New paper: Unearthing diversity in fungal dark matter

To be born an orchid is a most unlikely thing. First your parents must be pollinated, which is difficult. Orchids are both rare, and rarely pollinated due to the bizarre and dishonest means by which they go about attracting pollinators. Added to that, orchids often rely on a single species of pollinator to do the job.

Let’s say, however, that your orchid parents do manage to achieve fertilization. Your orchid mother will produce many thousands of tiny dust-like seed, which will be jettisoned into the wind. Unlike most seeds, you have no maternal energy investment to power your germination and first days as a seedling. Instead, you must rely on blind luck to land you within reaching distance of a strand of soil fungus. This fungus is the wet nurse to bring you into the world, invading the seed coat and hooking the young orchid up to a network of fungal strands that pervade the soil. Tapping into this network provides you with the first sips of carbohydrate and nutrient you need in order to build your first green leaf and begin to stand on your own roots. But it is not enough to land near any fungus. Many orchid species require fungal partnership with a specific species of fungus for this to occur at all. Multiplied together, it is a wonder that orchids ever overcome these odds to propagate themselves into the next generation.

The southwest of Western Australia is rightly famous as a global biodiversity hotspot. The area is particularly rich in orchids, and the spider orchids (Caladenia) are some of the most impressive and diverse of the region’s main orchid groups. In 1967, University of Adelaide researcher John Warcup discovered in association with Caladenia a new genus of fungi. Today those fungi are called Serendipita, and although we have known of them for around 60 years, there have been less than a handful of species discovered and described.

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The spider orchid Caladenia arenicola was one of those sampled in the study

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White spider orchid (Caladenia splendens)

Ubiquitous yet invisible

Although related to mushrooms, Serendipita fungi have not been observed producing the conspicuous spore-bearing fruit bodies we usually use to find and identify them. This makes them largely invisible, and I have therefore never observed them in the wild. Despite that, recent research using DNA sequencing has found them to be absolutely everywhere. Inside all kinds of plants, outside all kinds of plants, and distributed from the equator to Antarctica. It is clear then that there must be a hidden biodiversity of these species siting, waiting to be discovered.

My study took a wide sample of southwest WA spider orchid samples and assayed them for the presence of Serendipita fungi. We then sequenced the DNA of all the fungi we found, and used a new analytical technique for dividing that DNA sequence diversity into units that are probably species. This is currently the only way to sensibly identify Serendipita fungi, as they all look completely alike and do not produce spores in the lab.

We found a total of eight species of Serendipita fungi, including the original species discovered by Warcup back in the 60s. These came from a total of 18 species of orchid. At some sites where we sampled multiple orchid species, we found six species of Serendipita, meaning that the fungi were as diverse as the orchids!

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Lying just below the soil horizon, that swollen, yellow stem bit is called the “collar”, and its where all spider orchids keep their fungus.

Untapped agricultural potential?

Although we have chosen to study these Serendipita in association with orchids, their wide host association has got other researchers interested in their role in plant health and application to agriculture. For example, Warcup’s species and one other have been used in experiments (and patent applications) showing inoculation with Serendipita results in profound benefits for the host plant, including:

  • Increased plant weight in maize, poplar, parsley, tobacco, barley, wheat, switchgrass and Arabidopsis
  • Enhanced grain yield in barley
  • Accelerated plant development in barley
  • Greater seed set, increased growth and faster flowering time in tobacco
  • Increased wheat yield in poor soils
  • Improved nutrient uptake in chickpea and lentil
  • Improved salinity tolerance in barley
  • Enhanced protection against root and stem pathogens in barley
  • Improved resistance to stem pathogens in tomato
  • Stronger defense response against mildew leaf pathogen in barley
  • Increased essential oil content in fennel and thyme
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Figure 7 from Ray and Craven (2016): Root growth in winter wheat in Serendipita vermifera inoculated plants (left) versus control (right)

These proven benefits make Serendipita a potentially powerful tool to enhance plant productivity and stress tolerance in crops. Furthermore, application of Serendipita fungi could be an organic alternative permitting growers to lower the application of unsustainable and ecologically harmful synthetic fertilizers. Our knowledge of plant-Serendipita associations in the wild suggests that these relationships are more prevalent in nutrient poor soils such as those in southwest WA. They are probably one factor that allows our plant diversity to thrive in such weathered, poor soils. This means that species of fungi that have evolved with the nutrient poor soils (like those discovered in this paper) might be untapped tools to enhance agriculture taking place in those very same soils.

 

(Erratum: This story was edited to replace the figure attributed to Ray and Craven (2016). The first image I used was one showing Arabidopsis capability for mycorrhizal association. Arabidopsis is typically thought to be a non-mycorrhizal plant, which is why this is interesting. The image however showed slower growth in the mycorrhizal treatment. A related Serendipita has been shown to enhance root growth in Arabidopsis however. I have now updated the post with a more appropriate image of root growth gains in wheat. Thanks to Pawel Waryszak (@PWaryszak) for pointing this out.)

 

My study:

Whitehead, M. R., Catullo, R. A., Ruibal, M., Dixon, K. W., Peakall, R., & Linde, C. C. (2017). Evaluating multilocus Bayesian species delimitation for discovery of cryptic mycorrhizal diversity. Fungal Ecology, 26, 74-84.

Further reading:

Weiß, M., Sýkorová, Z., Garnica, S., Riess, K., Martos, F., Krause, C., … & Redecker, D. (2011). Sebacinales everywhere: previously overlooked ubiquitous fungal endophytes. Plos one, 6(2), e16793.

Weiß, M., Waller, F., Zuccaro, A., & Selosse, M. A. (2016). Sebacinales–one thousand and one interactions with land plants. New Phytologist, 211(1), 20-40.

Ray, P., & Craven, K. D. (2016). Sebacinavermifera: a unique root symbiont with vast agronomic potential. World Journal of Microbiology and Biotechnology, 32(1), 16.

Bokati, D., & Craven, K. D. (2016). The cryptic Sebacinales: An obscure but ubiquitous group of root symbionts comes to light. Fungal Ecology, 22, 115-119.

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Australia’s sexual swindlers.

Seduction. Pollination. Deception.

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I recently wrote an article for Wildlife Australia about Australian sexually deceptive orchids, their evolutionary biology, and historical and current research about them. You can download and read the article here: PDF. Thanks to Carol Booth for her collaboration and editorial guidance.

The latest of Australia’s sexually deceptive orchids that I have seen (below) are Caleana major, the Flying Duck orchid (left), and a spider orchid Caladenia clavigera (right). Both were photographed last week in Brisbane Ranges NP, Victoria.

Flowering this year is one of the best seasons of recent times both east and west of the country. So if you’re in Australia, don’t miss the chance to get out bush and enjoy it.

New article: The Territories

The Territories is Heath Killen’s new project. The site blends stories of Australia’s natural and cultural history under a unique aesthetic. I encourage you to check it out.

I was happy to make a recent contribution to The Territories, a story and photo gallery about Australia’s abundance of deceptive orchids:

“Sex, Lies and Pollination”

Rather than luring its pollinator with the promise of food this flower uses an equally, if not more, powerful motivator: sex. Undetectable to human senses, the orchid’s advertisement is a precise chemical mimicry of a female wasp’s sex pheromone. This is targeted marketing at its finest, as the use of a signature sex pheromone ensures that the orchid attracts only males of a specific species of wasp.

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The Toadlet Diaries 2: Gulf country.

In 2010 I was fortunate to accompany herpetologist Dr. Renee Catullo on a trip through Australia’s Top End collecting little brown frogs. Here are some of my field notes along with photography. While my photography has vastly improved, I’m not sure I’ve felt so inspired to write since that trip. I hope this series of vignettes communicate some of the flavour and excitement of the wet season in Australia’s monsoon tropics.

(Part one here)

31 January 2010

I was relieving myself a stone’s throw from the inundated Carpentaria Highway when I saw my first Brolga. Its lanky form drifted indolently against a pastel sky as the tropical sun poured out late afternoon’s final slanting blaze. I finished my business, picked up my binoculars and shovel, tucked the bog roll under my arm, snatched a nearby burrowing frog with my free hand and wandered back to where Steve had left our hired Landcruiser: bogged up to the axles in the soft roadside sludge.

We had been following a map to the “Lost City”, scrawled on a take-away order pad by a gnarly-toothed cook at Cape Crawford’s “Heartbreak Hotel”. (This sentence is entirely true and gives me great pleasure to write). I had hoped to see the exceedingly elusive Carpentarian Grass-wren there, but like Grass-wrens, Lost Cities are difficult to find. Renee planned to make a 200 km push down and back the Tablelands Highway that night so our search for the Lost City was truncated in favour of beginning the evening’s driving. Our U-turn was truncated on the shoulder of the highway, which had been under floodwater for the last 3 or 4 days and needed little persuasion to engulf the hired Landcruiser.

We had been stalking 300 kms of the Carpentaria Hwy for the last two nights and had seen one car in that time. It was 5.30pm on Sunday and we had enough food and water in the car to last us a few nights should it come to that, but in a great fluke of variance the next 30 minutes sent us three different cars. Our eventual saviour rocked up in a big old Landcruiser. As a spry indigenous woman jumped out of the passenger seat to retrieve a rope from the tray, a man as weathered, wide and red as our fair country hopped out of the driver’s seat. Our saviour was in a hurry, the rope quickly linked our cars back to back and he barked some instructions to an unsure Steve behind the wheel of our stricken vehicle. Soon wheels were spinning as his truck revved and squealed, switching about like a hooked barramundi. Steve eventually found 4WD, low range, reverse and our steed was yanked backwards from the muck.

Impeded on the Carpentaria Hwy

Impeded on the Carpentaria Hwy

That was the beginning of one of the most eventful evenings of the trip. We were now running a bit late, but counted ourselves lucky to have gotten away with an hour delay. The drive ahead saw us traveling south down the Tablelands Highway, a road that splits rocky cliffs of rust red upon which the ivory white bark of eucalypts is thrown into dramatic contrast by the light from the setting sun. We stopped on a vast flat grass plain after dark and watched the moon rise, a giant languid yellow disc that was to light the rest of our evening.

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It is worth mentioning that I only refer to the roads by name because there are so damn few of them here in the Top End. Each road takes on a character through its interaction with the elements, the lansdscape, and the idiosyncrasies of the disparate roadhouses, towns and remote communities it links across vast distance. These bitumen ribbons of country and the hours spent on them forms a large part of the Top End experience for residents and visitors alike.

Soon after dark the animals started throwing themselves in front of the car. A remote wet season highway at night is chaos. I’ve never seen so much wildlife ever, and you’ll be pleased to know most of it survived. Bustards, nightjars, owls and curlews appear in the headlights, I brake and they make a flapping flash in my periphery as they fly within centimetres of the windscreen. Agile wallabies bound in groups across the road ahead, or sometimes they just stand on the road shoulder, waiting for us to drive closer before darting out into our path. The road is littered with frogs, only discernable as the car drives on over them. But one can’t look out for them as it is much more important to spot the groups of Brahman cattle from a distance safe enough to slow down. At several points we’re slowed to sub 10 km/h as dozens of cows slowly bumble down the road in front of you for hundreds of meters. There is nothing to do but travel along behind until they find a spot to vacate the bitumen. In addition to the fauna there’s water to watch for, the road is flooded in some points up close to a meter, and the floods have dragged onto the road a flotsam of logs, branches and general crap to drive around.

Tablelands Hwy denizen with biologist for scale - Black-headed python

Tablelands Hwy denizen with biologist for scale – Black-headed python

When we swapped drivers I had run over what I was horrified to hear Renee later estimate as a total of 30 burrowing frogs. At the wheel, Steve the frog lover perhaps avoided a few more than I did, but unfortunately he was unable to avoid a nail tail wallaby. The nail tails are beautiful creatures up close, covered in soft, fine light caramel fur with faint white markings. A dark dorsal line runs from the back of their neck down their spine to the nail protruding from a spray of thick black bristles at the end of the tail.

That was one day in gulf country, out near Boroloola.

The Toadlet Diaries 1: Trench warfare frogging.

In 2010 I was fortunate to accompany herpetologist Dr. Renee Catullo on a trip through Australia’s Top End collecting little brown frogs. Here are some of my field notes along with photography. While my photography has vastly improved, I’m not sure I’ve felt so inspired to write since that trip. I hope this series of vignettes communicate some of the flavour and excitement of the wet season in Australia’s monsoon tropics.

3 February 2010

Birds, wind, insects, all still, all silent. An atmosphere of exhaustion settles in as the temperature draws near 40. Wanda Inn roadhouse sits baking between red clay and the azure expanse of the outback sky. This would be home for the night, and we’d best get some sleep before tonight’s activities.

Littoria caerulea find respite from day's dry heat by hanging out in the toilets.

Littoria caerulea find respite from day’s dry heat by hanging out in the toilets.

The area hadn’t seen rain for a while but on dusk the moodily flashing cumulus clouds in the distance promised a change in the weather. Soon after dark we find ourselves in frogless country, standing on the roof of the Landcruiser captivated by the lightshow of distant electrical storms. As time passes the breeze blows harder, and we drive closer to its origin. Soon we are buffeted by a stiff cool wind, petrichor fills the air, fat drops of rain spatter and we are surrounded on all sides by the intermittent discharge of three kinds of lighting. Coruscating bolts crack somewhere between us and the horizon, leaving their jagged after-image in negative on our retinas, snaking fingers of electrical tracery race bifurcating and branching in the clouds overhead, and distant bolts diffused through cloud and rain suddenly bathe the land in white, turning puddles into mirrors for the silver sky before plunging us back into darkness. The weather is completely in character for the Northern Territory: at once utterly romantic and dangerously thrilling.

We stop periodically to stand on the car and take pictures of the gathering storm (still no frogs calling) but when a blinding bolt cracks too close for comfort we quickly curtail our roof-standing. Discouraged by the lack of frogs, the talk turns to gin and tonic at our next stop, but when we get there, rather than a refreshing drink, the distinctive chip of the Stonemason toadlet greets us and the frogging is on.

And so the wind blows, fat drops spatter our skin as we stride through waist high grass and negotiate ankle-twisting holes, boot-sucking puddles, and mud that cakes to the mud that’s caked on the mud caked on our boots. We wiggle between the slick ground and barbed wire fences while the sky flashes chaotically, rumbling and booming, and we stalk around pools thronging with the disorientating din of burrowing frogs, occasionally glimpsing the wide eyes of the other when the land in an instant becomes awash in the white of a nearby burst of lighting. This was trench-warfare frogging.

Top End storm

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As you were, Australian researchers.

Waking up to look at this before a coffee and a shower was enough to put me into fight or flight mode this morning.

With hackles raised I read on and found a sciency corner of Australian Twitter users in a flap about Abbott’s 20% ARC cuts. #AbbottsRazor #ARCcuts etc etc

While the wording of these Tweets is strictly true, they are also completely misrepresenting the politics of these ARC funding estimates.

The numbers are below. The top row is the current budget handed down by Labour in 2013. The middle row is the Abbott Government amendment. The bottom row is the difference. Numbers represented in thousands (000’s).

2013-14

2014-15

2015-16

2016-17

TOTAL

May budget

$883,959

$879,983

$834,587

$788,710

$3,387,239

Amendment

$883,959

$853,110

$783,253

$716,205

$3,236,527

Difference

$0

$26,873

$51,334

$72,505

$150,712

YES. ARC funding will dive by 19% in the next 4 years. But this is a dive courtesy of the Labour Government’s May 2013 budget.

YES. Abbott is cutting funding further, but this amounts to 4% cut in total ARC spending over the next 4 years. The majority of the sliding investment trend came from the initial budget trajectory set out in May.

The time to make a flap about budget cuts was in May. And some of us had a good whinge then. The truth of this latest news is that it is a continuation of the prevailing “death by a thousand cuts” trend, as another shaving is whittled off our future investment in research and innovation.

But the big lesson here is to hold fire when it comes to social media. A forgiving person might acknowledge that this shows that scientists are only human, prone to the occasional passionate, emotional, reactionary outbursts. A harder judge might question whether researchers who don’t think critically and do a bit of their own “research”, deserve any ARC funding at all.

Thanks Alice Hutchings, for engaging your brain. And Tom Stayner for the title.

Postscript

Jeremy Shearman from the Genome Institute in Thailand has produced this graphic showing the effect of amendments on ARC funding over the last few years. The trend is one of providing more upfront dollars with increasingly steep sliding scales of less funding later.

ARC funding amendment history