Approaches to understanding the ecology and evolution of understudied terrestrial archaeal ammonia-oxidisers

Funded by The Royal SocietyPeer reviewedPostprintPostprin

Selective inhibition of ammonia oxidising archaea by simvastatin stimulates growth of ammonia oxidising bacteria

Acknowledgements The authors would like to thank Dr Robin Walker for access to the experimental plots at the SRUC, Craibstone Estate, Aberdeen. JZ was funded by a Natural Environment Research Council (NERC) grant (NE/K016342/1), MOB by a University of Aberdeen Elphinstone Scholarship and by TETFund through Adekunle Ajasin University Akungba (AAUA) Nigeria, YM by a NERC grant (NE/R001529/1) and CGR by a Royal Society University Research Fellowship (URF150571).Peer reviewedPublisher PD

Preferential temperature and ammonia concentration for in-situ growth of Candidatus Nіtrоѕосоѕmісuѕ ammonia oxidising archaea

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).Peer reviewedPostprin

The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions

The authors are members of the Nitrous Oxide Research Alliance (NORA), a Marie Skłodowska-Curie ITN and research project under the EU's seventh framework program (FP7). GN is funded by the AXA Research Fund and CGR by a Royal Society University Research Fellowship (UF150571) and a Natural Environment Research Council (NERC) Standard Grant (NE/K016342/1). The authors would like to thank Dr Robin Walker and the SRUC Craibstone Estate (Aberdeen) for access to the agricultural plots, Dr Alex Douglas for statistical advice and Philipp Schleusner for assisting microcosm construction and sampling.Peer reviewedPublisher PD

Gene duplication drives genome expansion in a major lineage of Thaumarchaeota

Acknowledgements This work and P.O.S. were financially supported by UKRI through the NERC grant NE/R001529/1. In addition, C.G.-R. and T.A.W. were both supported by a Royal Society University Research Fellowship (URF150571 and UF140626). C.Q. was funded through an MRC fellowship (MR/M50161X/1) as part of the CLoud Infrastructure for Microbial Genomics (CLIMB) consortium (MR/L015080/1). S.R. was funded through the BBSRC grant BB/R015171/1. The Thames Metagenome Database was funded through the NERC grants NE/M011674/1, NE/M011259/1 and NE/M01133X/1. We thank Dr Tony Travis for his support with Biolinux and acknowledge Prof Jim Prosser for his critical reading of the manuscript. The authors would also like to acknowledge the support of the Maxwell computer cluster funded by the University of Aberdeen.Peer reviewedPublisher PD

Grazing weakens competitive interactions between active methanotrophs and nitrifiers modulating greenhouse-gas emissions in grassland soils

This work was financially supported by Natural Science Foundation of China (41977033, 41907026, and 41721001), Fundamental Research Funds for the Central Universities (2019QNA6011), National Key Basic Research Program of China (2014CB138801), Shandong Provincial Natural Science Foundation (ZR2019BD032), China Postdoctoral Science Foundation (2020T130387 and 2019M652448). CG-R was funded by a Royal Society University Research Fellowship (UF150571). Special thanks to ChunMei Meng, Yu Luo, and Yan Zheng for their assistance in laboratory analyses.Peer reviewedPublisher PD

AOB Nitrosospira cluster 3a.2 (D11) dominates N2O emissions in fertilised agricultural soils.

CRediT authorship contribution statement Na Deng: Writing – review & editing, Methodology, Investigation, Data curation. Cecile Gubry-Rangin: Writing – review & editing, Methodology, Conceptualization. Xiao-Tong Song: Writing – review & editing, Methodology, Data curation. Xiao-Tang Ju: Writing – review & editing, Conceptualization. Si-Yi Liu: Methodology, Data curation. Ju-Pei Shen: Writing – review & editing, Data curation. Hong-jie Di: Writing – review & editing. Li-Li Han: Writing – review & editing, Methodology. Li-Mei Zhang: Writing – review & editing, Methodology, Data curation, Conceptualization.Peer reviewe

Seqenv : linking sequences to environments through text mining

Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the ‘‘nt’’ nucleotide database provided by NCBI and, out of every hit, extracts–if it is available–the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS How to cite this article Sinclair et al. (2016), Seqenv: linking sequences to environments through text mining. PeerJ 4:e2690; DOI 10.7717/peerj.2690 and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography