Seagrass, seaweed, and bivalves are ubiquitous foundation species in estuarine ecosystems that often have positive impacts on biodiversity. However, relatively little is known about their distribution patterns on the South Island of New Zealand (specifically, Zostera muelleri, Ulva spp. and shell deposits from the ubiquitous cockle Austrovenus stutchburyi) and their effects on local biodiversity across spatiotemporal scales. To address this research gap, nine estuaries were sampled in winter 2020 across tidal elevations and along a latitudinal gradient from 41°S to 46 °S, and in two estuaries around the Banks Peninsula (every month from November 2020 to October 2021). Small- and large-scale sampling methods were used to quantify co-occurrence patterns between foundation species (Chapter 2) and their effects on associated plant and animal communities (Chapter 3) in both the latitudinal and seasonal surveys. Such multifactorial baseline data collected across spatiotemporal scales are important to gauge how estuaries may be affected by future stressors, like eutrophication, warming, and other anthropogenic stressors.

In Chapter two, geotagged small scale digital photos and large-scale drone images were collected and analysed for percent cover of foundation species across latitudes and seasons. I found strong effects of latitude and season on the abundance of all foundation species, and results were consistent between scales. Zostera was most abundant in southern estuaries and in winter months whereas surface deposited shells were most abundant in northern estuaries and also in winter months. By comparison, Ulva was generally found in low abundances but was relatively common in the Avon Heathcote Estuary in summer months. I also found negative correlations between seaweed and seagrass suggesting that Ulva may have negative effects on Zostera, for example through competition for light or by creating adverse environmental conditions such as low oxygen levels.

In Chapter three, species-habitat-associations were quantified in quadrats (e.g., limpets attached to shells, crabs hiding under seaweed) and invertebrate abundances and taxonomic identities were quantified from cores collected in bare mud, seagrass beds and seaweed mats. Quadrats and cores were collected from the same latitudes and seasons as described in Chapter 2, but also included sampling across two elevation levels. The quadrate data showed that abundances and richness of habitat-interactions were highest in the central estuaries at low elevation and in summer months. This survey highlighted that dead bivalve shells, a habitat often ignored in estuarine surveys, were common across estuaries, seasons, and elevations (as also shown in Chapter 2) and that shells had positive effects on biodiversity.

Examples of habitat-interactions that explained much of the multivariate variability in community structures included Ulva-on-shell, Notoacmea-on-Diloma, Diloma-on-shells, Notoacmea-on-shells, and Micrelenchus-on-shells, again highlighting the importance of shells providing habitat for estuarine epifauna. The sediment core data showed the same overall pattern as the quadrate data, but also highlighted that estuarine foundation species are inhabited by more individuals and taxa compared to bare sediments and that abundances and richness was slightly higher in cores were seagrass and seaweed co-occurred compared to cores where foundation species were found alone. Taxa that explained most of the variation in community structure in the sediment cores included many molluscs (e.g., Diloma, Micrelenchus, Notoacmea, Austrovenus, Zeacumantus) again emphasising the importance of shell-forming molluscs in estuarine habitats.

The results were discussed in a context of latitudinal differences in temperature (for Zostera) and seasonal changes in temperature, light, desiccation, and grazing (for Zostera and Ulva) and possible differences in hydrodynamic conditions and sedimentation and erosion rates (for shells). Richness and abundances of animals were, compared to previous work done in the same regions in 2016, slightly lower, perhaps because these estuaries experienced unusually hot summers in 2017/18 and 2018/19, or they may experience stronger anthropogenic stress e.g., from eutrophication. For example, after a short marine heatwave in February 2020, I recorded a decrease in seagrass cover and less habitat-interactions, suggesting that effect from high temperature may be rapid but also short-lived. This study added multifactorial baseline data about foundation species and their associated ecological communities, from moderately-to-poorly sampled estuaries on the South Island of New Zealand. I conclude that (i) estuarine foundation species, like seagrass, seaweeds, and shells, facilitate biodiversity across spatiotemporal gradients, (ii) facilitation is slightly stronger when foundation species (here seagrass and seaweed) cooccur, and (iii) surface deposited shells are common in estuaries, also increases diversity, and therefore should be included in future surveys and experimental estuarine studies.