Linking marine fisheries species to biogenic habitats in New Zealand: a review and synthesis of knowledge


Morrison, M. A., Jones, E. G., Consalvey, M., & Berkenbusch, K. (2014). Linking marine fisheries species to biogenic habitats in New Zealand: a review and synthesis of knowledge. New Zealand Aquatic Environment and Biodiversity Report No. 130. 160 p. Retrieved from


Fisheries research and management has traditionally been focussed on the fish populations, while the habitats and environments which underpin their production have been largely ignored. This situation is changing, with an increasing awareness that habitats are important and can be degraded through human activities, both marine and land-based. While the wider field of marine ecology has been researching such fish-habitat themes for a number of decades, the species worked on are often small, site-attached, and relatively short-lived; while fisheries species tend to be larger bodied, and operate over much larger spatial and temporal scales. Given this, quantitatively linking fisheries species to habitats is a challenge, and an active field of research. One type of habitat that appears to be especially important for many demersal species are those referred to as ‘biogenic’ habitats.

These biogenic habitats are formed by plants and animals, and occur from the inter-tidal out to the deep sea. Well known biogenic habitats include salt marshes, mangrove forests, seagrass meadows, kelp forests, bryozoan fields, and shellfish beds. For the purposes of this review, biogenic habitats are defined as a) those living species that form emergent three-dimensional structure, that separate areas in which they occur from surrounding lower vertical dimension seafloor habitats and b) non-living structure generated by living organisms, such as infaunal tubes and burrows. A sub-set of these habitats are biogenic “reefs”, which are visually imposing, and are defined as “solid, massive structures which are created by accumulations of organisms, usually rising from the seabed, or at least clearly forming a substantial, discrete community or habitat which is very different from the surrounding seabed. The structure of the reef may be composed almost entirely of the reef building organism and its tubes or shells, or it may to some degree be composed of sediments, stones and shells bound together by the organisms.”

The functions provided by these habitats are diverse, and can include the elevation of biodiversity, bentho-pelagic coupling, sediment baffling, protection from erosion, nutrient recycling, the provision of shelter and food for a wide range of other organisms, and even the creation of geological features over longer time scales. They also directly underpin fisheries production for a range of species, through: 1) the provision of shelter from predation, 2) the provision of associated prey species, and in some cases, 3) the provision of surfaces for reproductive purposes e.g. the laying of elasmobranch egg cases; as well as, 4) indirectly in the case of primary producers through trophic pathways.

In New Zealand, historical data on biogenic habitat extents and changes over time are very poor, and largely limited to shallow estuarine systems where change is visually observable (e.g. salt marsh, mangroves, seagrass and oyster beds), and/or where the biogenic species is actively harvested ( e.g. green-lipped mussels), or strongly associated with fish catches (e.g. the bryozoan beds of Separation Point, and off Torrent Bay with coastal finfish; and the bryozoan reefs of Foveaux Strait with dredge oysters). For such species where data is available (often ‘just’ anecdotal accounts), strong declines have occurred, which appear largely attributable to land-based effects (e.g., sedimentation and elevated nutrient levels), and fishing impacts. Examples include the extensive loss of seagrass meadows (e.g. large areas in Whangarei, Waitemata, Manukau, Tauranga and Avon-Heathcote estuaries), green-lipped mussel beds (about 500 km2 in the Hauraki Gulf), bryozoan beds (about 80 km2 in Torrent Bay, about 800 km2 in Foveaux Strait), and deep-water coral thickets on sea-mounts. Mangrove forests, in contrast, are one of the few biogenic habitat habitats which have greatly expanded in extent, following initial losses during European settlement through land reclamation and the building of infrastructure. Cumulatively, the magnitude and extent of biogenic habitat losses are likely to have been very substantial, but are unknown, and probably will never be able to be calculated. Other biogenic habitat species for which evidence points to historical losses include horse mussels, kelp forests, oyster beds, and sponges, both in assemblages where they tend to dominate, and as part of mixed biogenic habitat assemblages.

In the New Zealand context, there is currently no marine habitat classification system at the scale of biotopes (defined as recognisable and re-occurring natural associations of plants and animals), with the sole exception being a validated broad level habitat classification for shallow north-eastern New Zealand rocky reefs (including kelp forests and algal mats). This makes the formal and systematic evaluation of biogenic habitats problematic, and so in this review we work our way through biogenic habitats based on their intuitively obvious visual identities, and associated habitat quality variations where quantified. World-wide, biogenic habitats have seriously declined in extent and quality over time scales of decades to centuries, with global reviews (subject to some geographic data gaps) all showing serious regional and global declines in wetlands, sea-grasses, kelp forests, and oyster reefs; other biogenic habitats, including subtidal ones, may also be in decline but data is unavailable. The many functions and species associated with these habitats have by association also been lost or severely reduced. These fundamental changes in ecosystem structure and functioning have until recently been largely ignored or overlooked, partly through the phenomena of ‘sliding environmental baselines’, where each succeeding human generation has a different view of what is ‘natural’ in the oceans. […]