Are bacteria or archaea the major players in nitrogen fertiliser loss in agricultural soils?

哪些微生物导致氮肥流失？氮是作物生产所需的主要肥料。在最近的过去，氮肥以无机形式添加到作物中，如铵盐。氨在硝化过程中被两组土壤微生物转化为硝酸盐：氨氧化剂将氨转化为亚硝酸盐，亚硝酸盐氧化剂将氨转化为亚硝酸盐。铵被保留在土壤中，但硝酸盐很容易被浸出，并在用于供应饮用水的地下水中积累到高污染水平。此外，氨氧化伴随着一氧化二氮的产生，一种强效的温室气体，它也是由硝酸盐的还原产生的。因此，硝化作用导致污染和氮肥的大量损失。氮肥的损失可以通过施用硝化抑制剂和无机肥料或使用释放氨缓慢的肥料（如堆肥肥料）来减少。直到最近，人们还认为最重要的土壤氨氧化剂是细菌。然而，这一观点被最近发现的属于另一个微生物领域的有机体——古细菌——所推翻，古细菌也能氧化氨。这些生物属于古细菌的一个亚群，crenarchaea，存在于所有土壤中，但从未在实验室中分离出来。因此，我们需要独立于培养的分子技术来评估它们的存在和重要性。这些技术表明，氨氧化古细菌通常比氨氧化细菌数量更多，而且似乎具有更大的活性。也有证据表明，它们可能比细菌更喜欢低浓度的氨。无机氮肥产生高浓度，因此，在使用有机肥料的可持续系统中，微生物氨氧化剂可能在硝化作用中发挥更大的作用。为了确定微生物氨氧化剂的重要性，我们将采用实地研究、微观实验和生理实验相结合的方法来解决四个目标。1. 测定细菌和古细菌氨氧化剂对氨浓度的相对反应。2. 测定不同肥料是否适合不同氨氧化剂群落。3. 细菌和古细菌对不同肥料转化的评价。4. 底土中微生物和细菌对氨氧化作用的测定。5. 微生物和细菌对硝化抑制剂相对敏感性的测定。我们将测定氨氧化细菌和crenarchaea的丰度和活性，在两个不同的场地，用无机氮肥或堆肥处理多年的土壤。分子技术将用于确定这两种微生物群的种群大小。amoA是氨氧化过程中的一个关键基因，编码部分氨单加氧酶蛋白，通过对其表达水平的量化来研究其活性。将利用从不同土壤中提取的细胞和在小型土壤微观环境中研究不同肥料和硝化抑制剂的影响。我们还将使用分子技术来确定氨氧化细菌或古细菌中的特定亚群是否受到氨浓度或硝化抑制剂的不同影响。这些发现将使农业、环境机构和工业的人们更加了解微生物在氮肥损失中的作用，以及不同微生物群对传统和可持续系统以及底土中硝化作用的影响。这些发现对研究生物多样性和生态系统功能之间的联系感兴趣的研究人员和环保主义者也很重要。

Which microorganisms are responsible for nitrogen fertiliser loss? Nitrogen is the major fertiliser required for crop production. In the recent past, nitrogen fertiliser has been added to crops in an inorganic form, as an ammonium salt. Ammonia is converted to nitrate by two groups of soil microorganisms in a process termed nitrification: ammonia oxidisers convert ammonia to nitrite, which is converted to nitrite by nitrite oxidisers. Ammonium is retained within the soil but nitrate is readily leached and can accumulate to high, polluting levels in groundwater used to supply drinking water. In addition, ammonia oxidation is accompanied by production of nitrous oxide, a potent greenhouse gas, which is also produced by reduction of nitrate. Nitrification therefore leads to pollution and to significant losses of applied nitrogen fertiliser. Nitrogen fertiliser loss can be reduced by application of nitrification inhibitors with inorganic fertilisers or by use of fertilisers which release ammonia slowly, such as composted manure. Until recently it was believed that the most important soil ammonia oxidisers were bacteria. However, this view was overturned by the recent discovery of organisms belonging to another microbial domain, the archaea, which can also oxidise ammonia. These organisms belong to a subgroup of archaea, the crenarchaea, which are present in all soils but which have never been isolated in the laboratory. We therefore require cultivation-independent, molecular techniques to assess their presence and importance. These techniques show that ammonia oxidising crenarchaea are usually more abundant than ammonia oxidising bacteria and also appear to have greater activity. There is also evidence that they may prefer lower ammonia concentrations than bacteria. Inorganic nitrogen fertilisers generate high concentrations and crenarchaeal ammonia oxidisers may therefore have a bigger role in nitrification in sustainable systems, using organic fertiliser. To determine the importance of crenarchaeal ammonia oxidisers, we will use a combination of field studies, microcosms and physiological experiments to address four objectives. 1. Determination of the relative responses of bacterial and crenarchaeal ammonia oxidisers to ammonia concentration. 2. Determination of whether different fertilisers select for different ammonia oxidiser communities. 3. Assessment of conversion of different fertilisers by bacteria and crenarchaea. 4. Determination of contributions of crenarchaea and bacterial to ammonia oxidation in subsoils. 5. Determination of relative sensitivities of crenarchaea and bacteria to nitrification inhibitors. We will determine the abundances and activities of ammonia oxidising bacteria and crenarchaea in two field sites, with contrasting soils, that have been treated for many years with either inorganic N fertiliser or composted manure. Molecular techniques will be used to determine the population sizes of the two microbial groups. Activity will be investigated by quantification of the levels of expression of amoA, a key gene in ammonia oxidation that encodes part of the protein ammonia monooxygenase. The influence of different fertilisers and of nitrification inhibitors will be investigated using cells extracted from the different soils and in small-scale soil microcosms. We will also use molecular techniques to determine whether particular subgroups within ammonia oxidising bacteria or archaea are influenced differently by ammonia concentration or by nitrification inhibitors. The findings will benefit those in agriculture, environmental agencies and industry by increasing understanding of the roles of microorganisms in nitrogen fertiliser loss and the impacts of different microbial groups on nitrification in traditional and sustainable systems and in subsoils. The findings will also be important to researchers and environmentalists interested in the links between biodiversity and ecosystem function.