Do novel acidophilic archaeal ammonia oxidisers solve the paradox of nitrification in acid soils?

硝化作用是氮在整个地球上循环的一个重要过程。该过程由两组微生物将氨转化为硝酸盐组成。氨氧化剂将氨转化为亚硝酸盐，然后亚硝酸盐氧化剂将氨转化为硝酸盐。虽然硝化作用对某些植物有益，但也会产生有害的后果。铵可以保留在土壤中，但在转化为硝酸盐后，它从土壤中浸出，污染可用于供应饮用水的地下水。它还会造成大气污染，因为氨氧化会产生一氧化二氮，一种强效的温室气体，也会破坏平流层臭氧。在实验室中培养的氨氧化剂都不能在低pH下生长，但硝化作用发生在酸性土壤中，实际上有证据表明，在低pH下，硝化作用的速率略高。世界上大约30%的土壤是酸性的（pH小于5.5），主要是由于微生物的活动，包括硝化菌的活动。它们代表了广泛的自然和管理栖息地，包括林业、农业和草原。因此，酸性土壤具有重要的环境和经济意义，了解这些土壤中导致硝化作用的机制是很重要的。已经提出了几种解释来解释低pH下氨氧化的原因，但没有一个能提供一个完整的解释，而且所有的解释都难以在土壤中证明。传统上，最重要的土壤氨氧化剂被认为是细菌，但我们现在知道，另一组丰富的土壤生物，古细菌，可以氧化氨。古细菌是古细菌中的一组，是与细菌不同的微生物生命领域。尽管它们在很多方面与细菌相似，但它们在进化上是不同的，并且以前被认为仅限于“极端”环境。我们最近获得的证据表明，两组太古菌氨氧化剂仅限于酸性土壤，表明适应在低pH下生长。然后，我们获得了一种生物的培养物，亚硝索talea devanaterra，它是其中一组的代表，并表明它是一种严格的，嗜酸氨氧化剂，只能在pH范围4 - 5.5内生长。在这样的pH值下，氨的可用性极低，因为大多数会电离成铵。因此，N. devanaterra必须在低pH值下具有独特的氨氧化机制，使其能够在酸性土壤中占据这个不可能的环境生态位。因此，该项目的一个主要目标将是确定N. devanaterra在低ph下生长的机制。我们还旨在获得在我们早期研究中确定的第二组嗜酸古细菌氨氧化剂的培养，并确定两组是否利用相同的机制。潜在的机制将通过测序和分析这两个菌株的所有基因，并确定哪些基因在低ph下生长时表达。这些机制将在实验室生长实验中进行测试。第二个主要目的是确定这些生物在酸性土壤的硝化作用中是否真的很重要。我们将使用土壤实验室系统（微生物）来确定它们在一系列酸性土壤中的生长能力，并确定它们的生长是否与氨氧化有关。我们将操纵土壤pH值，以确定pH值对其生长和活性的影响，我们还将确定在实验室培养中解释低pH生长的生理机制是否可以解释酸性土壤的生长。

Nitrification is an essential process in the cycling of nitrogen throughout the planet. The process consists of the conversion of ammonia to nitrate by two groups of microorganisms. Ammonia oxidisers convert ammonia to nitrite and this is then converted to nitrate by nitrite oxidisers. Although beneficial to some plants, nitrification can have deleterious consequences. Ammonium can be retained in soil but, after conversion to nitrate, it is leached from soil, polluting groundwaters that may be used to supply drinking water. It also contributes to atmospheric pollution, as ammonia oxidation is accompanied by production of nitrous oxide, a potent greenhouse gas that also contributes to destruction of stratospheric ozone. None of the ammonia oxidisers that have been grown in the laboratory can grow at low pH, but nitrification occurs in acid soils and there is actually evidence that rates are slightly greater at low pH. Approximately 30% of the world's soils are acidic (pH less than 5.5), mainly due to microbial activity, including that of nitrifiers. They represent a wide range of natural and managed habitats including forestry, agriculture and grasslands. Acid soils are therefore of great environmental and economic importance and it is important that we understand the mechanisms leading to nitrification in these soils. Several explanations have been proposed to explain ammonia oxidation at low pH, but none provides a full explanation and all are difficult to demonstrate in soil. Traditionally, the most important soil ammonia oxidisers were thought to be bacteria but we now know that the thaumarchaea, another group of abundant soil organisms, can oxidise ammonia. Thaumarchaea are a group within the archaea, a domain of microbial life distinct from the bacteria. Although they resemble bacteria in many ways, they are evolutionarily distinct and were previously thought to be restricted to 'extreme' environments. We recently obtained evidence that two groups of thaumarchaeal ammonia oxidisers are restricted to acid soils, suggesting adaptation to growth at low pH. We then obtained a culture of an organism, Nitrosotalea devanaterra, which is representative of one of the groups and showed it to be a strict, acidophilic ammonia oxidiser that grows only within the pH range 4 - 5.5. At these pH values, ammonia availability will be extremely low, because most will be ionised to ammonium. N. devanaterra must therefore possess unique mechanisms for ammonia oxidation at low pH that enable it to occupy this improbable environmental niche in acid soils. A major aim of the project will therefore be to determine the mechanism by which N. devanaterra grows at low pH. We also aim to obtain a culture of the second group of acidophilic thaumarchaeal ammonia oxidisers, identified in our earlier studies, and to determine whether both groups utilise the same mechanism. Potential mechanisms will be investigated by sequencing and analysing all of the genes in both strains and identifying which genes are expressed when they are growing at low pH. These mechanisms will then be tested in laboratory growth experiments.The second major aim is to determine whether these organisms are actually important in nitrification in acid soils. We will use soil laboratory systems (microcosms) to determine their ability to grow in a range of acid soils and determine whether their growth is associated with ammonia oxidation. We will manipulate soil pH, to determine the influence of pH on their growth and activity, and we will also determine whether the physiological mechanisms that explain growth at low pH in laboratory culture explain growth in acid soils.