity? What kinds of impacts are those ever-present anthropogenic noises having on marine soundscapes? Are they significantly altering the life functions of acoustically active species? Are they influencing biodiversity? As more and more ecoacousticians turn their attentions – and their ears – to the sea, these and other mysteries will be solved. In the meantime, perhaps this technique can help set us up for success in the ongoing effort to protect diversity in our oceans.

A school of Two-Spot Demoiselle fish – common rocky reef inhabitants – in the Mokohinau Islands, NZ. © Sydney Harris

A school of Two-Spot Demoiselle fish – common rocky reef inhabitants – in the Mokohinau Islands, NZ. © Sydney Harris

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2 thoughts on “Revealing Biodiversity on Rocky Reefs using Natural Soundscapes

  1. Pingback: March 8, 2016: Red Gurnard – SCFoW

  2. Pingback: Exploring Microbial Diversity: From the Sequence to the Cell | methods.blog

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