Microbial nitrogen-cycling and cooperation in the terrestrial subsurface

The microbial nitrogen cycle is predicted to play a major role in nitrogen transformations in the terrestrial subsurface. The cycle comprises six distinct biological N-transformation processes, including ammonification, nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation (anammox), and assimilation. The microorganisms that perform these processes can be sources and sinks of nitrate – a major anthropogenic contaminant of aquifers. Therefore, it is crucial that we understand how natural and anthropogenic driven variation in aquifers impacts the microbial communities and their functional contributions, including nitrogen removal. To determine the distribution and activity of nitrogen cycling microorganisms in aquifers, this thesis applied a variety of molecular approaches to groundwater samples collected across a range of aquifer lithologies and physicochemistries. Groundwater with varying nutrient and oxygen contents was sampled from 55 sites distributed over 860 km2 of New Zealand. Metagenomes and metatranscriptomes were analysed from a subset of oxic and dysoxic sandy-gravel aquifer sites, and genes/transcripts involved in major nitrogen-cycling pathways were quantified from 55 and 26 sites, respectively. Data indicate that non-assimilatory nitrogen-cycling (ammonia oxidation, nitrate, nitrite and nitric oxide reduction and denitrification) potential was prevalent regardless of site-specific physicochemistry, but pathway relative abundances differed. Anammox helps to drive N loss from aquatic systems, and is expected to be associated with low oxygen and carbon availability. While anammox-associated bacteria (class Brocadiae) diversity decreased with increasing dissolved oxygen in groundwater, Brocadiae 16S rRNA genes and hydrazine synthase (hydrazine synthase, hzsB) genes and transcripts, which are indicative of the anammox process, were detected across a wide range of bulk groundwater dissolved oxygen (DO) concentrations (0–10 mg/L). Distinct groups of these genomes dominated the anammox-associated community at dysoxic and oxic sites, further reflecting the influence of dissolved oxygen on Brocadiae composition. Anammox gene and transcript (hzsB) concentrations correlated significantly and positively with those involved in bacterial and archaeal aerobic ammonia oxidation (ammonia monooxygenase, amoA), which could represent a major source of nitrite for anammox. This trend was confirmed with metatranscriptomic data, which revealed the co-occurrence of aerobic (nitrification, including ammonia oxidation) and anaerobic (denitrification, nitrite-dependent anaerobic methane oxidation, and anammox) processes in dysoxic groundwater (0.3–1.1 mg/L bulk dissolved oxygen), indicating the availability of oxic-anoxic interfaces. Concurrent activity by ammonia oxidizers, anammox bacteria, and methanotrophic bacteria, indicates potential synergism and metabolic “hand-offs” through shared metabolic products (e.g. nitrite). In addition, the portion of complete versus incomplete denitrifiers was substantially higher under low oxygen conditions. Genes and transcripts encoding atypical Sec-dependant N2O reductases (NosZ) were the most common type, and although usually associated with incomplete denitrifiers, were found here to be also associated with complete denitrifiers. Nitrospirota species are usually regarded as key contributors to nitrification. Genomic and transcriptomic analysis indicates that a Nitrospirota species from groundwater-derived genus, 9FT-COMBO-42-15, has the capacity for versatile autotrophic sulfur and anaerobic nitrogen metabolism, including dissimilatory nitrate reduction to ammonium and complete denitrification coupled to sulfur oxidation. As the phylum comprises considerable uncharacterised diversity, the newly-recovered genome was analysed alongside sixty-seven other genomes spanning all nine Nitrospirota orders to determine the metabolic capacity for carbon fixation and nitrogen and sulfur cycling across the phylum. This analysis revealed that species belonging to Nitrospirota comprise three clades that have distinct environmental niches and metabolic attributes, largely influenced by oxygen availability. This thesis provides insights into factors influencing nitrogen-transformations in groundwater, such as oxygen availability across a diverse range of aquifer conditions. Data indicates anammox bacteria contribute to loss of fixed N across diverse anoxic-to-oxic aquifer conditions, and that this is likely supported by nitrite from aerobic ammonia oxidation. Moreover, the phylogenetic and genomic analysis of Nitrospirota species recently recovered from diverse groundwater environments, and other environments (such as subseafloor crustal fluid, alpine thermal spring water, sulfur rich hydrothermal vent sediments and soils), sheds light on the divergent metabolic capacities between well-characterised Nitrospirota (characterised predominantly by aerobic nitrifiers) compared with the widespread capacity for anaerobic nitrogen and sulfur metabolism among newly-defined families that lacked metabolic characterisation.

Name thesis:degree_name

PhD

Level thesis:degree_level

Doctoral

Discipline thesis:degree_discipline

Biological Sciences

Grantor dc:publisher

ResearchSpace@Auckland

Year dc:date.issued

2021

Author dc:creator

• Mosley, Olivia Ellie

Advisors dc:contributor.advisor

• Handley, Kim M.
• Lewis, Gillian

Statement dc:rights

• Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated.
• Restricted Item. Thesis embargoed until 4/2023. Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

Licence dc:rights.uri

• https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm

Handle dc:identifier.uri

https://hdl.handle.net/2292/58816

OAI identifier oai:identifier

oai:researchspace.auckland.ac.nz:2292/58816