Herbaria

Herbaria are collections of plant and fungal specimens. A collection of fungi is sometimes distinguished as a fungarium. In the case of plant pathogens, these specimens are usually pressed and dried, and stored in paper packets. Sometimes they are mounted on paper.

The front of a paper herbarium packet, showing all the important details about the specimen.

The contents of a paper herbarium packet; the specimen is placed loosely and the packet is folded around it.

Herbarium specimens provide a record that a particular taxon was found in a specific place, at a specific time. If taxonomy changes, the specimens can be redetermined and we will still know what they were — compare this to a written record, which only tells us what the recorder thought something was at the time. The following is an example of a specimen mounted on paper, but there is a major problem. Can you see what is wrong?

A flower smut specimen that has been mounted on paper.

There is no date or location beyond “England”, and there is no other information! This specimen could be the only record of the species from a certain site, but we will never know. It is very important to label your specimens. The one thing we can do is determine and redetermine the identity of the specimen — the post-it note shows my determination of the specimen as Microbotryum flosculorum (de Candolle) Vánky, 1998, and if this species is ever split up or merged with another species, future researchers will be able to redetermine it.

Information with a specimen or record

You must include the following with any herbarium specimen or iNaturalist record:

Location: At the very least GPS coördinates or a grid reference, often with a placename too. You can be vague if you want but I like to be accurate enough that if someone wanted to refind the host plant they would have a decent chance.
Date: This is useful for understanding when pathogens appear and how this is changing with climate change.
Host plant: This one is really important! If you are only taking a single leaf, other people will not be able to identify the host plant. Many old records are less valuable because the host plant has not been included, as old species have been split into many different host-specific species, and without knowing the host plant we do not know which of the new species the record refers to.; An alternative if you aren't sure what the host plant is, is to make a separate collection of the host plant itself and make sure the records are linked in some way. You can also simply include enough of the host plant that ID is possible from your specimen, as in my Entyloma specimen shown above.
Collector: The name of the collector, i.e. your name!

You should aim to include the following with your specimens and records:

Taxon name: You might be surprised that this isn't essential, but you can donate indeterminate specimens (“indets”) to a herbarium. They can always be determined later, and if you think it is an interesting specimen that is worth keeping then there is not reason not to just because you don't know what it is.; It's also worth noting that you don't have to identify something to species, you can leave it as a higher taxon such as Entyloma or even a very broad group like Pucciniales (Rust Fungi). Any level is useful information.
Habitat notes: These can be useful for researchers studying the ecology of pathogens.
Collector number: Most collectors have a continuous series of numbers that uniquely identify every specimen they have ever collected. For example, the first specimen I ever collected is JD1, the thirty-seventh is JD37, etc.
Determiner: If someone else identified the specimen for you, write their name. If someone else helped you to identify the specimen, write your name and their name, etc.
iNaturalist record number: This means the specimen can be linked to your iNaturalist record, with associated photographs. This is the number at the end of the URL, eg for the packet shown above the URL is https://www.inaturalist.org/observations/228476520, so the number is 228476520.
Other notes: For example, is this the first record from the area? Is the taxonomy controversial?

Keeping a personal herbarium

It is very easy to start and maintain a personal collection of specimens. I use brown paper bags, which you can buy in bulk cheaply online. They are quite rough and ready but they work, and are easy to take into the field.

I dry specimens by placing them between a few sheets of toilet paper, then sandwiching them between books. Sometimes I have to swap the paper several times before they are dry.

Ideally you should store your specimens in a cool, dry place such as a cardboard box. There are lots of pests to watch out for! I find Psocids (booklice) sometimes like to nibble at my specimens... Freezing affected specimens can save them: it is standard in the Ulster herbarium to leave specimens for six weeks in a freezer after they have been donated. This is one reason why important specimens should be given to research herbaria, which use integrated pest management and generally put specimens into deep freeze for several weeks before they enter the main collection, to avoid bringing in any pests.

Comparing a packet from my personal collection (top) with a much nicer packet from the Belfast Herbarium.

Creating nice herbarium packets from iNaturalist data

Now that I am doing a PhD I am determined to keep my herbarium neat and organised (at least the specimens I need to keep track of!).

Downloading iNaturalist data as a csv file will allow you to create nice herbarium packets automatically. LibreOffice has a Label function that allows you to generate labels from rows in a csv. MS Office presumably does too. I first parse the description (which I use to record the host etc) and other fields in R using the stringr and lubridate packages to create some new fields and then my csv is ready.

Download the label template here.

In R

It is up to you how much (if any) data manipulation you should do in R or another language of your choice. For the full code I used to generate the data for my labels see here.

One particularly useful thing to do with the lubridate package is to put the date in a nice format, as the format iNaturalist gives you (in the observed_on field) is ugly:

data$date <- parse_date_time(data$observed_on, orders = "ymd")

        date_format <- stamp_date("1 January 2026")

        data$date <- date_format(ymd(data$observed_on))

This creates a new column date with dates in the format "1 January 2026"

Another useful thing is getting host information from the description of the record. This is easy if you are consistent in how you outline your description. In my case I always use the first line of the description to describe the host, always in the format “ex Bellis perennis” followed by a newline. I use stringr to parse this. Note I am also using the dplyr package here:

data$host <- data$description %>%

    word(1, sep="\n") %>% # first line
    str_remove("ex ") # remove only the first instance of "ex "

This creates a new column host containing only the scientific names of the host of each specimen.

Database side

In LibreOffice Base create a new database
Copy the data (CTRL+a then CTRL+c) from your csv file and right click on the tables area (bottom right in the pic below) then click paste

In the "Copy table" dialogue give the data a name then click Create
Click yes to unique index
Click yes to warning

In LibreOffice Writer

File → New → Labels
Select the database and table you want to take data from
You have to individually select each field in the order you want it then click the arrow to add it to the label
Click new document to create the label
Format → Page Style
Under "Page" tab:

Change Paper Format to preset "A4"
Change margins to 2, 2, 2, 1, 0cm

Edit the label box to have the following properties:

Anchor to paragraph
Right click on edge → Properties → Position and Size and untick Position and Size under the "Protect" heading

Move the box to below the first line of text then copy and paste the guidelines from the template above it (all of the lines above the label box), moving the box to the bottom of the page. Note the lines should be 12pt Times New Roman
Edit to your heart's content. Note you can copy-paste a field and double left click it to edit the field, if you left one out. Also note you can make fields italic, bold etc. Also also note if any field is blank for a certain observation the entire line of text gets left out (even if other fields aren't blank!).

Folding the packet

The sheet should be text-down on the table with the label towards you, so your folds are all into the blank side
Fold along the horizontal line immediately above the label

Make another parallel fold by bringing the other side of the sheet to meet the first fold

Fold the edges in using the guidelines

Fold the label back up to form the front of the packet

The specimen goes into the pocket you see when you lift up the label flap. You can fully unfold the page for easy access, which is often useful for delicate specimens.

Donating to research herbaria

Important (and unimportant!) specimens should be donated to research herbaria, where they will be kept and maintained indefinitely. If a taxon is new to an area, or may be a new species altogether, you should make sure to donate a specimen. If you want to keep your own, you can just make duplicates of a specimen — this is also a good idea if you want to donate to a local herbarium and a large one like Kew.

To donate, you should get in touch with the herbarium curator, generally by email. Note that a few larger institutions (notably Kew) have different curators for the herbarium sensu stricto (i.e. just plants) and the fungarium.

I have made a very non-exhaustive list of things to look out for and collect for research herbaria here.


This project is possible thanks to a grant from the Irish Naturalists' Journal.	Field Guide to Plant Pathogens by Jake Dalzell is licensed under CC BY-NC 4.0	This site is hosted by Neocities.