Making and breaking DMS by salt marsh microbes - populations and pathways, revealed by stable isotope probing and molecular techniques

Lead Research Organisation: University of Warwick
Department Name: Warwick HRI

Abstract

There is an evocative gas, called dimethyl sulfide - DMS for short - which most of us have smelled, since it is a component of the smell of the seaside. But it is far more important than that. Around 300 million tons are made each year by marine microbes, around 10% of which escapes into the atmosphere. Not only does this bring back memories of days by the sea, but DMS is chemically modified in the air to compounds that cause clouds to form over the oceans, affecting weather and climate. And, when it rains, these compounds come back to earth in a major step in the global circulation of the essential element sulfur. And one more thing. Even in tiny amounts, DMS attracts different marine animals - fish, penguins and tiny crustaceans all swim, fly or paddle towards it as fast as they can. The reason is that they know that where there is DMS there is food. This is because DMS is a by-product of biochemical processes that occur when different microbes devour another sulfur-containing molecule, with a ridiculously long name - dimethylsulfoniopropionate. This DMSP is made in prodigious amounts by tiny plankton organisms in the oceans, by seaweeds and by a very few land plants that live by the sea. At UEA, we discovered how microbes make the DMS and in Warwick, the ways in which other marine microbes can further transform this gas are studied. We use molecular biology, gene cloning and DNA sequencing to identify the genes in a whole range of microbes that let them undertake these reactions. For both processes, we found that some very unexpected organisms can make or can break down DMS and that they can do this in completely different and surprising ways. Most of these studies are on purified strains that we grow in the lab. This lets us identify the genes and their individual functions, but it does not tell us which are the most important pathways and which of the microbes are the key players in natural environments. This is because the great majority of bacteria that live 'out here' in the natural world have never been cultured. Luckily, some very recent techniques let us study such 'difficult' microbes. One neat trick, invented by Professor Murrell, is to feed natural populations of microbes with a version of the substrate that is chemically identical to the normal one but which is, literally, heavier. So, in our case, we will use forms of DMS and DMSP in which the carbon atoms have an atomic weight of 13, not the more conventional 12. When a microbe digests such a heavy molecule, the heavy carbon is incorporated into its molecules, including DNA. By purifying this heavy DNA from the light form and by looking for signature sequences in the genes, the microorganisms and fungi that used the DMS or the DMSP can be identified and the mechanisms by which they do so can be inferred. We will do these experiments on mud from the salt marshes of North Norfolk. These are home to the grass Spartina, one of the few land plants that makes DMSP. This plant is also important because it is has been spread by human hand across the world and is now a serious pest on many coasts all over the world, killing off many native species. Not surprisingly, there is a lot of DMSP around Spartina roots, which teem with bacteria and fungi that consume or make DMS. We will therefore conduct a census of these microbes, some of which may be new to science. Our findings should relate to other hotspots for DMS and DMSP, such as corals and the massive blooms of plankton in the oceans. Although very small, the sheer numbers of microbes mean that they affect our environment more than most of us realise. Given the environmental consequences of the DMS gas, it is important to know which types of bacteria and fungi that affect its production and destruction and which of the various potential pathways are involved. This may help us model how environmental changes such as climate change alter the balance of these processes.
 
Description 1. Identification of DMS and DMSP degrading bacteria in saltmarsh sediments using DNA and RNA stable isotope probing
2. characterisation of bacterial diversity in saltmarsh sediments in seasonal cycle using high throughput sequencing
3. discovery of plant phyllosphere of saltmarsh plants as an environmental compartment that exhibits high potential DMS degradation rates
4. Single cell isolation and genomic characterisation of single DMS degraders belonging to the Piscirickettsiales
Exploitation Route We are planning to exploring the role of phyllosphere bacteria in degradation of other relevant volatile compounds in saltmarsh environments. Clearly, the role of microbial communities in various compartments in saltmarshes and their role as a source and sink of volatiles of atmospheric relevance is currently not well understood and requires additional work in order to allow the saltmarsh system to be modelled adequately in terms of biogeochemical models.
Sectors Environment

 
Title Dimethylsulfide and dimethylsulfoniopropionate metagenomics data from stable isotope probing experiments with saltmarsh sediment samples from Stiffkey saltmarsh 
Description 12C and 13C fraction metagenomic sequence of dimethylsulfide and dimethylsulfoniopropionate stable isotope probing experiments with saltmarsh sediments; data have been submitted to EBI metagenomics portal 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact data are publicly available