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Septoria, a leaf spot fungus destroying harvests – learn to destroy it instead!

Spots of septoria infection on a tomato plant leaf.

Septoria is a species of fungus that infects vegetables, trees and ornamental plants. In some cases damage is insignificant, in others there’s no hope.

Key Septoria facts

NameSeptoria species
Common names – leaf spot
Type – leaf spot fungus

Season – spring until fall
Target plantsSolanaceae (nightshade family, like tomato & potato) & others (all septoria host plants here)
Infected plant parts – leaves & stems

Main Septoria spot identification

  • numerous round spots
  • red-yellow-purple rim
  • swollen rim
  • brown or black center
  • tiny black pinheads on underside of spots

Learn to treat against Septoria and protect plants and vegetables from it.

Preventing Septoria infection

Septoria is difficult to get rid of, so do your best to prevent it altogether. Understanding the environmental conditions that trigger the disease help prevent it.

Conditions that trigger Septoria on plants

Long periods of high temperatures (minimum 60° F / 15°C, more commonly 80°F / 25°C) and high relative humidity both weaken target plants and trigger Septoria growth.

Leaves that stay wet for a long time are its favorite. Water on the leaf serves three purposes for the fungus:

  • Water lowers the plant’s defenses. Indeed, it weakens the boundary between the inside and outside of plant cells.
  • Water dilutes the immune response of the plant. Fighter-proteins the plant releases disperse all over the leaf instead of concentrating near the infection.
  • Water is what the fungus needs to send tiny root-like tendrils between cells into the plant.

Expect infection when you have the following:

previously infected plants/terrain + high temperatures + high moisture + wet leaves for over 6 hours

Here are 9 important ways you can reduce Septoria infections in your plants.

1 – Take great care in how you water

  • Don’t get leaves wet.
  • Water on the soil directly. Use long-spout watering cans,  an extension to the hose, or drip irrigation.
  • Avoid splashing.
  • Water in the morning. Do not water in the evening or plants will stay wet all night. Also, watering in the evening favors guttation. Guttation is one of the ways diseases like Septoria spread.

2 – Increase air circulation and space between plants

This helps leaves dry faster when they do get wet, for example in case of rain. It also makes it harder for Septoria to propagate from one plant to the next when they’re further apart.

Here’s a table that shows how certain actions influence air circulation and decrease contamination.


Action Air circulation Spread of septoria
raised gardening
or container garden
increases air circulation,
moisture drops to between beds
plants are further up
and harder to reach
spacing plants airflow facilitated neighbors further away
staking plants avoids moisture-collecting canopy,
soil surface dries up faster
neighbors further away,
infecting upwards harder
than spreading sideways
remove lower
soil surface dries up faster,
airflow facilitated
leaves are further up
and harder to reach


  • Go for a raised garden which increases air circulation.
  • Space the plants for air to flow through.
  • Stake taller plants like tomatoes so they grow tall instead of forming a canopy.
  • Remove lower leaves up to at least a foot.

One last point if you’re growing a vegetable patch: orient rows according to dominant winds in your area. Place them so the wind flows through the rows and not across them.

3 – Keep target plants away from each other

This is one of the virtues of companion planting. Having several crops grow together means pests from one crop land on another – on which they can’t grow and spread!

  • Intercropping is also very relevant for the same reason.

Various hedge shrubs are vulnerable to Septoria fungal infections, such as cherry laurel for instance.

  • Growing a mixed hedge is a sure way to reduce the impact of an infection on hedge shrubs.
  • Include shrub varieties that are resistant to Septoria, such as yaupon holly.

Additionally, growing different varieties of plants together increases their immunity. It increases diversity of epiphyte micro-organisms that settle on leaves and stems. Having more diversity there means it’s harder for disease-inducing germs to settle in.

Be on the watch for weeds that also host Septoria. These are listed below, in the “Varieties and types of Septoria and the plants they infect” part.

4 – Use green manure, till and mulch

Generally, green manure is a great way to enhance soil health.

  • Specifically, certain plants, when used as green manure, have been shown to protect against fungal diseases such as Septoria.
  • These include plants of the mustard family, such as mustard and rapeseed.

Till before sowing or planting to flip the ground over. This will bury spores so they can’t splash up.

Mulch to trap any remaining spores at the beginning of the planting season.

5 – Preventive sprays

Every fortnight in the growing season, it’s very beneficial to use natural fermented weed sprays on your preferred plants.

  • Prepare them from whichever weeds you have at hand.
  • Spray early morning, this time including leaves.
  • This will reinforce your plants’ immune systems and fend off pests and diseases.

6 – Grow on a different plot every season

Septoria spores will remain active for up to three years on topsoil and plant debris.

  • Crop rotation will ensure the same disease won’t strike again. Best is four years, but even one year of not planting will greatly reduce the next infection.
  • Spores of some species can travel in the air for miles, especially for soybean. Other Septoria spores are much heavier and will remain within several dozen yards of where they originated.
  • If you haven’t much space, add obstacles to hinder airflow from a contaminated area. Hedges or bamboo lattices will help somewhat.

7 – Avoid infected seeds

Some Septoria strands also contaminate seeds of their host plant. If you’re planting soybean or tomato, ensure that seeds come from disease-free plots of land.

  • You can heat-treat your own seeds to keep them. (120°F for 20 minutes)

8 – Behavior that worsens disease spread

On top of what we mentioned above, one more unexpected tip:

  • don’t handle or brush through the plants in the early morning  if you notice guttation drops.
  • Don’t work in infected fields if it has rained recently and leaves are still wet.

Septoria can spread from one plant to the next through these dew-like drops. Since infection may have started even before the plant shows any symptoms, it’s more prudent not to handle the plants at this time of the day, or whenever they’re wet.

9 – Watch out for frost on larger plants

In larger trees and plants, Septoria will wreck more damage on parts of the plant that are more exposed to frost. Indeed, this fungus releases toxins that decrease frost resistance of leaves.

  • Leaf tissues break as water in them turns to ice.
  • The fungus colonizes wounded tissue much more easily.
  • Winterize your plants to keep them from freezing.

Treating Septoria

Spot of a septoria fungusIt must be said: the best treatment is prevention. Getting rid of a disease is harder than not catching it.

Nonetheless, there is a lot you can do. First, go through all actions related to prevention shared above. After that, follow these steps:

Remove all infected leaves and stems

If a plant is more than a half infected, remove it entirely.

If less than half infected, remove all diseased leaves with clean shears.

  • Dip the shears in methylated spirits or alcohol between cuts.
  • Carefully place cut material in a plastic bag to avoid spreading spores around.
  • Clean and disinfect all equipment used before leaving the plot to avoid spreading spores.

Dispose of the infected material in either of the following ways:

  • bury in a hole at least two feet deep.
  • or burn the trimmings.

Don’t compost materials infected with Septoria. Temperatures of over 130 °F (55°C) are needed continuously for over 72 hours to kill spores off. It’s very difficult to obtain this without specific hot-composting practices.

Spray with fermented tea

Many kinds of fermented teas can strengthen the plant and make it harder for Septoria to spread. You can use compost tea or make your own fermented tea from weeds.

Spray weekly to contain the infection. Best is to spray early morning to match with guttation. It also ensures leaves dry off faster.

Bordeaux mixture

Another option known to repel fungal diseases, including Septoria, is Bordeaux mix.

  • This copper-based spray is accepted as an organic treatment as long as it’s used adequately.
  • Organic growing regulations describe how much and how often it should be sprayed.
  • Copper accumulates in the soil and proper use avoids soil contamination.

Chemical treatments

There are chemical solutions to get rid of fungus, but using them is a double-edged sword.

  • When chemical fertilizers are used, pests develop a resistance to them and grow stronger. Every following infection will require more poison.
  • Also, chemical products weaken the plant and devastate all micro-organisms present on the plant. Many of these epiphyte micro-organisms are beneficial to the plant and hinder the spread of fungus.
  • Furthermore, field trials have shown that chemical fertilizers are only marginally more effective than fermented teas.

Note: check labels for when to stop spraying if you intend to eat fruits and vegetables from chemically-sprayed products.

After the season is over

  • Clean all garden tools diligently. Wipe with alcohol to disinfect everything before storage.
  • Plan the following year’s crops and organize crop rotation. Ensure the furthest possible distance to the contaminated plot.

If you can’t practice crop rotation, one option that may be effective is to solarize your soil.

Identifying Septoria leaf fungus

Make note of the following characteristics:

  • shape, color, location, pattern, swelling, wet/dry aspect
  • Bring several samples with you when visiting an expert like the local gardening association or Agriculture Department office. Try to include a whole infected plant if possible, pulling roots out.

Shape and size of Septoria spots

  • Spots are usually circular.
  • The round shape isn’t necessarily interrupted if the spot crosses a leaf vein.
  • Spot size is usually 1/4th of an inch (5mm) across when they start sporulating.


  • Center is either tan or gray (usually depends on the plant species).
  • Rim is brown.
  • Neighboring leaf cells are either yellow (common for tomato) or red/violet. This is where the plant is still fighting the infection off. It’s rather narrow, about a hundred mils wide (a couple millimeters). The natural green color of the leaf is lost because chloroplasts are already destroyed by the fungus. It’s a localized chlorosis.
  • Possible black spots further off, signalling secondary infection sites starting.
  • With a magnifying glass, tiny black pinheads can be seen on more mature spots, on the underside of leaves. This are where new spores form. The scientific name of these tiny specks is “pycnidia”.

Location of spots on plant

  • Spots usually appear on the leaves.
  • Older, lower leaves near the ground are infected first.
  • Disease slowly “climbs” up the plant to younger leaves.

More rarely, young stems may show signs of infection. Fruits are usually last to be infected.


  • Somewhat random pattern, usually towards the center of the leaf.
  • Not necessarily along leaf veins.
  • Not “locked” in the space between leaf veins.
  • Numerous spots.


  • The edges or rim of the spot are slightly swollen compared to nearby healthy leaf.
  • The center of the spot is much thinner, and flat like parchment.


  • Spots don’t leach sap or water.
  • Center of the spot is dry on the topside, sometimes a bit wet on the underside.

Microscopic identification

A laboratory will identify Septoria reliably by looking at the shape and size of the spores and spore-sacs (conidia and pycnidia). A microscope is used for this.

Life cycle of the Septoria fungus

Like other black spot diseases, Septoria is dormant in winter.

  • Spores called conidia (equivalent to seeds for fungus) overwinter in old infected plant material.
  • Some spores are released and land on neighboring weeds, bark, or soil.
  • Garden tools and implements can host the spores as well if not properly cleaned.

When the growing season starts, spores spread to the environment. Most common is during watering or rain, as water is splashed about.

  • On wet leaves, Septoria can start penetrating inside the plant leaf. It uses thin filaments called “hyphae” to infiltrate the space between cells.
  • Spots form as the fungus spreads locally.
  • On dead material, in the center, the fungus forms new spores.
  • Spores are propelled into the air by drying pycnidia (the tiny black pinhead-like spore sacks). If wet, the pycnidia soften up and burst, releasing the spores in the water on the leaf.
  • Spores land on neighboring leaves. Water splashes them higher up.
  • The cycle starts over in a new location until the entire plant is contaminated.

Spores of Septoria being released by ripe pycnidiaThis cycle repeats every 3 to 4 weeks, as long as conditions are maintained. After the first infection, these are called “secondary cycles“.

At the end of the season, an infected plant is all withered up, covered in spores. Debris falls to the ground. Septoria spores can resist frost and freezing and in the following spring the cycle starts over.

  • Collecting all infected plant material is crucial to reducing infection the following year.
  • Adding a thick layer of mulch will also help trap spores below ground.

Varieties and types of Septoria

Each strand of this fungus usually only infects a single host plant species, or a single family. Several, though, are able to contaminate several host plants.

The most famous variety is one almost all gardeners have encountered: Septoria lycopersici, the tomato black spot.

Since conditions that trigger growth are similar to all species, infection may start at the same time on different plants.

  • Septoria host plants and types of Septoria (vegetables, fruit trees, garden flowers, houseplants, herbs, citrus…)
  • Note that they’re also generically called “Septoria leaf spot“, too.

Weeds that Septoria can survive and multiply on

Although not necessarily ideal hosts for Septoria, the following weeds make it possible for the fungus to grow and spread:

  • horsenettle
  • jimsonweed, a type of datura
  • groundcherry, of the Physalis family
  • black nightshade

Plants resistant to Septoria infection

Disease-resistant varieties and cultivars have yet to be found for most food crops.

For example, only a fraction of all varieties of wheat grown on earth are resistant.

None of the commonly cultivated tomato cultivars are resistant to Septoria.

However, there is hope that resistant hybrids can emerge. Wild tomato, previously grouped under the label “Lycopersicon”, have shown strong resistance to the disease.

Generally, among ornamental plants and vegetables, some varieties are less prone to infection than others.

A few herbs resistant to Septoria

Basil and thyme (including wild thyme and lemon thyme) are resistant to Septoria.

Shrubs and ornamental plants that resist this fungus

A few great hedge shrubs have never yet been seen to host Septoria infections:

Diseases Septoria might be confused with

Especially in the early stages, Septoria resembles the following diseases:

  • Alternaria, rust, bacterial blight, black spot, anthracnose, black dot disease, fusarium wilt

Learn more about Septoria

Septoria leaf spotSeptoria is one of the world’s most problematic plant diseases. It affects food crops and ornamental gardening.

As for most fungus diseases, controlling growing conditions is essential. The first goal should be to avoid appearance and spread of the disease.

There are only few options for biological control of Septoria. These include fermented teas. One major hope is breeding and selection to identify plants that succeed in fighting the disease off.

Biological control against invasive plants

However, sometimes Septoria can be of use. In one experiment in Hawaii, the fungus was tested as biological control on a locally invasive plant.

This plant, called banana poka, is a type of passion flower. It had overrun entire mountains.

Contaminating the plant with Septoria passiflorae succeeded in eliminating 95% of the invasion on some test sites!

Similar experiments with Septoria helped control spread of another invasive flower shrub in Hawaii, Lantana camara.

Names and taxonomy of Septoria

As shown in our list of plants vulnerable to Septoria, there are a great many species of this fungus. Currently, they’re classified together mostly because of similarities in how they appear and spread.

Each sub-species or variety is set apart from its peers simply because it infects different host plants.

More recently, DNA analysis of various strands is attempting to classify these fungus according to genetic closeness. This has already revealed that some species thought to be Septoria are actually closer to other types of fungus.

Furthermore, in laboratory conditions, strands thought to be specific to a certain plant were able to infect different plants. There is still much to learn about this surprising fungus!

Read also:

Smart tip about Septoria

After a serious infection, it may be wisest to not plant any target plants in the following year. Ask a neighbor if you can grow tomatoes in his or her garden, or set up a community garden nearby instead!

Image credits (edits Gaspard Lorthiois):
Bugwood.org: Bruce Watt, Mary Burrows
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