One of the foremost microbiologists of his generation, Sir Howard Dalton was appointed chief scientific adviser to the Department for Environment, Food and Rural Affairs (Defra) in March 2002 in the hope that he would bring scientific rigour — and much needed credibility — to the department.

Defra had been created after the perceived failure of the Ministry of Agriculture, Fisheries and Food, still tainted by the BSE crisis of a decade earlier, to deal effectively with the foot-and-mouth outbreak of 2001. Dalton found the BSE crisis particularly disappointing, a case where PR and science had broken down: “There was a real issue over public understanding of the way the science was being used. There was a lot of sensible advice . . . but how it was being picked up and used was another issue.” To some extent Dalton had the same problem: while he made sure to channel the best available advice, often complex and contradictory, to the Government, the policy it shaped was often rather more simplistic.

Dalton was born in New Malden, Surrey, the son of a lorry driver. Showing a precocious talent for science, he won a place at Raynes Park Grammar School and went on to Queen Elizabeth College at London University to read microbiology. He took his doctorate at the University of Sussex. He then worked as a post-doctoral fellow,at Purdue University, Indiana, 1968-70. There, to avoid any possible risk that he might be drafted for Vietnam, he paid the Universal Life Church of California $25 to ordain him. In 1970 he returned to the University of Sussex, where he worked on methane monooxygenase — an enzyme that converts methane gas into methanol.

In 1973 he became a lecturer at the University of Warwick, and continued work on the pathways used by the bacteria around plant roots to fix atmospheric nitrogen in the soil. He studied the metabolism of bacteria growing in unusual positions, using organisms isolated from the hot spring waters of Bath, high in metallic elements and methane. From this developed his interest in biotransformation; in particular, ways of harnessing the power of biological and biochemical pathways and using them in industrial processes. He was appointed Professor of Microbiology in 1983.

At Defra, Dalton ensured that the department had access to a broad pool of virologists and oversaw a forward vaccination centre that could be ready to act three days after an animal health scare. He formulated a policy to cope with bluetongue outbreaks and directed work to find an effective preventive vaccine, although slaughter remained the department’s primary response.

Dalton’s advice was held dear by Tony Blair, who shared his feelings on genetically modified foods. Although Dalton initially felt that the country was being steamrollered into accepting large-scale trials of GM crops without a calm assessment of the impact, he came to see public hostility as a blow to British commercial science, which had been the world leader in this field. Always emphasising that GM crops were never going to be “wholly good nor wholly bad”, he insisted that Britain would one day grow GM crops in a properly controlled environment, and hoped that this could be as early as 2009. In the spring of 2005 Dalton joined Defra’s Committee on Radioactive Waste Management, which was suffering the fallout of wrangles and resignation over what to do with Britain’s nuclear waste. Again his remit was to apply proper science — and human reasoning — to a deeply divisive and politicised subject.

Dalton was idealistic and had a talent for making complex ideas seem straightforward, but the science he loved to see “presented in a forum in which it is open to challenge” was subject to a government department increasingly sensitive to such challenge. This paradox could never be fully resolved. Dalton’s work for Defra was rarely regarded as pure science by the media or by a public steeped in cynicism after a decade of “spin”. Each successive BSE scare was seized upon, quite unfairly, as evidence that Defra’s science was as flawed as ever, and the H5N1 strain of bird flu, which reached the Netherlands in 2003, required him to advise and reassure the public repeatedly.

This backfired in October 2005 during a technical briefing that concerned a parrot that had died in quarantine. It was assumed to have contracted the virus from some Taiwanese mynah birds, a “working hypothesis” that angered the Taiwan Government. When it transpired that there might be two dead parrots, and that Defra was unsure which had died of H5N1, the episode seemed even more Pythonesque. Neither Dalton nor the Chief Vet, Debby Reynolds, could tell their audience of Conservative front-benchers which clade, or sub-type, of the H5N1 virus family was responsible — an important point since the type deadly to humans had never been found in Taiwan. Such confusion reminded newspapers of the case of Georgina Downs, whose case against the Government for pesticide spraying near her home in Chichester was turned down by the Minister for Rural Affairs after taking advice from Dalton, although Dalton said in August 2004 that Downs’s evidence had never been passed on to him.

Climate change was a perennial theme during his five years at Defra. In January 2006 he went with the British Antarctic Survey to inspect first-hand the effects of climate change on the ice sheets. He concluded that: “There is no doubt on a global level we’re not doing enough to tackle climate change.” He insisted, however, that he was hopeful, and that “science and technology can help us to curb our greenhouse gas emissions and still allow us to live in a modern society”.

Dalton did not go along with all government ideas on the environment and green energy, some of which he regarded as faddist and impractical. When asked about plans for wind turbines, which he had always regarded as too expensive, he said: “Do we really want windmills all over the countryside and covering swaths of the ocean? I don’t think so. They are a hell of a bloody eyesore.” Dalton was unafraid of controversy and, a lifelong believer in the potential of biofuels, gave his backing to David Miliband’s plans, as Secretary of State for Environment, Food and Rural Affairs, for turning over land to fuel crops. This angered other scientists, particularly Professor Roland Clift, the founding director of the Centre for Environmental Strategy, who told a seminar of the Royal Academy of Engineering that the whole idea was a “scam” that would create more greenhouse gases than it removed.

Dalton remained committed to Warwick university for more than 30 years, giving his name to a research group, and to the cause of proper funding for scientific research. He was elected a Fellow of the Royal Society in 1993, and was president of the Society for General Microbiology, 1997-2000. He was awarded the Royal Society Leeuwenhoek medal lecture for 2000, and was knighted in the 2007 New Year’s Honours List.

With his wife, Kira, whom he married in 1971, he was in the process of building a medical centre in The Gambia, and innoculating its children against malaria. The couple had helped to construct six schools in the country.

His great passion was for real tennis, and he died during a game on the courts at Leamington Spa, Warwickshire. He had long-standing arterial problems, and had suffered a heart attack on the courts on his 48th birthday. His wife survives him, along with their son and daughter and two stepsons from his wife’s previous marriage.

Professor Sir Howard Dalton, FRS, chief scientific adviser, Defra, 2002-07, was born on February 8, 1944. He died on January 12, 2008, aged 63