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Globally decreasing bird numbers – Part 2: Endophytic fungi

Barry Muir – Guest Contributor

In Part 1 of this series of articles, I discussed the principles of climate change to set the background for what follows. There are three types of fungi absolutely vital for the survival of birds, and which I will discuss in this and future articles. The first are called endophytes, the second mycorrhizae, and the third entomopaths. I will discuss endophyte (Greek endo = inside, phytos = plant) fungi first – there are also endophyte bacteria, but these are not considered here.

Endophytes are microscopic fungi that live inside leaves, flowers, seeds, fruit, stems, trunks and roots of all plants – terrestrial, aquatic and marine. They are mostly symbiotic with the plants, receiving sugar from photosynthesis and shelter from the elements, in return for providing the plant with special services. It is these special services that are vital to plants, animals and us.

A typical endophytic fungus inside a plant cell. From: Chatterjee et al. (2019). pone.0214744

Plants can pass their endophytes (both bacterial and fungal) on to their offspring, either by having the fungi inside their seed where they can begin their work in the seedling and then adult plant, or via transport. Spores from some endophytes are transmitted in nectar, pollen, just by release into the air or carried on the skin, feathers and fur of animals. A species of endophytic fungus may occur in several species of plants, not just within the same species of plant.

So, what has this got to do with birds? Endophytes are now recognised as being vital to a plants’ ability to react positively to climate change (Xiaoting Wei et al., 2021), but the colours of many flowers and the odours (perfumes) they emit are also made by endophytic fungi, not necessarily by the plant itself. This means that anything that changes the endophytes (eg the colour, perfume, or taste of nectar, fruit, or seeds) makes these foods less attractive to birds and insects that feed on them. 

The Double-eyed Fig-Parrot eats fruits (particularly figs), as well as seeds, flowers and insect larvae. Image: Jennifer H Muir.

A warming climate, or perhaps the increase in carbon dioxide, or both, is killing or potentially altering the chemistry of many endophytes. Honey Bees are in global decline partly because of starvation. Bees no longer like the nectar, or are not attracted to the flowers because the colour is wrong, or the perfumes that attracted the bees over many kilometres are now too weak to attract them. This weakening has allowed diseases to take hold in bee colonies which were previously strong enough to resist infection. Any bird or other animal that eats bees, or other nectar, or pollen-feeders is in trouble.

Colour, perfume and taste of nectar in flowers are vital to attract bees for pollination. Image from Aridi R. (2020) Smithsonian Magazine.

Some endophytes are involved in production of complex chemicals that serve to protect the plant from bacterial, fungal, or animal attack: in effect, antibiotics or toxins. Many of these chemicals are exploited by we humans as herbal medicines and perfumes, and the fungi manufacture the flavours of vegetables, fruits, wine and other foods.

These chemicals also have more complex roles such as emitting gases that ‘warn’ endophytes in nearby plants that they are under attack (Connors – see web address in Reference list below). Thus, the endophytes in the recipient plants can produce distasteful or poisonous chemicals to deter the pests.

A great example of this is apparent when watching sheep or cattle graze. They constantly move around and do not stay feeding for too long in one place. The grass where they are eating emits gases that ‘tells’ nearby grass it is being attacked, so the grass becomes distasteful, and the animals move away to an area where the grass hasn’t got the message yet! Similarly. plant toxins such as caffeine, nicotine, strychnine, etc., are all manufactured by endophytes to protect their host plants. A few animals, such as some caterpillars, can store these toxins to make themselves distasteful or toxic. Those of you who read my article on phytoncides [BirdLife Northern Queensland (BLNQ) Contact Call: 08 January 2024 – “Go Bush and Take a Deep Breath”] will remember that endophytes are involved in the manufacture of these health-giving gases.

While climate warming may reduce the abundance or species richness of some endophytes (Oita et al. 2021), in some cases, the endophytes are turning into bad guys and now attack the plants they previously protected. This reduces numbers of plants, including those that produce nectar, pollen, fruit and seed on which many birds and other animals (including us) depend for survival. Certain insects are, however, favoured by climate change (Lehmann et al. 2020), either directly or because food toxicity from certain endophytes is decreasing. The reduction in plant toxicity is resulting in insects and other animals attacking plants they previously didn’t feed upon.

It is not just climate change that is altering endophytes and insects: pollutants including vehicle exhausts (Reitmayer et al. 2019, Ryalls et al. 2022), and the use of chemical pesticides, is also altering or killing many endophytes and affecting the host plants. Birds and insects are literally starving to death. Loss of both nectarivores and insectivorous birds is, in turn, providing less food for birds of prey and scavengers.

A more indirect impact of climate and pollution is the stress these influences have on insects. Stress makes the insects more susceptible to disease, just as stress decreases our ability to fight off illness. Another group of fungi, the entomopaths, attack stressed insects and kill them, again reducing numbers of food species, but that is a story for later.


For a readable rundown of endophytes I recommend an elderly (2004) paper by Owen & Hundley, or a wealth of papers in Phytobiomes journal published by The American Phytopathological Society. Both are available online.

Lehmann, P et al. (11 others) (2020). Complex responses of global insect pests to climate warming. Front. Ecol. Environ. 8(3):141–150. doi:10.1002/fee.2160

Mamac, L. (2022). Why Aussies are seeing fewer backyard birds. Asian Scientist August 25, 2022.

Oita et al. (9 others) (2021). Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale. Communications Biology 4:313.

Reitmayer et al. (5 others) (2019). Acute exposure to diesel exhaust induces central nervous system stress and altered learning and memory in honeybees. Scientific Reports 9:579.

Ryalls JMW et al. (6 others) (2022). Anthropogenic air pollutants reduce insect-mediated pollination services. Environ. Pollut. 297:118847.

Xiaoting Wei et al. (5 others) (2021). New insight into the divergent responses of plants to warming in the context of root endophytic bacterial and fungal communities. PeerJ. 9:e11340. doi: 10.7717/peerj.11340. PMID: 34123582


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