Scientists, politicians and activists expect the first commercially cultivated GM crops to be planted in England in 2017 after an EU vote for new GM crop rules last week, but the battle for biotechnology is far from done.

GM serves as a proxy and arena for a dizzying range of debates in the EU splitting industry and environmentalists. These cover trade deals, agricultural herbicide use, subsidiarity (dealing with social issues at a local level), evidence-based science and the precautionary principle.

With an average GM crop costing between $200m-$300m to bring to market, and potential returns that run into billions, lobbyists on all sides are sharpening their pencils in the corridors of Brussels.

The first item on their agenda may be a commission review of GM authorisation rules expected by May. The EU’s president, Jean-Claude Juncker, ordered the rethink into ways that GM authorisations could be blocked after states criticised the current need for a qualified majority of EU leaders at Council meetings.

The health and food safety commissioner, Vytenis Anriukaitis, has already alarmed biotech industries by suggesting that current legislation creates “conflict” because it ignores sovereignty and subsidiarity.

There are also trade issues, with the US viewing EU regulation on GM as a trade barrier. Negotiators have exerted pressure for a freer regime in talks on the Transatlantic free trade deal known as TTIP, and the EU’s agriculture commissioner, Phil Hogan, felt obliged to pledge last week that Europe would continue to label GM products under any future TTIP deal.

The new GM rules which MEPs voted in favour of last week should come into force this spring, but they cut two ways. They allow countries to grow GM crops that have first been authorised by the European Food Safety Authority (Efsa), but enable states to ban single GM crops on the basis of evidence that does not contradict an Efsa opinion.

The details of how new biotech regimes in the EU will be constructed, enforced – and, crucially, how liability will be allocated within them - remain sketchy, with questions of cross-border protection to the fore.

“If, as expected, the UK government uses this new legislation to approve more GM then there needs to be adequate separation distances between GM and non GM crops to protect the environment from contamination,” the Green MEP Keith Taylor told the Guardian.

The issue could spark rows between countries – and within the UK too, as England is far keener on GM cultivation than Scotland or Wales.

GM-sceptic states such as France and Hungary are likely to prohibit cultivation on their land, but environmentalists expect some of the 19 countries which rejected authorisation of GM Maize 1507 last February to wilt before the high bar set for banning GM produce under the new rules.

Cross-pollination from GM crops can take place through seeds carried by the wind, animals, vehicles or people, as well as from storage silos that have not been scrubbed clean.

Efsa recommends buffer zones and rotation schemes to confine GM crops to cultivation fields, but campaigners view the 200 metres separation distance favoured by the UK as inadequate, proposing buffer zones measured in kilometres instead.

It is unclear when the eight crops in the regulatory pipeline may receive their final green lights. Those closest to market, such as Dupont Pioneer’s ‘Supercorn’ Maize 1507, have insect-resistant qualities not relevant to conditions in the UK. Greenpeace says it expects pro-GM English farmers to make a point by planting them in 2016 anyway.

The chair of Efsa’s GMO panel, Professor Joe Perry said that he thought another herbicide-resistance Dupont GM Maize, known as 59122 would be “quite appropriate for UK”. It is at an advanced stage of its regulatory passage.

“There would be a lot of interest among UK farmers in growing it, because maize is quite vulnerable when it is just coming out of the ground,” he told the Guardian.

Much of the GM debate involves the herbicide resistant nature of such crops – and the licensed toxins that agribusiness include in their GM packages.

“If you use these herbicides too much or without proper management, the weeds you are trying to kill can evolve a resistance – a bit like antibiotic resistance,” Perry said. “The herbicide-tolerant GM systems are also so efficient at killing weeds that they can lead to a reduction in biodiversity – in weeds and the insects that live among them - and therefore a reduction in food for farmland birds.”

The question of whether GM crops encourage plant-resistance and the over-use of toxic herbicides such as glyphosate and glufosinate has been a hotter potato than BASF’s GM Amflora spud (which the EU authorised, and was subsequently banned by the EU General Court).

Glufosinate is due to be prohibited across the EU from 2017, although GM Maize 59122 has been designed to tolerate it.

The EU’s chief scientific adviser, Ann Glover, drew ire from environmentalists when she said that the EU’s long-standing precautionary principle was “no longer relevant” for GM, and that it would be “unethical” not to use such biotech produce when other approaches had failed, because of the role that GM could play in alleviating global hunger.

Glover will be leaving her position at the end of this month, partly because of the fallout from her clashes with green NGOs over GM and endocrine disrupting chemicals. In a sign of the stakes at play, British Conservative MEPs last week threatened a spat with the commission if her chief scientific adviser position was not maintained, after she has gone.