Saltwater Intrusion Impacts Microbial Diversity and Function in Groundwater Ecosystems

Karen M. Houghton1, *
, Mano Fournier1, Conny Tschritter1

1 GNS Science, Wairakei Research Centre, 114 Karetoto Road, Taupō, New Zealand

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© 2023 Houghton et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the GNS Science, Wairakei Research Centre, 114 Karetoto Road, Taupō, New Zealand; Tel: +64 7 376 0139; E-mail:



Groundwater ecosystem services provided by microbial communities are essential for the maintenance of water quality. For example, nitrate contamination is a recognised health and ecosystem issue in most groundwater systems, often alleviated through microbial processes. The effects of climate change, including increasing salinity from rising sea levels, or over-abstraction, on these communities are largely unknown.


This study uses a combination of culture-dependent (growth curves, isolation of bacteria) and culture-independent (16S rRNA gene sequencing) methods to identify the potential effects of saltwater intrusion on groundwater microbes and their ecosystem functions.


Some groundwater microbial communities are negatively impacted by increasing chloride concentrations, including declines in bacteria responsible for nitrate and ammonia removal. These ecosystems should be prioritised for future protection from sea level rise or increased extraction of groundwater for agriculture and other uses. Other microbial communities are stimulated in the presence of chloride, often caused by an increase in abundance of salt-tolerant heterotrophic bacteria using sugars, peptides, or organic acids for energy.


There have been no previous studies investigating the impact of chloride on Aotearoa New Zealand groundwaters. The identification of keystone species that are affected by increasing salinity, which have a disproportionately large effect on the ecosystem and low functional redundancy, is essential. Water management decisions about future abstraction limits and defences against sea level rise can be underpinned by robust scientific knowledge about microbial community sensitivity to salinity.

Keywords: Chloride, Ecosystems functions, Groundwater, Microbial diversity, Salt, Toxicity.