NO-ONE can say commuters have not been taken fully into account in the development of a second Rail link between Oxford and London.

But not many could have predicted that it would be the commuting residents of Wolvercote Tunnel that could potentially derail the £130m scheme.

The risk of harm to bats and great crested newts resulted in a Government planning inspector refusing to recommend approval of the scheme last month.

And it led to Transport Secretary Justine Greening firing off letters to Chiltern Railways and Natural England urging them to resolve the problem and quickly.

The tunnel, it emerged, was used by numerous bat species including common and soprano pipistrelle, noctule, natterer’s, Daubenton’s, brown long-eared, and myotis bats.

The inspector was told during the public inquiry into the project that the tunnel was used for “swarming, foraging and as a temporary roost site.”

It also serves as a commuter route for the bats, which feed along the railway’s route through North Oxford.

The inspector was persuaded that more trains passing through the tunnel – which takes the Oxford to Bicester line under Wolvercote roundabout on the A40 – and at higher speeds would increase the risk of harm to the bats and see roosts in the tunnel “rendered unusable.”

So the Transport Secretary gave the rail company and the nature body until this week to agree on proposals to minimise dangers for the bats and to mitigate any harm the scheme would cause to great crested newts in a habitat nearby.

Bats, newts and human commuters should all feel some relief. For the deadline has been met, with the threat to Chiltern’s proposed Oxford-Bicester-London Marylebone service apparently lifted.

Ms Greening is now expected to give her formal consent to the scheme early next year.

As reported in Tuesday’s Oxford Mail, Chiltern Railways and Natural England have told the Government that they are close to solving the bat problem to get the long awaited scheme back on track.

Chiltern Railways spokesman Emma Gascoigne said: “The Secretary of State gave us until Tuesday to demonstrate that we are likely to reach a conclusion in our negotiations. That is something which we have done.”

Natural England spokesman Melissa Gill said: “Natural England met Chiltern Railways and agreed a way forward in respect of the outstanding issues surrounding bats in the Wolvercote tunnel.”

If Ms Greening signals that the way is now clear for work to start, Chiltern will suspend train services between Oxford and Bicester Town next year to begin work to upgrade the route and build a connection from Bicester Town station to the Chiltern main line.

The first trains could be running to London Marylebone in 2013-14, providing competition for First Great Western’s existing services between Oxford and London Paddington.

And from 2017 they are set to be joined by services between Oxford, Milton Keynes and Bedford, following Government backing for the East West Rail project in Chancellor George Osborne’s Autumn Statement a fortnight ago, which will revive a route closed to passenger trains in the 1960s.

Natural England said that if a transport works order is issued by Ms Greening, a ground-breaking lighting system will be included as a key part of the plan to protect the bats.

This will effectively give the Wolvercote bats their own traffic lights to warn them about approaching trains. It will be the first such system to be installed in the UK in a railway tunnel.

A trial took place at Wolvercote in August to see whether triggering lights inside the tunnel when a train is on the way would alert the bats and encourage them to fly out or move to safer roosts inside.

A high proportion of bats are light-sensitive and avoid lit areas. But much depends on bats being able to associate the lights coming on with the arrival of a train.

This system would certainly maintain Oxfordshire’s tradition of ensuring the wellbeing of bats.

Horspath Tunnel, which used to carry the Oxford to Thame and Princes Risborough railway line through the eastern end of Shotover Hill, was turned into a bat hibernaculum, or winter hibernating refuge, nearly a decade ago, after it had stood disused for almost 40 years.