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Bringing Citizen Science To Lake Pupuke

GUE diver and aquatic eco-toxicologist Ebrahim Hussain applies some serious citizen science to get to the bottom of the trouble in Lake Pupuke, New Zealand. Project Baseline is alive and kicking, thank you very much!

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by Ebrahim Hussain

I have always been passionate about aquatic ecosystems and how they work which inspired me to become an aquatic ecotoxicologist. I have always tried to document observations in an attempt to better understand environmental changes. The biggest challenge I have faced was getting my observations to organizations that are able to use them in a constructive manner. We all constantly see changes in our environments but are often unable to make a positive change.

Citizen science is a greatly underutilized resource by regulatory agencies. There are a myriad of citizen science groups that actively want to participate in the monitoring of their local ecosystems, but they lack the guidance or platform to do so. The Project Baseline Initiative provides an amazing platform for people to display their findings, and in combination with guidance from local authorities, the resulting projects can be an overwhelming success. This article will hopefully take you through my journey to improve a local lake that means a lot to me and the people who use it.

Lake Pupuke is a 186 ft/57m deep volcanic crater lake with a surface area of 110 hectares that drains a 105 hectare urban catchment in Auckland, New Zealand’s North Shore. The influence of this urban catchment on lake water quality is enhanced by the fact that the lake has no direct in and/or out flows and consequently has a high water retention time. Water enters the lake via a variety of diffuse sources (runoff, groundwater & precipitation) and exits through evaporation and intermittent drainage channels.

The lake is used for a variety of recreational purposes and is a venue for national and international events. The lake is also widely used by dive schools and boat clubs from across the region as a training facility.

A Lake Under Threat

I have been diving in Lake Pupuke since 2013, and I quickly came to realize that this lake was under threat. The water clarity had decreased, and according to the local dive schools, this deterioration had been noticed for many years prior. In the summer of 2014 a thick algal bloom developed which had not been recorded previously. The initial concern was the potential human health risk associated with algal blooms, but samples taken by the Auckland Council identified the bloom as Ceratium hirundinella which is a nontoxic species.

It was quite puzzling that even though Ceratium has always been present in the lake it had never formed large scale blooms until 2014. It was thought that this bloom was a once-off event until it occurred the following year and every summer since.


Ebrahim Hussain installing a dissolved oxygen & temperature sensor on the monitoring station. Photo by Andrew Davidson.

In an attempt to understand what had caused this change, I began looking at the Council’s long-term monitoring data, and to my surprise, I could not find anything that pointed to the exact cause of these recurring blooms.

I initially looked at temperature and nutrient loads which are the most common drivers for algal blooms and found that the lake had not been significantly warmer than previous years, and the trophic level index, while elevated, was within the same variance seen over the past ten years. However, there was no associated metadata to support any conclusions. It was clear to me that we could not fully understand what was happening in the lake through seasonal surface-based water quality sampling alone, and that regular subsurface observations were needed.

Enter Project Baseline

That is when I came across the Project Baseline Initiative, and it was the perfect platform for the type of work I wanted to conduct. The primary focus was to collaboratively work with volunteers, local communities, research organizations, and the Auckland Council to collect data that would complement the work already being done by the Council, as well as to specifically address the subsurface knowledge gaps. By doing this we are able to make use of both Council-funded and citizen science-driven data acquisition to support and inform a more holistic management strategy for Lake Pupuke.

We initially started collecting very basic data, such as visibility, temperature, and general meteorological information, but this quickly ramped up once we started noticing what was happening underwater.

Todd Kincaid & Louise Greenshields preparing the sediment coring tubes. Photo by Ebrahim Hussain.

We installed continuous temperature sensors, which log data every 15 minutes, at various depths to get a better understanding of the seasonal thermal stratification in the lake. Our data indicates that the lake usually stratifies from October until June, with an average winter temperature difference of 0.7°C between surface and bottom waters, and a summer difference of 10.2°C.

Stratification in lakes of this depth is a natural result of the surface water layers being heated by the sun. This heating causes the formation of a thermocline where the warmer water layer sits above the cooler, denser bottom water. This process separates the water column into three distinct layers, the epilimnion which is the warmest layer on the surface, the cooler metalimnion in the middle, and lastly the hypolimnion which is the coldest layer at the bottom of the lake. This separation of layers reduces the mixing of heat, oxygen and nutrients between the surface and bottom waters.

It is important to track these changes in stratification because it is directly related to the potential oxygen cycling and internal nutrient loading within the lake.

We installed continuous dissolved oxygen (DO) sensors within these distinct thermal layers to assess this oxygen cycling, and what we found was surprising. In winter the DO% on the surface ranges from 86% to 98% and gradually drops in even gradations down to about 40% at 55m. In summer the DO% ranges from 80 to 90% on the surface down to less than 3% at 55m. This is expected, but what took us by surprise was the presence of midwater anoxic layers, one near the surface between 7m-9m, and a second layer in the metalimnion between 12m-16m.  

The Results

After seeing this, we began investigating other potential DO dead zones in the lake using multi-parameter water quality meters and have since identified additional areas. There was evidence of anoxia in the macrophyte beds that surround the lake, so we deployed additional sensors, and our finding confirmed our initial assumptions with summer DO% dropping to less than 3%.

This is critical information, as anoxic sediment conditions actively promote the remobilization of nutrients which further contribute to the eutrophication of the lake and drive algal bloom formation. These conditions can also cause the release of ammonium & hydrogen sulphide which are all toxic in high concentrations.

The next question we had was what was causing this anoxia. It is natural for a lake this deep to have anoxic bottom waters during summer, but we did not know what was causing this anoxia midwater and in the macrophyte beds. The dense macrophytes stop water from freely flowing into the shallows, and there is a lot of visible organic material that is decomposing on the bed, which all contributes to the anoxia.

The increased load of organic material, composed of dead macrophytes & phytoplankton, seemed to coincide with the appearance of the algal blooms. To prove this we installed light sensors that continuously measure the photosynthetically active radiation attenuation at various depths. The data shows that at on average there is almost no usable light past 4m after 13:00 and zero light penetration past 10m during the summer blooms. This lack of light caused the macrophytes to die, and coupled with the dead phytoplankton settling down, created an influx of decaying matter on the lake bed. We now regularly conduct macrophyte extent surveys to document seasonal die back and regrowth.

Phytoplankton, Chlorophyll-a & biological oxygen demand sample bottles as well as a photosynthetically active radiation sensor ready for deployment. Photo by Ebrahim Hussain.

We knew where the additional organic material was coming from and what was causing the anoxia in both the macrophyte beds and the hypolimnion. The next question was how many nutrients are being released from these areas and what is causing the midwater anoxia. To answer this, we started a collaborative project with the Auckland Council and the Cawthron Institute.

The first step was to install sediment traps at various depths to understand how much organic material is produced midwater and how much settles down to the bed. The second step was to take a suite of sediment cores from the areas of concern we had previously identified to understand the amount of nutrient remobilization that occurs under various environmental conditions. The third and final step was to take targeted water quality and phytoplankton samples from the midwater anoxic layers to understand how/why they are formed.

Ebrahim Hussain & Tyler Ungureanu purging bottles in preparation for water quality sampling. Photo by Harry Josephson-Rutter.

The majority of the sampling required has been done except one more round of winter sediment traps. Once this has been completed, all the data will be analyzed and will fill a critical knowledge gap regarding internal nutrient cycling. This in turn will help guide the next steps for the wider project as well as inform potential mitigation measures.  

Project Baseline has provided an amazing tool to facilitate the collaboration between citizen science and local government by formalizing community-driven data collection. The Project Baseline Lake Pupuke Initiative is a proven example of how citizen science can be used to satisfy critical knowledge gaps and directly feed into regulatory strategies with the common goal of creating a better, healthier environment.


Ebrahim Hussain is an Aquatic Scientist working at the Auckland Council. He began diving when he was 12 years old and has never looked back. Hussain studied aquatic ecotoxicology and zoology at university, and it was clear that he wanted to spend his life studying these subsurface ecosystems and the anthropogenic stressors that impact them. Hussain founded Project Baseline Lake Pupuke with the goal of contributing to preserving and enhancing this natural beauty as well as encouraging others to get involved in actively monitoring their natural surroundings.


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Getting Back in the Water with Caveman Phil Short

With local diving slowly opening in the wake of the pandemic, InDepth caught up with British cave explorer and educator Phil Short to see how he navigated his post lockdown re-submergence. And what about those 14, 15, 16 month old oxygen sensors?

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by Michael Menduno

Header photo by Michael Thomas. Phil Short swims under Wookey Chamber 14.

With diving just beginning to resume in various parts of the world after what felt like an interminable shutdown, we thought it would be interesting to check in with some of our friends to see how they were approaching their return to the underwater world after such a long hiatus. 

British caver Phil Short sporting his colours. Photo courtesy of Phil Short.

Ironically, it’s been the longest that 51-year old British cave explorer, scientific diving officer, exosuit pilot, educator and film consultant Phil Short, principal of Dark Water Explorations Ltd. has been out of the water in his entire 30-year diving career. How did one of tech diving’s indefatigable pioneers plot his re-submergence, and what would he offer up to colleagues about to take the plunge? 

We chatted up Short just as he was booking his first dive project trip abroad; this is what the ardent caveman said.

InDepth: Maybe we can start with you explaining a little about the circumstances in the UK. I know you were on lock down as far as diving was concerned, and they are now in the process of opening up.

Phil Short: Basically, when the COVID-19 crisis began, the country went into lockdown for all nonessential activities. So obviously, any type of sport and recreation was included in that. And then, after about two months, they slowly started to reduce the restrictions, certainly for more normal activities and allowed certain sports to take place again. There was a lot of controversy over diving, because COVID-19 is a respiratory or lung-borne disease. So there was concern that it could create additional potential hazards with lung expansion injuries and embolisms.

In the UK, we have a group called the British Diving Safety Group, which is made up of various organizations including diving training agencies: the British equivalent of the Coast Guard, the Health and Safety Executive (HSE), which is our version of OSHA and the diving industry trade organization, and SITA (Scuba Industries Trade Association). I am a member, and we met to determine what the safest and most prudent, most expedited means were to get people back in the water. We consulted with the hyperbaric medical community, COVID-19 related medical experts, the agencies with the authorities that control charter boat operations, and with the HSE. 

The first permissions were for small groups. Basically, you and one buddy could do shore dives. We adopted recommendations by the NSS-CDS as to how gas sharing should take place, and safety or S-drills so you are not breathing from each other’s equipment. 

So when did you go diving?

As a member of the BDSG committee, I was very diligent not to go in the water until the evening we announced that it was permissible to go beach or shore diving. The next morning, 28May 2020, I left my house at 4 AM to go and do a beach dive on a landing craft from the second world war, a genuine World War II wreck. I descended at 6:23 AM and it was just heaven because I had been out of the water for 86 days because of the restrictions. And it was just great to get back in.

Where did you make your last pre-COVID-19 dive? 

My previous dive had been on the island of Lanzarote in the Canary Islands off of West Africa teaching a trimix rebreather class. It was a 93m/303 ft dive. I got on the plane, flew home, and the lockdown started almost immediately. And then 86 days later, I was doing a 12m/39 ft dive off the beach in the UK. It was my longest break in diving in the 30 years I’ve been in the industry.

The Wreck of P&O Liner Salsette off U.K South Coast 12th July 2020 (Post COVID Lock Down.) Photo by Marcus Blatchford.

Let me ask you, did you have a conscious strategy or approach to getting back in the water? You didn’t start back in at 90 meters.

Yes, it was conscious. Certainly rebreathers, it’s not just like riding a bike. You do need to keep current. I recommend to my students to be doing at least one skill dive on the rebreather per month, minimum, to maintain currency. 

So I decided that for the first dive, once the permissions had been given, to go make the beach dive on doubles. I’ve got a nice little twin 8.5L set that’s small enough for walking over the beach. It still had the redundancy, but it was simple scuba and a simple depth of just 12m/39ft. Basically, the first thing I did when I got in the water was descend just a few feet and made sure that I was proficient with doing a shutdown and isolation drill on the doubles. 

Then I went for the dive on a good nitrox with a long no-decompression time and surfaced way before I was getting anywhere near decompression. I took it gently. First time back in 86 days, I took it gently, and then over the last six or seven weeks, I’ve started to build up from there.

I know you’ve talked and probably compared notes with colleagues and other divers. Do you think people there are approaching getting back in the water sanely or is it a bit of a madhouse? How would you characterize things in the UK?

I would say, as often happens, it’s mixed. So, based on recommendations of the agencies and their instructors, the majority of people are getting back into it gradually like I did myself. But there’ll always be those who say, “Oh, I’m a good diver. I don’t need to do that. I’ve not been allowed to dive for two or three months. I want to go do what I want to do.” And they go straight out and do a 50 or 60m dive, which I think is just foolish. 

Even ignoring the COVID-19 situation, if you were out of diving because of having a kid, or experiencing a job change or anything like that, or after a big layoff, I think it would be prudent to get back in gently and then slowly build up. So, my first dive was shallow with open circuit doubles. My next dive was a very limited penetration, shallow cave dive on open circuit, side mount, again with redundancy. A no-decompression dive but back in my natural environment of caves for a little swim around. 

Wookey Hole Cave (The birthplace of cave diving) at the base of the Mendip Hills U.K. (Post COVID Lock Down). Photo by Michael Thomas.

Gradually over the weeks, because I had better access to caves than I did to the sea, I did more and more cave dives and slowly built up in duration and distance, but still on open circuit. I then got permission from the owner to access one of the inland lakes, and we did some pre-official opening work for the owners of the site. I got back in on the rebreather but again, no-decompression, relatively shallow, no more than 30m/100 ft. Next, I integrated stages and my DPV (diver propulsion vehicle). 

My first teaching was a Level one, Mod One rebreather course that I team-taught with a fellow UK instructor. It was a perfect way to get back in gently because we were running 10 hours over 8 to 10 dives of constant skills for the students. So that was a real refresher. And then finally last weekend, a group of us that had all been doing that type of gradual build up got out on a boat off the south coast of the UK, on a 33 m/108 ft deep wreck on Saturday. On Sunday, we dived a very well-known wreck, the SS Salsette, in 45 m/147 ft of water in beautiful conditions. Calm sea, good visibility, and a real wreck. So I had made a gradual buildup over seven or eight weeks to get to that point, rather than jumping straight back in.

Sweet. You mentioned rebreathers (CCR). Currently, there is a global shortage of oxygen sensors underway as a result of the pandemic. Oxygen sensors are being diverted to the medical industry, which is under siege right now from COVID-19. Any concerns or worries that people will go diving with out-of-date cells? Do you think that’s an issue? 

It definitely concerns me. I’ve been a CCR instructor at all the levels, almost exclusively for the last 15 years, and I’ve seen people go out and happily spend five, six, seven, 10,000 pounds on a brand new rebreather and the training and then go out and be cheap on a £16 fill of Sofnolime or a £16 fill of oxygen. And you’re like, what are you doing? You paid £10,000 for this equipment and you’re risking your life on a £16 refill of consumables? People are so desperate right now to get back to their hobby; they feel like it’s been taken away from them, that I worry they may not always act sensibly. 

Short checking the oxygen sensors on his rebreather. Photo courtesy of Phil Short.

It’s been a battle over the last five or six years to get people to really wake up and pay attention to the fact that these sensors are your life support. There was a very high-profile accident that was caused by overrun sensors a few years back with a quite-well-known person in the industry. He effectively died on the bottom, was rescued by his buddy, then was helicoptered to the hospital where he was put into an induced coma. He came out of it several days later and he was very, very lucky to survive. And very, very lucky to come back to actual diving again. But that was all caused by old, overbaked sensors. 

So what do you see happening?

I think what’s going to happen, you know, is that some people ran out of fresh sensors a couple of months ago so now it’s 14 months, 15 months, 16 months. And some may be thinking, “It’ll be okay, it’ll be okay. They’re reading fine, they’re working fine.” Some people might be doing linearity checks, doing oxygen flushes at 6 m/20 ft to check if they read high when appropriate. 

But really, the companies like AP Diving, JJ-CCR, Vobster Marine Systems, and others have put a lot of time, a lot of effort, and a lot of money into researching and independently testing these life-support machines for functionality, with certain parameters. Much like car manufacturers do so you can drive your family and your kids in a safe car. [Hammerhead CCR developer] Kevin Jurgenson summed it up once brilliantly when he put out a statement saying, ”Okay, people are questioning the duration that a sensor can last. Some people would say 12 months. Others would say 52 weeks. Some would say 365 days.” And he carried on to include hours, minutes etc. Basically saying, a year is a year. Whichever way you try to stretch it, it’s a year. No more.

Personally, I would not violate that because those three simple galvanic fuel cells that represent probably somewhere between $200 and $300 depending on the manufacturer and the unit, representing a tiny percentage of the expense that I’ve outlaid to become a rebreather diver, is not worth my life. 

As I mentioned, I am now back on my rebreather after starting on open circuit, and if my sensors eventually pass their 12-month date, I’m very happy to return to open circuit for as long as I have to while I wait to buy some new cells. 

I have always believed in my educational career of thirty years in the diving industry to lead by example. Those are my feelings. I know from experience when you make comments like that, and it’s effectively the same as raising your head above the trench in a warfare situation. People are going to take shots; but bring it on. If you’ve got a sensible, scientific argument for extending your cells past 12 months, then I’m happy to discuss it. But I don’t think there is one.



So the moral is, if you have sensors that are past either one year, 12 months, 365 days, 8760 hours, 525,000 minutes, or 31.5 million seconds, then you need to go back to open circuit, or not dive until you can get some new ones?

I believe so. The manufacturers whose rebreathers I have dived and taught on over the last 10 years are people that were passionate about rebreather safety. And much like [Sheck] Exley, who focused on improving cave training and cave safety by writing Basic Cave Diving: A Blueprint for Survival, these manufacturers—people like Martin Parker at AP Diving and Jan Petersen at JJ CCR have gone the extra mile to improve safety.

You know full well from the aquaCORPS days, if you look at the safety record of CCR diving now, versus 15 years ago, we made a difference. It has become safer. Why ruin it, because of impatience and a short-term, relatively short-term, restriction on availability of consumables?

Right. In fact, I have talked to Nicky Finn at AP and also Jakub Sláma at Divesoft who have been in touch with sensor manufacturers regarding shortages, and it seems that the situation may be stabilizing and or easing up, assuming we don’t have a second wave of COVID-19 infections. So hopefully, the situation will improve.

Actually, I’ve heard that from several manufacturers, and I think it will improve quicker than was first anticipated. And that’s even more of a reason for not doing anything foolish and being a little bit patient with this to be safe.

Last question: What’s next for you? Got any big projects coming up? 

I just booked my first flight to travel out of the UK again. This time to Croatia. I’m going to be designing and building a water dredge system for recovering and capturing sediment on an archaeological site for a project that we are going to do in October. This is a follow-up project from one we did in 2017 to recover a US World War II pilot from a wrecked B24 bomber that ditched in the Adriatic Sea. We’re going back to do another recovery on a different wreck. 

The dredge system will be designed to work at the appropriate depth level so that we can basically recover the sediment without losing anything. Specifically, we’re not going to miss any of the crew that are found through that dredging. So, I’ve got a 10-day trip to build that system, test it in the same depth of water, and have it ready for the project. 

“Short suiting up at Woods Hole Oceanographic Institute (WHOI) for Nuytco Exosuit pilot training ” Photo by Ed O’Brien, WHOI diving safety officer.

When I come back from that, I’m flying out to Switzerland to train on the Divesoft Liberty sidemount with a good friend and former student of mine, Nadir Quarta. It will be my first sidemount rebreather. I’ve got no intention of moving away from my JJ as my primary rebreather, but I’ve got quite a few cave projects that require a side mount that I can’t do in my back-mount JJ. They don’t offer a sidemount, and because of distance and depth, I can’t do it on open circuit. I put a lot of thought into which unit to use, and am very impressed with Divesoft’s engineering and build. They’re also very courteous and professional to deal with. I like working with people like that.

After training, I plan to attend a Swiss technical dive conference, Dive TEC! in Morges as a speaker, where I will be talking on my 30-year journey as a cave diver and explorer.

Fun times ahead! Thank you, Phil. I look forward to talking to you again soon.

Thank you!


Michael Menduno is InDepth’s executive editor and, an award-winning reporter and technologist who has written about diving and diving technology for 30 years. He coined the term “technical diving.” His magazine “aquaCORPS: The Journal for Technical Diving”(1990-1996), helped usher tech diving into mainstream sports diving. He also produced the first Tek, EUROTek, and ASIATek conferences, and organized Rebreather Forums 1.0 and 2.0. Michael received the OZTEKMedia Excellence Award in 2011, the EUROTek Lifetime Achievement Award in 2012 and the TEKDive USA Media Award in 2018.

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