The Flora & Fauna Hub: what's actually living in and around your lake

Most lake communities know their lake through what people catch, see and remember. That knowledge is real, and it is systematically blind to exactly the things that matter earliest. Flora & Fauna is where the other kind of knowledge lives.

Lake Pulse · Portal · Analytics → Flora & Fauna
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Start with what your lake already knows

Ask around any lake and you will get a species list. It will be good on walleye and bass, solid on loons and eagles, opinionated about weeds, and roughly silent on everything else. It skews toward organisms that are large, visible, active in daylight, and near shore — because that is where people are.

The problem is that the organisms that change a lake's future are usually none of those things. Zebra mussel veligers are microscopic. Starry stonewort arrives as a fragment on a trailer. Juvenile carp are invisible from a dock. By the time a lake community can see a new arrival, the cheap window for doing something about it has usually closed.

A lake's biology is the earliest signal it gives you, and it is the one almost nobody is reading.

What eDNA is, in plain language

Every living thing sheds. Fish shed skin cells and mucus. Plants shed pollen. Insects shed fragments of shell. All of it carries DNA, and all of it ends up suspended in the water.

Environmental DNA — eDNA — is simply that shed material, collected from a water sample. You push about a litre of lake water through a fine filter with a syringe. Whatever was floating in the water gets caught. A laboratory then sequences the genetic material on that filter and matches it against a reference library of known species.

What comes back is a list: fish, plants, algae, invertebrates, sometimes pathogens. No nets, no electrofishing, no diver, no specialist training. Five minutes at the water's edge.

A useful way to think about it: a room where a party has just happened is full of evidence about who attended, even after everyone has left. Fingerprints on glasses, hair on the sofa. eDNA is that evidence, for a lake. It tells you who has recently been in the water.

What eDNA is good at

• Finding things nobody has seen yet — the entire economic argument for running it
• Covering a lot of species at once, cheaply, from one sample
• Producing a result that does not depend on who collected the sample, which makes it unusually good for year-over-year comparison
• Documenting what is there — a recorded native fishery and plant community is the evidence you want on file before anyone proposes a project on your lake

What eDNA cannot tell you

• How many. A detection means genetic material was present, not how many organisms produced it.
• That something is absent. A non-detect means the assay did not find it in that sample, at that place, at that time. Nothing more.
• Everything that is there. Sequencing can only name what exists in the reference library. Poorly covered species come back as a genus or a family.
• That the organism is alive, or local. DNA persists for days to weeks and it travels. A detection can come from something long dead, from a bird's feet, or from water that flowed in from upstream.

What eRNA is, and why it answers a different question

DNA is the blueprint. Every cell carries the full set, all the time, whether or not it is being used. It is durable, which is exactly why eDNA works — and also exactly why eDNA can mislead you.

RNA is the working copy. A cell makes RNA only when it is actively using a particular instruction, and RNA falls apart within hours once the cell stops or dies. It is fragile by design.

That fragility is the whole point. If you find environmental RNA, something living was active at that spot very recently.

A useful way to think about it: eDNA is a name in the guest book. eRNA is a light on in the window.

The questions each one answers

Question	Tool
What species have been in my lake?	eDNA
Has this invasive arrived yet?	eDNA — it is the early-warning tool
Is that detection a living, local population?	eRNA
Is the algae in my lake actually producing toxin right now?	eRNA
Did our treatment actually work?	eRNA — activity, not presence

The two work as a sequence, not as alternatives. Run eDNA to find out what is there. Run eRNA when a detection matters enough that you need to know whether it is alive, active, and worth spending money on.

The Flora & Fauna Hub

Every one of those surveys produces a report. Historically that report arrives as a PDF, gets forwarded to a board, and is never opened again. Three years later somebody asks whether the lake has more or fewer species than it used to, and nobody can answer, because the 2023 report is in someone's email and the 2026 report came from a different laboratory in a different format.

Flora & Fauna is the fix. It sits under Analytics in your lake's Portal and it is the single home for every biological record your lake has ever produced — eDNA, eRNA, historical survey data, and the reports you already have sitting in a folder somewhere.

Flora & Fauna is a Plus, Lake Admin and PRO feature. Sequence data is expensive to store and expensive to keep safe, and a permanent biological archive only makes sense for lakes that intend to keep measuring. That is what those tiers are for. On the free tier you can still see your lake's species list; the archive, the uploads and the analytics live behind the subscription.

Here is what is in it.

Any report. Any lab. Any year.

Everything above depends on one unglamorous thing working: that a report produced by one laboratory in 2022 can be sensibly placed next to a report produced by a different laboratory in 2027.

Today, it mostly cannot. Every laboratory uses its own analysis pipeline, its own reference database and its own naming conventions. Two labs can look at the same water and return different species lists, and neither is wrong. They are simply not speaking the same language. That single fact is why so much biological data has no shelf life.

The one thing to do before your next survey: ask for the FASTQ files

When a laboratory finishes your samples, you normally get a report — a species list, some charts, a PDF. That report is the laboratory's interpretation of your samples, made on the day, using the reference library and software they had at the time.

Underneath that report is the actual data: files of raw sequence reads, in a standard format called FASTQ. These are the unedited output of the sequencing machine — millions of short genetic fragments recovered from your filter, before anyone decided which species they belonged to.

The report is the photograph. The FASTQ is the negative. You can always make a new print from the negative.

This distinction is not academic, and it will cost you if you ignore it:

• Reports go out of date. Raw data does not. Reference libraries improve every year. A fragment that came back in 2024 as "unidentified minnow" may be identifiable to species by 2028 — but only if somebody kept the fragment.
• Species names change. Taxonomy gets revised constantly. A report is frozen at the moment it was written; raw data can be re-read against current names.
• Comparability lives in the raw data. Two labs' reports cannot be sensibly compared. Two labs' FASTQ files, run through one common method, can be. This is the whole mechanism.
• It is your data. You paid for the sequencing. The reads belong to your lake.

What to ask your laboratory for

Ask before you place the order, and get it in writing. Some labs — the good ones — return raw data as standard. Others will provide it on request. A few charge for it, and a few will not release it at all, which is worth knowing before you send them your samples rather than after.

Request all of the following:

• Raw FASTQ files for every sample, unfiltered and untrimmed, with the sample identifiers matching your submission form
• The negative and field control files too. Controls are how anyone later judges whether a detection was real or contamination. A run without its controls is very hard to defend.
• The run metadata — which genetic markers were used, the sequencing platform, the run date, and the pipeline and reference library versions used to produce your report

A short sentence in your order email is enough: "Please confirm that raw FASTQ files for all samples, including controls, plus run metadata, will be provided with our results." If the answer is no, that is a real piece of information about the vendor.

Then upload them here

Drop the FASTQ files into Flora & Fauna alongside the report. They are large — expect hundreds of megabytes, sometimes several gigabytes for a full run — so upload over a decent connection and expect it to take a while. It is a one-time job per survey.

Sequence archiving requires a Plus or Lake Admin subscription on your lake. Storing raw sequence data permanently, backed up, and in a form that can be reprocessed years later is a real ongoing cost, and it is one of the things those subscriptions pay for. If your lake is on the free tier, get the files from your lab anyway and keep them somewhere safe — you can upload them the day you subscribe. What you cannot do is get them back from a lab that has deleted them.

Two things happen once they are in. Immediately, your lake has a complete, permanent, portable record rather than a PDF. And when Common Measure comes online in 2027, those stored files can be run through a common reference frame — which is what turns a stack of unrelated reports from different labs and different years into a single, comparable biological history of your lake.

If you do nothing else after reading this: email whoever did your last eDNA run and ask them for the FASTQ files. Even if the survey was three years ago. Even if you have no immediate use for them. Labs do not keep customer data forever, and the request costs you one email.

If what you are chasing is a specific invader rather than a picture of the whole community, the detection question sits inside a wider one: how invasive species arrive, why they are established before anyone sees them, and what to do in the first ninety days.

What this is not

Worth saying plainly, because it will matter the first time somebody quotes your report:

• eDNA metabarcoding is not an EPA-approved method. It is a survey and screening tool. Results are not suitable for regulatory or compliance determinations. If you get a detection that matters, your state agency has its own confirmation protocol and that is the one that counts.
• Flora & Fauna is a record, not a diagnosis. It tells you what has been found. It does not tell you what to do about it.
• Lake Pulse sells measurement and monitoring, not treatment. What you build here positions you to solve a problem, and to prove afterwards whether it worked.

How to start

1. Upload what you already have. Old reports, agency surveys, plant maps. Whatever is in the folder. The record starts the day you stop letting it sit in email.
2. Email your lab and ask for the FASTQ files from every survey they have run for you. This is the highest-value thing on this list and it takes five minutes. Do it whether or not your lake is subscribed yet — the files are the part you cannot recover later.
3. Put your lake on Plus or Lake Admin if you intend to keep measuring. That is what turns a folder of files into a permanent, reprocessable record.
4. Run a three-site eDNA survey. Spread the sites across habitats, not along one shoreline. Include the boat launch — it is where new organisms arrive and where a detection is most actionable.
5. Sample the same three sites next year, and the year after. One survey is a snapshot. Three surveys are a trend, and a trend is the thing that changes decisions.
6. Escalate to eRNA only when it matters. When a detection would trigger real spending, find out whether it is alive and active first.

Disclosure. Lake Pulse's CEO is involved in the development of Common Measure. We think a neutral, lab-agnostic reference standard is the right foundation for biological monitoring — including when it is not our own data going into it — and we would rather say so up front than have you find out later.