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

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.

The aim of the proposed research is to understand the mechanisms of ammonia oxidation by archaea in natural acidic soils. The findings will therefore impact significantly on our ability to monitor and maintain soil fertility and health and to assess the importance of atmospheric and groundwater pollution derived from acid soils. The work is therefore of direct relevance to stakeholders and policy makers with responsibility for responding to and implementing the findings and recommendations of the EU Soil Framework Directive.

We are currently ignorant of the role or archaea (either direct or indirect) in production of the greenhouse gas nitrous oxide. Ammonia oxidising bacteria contribute significantly to emissions nitrous oxide, but due to a lack of cultivated soil strains, we have not been able to address their contribution in the soil environment. These studies will therefore determine the role of ammonia oxidising archaea in nitrous oxide production in acid soils but will also determine this potential in other soils and other ecosystems, informing estimates of global emissions by these organisms.

The findings also have potential environmental and economic relevance through greater understanding of nitrification in acid soils and the consequences of changes in land use and management strategies. We believe that archaea dominate nitrification processes in acid soils and therefore have a central role in the production of nitrate. They may therefore be involved in losses of N-based fertilisers which are considerable ($15.9 billion in 1999), contributing to nitrate production in managed systems and contributing to nitrate pollution. Greater knowledge of the role of archaea in acid soils is also required for an understanding nitrogen cycling in unmanaged systems, to predict the impact of atmospheric nitrogen deposition and mitigation strategies in both forest and non-forest ecosystems.

Who will benefit from this research?

As indicated above, major beneficiaries will be policy makers, legislators and regulators, including DEFRA, SEPA, the Environment Agency, the Forestry Commission regional and national government and the EU. It will both inform on the significance and mechanisms controlling nitrification in acid soils and also improve methodology for assessing the significance of bacterial and archaeal diversity and abundance on this process, increasing reliability and confidence in monitoring techniques.

The research will also benefit scientists with research areas focused on nitrogen cycling, including soil scientists and systems biologists modelling emissions of nitrous oxide and its contribution to climate change. The work will also be of direct relevance to those concerned with inorganic nitrogen pollution of natural ecosystems (nitrogen deposition and acidification) as well as pollution derived from managed soils (nitrous oxide emissions, eutrophication, nitrate pollution of water courses) from a regulatory and legislative perspective.

How will they benefit from this research?

This work will answer long-standing questions about which organisms are primarily responsible for nitrification in soils, particularly in acidic soils. Fundamentally, we aim to gain an understanding of their physiology, with regard to both nitrogen cycling in soil but also their metabolic diversity. The findings will improve mechanistic understanding of the drivers of nitrification in acid soils and our ability to predict nitrification rates and their response to environmental change. It will also improve methods for assessment of soil health in both natural soils and managed ecosystems, particularly their contribution to soil acidification, plant nutrition and toxicity, nitrogen fertiliser loss and nitrous oxide emissions. With specific reference to soils subject to nitrogen pollution, this research will be relevant to those attempting to understand the usefulness of land management strategies to counteract acidification.