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Biogenic habitats are foundational habitats for species assemblages and drive a range of ecosystem functions. The Hauraki Gulf/Tiikapa Moana is the most intensively used coastal area in Aotearoa/New Zealand, and decades of commercial fishing, sedimentation and industrialization have degraded biogenic habitats in the Gulf. In response, the marine spatial plan 'Sea Change' includes proposals to create new and extend existing marine protected areas (MPAs) and restrict the area open to mobile bottom‐impact fishing methods to conserve and help the recovery of biogenic habitats.To assess the benefits of different spatial planning scenarios for biogenic habitats, information on their spatial distribution is needed, but data limitations are a significant challenge. Here, an approach is detailed that maximized the information extracted from limited species occurrence data, by incorporating expert knowledge to develop and evaluate models of biogenic habitat‐forming taxa.Ensemble habitat suitability models (using boosted regression tree and random forest models) were created for 20 biogenic habitat groups. Using withheld data for validation, area under curve (AUC) scores ranged from 0.58 to 0.95 and true skill statistics (TSS) ranged from 0.37 to 0.84, though three models were further evaluated as insufficient representations of known ecological habitats by expert assessors.Models produced here provide substantially increased information to inform progress on implementation of the Sea Change plan. Two stakeholder processes have been held, resulting in the development of spatial plans for bottom trawl mitigation that are currently under public consultation. Systematic surveys that gather abundance and high‐resolution environmental data should be a priority to improve the utility of predictive models and inform future management processes in the Hauraki Gulf, and funding has been allocated to support additional data collection to determine the effectiveness of spatial management measures in the Hauraki Gulf. [ABSTRACT FROM AUTHOR]

In northern New Zealand, there is speculation that predation by a recovering shorebird, the South Island Pied Oystercatcher (Haematopus finschi), has caused the continuing decline of an endemic surf clam, the toheroa (Paphies ventricosa). Consequently, there have been requests by the public for these protected birds to be culled to protect and restore the toheroa. To better inform management and decision-making for these species we set out to understand the impact of oystercatcher predation on toheroa at Ripiro Beach in New Zealand. A study was conducted to establish the spatio-temporal overlap of toheroa and oystercatcher distributions, determine oystercatcher prey selection, and assess the impacts of oystercatcher predation on toheroa population size structure. Monthly surveys over a 12-month period indicated limited spatial overlap between the two species, and that most toheroa beds on Ripiro Beach are not subjected to oystercatcher predation. In areas where oystercatchers and toheroa co-occurred, oystercatchers consumed a variety of prey including polychaetes, small and medium-sized toheroa and a non-threatened surf clam (P. subtriangulata). While oystercatchers do feed on toheroa (and may be capable of locally reducing abundance of small toheroa in a population), feeding on larger individuals (>50 mm in length) was not observed. These results suggest that culling of oystercatchers would be of no benefit for the recovery of toheroa populations. It is likely that less obvious factors are impeding the recovery of toheroa in New Zealand. This study highlights the importance of understanding predator-prey interactions before implementing management actions such as lethal control. [ABSTRACT FROM AUTHOR]

The toheroa (Paphies ventricosa) is an Aotearoa (New Zealand) endemic surf clam that remains threatened following population collapse due to overfishing in the twentieth century. Despite protective measures being in place for more than 4 decades, toheroa populations have inexplicably failed to recover. As part of an investigation into the possible role of disease in preventing their recovery, an exploration of the bacterial composition in toheroa was conducted over their entire geographic range. The bacterial composition in toheroa tissues was dominated by Spirochaetaceae, Mycoplasmataceae, and Endozoicomonadaceae, and varied at both large (between geographically separated sites) and small spatial scales (beds < 10 km apart). At small scales, it was habitat, in this case the presence or absence of freshwater outflows, which appeared to be a major influence on bacterial composition. Given that the decline of toheroa has also coincided with changes in land use that have reduced the amount of freshwater reaching the toheroa beaches, it is possible that habitat-related shifts in the abundance of certain bacterial symbionts are affecting the health and impeding recovery of this iconic and culturally significant species. [ABSTRACT FROM AUTHOR]

[Display omitted] • Histopathology is used to assess toheroa health. • The prevalence of IMCs was geographically dissimilar. • IMC infection and health-related features are modelled. • Toheroa condition was linked to IMC intensity. The toheroa (Paphies ventricosa) is endemic to Aotearoa (New Zealand). Following decades of overfishing in the 1900 s, commercial and recreational fishing of toheroa is now prohibited. For unknown reasons, protective measures in place for over 40 years have not ensured the recovery of toheroa populations. For the first time, a systematic pathology survey was undertaken to provide a baseline of toheroa health in remaining major populations. Using histopathology, parasites and pathologies in a range of tissues are assessed and quantified spatio-temporally. Particular focus is placed on intracellular microcolonies of bacteria (IMCs). Bayesian ordinal logistic regression is used to model IMC infection and several facets of toheroa health. Model outputs show condition to be the most important predictor of IMC intensity in toheroa tissues. The precarious state of many toheroa populations around Aotearoa should warrant greater attention from scientists, conservationists, and regulators. It is hoped that this study will provide some insight into the current health status of a treasured and iconic constituent of several expansive surf beaches in Aotearoa. [ABSTRACT FROM AUTHOR]

The toheroa Paphies ventricosa is a large Aotearoa New Zealand (ANZ) endemic surf clam of cultural importance to many Māori, the Indigenous people of ANZ. Extensive commercial and recreational harvesting in the 20th century dramatically reduced populations, leading to the collapse and closure of the fishery. Despite being protected for >40 yr, toheroa have inexplicably failed to recover. In 2017, intracellular microcolonies (IMCs) of bacteria were detected in 'sick' toheroa in northern ANZ. Numerous mass mortality events (MMEs) have recently been recorded in ANZ shellfish, with many events linked by the presence of IMCs resembling Rickettsia-like organisms (RLOs). While similar IMCs have been implicated in MMEs in surf clams elsewhere, the impact of these IMCs on the health or recovery of toheroa is unknown. A critical first step towards understanding the significance of a pathogen in a host population is pathogen identification and characterisation. To begin this process, we examined 16S rRNA gene sequences of the putative IMCs from 4 toheroa populations that showed 97% homology to Endozoicomonas spp. sequences held in GenBank. Phylogenetic analysis identified closely related Endozoicomonas strains from the North and South Island, ANZ, and in situ hybridization, using 16S rRNA gene probes, confirmed the presence of the sequenced IMC gene in the gill and digestive gland tissues of toheroa. Quantitative PCR revealed site-specific and seasonal abundance patterns of Endozoicomonas spp. in toheroa populations. Although implicated in disease outbreaks elsewhere, the role of Endozoicomonas spp. within the ANZ shellfish mortality landscape remains uncertain.