There is a strong Asterix vibe to the annual cork oak harvest of the Alentejo in Portugal. Deep into one of the 350 remaining cork oak forests (in my case Herdade dos Fidalgos, near Lisbon) sometime between June and August you'll suddenly come across a team of about 20 men, ranging in ages from 16 to 70, striking huge twisted trees with axes. Then, with a sensitivity you would not associate with an axe, they prise the juicy bark from the tree and it is levered from the trunk in great, satisfying pieces. From the base, right up to the beginning of the branches, it is peeled away to reveal the oak's red, nude surface underneath.

When the tree is completely harvested, the axeman takes a swig from his water barrel and moves on to the next. Periodically, a truck comes to collect the pieces of cork and take them to nearby sheds where they will be weathered for months before being processed. The truck is the only obvious exception to a process that hasn't changed since the 18th century, when montados (open cork oak woodlands) and forests here in Portugal, in southern Spain, Morocco, Algeria and Turkey began to be exploited commercially to produce wine corks. A white number is painted on the tree. It will be nine years before it's disturbed again.

"You need to be very skilled so that you can be sensitive with the axe," says Daniel Pereira, who at 26 is one of the younger harvesters. He's a jovial type and laughs as he talks. "Some of these trees are more than 100 years old. I don't want to be the one to damage them.

"I spent four years learning to harvest. This is the job everyone wants to do. It's very well paid." Pereira turns serious: "There is nothing like cork."

And there really isn't. For starters, cork is the only tree bark that doesn't contain lengthwise fibres, which is why you can (sensitively) chop into it with an axe and return nine years later for a repeat performance. Pliny the Elder gave the cork oak a mention in his Naturalis Historia: his brethren used cork for their sandals, and corks as wine bottle stoppers were found in amphorae at Pompei. A cork oak can live for more than 200 years.

The best of the pieces harvested here, the thickest and smoothest cork, will be punched into wine corks for some of the finest vintages from the best wineries on earth. The other pieces will provide granules for the more workaday wines – the type I'm more familiar with. It's as if globalisation never happened: instead of outsourced, sub-contracted workers slaving away for a pittance, here we have local men, happily swinging axes in the depths of the forest near to where their families have often lived for generations.

Pereira and his colleagues can harvest 10 large trees or 20-30 medium-sized trees in a day. I ask if the workers are unionised (a standard ethical-sounding question when you're standing idly by trying to justify people working very hard). The boss laughs: "These guys don't really need a union. Their jobs are well paid." For each day they will earn around €120. In a rural area of big unemployment that's three months of big bucks that sustains them through smaller repair and farming jobs during the rest of the year.

The cork oak's ecological contribution is just as munificent. The trees naturally occur in mixed-plant woodlands – the Rolls-Royce of forestry – and their root systems are excellent water regulators in this semi-arid landscape. They also anchor the soil and offer shade to the biodiverse species. According to a WWF report, the remaining 108,000 hectares of Portuguese cork oak forests are instrumental in preventing this region from turning into a dustbowl. Each tree sustains 100 species; it is pretty much the only place in which the rare short-toed eagle and extremely rare Iberian lynx will consider living. It is a living, breathing European ecosystem and effective carbon sink (conservative estimates say the cork forests sequester 10m tonnes of CO 2 every year) and really, how many of these do we have knocking about?

But this magic forest is in the grip of an acrimonious and long-running debate. It rests on a consumer decision to which most of us will have given little thought: last time you bought a bottle of wine did it have a natural cork, a plastic stopper or a screw cap (increasingly likely from a UK supermarket, the biggest retailers of wine with 75% of the wine retail market)? Did you even notice?

It might seem a prosaic choice, but when you include the cork industry, the environmentalists, the screw cap "innovators", the wine writers and makers, the debate takes on a tone of operatic intensity. Natural cork has seen its pre-eminence as a wine bottle stopper kicked into touch by synthetic upstarts including plastic corks and screw caps. In the past 15 years the market share of "nature's nearly perfect product", as American writer George Taber has described it, has declined from 90% to just over 70%. The value of cork is half what it was a decade ago, there are more than 30 synthetic cork producers worldwide and 85% of Australian wine and 45% of New Zealand's are now under screw caps.

It would be premature to pronounce the death of the wine cork, yet it has already been done. In 2002 a solemn trumpet solo at New York's Grand Central Station announced the arrival of a hearse, from which funeral directors lifted a casket containing "Thierry Bouchon" – a dummy made of cork (tire-bouchon is French for corkscrew). The world-renowned wine writer Jancis Robinson delivered a eulogy which began, "Oh Cork. Oh Cork. Oh Corky, Corky Cork. How we shall miss thy cylindrical barky majesty…" The man behind this elaborate stunt – a pastiche of a scene from Joris-Karl Huysmans's late-19th-century novel A Rebours (Against the Grain) – was Randall Grahm, founder of California's Bonny Doon winery. "I didn't quite anticipate it would mark such a flash point," says Grahm.

The Portuguese cork industry was not laughing. It's unlikely most witnesses of the stunt or readers of the widespread press coverage got Grahm's obscure literary joke, but they did get that he'd put 80,000 cases of his Cai de Solo wine in screw-capped bottles. This was the largest US bottling to date of a fine wine – before this, screw-capped fine wine was an oxymoron. As Robinson announced in the course of the eulogy: "The great big supertanker SS Screw Cap has set sail and there will be no turning back."

There had been serious provocation. The wine industry had one very specific enemy: cork taint. "It was completely frustration with cork taint that led me, in 1996, to work with synthetic closures for a few of our wines," Grahm tells me. "What began out of frustration – the unreliability of cork and the non-performance of synthetic closures – led me to screw caps. Having used them now for almost 10 years, I have been so pleased with how they work that it is very difficult for me to imagine going back to cork."

Cork taint is the tragic (at least to an oenophile) point at which a cork becomes contaminated with 2,4,6-trichloroanisole, or TCA. Discovered by a Swiss researcher in 1981 who detected TCA in a $400 bottle of wine, it's described as smelling like a cross between mouldy newspapers and old socks. Most of us can't detect it until it goes above 6ppt (parts per trillion), but expert noses are thought to sense it below 2ppt.

However, even the top olfactory glands aren't infallible. A team of professional sniffers can apparently only sniff 200 corks in one siting, still needing a break every 50 corks or so. As "synthetic closures" made a play for the hearts and minds (and noses) of the wineries, experts and finally consumers, some 10-25% of cork was rumoured to be tainted. But the "fat and arrogant" (Taber again) monopolistic Portuguese cork industry that produced 3bn wine stoppers every year did itself no favours. According to Robinson: "If the cork industry had taken the problem seriously from the start and had cultivated better relations with the wine industry, cleaning up its act years before it did, it would not have lost so much business."

"It is true we made it easy for the screw caps," says Claudio de Jesus, dolefully. The 46-year-old marketing director of Amorim, in Portugal – a leading global cork producer – is one of the new guard. In 2001 he left his job as a Wall Street trader to return to his native Portugal and wrote to Amorim offering to help to engineer a renaissance.

As luck would have it his arrival coincided with António Amorim, the fourth generation of the family firm, becoming CEO. He had a different attitude. "The industry had made life too cosy for the screw cap," says De Jesus. "We paid a heavy price. The cork industry had a credibility problem and there was only one way to repair it: tell the market what you're doing and ask it to come and check."

The two set out to eradicate TCA in cork. They spent big money on chambers to boil and wash cork, on a laboratory with gas chromatography machines – the same as those used in the forensic TV drama CSI – to trace and find any TCA offenders, and became intent on removing the taint of cork taint. They seem to have had some success; the oenologist Christopher Butzke, who was once very down on cork, now says it has achieved a performance rate of 99% and that TCA is no longer a big issue for either wine makers or consumers.

De Jesus holds a cork up to the light between his finger and thumb. It's one of the upscale ones, punched from a single piece of cork that will end up in a bottle of fine wine. He's moved on from extolling the new scientific precision of cork production to the innate and superior quality of nature. "Whether it's beans, a horse, a cork – you recognise quality in nature, right?"

I wonder why they don't secure the future of the forests by pushing the diversified uses of cork as opposed to battling for wine cork business – Stella McCartney makes shoes from it, there's a guy doing cycle helmets, BP even took a look at it during the early days of the Fresh Kills crisis to see if there were ways of expanding its potential to suck up disastrous oil spills. "Cork has many applications," says De Jesus. "It's an amazing substance, but wine corks are what we do. Each cork oak stopper has 800m breathing cells, and an elastic memory that tries to expand. Man-made technology cannot replicate that." His lip curls slightly. "Château Margaux became great with a cork in it."

However the British consumer seems to have developed a taste for a cork-free lifestyle. Tesco led the way: 40% of all Tesco-sold wines are now screw caps and you can add to that another 15-20% using synthetic or "technical corks" (ie man-made). Simon Waller of Supreme Corq, one of the biggest producers of synthetic corks, tells me that "there has never been a better time to be a wine consumer: techniques shared, best practice, screw-cap technology and 10% over-supply meaning low prices."

I suppose we could drink and be merry, but what about those forests? "Increasingly we are taking account of environmental issues in all our purchasing decisions," says Andy Gale, technical manager of Tesco beers, wines and spirits. "But cork, despite the improvements made, is still an imperfect closure."

Jancis Robinson confesses to being "probably more of a nag about sustainability than most wine writers, having campaigned against heavy bottles [arguing their excess materials and transport costs are far from eco-friendly] and certainly this argument is for me one of the most compelling in favour of natural cork." But even she adds: "It never did make sense to have wine the only product in supermarkets that needed a special implement to open. I can't see mass-market consumers returning to corkscrews for the sake of the Alentejo ecosystem."

That's a shame. The 2010 cork oak harvest has now come to an end. There's a track at Herdade Dos Fidalgos where the future is viscerally played out. On one side are the cork oaks that take 80 years to reach their first harvest, their canopies stretching over smaller plants. On the other side there's a fast-growing eucalyptus plantation presiding over some very dry soil. The eucalyptus will be ready to be sold for the voracious pulp and paper market in a matter of months. If the market drops further for cork, the decision for the landowner becomes a no-brainer. They plant fast-growing eucalyptus, ecosystem be damned. Common-sense sustainability dictates that there's a unique and relatively local ecosystem here that needs our support. Besides, the sound of a real cork leaving the bottle is a rare bacchanalian way to do the right thing.

To cap it all: the options



Natural cork: Cork has more than 400 years' experience in stopping wine bottles but it is also charged with spoiling 3-5% of global wine. Spanish law now dictates that wineries in 11 regions must use natural cork to receive a DO (Denominacion de Origen) quality status. This won't do much to counter charges of a southern European monopoly.

Screw cap: Once the surest way to get yourself barred from the dinner-party circuit, screw-caps are now billed as the solution to both cork taint and the less-technical issue of "where's the bloody corkscrew?". Guala Closures, one of the world's biggest manufacturers, claims sales are growing at half a billion a year, and screw-caps are getting clever with plastic filters and layers to deliver oxygen to maturing wines.

The plastic stopper: Entrepreneur Dennis Burns, a producer of pro-tech hockey helmets in the US, decided to use a similar polyethylene composite to make a synthetic wine "cork" with no chance of taint. Burns's Supreme Corq is one of the biggest of the 30 synthetic cork producers worldwide. Its rival, Nomacorc, produced 1.4m plastic corks last year – enough to circle the earth 1.33 times. The synthetic boys don't buy cork's ecological superiority: "Many are just cork granules and dust bonded with solvents," says Simon Waller of Supreme Corq. "They are no more biodegradable than our product."

The zork: It's new(ish) and loud and hails from New Zealand. The Zork (a hybrid of "zero" and "cork") is a low-density plastic closure that boasts sophisticated tamper-evident design and inner foil oxygen barriers. The innovation will need to be more sophisticated than the colour – bright pink or red, which may put off serious wine drinkers. It's gaining popularity in US wine bars for by-the-glass fizz.