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

有一种令人回味的气体，称为二甲基硫醚-简称DMS-我们大多数人都闻到过，因为它是海滨气味的一种成分。但它远比这重要得多。海洋微生物每年制造约3亿吨，其中约10%逃逸到大气中。这不仅让人回想起在海边的日子，而且DMS在空气中被化学修饰成化合物，导致海洋上空形成云层，影响天气和气候。而且，当下雨时，这些化合物回到地球，这是基本元素硫全球循环的重要一步。还有一件事即使是微量的二甲基硫，也会吸引不同的海洋动物--鱼类、企鹅和微小的甲壳类动物都以最快的速度向它游去、飞去或划动。原因是他们知道哪里有DMS，哪里就有食物。这是因为DMS是生化过程的副产品，当不同的微生物吞噬另一种含硫分子时，会发生这种副产品，它有一个可笑的长名字-二甲基磺基丙酸酯。这种DMSP是由海洋中的微小浮游生物、海藻和极少数生活在海边的陆地植物产生的。在UEA，我们发现了微生物如何制造DMS，在沃里克，我们研究了其他海洋微生物进一步转化这种气体的方法。我们使用分子生物学，基因克隆和DNA测序来识别一系列微生物中让它们进行这些反应的基因。对于这两个过程，我们发现一些非常意想不到的生物可以制造或分解DMS，并且它们可以以完全不同和令人惊讶的方式做到这一点。大多数研究都是在实验室中培养的纯化菌株上进行的。这使我们能够识别基因及其各自的功能，但它不能告诉我们哪些是最重要的途径，哪些微生物是自然环境中的关键角色。这是因为大部分生活在自然界中的细菌从未被培养过。幸运的是，最近的一些技术让我们可以研究这些“困难”的微生物。Murrell教授发明的一个巧妙的技巧是，用一种化学性质与正常底物相同但实际上更重的底物来喂养自然界的微生物种群。因此，在我们的例子中，我们将使用DMS和DMSP的形式，其中碳原子的原子量为13，而不是更传统的12。当微生物吸收这样一种重分子时，重碳被结合到它的分子中，包括DNA。通过从轻形式中纯化这种重DNA并通过寻找基因中的特征序列，可以鉴定使用DMS或DMSP的微生物和真菌，并可以推断它们这样做的机制。我们将在北诺福克盐沼的泥上做这些实验。这些是草米草的家，米草是为数不多的制造DMSP的陆地植物之一。这种植物也很重要，因为它已经被人类传播到世界各地，现在是世界各地许多海岸的严重害虫，杀死了许多本地物种。毫不奇怪，在米草的根部周围有很多DMSP，它们充满了消耗或制造DMS的细菌和真菌。因此，我们将对这些微生物进行普查，其中一些可能是新的科学。我们的研究结果应该与二甲硫醚和二甲硫醚悬浮物质的其他热点有关，如珊瑚和海洋中浮游生物的大量繁殖。尽管微生物的数量非常少，但它们对环境的影响比我们大多数人意识到的要大。鉴于二甲基硫醚气体的环境后果，必须了解影响其产生和销毁的细菌和真菌类型以及涉及各种潜在途径中的哪一种。这可能有助于我们模拟气候变化等环境变化如何改变这些过程的平衡。

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.