NEON protocols, part 2 (non-periodic)

After a pleasant Christmas I'm back to wrap up this short series on the various activities I got to take part in over the field season with NEON (the National Ecological Observatory Network). Part 1 covered the protocols we performed throughout the season. This post will look at the remainder.

These protocols I'm calling, for lack of a better term, non-periodic. They had windows of time (typically a few weeks to months) during the year during which they could be conducted, and our job was to perform them in as many different plots as possible during that time. (With some limitations, certain protocols only applied to certain types of plots.)

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Plant Diversity (DIV)

This was the first non-periodic protocol we did, and is also probably my favorite. The window opened around the time I began in April, and closed in early summer. The basic concept is simple: we looked for as many plant species as we could find in a plot.

A beautiful field of Elaphoglossum wawrae ferns.

In practice, it was a little more complicated. We were looking for vascular plant species, so didn't count mosses or other bryophytes. We also counted at various scales and locations around the plot. Each plot was a 20×20 m square, and we would count species at certain 1 m² subplots within it, at 10 m² subplots, and within the four 100 m² quadrants that made up the plot.

Maile (Alyxia stellata) fruit; they often grow in chains, one out of the other.

Looking at different spatial scales provided some interesting information on the biodiversity at each plot. In some plots, most of the species in the plot could be found within a single 1×1 m square, while in others there would be comparatively few in such a small area but a large number in aggregate across the entire plot.

ʻIeʻie (Fraycinetia arborea) fruits, somewhat rare to see.

This protocol was essentially a big treasure hunt for plants, and I enjoyed it a lot. It happening early in the season was helpful (as it really kickstarted our plant species knowledge), but I was sad that it also ended early, since it was so much fun. It was great for really getting to know the various different climates and environments around the Natural Area Reserve (NAR), from lava fields less than two hundred years old with grasses and sparse ʻōhiʻa, to dense koa forest, to lower and wetter rainforest disturbed by pigs, and a few more besides.

Coarse Downed Wood (CDW)

This protocol was about tallying up and recording information about downed trees. For each plot, we'd walk 90 m out from the center along three transects (lines) 120° from each other and record dead wood we encountered along the way. This was…among my less-favorite protocols, for reasons I'll get to. Its window also opened early in the season, but didn't close until near the end. We stopped doing it around the end of June because other protocols (see below) crowded it out, and I wasn't sad to see the end of it…until we ended up doing it again a few months later once things finally calmed down a bit and we realized we still had a few weeks left in the window and a few more plots to perform it at.

In theory, it was simple: follow a line through the woods using a compass, measure out 90 meters, and record dead wood that the line crossed. Each piece of dead wood was termed a “particle” (a term I found amusing from a physics standpoint). There was a nuance that particles below a certain diameter weren't tallied (so you weren't recording every dead twig), and that minimum diameter was a function of distance along the transect (so – just making up some arbitrary numbers – a branch 10 cm in diameter encountered at 2 m along the transect would be recorded, but if it were encountered more than 30 m along the transect it would no longer be recorded as it would be considered too small to count. I didn't fully understand it, but there were published statistical reasons behind this.).

That still wasn't too complicated, but if you got into a situation where the transect encountered multiple forks of the same dead branch or tree, it got way more complicated with a bunch of measurements that needed to be done to determine an ‘average diameter’ to see if it got recorded. Frustratingly, this could result in spending 10 minutes making measurements and doing calculations only for the resulting value to be too small, and all that work being for naught. Thankfully that was rare, but I definitely didn't enjoy it when it happened.

Most of the time, the transect would cross a particle at one point along its length, which made measurement of its diameter simpler, but not necessarily easy. With many plots in mature rainforest, a lot of the dead wood we encountered was in advanced stages of decomposition; it was often hard to get a diameter (or even determine limits) as the log was slowly turning into dirt (“tree puddles,” we called them).

On top of such difficulties, running transects through the forest could be quite arduous. The transects went straight on, with no consideration for the roughness of the terrain or plants through with they passed. Those same dead trees we were recording could, when crossing our path, make getting past them pretty difficult – it's remarkable how many trees fall in such a way, suspended slightly above the forest floor, that it's hard to get either under or over them. The final plot we performed CDW at had a patch of uluhe (Dicranopteris linearis) so dense that we had to go around, but in general we went straight through thick, thin, and thicket.

Dicranopteris linearis, one of three fern species called uluhe in Hawaiian. It forms dense thickets.

It would be remiss of me not to mention that CDW could be very easy and quick in plots on newer land that didn't have any large dead trees yet. In some plots, walking a 90 m transect could take two hours or more; in others, it could take ten minutes. And while I personally didn't enjoy it much, it was the favorite protocol of a few of my coworkers, unlike:

Below Ground Biomass (BGB)

Hoo boy. Where to start with Below Ground Biomass? (It actually had a second official name, but I don't remember it as we all just called in BGB.) Where CDW had its share of people who both liked and disliked it, pretty much no one enjoyed BGB (it's definitely my least-favorite protocol). The basic premise was simple: at certain plots, we would extract a ‘brownie’ of soil, including all the roots in it. We would then carefully rinse the dirt away and strain out the roots, which we would then pick over and sort into bins based on their diameter. I forget the exact cut-off points, but they were in the single-digit millimeter range; these were small roots. The extracted roots would then be dried, weighed, and a portion of them would be ground up to be sent off for analysis.

While the soil retrieval and washing weren't too bad, the root sorting was simultaneously mind-numbingly tedious and exhausting. We spent several weeks over the middle of summer doing little else other than sitting bent over a tray of roots in water in the lab, picking out teen-tiny roots one by one with forceps. I didn't mind it too much the first few days…but by the time we finally finished it we were all ready to snap at the sight of another root. I forgot to take any photos of this protocol, but frankly, you're not missing much.

One notable incident involving this protocol was the first time I was using the Wiley mill to grind up some roots after we'd finished sorting and drying them. These machines are not cheap, to put it lightly, so when I managed to get it into a non-starting state when accidentally over-stuffing it with roots I had some very worried thoughts pass through my head. Thankfully, the fix was simple; I'd simply blown a $5 fuse that was easily replaced, though it had to be sourced off-island because it wasn't a common configuration.

Soils (SLS)

I almost forgot this one, because it was a relatively easy protocol that went by quickly. This despite the fact that we performed it twice during the season, once around May/June and again around September (to capture soil chemistry at different seasonal conditions). Similarly to BGB it involved collecting soil samples from plots, but the analysis of those samples was much simpler: just a little lab work to prepare them for shipping to a central laboratory for further analysis (and most of that only had to be done the first time, in June). The most difficult part of SLS was simply finding deep enough soil to get a sample; we had to sample from a list of random coordinates in the plots, which would sometimes be pointing at roots, places where the soil was a half-inch deep, and other unhelpful locations. In such cases, we'd cross off the coordinates and move to the next until one happened to coincide with sufficiently-deep soil. Still, even with that slowdown, this protocol only took about two weeks each time, with soil samples being collected from multiple plots per day (versus other protocols that could take multiple days to finish a single plot).

Vegetation Structure (VST)

One such protocol was Vegetation Structure, the last protocol in the season. VST was another divisive one, though in the opposite direction from CDW: some of my coworkers disliked it, but I actually quite enjoyed it. Where CDW measured dead wood, VST involved measuring the living; specifically, trees and small woody shrubs. The exact measurements varied slightly by size and category, but generally included things like a stem or trunk diameter and height, plus sometimes various other bits of data like the extent of the crown, the health status of the plant, or the position in the forest (ranging from Open Grown to Full Shade). 

Me marking a decumbent (but still living) hapuʻu pulu (Cibotium glaucum).

As part of the protocol we'd tag each plant measured and mark where we measured the diameter so that future field techs could reproduce the measurement. Many plants were already marked from the last time VST was done (five years ago for some plots), but new plants would grow large enough to be measured in the intervening time so we usually had a few ‘adders’ in each plot.

Me rewiring a tag around a maile stem (foreground).

I liked VST, but I can understand why some people found it arduous. One facet even I agreed on was the requirement for measuring the extent of the crowns of trees. In a thick forest, for mature trees (or even young but tall ones) this can be, to put it mildly, difficult. The best method usually involved two people making their way out to beneath the edges of the crown on opposite sides (as best they could guess) and measuring the distance between them. This was prone, we felt, to a high level of systematic error as it was often not at all easy figuring out where a particular tree's leaves and branches extended to or how directly ‘underneath’ it we were, especially when such leaves were 15 or more meters in the air and surrounded by leaves from other trees. The height of a tree could also be difficult to ascertain, even with the electronic range finders we were using, and prone to large systematic error.

Old growth koa forest (one of only two plots). The orange color is lichen that grows on koas preferentially.

Still, other than having to scrabble around in leaf litter to find tags on downed hapuʻu tree ferns, I generally enjoyed VST. I was able to put my Python skills to use with the data we collected this year to make some graphs for the annual report we were obligated to provide as part of our agreement to be able to use the NAR. Some protocols (including VST) only get done every five years in some plots; this was one of those years, and since the Hawaiʻi NEON site was established relatively recently in 2018 this was only the second time some of those measurements had been taken. It was really exciting to see how the trends looked, and I could even pick out different environments in the plots clustering in certain parts of the phase space.

One notable result from this year was that a lot of our trees actually shrank in diameter compared to five years ago. That's because this was a really, really dry year and the trunks had shrunk from lack of water. The trees had generally gotten taller, so they were definitely still growing, they just weren't growing out as much. Hopefully next year brings some rain, we could really use it. (But given how miserable working in the rain was when it did happen, a part of me is glad this year was a dry as it was.)

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So there you have it: a rough outline of what the 2025 NEON field season looked like. We started out with DIV and CDW, transitioned into SLS then into BGB for an interminable few weeks over the summer, started VST (and SLS again), realized we were making excellent time on VST and that the CDW window was still open, so finished off CDW and VST near the end of the season. And of course, in the background, all the periodic protocols were being conducted as well. It's quite the symphony of science being coordinated and conducted by NEON, carried out at sites across the US each year. It should hopefully run for about another twenty years, and it'll be interesting to see just what kinds of things we learn from such a large-scale project. As an open-access project, all the data collected are available here; as an astronomer, with a commitment to open knowledge, that was one of the things that initially drew me to this job.

My family's coming to visit on New Year's Eve, so this'll probably be my last post for the year as I prepare for that, and what a year it's been! I've given up on trying predict the future and where I might end up working, but in the near term: next semester I'll be teaching a few courses in physics and astronomy at my alma mater, the University of Hawaii at Hilo. Having never taught in a formal setting before I'm quite nervous, even as everyone tells me what a good teacher I'll make. We'll see I suppose! Big changes ahead next year. Hauʻoli Makahiki Hou, a hui hou!

NEON protocols, part 1 (periodic)

It's been a month since my job with NEON ended, and as another chapter of my life draws to a close I wanted to take one last look back at the various data collection activities we carried out. Each of the protocols below had an extensive document describing its execution in detail, which we had to be brought up to speed on before performing the protocol (and would not-infrequently refer to in the field for clarification). I probably don't remember them perfectly so I might get specifics wrong, and also the protocols are always subject to updating and revision based on best practices and experience gained in the field, so don't rely on this for future NEON field seasons!

Of the protocols, there were two broad categories: one type was repeated at a certain cadence – weekly, fortnightly, monthly – while the other was confined to certain windows of time in the year during which we'd try to get it done for as many plots as possible. I'll start with the repeating protocols, as those were the constant background cadence we became used to, then go through the season in chronological order covering the rest in a second post (as this one ballooned to longer than I expected). I've tried to include some photos where I can, but I didn't always remember to take them for every protocol.

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Phenology (PHE)

Phenology (a word I hadn't heard before starting with NEON) is, according to Merriam-Webster: “the study of periodic events in biological life cycles and how these are influenced by seasonal and interannual variations in climate, as well as habitat factors (such as elevation).” For us, it involved a weekly walk along an eight-hundred-meter stretch of road and checking on…I think it was some two hundred individual plants along the way. For each plant we'd record various data (though the specifics varied by plant type). Some typical data points would be things like does this plant have any new leaves growing? Are any of its leaves changing color or falling? Does it have flowers? (And if so, how many, and what fraction are fully open?) Likewise for fruit – are any present, and how many of them are ripe?

Thankfully, for our sanity, we didn't have to count every single instance of a flower or fruit on a plant, as the survey divided things up into bins of increasing numerical size:

• <3
• 3–10
• 11–100
• 101–1,000
• 1001–10.000
• >10,000

On small shrubs it'd be easy to say, for instance, that there were only two fruits (<3), while on some large trees (especially ʻōhiʻa) we could easily see upwards of ten thousand young leaves budding at certain times of year. (ʻŌhiʻa leaves come in bunches of a certain average amount, so we could simply count those and multiply.)

For instance, above is a closeup of a pūkiawe plant, one of the species we looked at. It grows as a shrub to a small spindly tree depending on environment, and puts out lots of tiny leaves and fruits. Those fruits are about the size of a BB and a large individual could have over a thousand, not to mention upwards of ten thousand leaves (thankfully those also came in clusters for easier counting). Most species weren't as complicated to measure as pūkiawe (they were definitely on the more time-consuming end of the spectrum), but it'd still take around 4–6 hours to cover every plant.

As mentioned, this was our most frequent protocol, happening every single week. In our tropical climate we didn't see quite such dramatic changes over time as the mainland U.S. would with deciduous trees, but we could still see things like the ʻākala (Hawaiian raspberry) budding, flowering, and fruiting over the summer months.

Beetles (BET)

Happening every two weeks, beetles was another frequent protocol that ran almost the length of the season. We left three ground-fall traps at specific locations around six plots (for a total of eighteen traps) scattered across the Puʻu Makaʻala Natural Area Reserve (NAR), and every fortnight we'd collect the contents of those traps for sorting and identification of any beetles they contained. We were looking specifically for any species in the Carabidae family, a family of mostly-ground dwelling beetles with species around the globe (though the native Hawaiian species are arboreal, funnily enough). We found both native and invasive Carabidae species, with certain plots being known for the distribution either way, or for being the only plot that some species had been found at. While we didn't discover any new species this season, previous seasons turned up two entirely new species, so there are potentially more out there waiting to be found!

At the end of the season, after all the beetles had been identified, we started working on pointing them. Not “pinning” them, as they were too small for that (around 5–6 mm, on average), though the goal is the same: preservation for later viewing. The “det D. Berke” on the label in the photo above signifies that I identified this particular specimen (a common native species), which is pretty neat! We didn't manage to finished pointing all the beetles before us seasonal staff left, but we got through quite a lot of ~240 beetles – I personally pointed upwards of 70 over a few weeks. (I found it quite relaxing after a day out in the field when we had an hour or two left on the clock back at the office, like a miniature arts-and-crafts project.)

Beetles sorted out of a trap, ready for identification under the microscope.

Mosquitoes (MOS)

Mosquitoes happened once a month, but was probably the most disruptive protocol we did. It involved three parts:

1. A team would go up in the afternoon to set ten mosquito traps at various location in the NAR. These had to be set within four hours of sunset, and would sit overnight.
2. Another team would go up early the next morning and check all the traps for mosquitoes, taking any catches and resetting the traps. (This checking had to happen within four hours of dawn.)
3. Yet another team would go up in the afternoon and check all the traps a second time after they had sat out during the day, then collect them and bring them and any catches down.

A mosquito trap.

The protocol wasn't particularly difficult, but it did involve some of the more technical work we did, as we carefully calibrated CO₂ canisters to put off a stream of carbon dioxide to attract mosquitoes towards a little fan blowing into a canister. Most of the traps were located near roads (as in the photo the above), though there was one lovingly termed “the long walk” which took nearly 10 minutes to reach. (Which doesn't sound like much, until you're carrying a heavy CO₂ canister and the rest of the equipment down a muddy trail…)

We usually didn't catch a lot of mosquitoes, which was a good thing. Mosquitoes carry avian malaria, which is driving the extinction of multiple native Hawaiian bird species at lower elevations. Mosquitoes can only survive temperatures down a certain level, though, and at the height of Puʻu Makaʻala it's mostly too cold, so birds which can retreat to higher elevations are generally still safe. (Shorter islands, such as Kauaʻi, are watching their native bird populations die out in slow motion without being able to do much about it, as there simply isn't high enough elevation for the birds to retreat to as the atmosphere warms and the mosquito-free range shrinks.) On a typical bout we might catch 0–2 mosquitoes, and usually only in the lower-elevation traps. This is compared to places on the mainland where, with the same traps, they might catch hundreds or thousands of mosquitos – I remember watching a training video for this protocol, where the presenter up-ended a catch cup and a literal pile of mosquitoes several centimeters in height fell out. Thankfully, we didn't have to deal with that, and almost never had to worry about getting bitten during our time in the field.

Leaf Litter (LTR)

Another monthly protocol, this one involved collecting leaf litter from aerial ‘traps’ in the forest and separating it into various components. These traps were pretty simple, just some mesh suspended by PVC pipe – they didn't need to be complicated, just a standardized area to collect what fell from above.

Me, collecting leaf litter from a trap near the end of the season.

Once the litter was collected into bags (from I believe 20 traps in different plots), we'd heat it to dry it out and then sort it into various functional groups. These were things like leaves, twigs, ‘woody’ (bits of bark),  flowers, seeds, ‘other’ (for, e.g., lichen and other rare things that didn't fit other categories) and ‘mixed’, a catch-all term for leftover material. According to the protocol, each bag was only to be sorted for one hour maximum, at the end of which any remaining unsorted material would go into ‘mixed’. This was partly for mainland domains where the amount of leaf litter in fall could be overwhelming, but we found it useful as well when all the easily-identifiable stuff has been sorted out and what's left is just tiny detritus. (Sorting could also end early if the remaining unsorted material was no more than 10% of the mass of the sample, which was usually pretty easy to judge.)

A tray showing an in-progress sort; in the bottom-left is the remaining unsorted material, then going clockwise we have a small amount of ‘other’, some twigs, a little woody material, a lot of leaves, flowers (mostly pistils and stamens from ʻōhiʻa lēhua flowers), and two seeds.

While this litter was a monthly protocol, there was also another type of litter that happens just once a year, around September. This protocol (ground litter) involved gathering litter from areas demarcated on the ground which were larger than the aerial traps. While the monthly litter collection focused on small litter (sticks too large would be discarded), ground litter collection was something of the opposite, only interested in sticks and leaves (such as tree fern fronds) larger than a certain limit.

(While mosquitoes had “the long walk”, litter had the really long walk to get to some of the plots where collection happened, something like half an hour's hike along a fence pushing through ferns.)

Imageomics

There was one additional repeating activity we did, though this wasn't a normal NEON protocol; a number of people from different universities teamed up to use NEON's Research Support Services, where outside research groups can contract to get support from NEON personnel for their research. In our case, they set up a number of trail cameras and audio recorders around the NAR, with the goal of developing machine-learning systems to automatically identify native and endangered birds for better tracking. They set up the system in January of this year, and we mostly just swapped batteries and SD cards on a regular basis to keep things moving (plus uploading data from the cards, and the occasional bit of troubleshooting for cameras that weren't working). I believe they gave a presentation at a machine vision/machine learning conference last month so hopefully the project is going well, but I don't know too much about it otherwise. It was a fairly easy activity, though, and let me see some parts of the NAR that we normally otherwise wouldn't.

I saw these nēnē fairly close up in one of the areas we wouldn't normally be.

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I originally intended to talk about all the protocols in this post but even just the repeating ones turned out to be a fruitful subject. I'll have another post covering our non-periodic protocols soon where we'll wrap up by going over what my field season looked like. A hui hou!