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

有一种叫二甲基硫化物的气体，简称DMS，我们大多数人都闻到了，因为它是海边气味的一种成分。但它远比这重要得多。每年约有3亿吨海洋微生物产生，其中约10%逃逸到大气中。这不仅唤起了人们对海边日子的回忆，而且DMS在空气中被化学修饰为导致海洋上空形成云的化合物，从而影响天气和气候。而且，当下雨时，这些化合物会返回地球，这是基本元素硫在全球循环中的重要一步。还有一件事。即使数量很少，DMS也会吸引不同的海洋动物--鱼、企鹅和微小的甲壳类动物都会以最快的速度游、飞或划向它。原因是他们知道哪里有DMS，哪里就有食物。这是因为DMS是不同微生物吞噬另一种含硫分子时产生的生化过程的副产品，这种分子的名字长得可笑--二甲基磺酸丙酸酯。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，数量惊人。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式。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的基因，这些基因使它们能够进行这些反应。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，它们可以以完全不同的、令人惊讶的方式做到这一点。大多数这些研究都是在我们实验室培养的纯化菌株上进行的。这可以让我们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参与者。这是因为生活在自然界中的绝大多数细菌从未被培养过。幸运的是，一些非常新的技术让我们能够研究这些“困难的”微生物。默雷尔教授发明了一个巧妙的技巧，就是用一种与正常底物化学成分相同的底物来喂养自然微生物群体，但从字面上看，它更重。因此，在我们的研究中，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。当微生物消化如此重的分子时，重碳被结合到它的分子中，包括DNA。通过从轻形式中提纯这种重DNA并寻找基因中的签名序列，可以识别使用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浆上做这些实验。这些是草本植物斯巴达纳的家园，它是为数不多的产生DMSP的陆地植物之一。这种植物也很重要，因为它已经通过人类的手传播到世界各地，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。不足为奇的是，大米草根周围有大量的DMSP，其中充满了消耗或制造DMS的细菌和真菌。因此，我们将对这些微生物进行普查，其中一些可能是科学上新发现的。我们的发现应该与DMS和DMSP的其他热点有关，例如珊瑚和海洋中浮游生物的大量繁殖。尽管微生物的数量很少，但它们对环境的影响比我们大多数人意识到的要大得多。考虑到DMS气体的环境后果，重要的是了解哪些类型的细菌和真菌影响其生产和破坏，以及涉及到各种潜在途径中的哪些。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.