The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers

AA was supported by a Natural Environmental Research Council grant (NE/L006286/1) and CGR by a Royal Society University Research Fellowship (UF150571).Peer reviewedPublisher PD

Differential sensitivity of ammonia oxidising archaea and bacteria to matric and osmotic potential

MOB was supported by a University of Aberdeen Elphinstone Scholarship and by TETFund through Adekunle Ajasin University Akungba (AAUA) Nigeria. CGR was funded by a Royal Society University Research Fellowship (UF150571) and CT by the Natural Environment Research Council (NERC, NE/L006286/1) and AXA Chair in Ecosystem Engineering and Microbial Ecology.Peer reviewedPostprin

Ammonia oxidation is not required for growth of Group 1.1c soil Thaumarchaeota

© FEMS 2015. FUNDING EBW is funded by Centre for Genome Enabled Biology and Medicine, University of Aberdeen.Peer reviewedPublisher PD

Oxygen preference of deeply-rooted mesophilic thaumarchaeota in forest soil

The Illumina sequencing was performed in the Centre for Genome-Enabled Biology and Medicine (CGEBM) (University of Aberdeen, UK). We would like to thank Noémie Hauss for her help with the sampling and incubations, the Erasmus program for supporting Noémie Hauss and Dr Tony Travis for his support on Linux. EBW was supported by a PhD studentship from the University of Aberdeen, by a Natural Environmental Research Council grant (NE/L006286/1) and CGR by a Royal Society University Research Fellowship (UF150571).Peer reviewedPublisher PD

Nitrous oxide production by ammonia oxidizers : Physiological diversity, niche differentiation and potential mitigation strategies

Funding Information: This work was financially supported by the AXA Research Fund (GWN), a Royal Society University Research Fellowship UF150571 (CGR) and all authors are members of the Nitrous Oxide Research Alliance (NORA), a Marie Skłodowska‐Curie ITN and research project under the EU's seventh framework programme (FP7).Peer reviewedPostprin

Genome Sequence of “Candidatus Nitrosocosmicus franklandus” C13, a Terrestrial Ammonia-Oxidizing Archaeon

“Candidatus Nitrosocosmicus franklandus” C13 is an ammonia-oxidizing archaeon (AOA) isolated from soil. Its complete genome is 2.84 Mb and possesses predicted AOA metabolic pathways for energy generation and carbon dioxide fixation but no typical surface layer (S-layer) proteins, only one ammonium transporter, and divergent A-type ATP synthase genes

Differential ecosystem function stability of ammonia-oxidizing archaea and bacteria following short-term environmental perturbation

Rapidly expanding conversion of tropical forests to oil palm plantations in Southeast Asia leads to soil acidification following intensive nitrogen fertilization. Changes in soil pH are predicted to have an impact on archaeal ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete (comammox) ammonia oxidizers and, consequently, on nitrification. It is therefore critical to determine whether the predicted effects of pH on ammonia oxidizers and nitrification activity apply in tropical soils subjected to various degrees of anthropogenic activity. This was investigated by experimental manipulation of pH in soil microcosms from a land-use gradient (forest, riparian, and oil palm soils). The nitrification rate was greater in forest soils with native neutral pH than in converted acidic oil palm soils. Ammonia oxidizer activity decreased following acidification of the forest soils but increased after liming of the oil palm soils, leading to a trend of a reversed net nitrification rate after pH modification. AOA and AOB nitrification activity was dependent on pH, but AOB were more sensitive to pH modification than AOA, which demonstrates a greater stability of AOA than AOB under conditions of short-term perturbation. In addition, these results predict AOB to be a good bioindicator of nitrification response following pH perturbation during land-use conversion. AOB and/or comammox species were active in all soils along the land-use gradient, even, unexpectedly, under acidic conditions, suggesting their adaptation to native acidic or acidified soils. The present study therefore provided evidence for limited stability of soil ammonia oxidizer activity following intensive anthropogenic activities, which likely aggravates the vulnerability of nitrogen cycle processes to environmental disturbance

Linking Nitrous Oxide and Nitric Oxide Fluxes to Microbial Communities in Tropical Forest Soils and Oil Palm Plantations in Malaysia in Laboratory Incubations

Funding Information: We thank the NERC LOMBOK field assistants for their help with soil sampling, especially Lawlina Mansul and Arnold James. We also thank Graeme Nicol for initial discussions in this project. Funding. This project was funded as LOMBOK (Land-use Options for Maintaining BiOdiversity and eKosystem functions) by the NERC Human Modified Tropical Forest (HMTF) research programme (NE/K016091/1). CG-R was funded by a University Royal Society Fellowship (UF150571).Peer reviewedPublisher PD

Effect of spatial origin and hydrocarbon composition on bacterial consortia community structure and hydrocarbon biodegradation rates

This work was supported by the Natural Environment Research Council [NE/L00982X/1 to UW, JA and EG]. CGR was supported by a University Research Fellowship from the Royal Society [UF150571].Peer reviewedPublisher PD

Chronic environmental perturbation influences microbial community assembly patterns

Acknowledgements Next-generation sequencing and library construction was performed by NCIMB Ltd., Aberdeen and CGEBM, Aberdeen. The authors would like to acknowledge the support of the Maxwell computer cluster funded by the University of Aberdeen. Dr Axel Aigle is acknowledged for assistance in molecular analysis. This work was supported by the Natural Environment Research Council [NE/L00982X/1] with financial support from BP UK Ltd and Intertek Group PLC. CGR was supported by a University Research Fellowship from the Royal Society [UF150571]Peer reviewedPostprin