Search

R code and eDNA input files to train a taxon-independent community index (TICI) for 53 riverine monitoring sites in New Zealand

New Zealand (NZ) has a diversity of large river ecosystems that provide essential ecosystem services but are impaired by multiple ecological impacts. River restoration is an active field worldwide and there is good potential for river restoration practitioners in NZ to draw on lessons from elsewhere, although there is also a need to tailor approaches to national and local contexts. Here, we provide a critical review of large floodplain river restoration to guide environmental management in NZ and inform research and management priorities. The review is structured using a driver-pressure-state-impact-response framework, with a focus on responses, i.e. large river restoration methods. Thirty-one river restoration methods aligned with 14 broad restoration goals were evaluated collaboratively and semi-quantitatively. Evaluation outcomes are presented to inform regional and national scale restoration planning. Recommendations were identified to address eight key knowledge or policy gaps: (1) understanding cumulative impacts facing large river systems, (2) prioritising restoration measures at the landscape-scale, (3) promoting lateral connectivity in large river floodplains, (4) incorporating knowledge of geomorphology into river management, (5) enhancing understanding of cultural priorities and community aspirations, (6) assessing how costs and benefits of river restoration vary among timescales, (7) understanding the feasibility of restoration methods that have received limited application in NZ and (8) improving protection of threatened native fish species.

Data collected on zooplankton community composition over longer time periods (> 10 years) are rare. We examined among-lake spatial and temporal trends of zooplankton communities from a monitoring programme undertaken in the Waikato region, New Zealand. A total of 39 lakes were sampled over a period of 12 years, between 2007 and 2019, with varying degrees of temporal effort. We focussed particularly on eight lakes, considered here as ‘long-term lakes’, where samples were collected with greater regularity (including 5 with 12 years of data). Among lakes, suspended sediment concentrations and indicators of lake trophic state were inferred to be important in determining the zooplankton distributions; as this region is dominated by shallow lakes, the relative importance of suspended sediments was high. Among the long-term lakes, the greatest dissimilarities in zooplankton community composition among years were in Lake Waahi, where the Australian Boeckella symmetrica was first detected in 2012. That is, the greatest temporal changes to zooplankton composition during the study period were due to the invasion by non-indigenous species, rather than changes in trophic state or other environmental variables; non-native species commonly dominated the individual counts of species through much of 2014 and 2015, with most samples since 2016 being again dominated by native species. Following this lake, the largest and shallowest lakes in the dataset—Whangape and Waikare—exhibited the greatest variability in community composition among years.

Introduced common carp (Cyprinus carpio) are a recognised threat to New Zealand’s freshwater ecosystems. In 2011, an invasive fish removal programme was undertaken in 16.8 ha Lake Ohinewai, a Waika...

Unbiased estimates of the current state of target ecosystems and identification of potential causal factors are key to managing stressors over large scales, and for guiding policy and decision makers to set realistic targets and expectations in light of economic pressures. A probability survey design for 176 target wadeable, perennial streams mapped on developed land in the Waikato Region, New Zealand, sampled over three austral summers (2013 to 2015), was used to i) estimate the extent to which “Poor” stressor and biological condition states occur, ii) determine the co-occurrence likelihood of “Poor” biological and environmental condition, and iii) identify and estimate the relative importance of key environmental stressors. The probability survey design also allowed the quantification of uncertainty around mean estimates of extent and risk. These analyses reveal that between 25 and 50% of mapped target stream length can be considered to be in “Poor” condition based on biological indices derived from macroinvertebrate and fish community data. For assessed stressors, Poor condition was estimated for 10 to 50% of the target stream network depending on the stressor. Poor biological condition was likely to co-occur with Poor stressor condition for 10 of the 12 assessed stressors for macroinvertebrate indices, and 5 of the 12 stressors for the fish index. These analyses identify that management actions targeted at improving instream habitat quality, particularly reducing fine sediment deposition, when applied across the entire stream network are likely to yield the most widespread improvement in biological condition indices. Our findings also highlight the importance of extending policy development beyond a singular focus on water quality if ecosystem health objectives are to be met.

New Zealand's Waikato River has had a short but intense history of development, primarily through land-use change and flow regulation in the upper river, and in the lower river through flood control works, non-native species invasion, and land-use intensification. The river undergoes sharp transitions across montane-flood plain-coastal environments over a short distance and under similar climate. Together with specialized life-history requirements of many native fish, these features provide valuable insights into large river ecology and management. Testing approaches to determine outcomes of water quality changes have highlighted the value of functional indicators over traditional biotic measures for monitoring anthropogenic impacts. Initiatives to enhance native fish populations in the lower river have included remediation of migration barriers to improve access to tributary habitat, enhancement of tidal spawning habitat, and traps and gates to limit movement of large pest fish into flood plain lakes for spawning. This example of a southern temperate large river system highlights the importance of recruitment habitat and connectivity for native fish communities dominated by migratory species. Their slender bodies provide opportunities to create semipermeable barriers that enable access to flood plain habitats while restricting larger invasive fish. Recent initiatives have increased momentum to restore the ecological health of this river, but the underpinning science to guide priority actions is often lacking, and there is limited monitoring over the scales and time frames required to evaluate effectiveness.

Fish mortality through floodplain pumping stations is a recognised global issue, but few studies have quantified the degree of mortality that occurs during pumping. We investigated the potential of passive acoustic monitoring (PAM) as a tool to record sounds made by fish and their likely mortality as they passed through pumps during downstream migration. The acoustic properties made by freshly killed eels that were fed through an existing pump station were compared to those made by goldfish (Carassius auratus). Processing and analysis of acoustic data enabled the development of an ‘eel-specific’ algorithm for detecting eels passing through the pumping station. The duration of sound and filtered intensity were useful characteristics enabling reliable separation of the two fish species. The algorithm was then applied retrospectively to soundscape recordings obtained during a typical eel migration period at the test site. Although the tool is unlikely to be able to differentiate the sound of goldfish from ‘other’ potential sounds of short duration (e.g. sticks), differentiating eels from other sounds was demonstrated. We conclude that this tool has considerable potential for improving the understanding of the timing of eel migrations and likely mortality through pumping stations. The tool may also be used to inform the development of both remote and manual pump management options for reducing pump-related eel mortality.

Summary 1. Culvert pipes are regularly used around the world for conveying stream flows underground, through embankments or under road crossings. Installation of these features can have significant negative effects on the passage of freshwater biota and potentially exclude many species from large areas of river networks. 2. We investigated the installation of mussel spat ropes as a potentially rapid and cost-effective tool for improving passage of freshwater biota through culvert pipes where internal barrel conditions impede passage. We assessed passage success for two fish species, juvenile rainbow trout Oncorhynchus mykiss (Walbaum 1972) and adult inanga Galaxias maculatus (Jenyns 1842), and one migratory shrimp, Paratya curvirostris (Heller 1862), through culverts of differing length (3 and 6 m), slope (15 and 3°) and flow (024 and 075 L s 1 ). We hypothesized that ropes would enhance the passage success of these three species, but success rates would differ between species and trial combinations. 3. Ropes resulted in a reduced water velocity within culvert barrels and significantly improved passage success for all three species. Shrimp benefited most by the presence of ropes, being unable to negotiate any of the pipe combinations in their absence, but exhibiting varying rates of success across all combinations with their presence. Both G. maculatus and O. mykiss were able to negotiate some of the non-roped pipe combinations, but as the level of difficulty increased, successful passage was only achieved with the ropes present. 4. Synthesis and applications. We conclude that this relatively inexpensive and easy-to-install tool has the potential to substantially improve passage for a range of aquatic biota through various culvert scenarios. We consider that ropes would be particularly useful in situations where internal culvert access is difficult and where various culvert parameters (slope, flow, length) result in internal barrel hydraulics that would normally limit or exclude passage of aquatic biota.

Using natural abundances of stable carbon (δ13C) and nitrogen (δ15N) isotopes, we quantified spatial and temporal patterns of carbon flow through the main channel food web in the lowland section of New Zealand’s longest river, the Waikato River. The study was undertaken with the objective of determining whether the Waikato River conforms to contemporary theoretical concepts regarding carbon flow in large river food webs. Potential organic carbon sources and invertebrate and fish consumers were sampled from three different hydrogeomorphic zones on six occasions, representing a range of seasonal and flow conditions. In line with the predictions of the riverine productivity model and riverine ecosystem synthesis, autochthonous algae and biofilms were the most important basal carbon source contributing to consumer biomass. These were often supported by C3 aquatic macrophytes and allochthonous C3 riparian plants. The relative importance of organic carbon sources differed between zones and appeared to change depending on season, presumably in response to water temperature and flow, particularly in the unconstrained zone of the lower river. We also demonstrate that to draw robust conclusions, consideration must be given to quantifying the isotopic signatures of organisms lower in the food web, as these can change significantly between sampling times and hydrogeomorphic zones.

Quantifying the contributions of carbon sources that support food webs in large rivers is an important and growing field of ecological research with implications for future management and rehabilitation. Here we review theoretical concepts and recent empirical evidence that address carbon flow through aquatic food webs in large rivers. The literature reviewed focuses on studies using stable isotope analysis, which is a tested framework for identifying the origin of carbon sources that are assimilated by primary consumers and subsequently transferred through the food web to support higher consumers. Theoretical concepts addressing carbon flow in large river food webs have tended to stress the importance of organic matter originating from different sources, such as floodplains (Flood Pulse Concept), local riparian and aquatic primary producers (Riverine Productivity Model), or leakage from upstream processing of terrestrial organic matter (River Continuum Concept). Recent empirical evidence from a ...

The application of mussel spat rope for enabling the passage of redfin bully Gobiomorphus huttoni through culverts, which create velocity barriers, was trialled in the laboratory. No fish were able to access the un-roped control pipes whereas 52% successfully negotiated the pipes in the rope treatments. The success of fish ascending treatment pipes suggests mussel spat rope may be effective for enabling the passage of this and other similar fish species through otherwise impassable culverts with velocity barriers.

Responses of macroinvertebrate communities to human pressure are poorly known in large rivers compared with wadeable streams, in part because of variable substrate composition and the need to disentangle pressure responses from underlying natural environmental variation. To investigate the interaction between these factors, we sampled macroinvertebrates from the following: (i) submerged wood; (ii) littoral substrates 1.5 m) benthic habitats in eleven 6th- or 7th-order New Zealand rivers spanning a catchment vegetation land cover gradient. Cluster analysis identified primary site groupings reflecting regional environmental characteristics and secondary groupings for moderate gradient rivers reflecting the extent of catchment native vegetation cover. Low pressure sites with high levels of native vegetation had higher habitat quality and higher percentages of several Ephemeroptera and Trichoptera taxa than sites in developed catchments, whereas developed sites were more typically dominated by Diptera, Mollusca and other Trichoptera. Partial regression analysis indicated that the combination of underlying environment and human pressure accounted for 77–89% of the variation in Ephemeroptera, Trichoptera and Plecoptera taxa richness, %Diptera and %Mollusca, with human pressure explaining more variance than underlying environment for %Mollusca. Analysis of replicate deepwater and littoral samples from moderate gradient sites at the upper and lower ends of the pressure gradient indicated that total Trichoptera and Diptera richness and %Diptera responded to land use differences in these boatable river catchments. Responses to human pressure were substrate specific with the combination of littoral and deepwater substrates providing the most consistent response and yielding the highest number of taxa. These results indicate that multiple substrate sampling is required to document the biodiversity and condition of boatable river macroinvertebrate communities and that spatial variation in the underlying natural environment needs to be accounted for when interpreting pressure–response relationships. Copyright © 2012 John Wiley & Sons, Ltd.

The movement of koi, a highly colored variant of common carp Cyprinus carpio, was monitored for 18 months in the Waikato River, New Zealand, with both radiotelemetry and acoustic telemetry. Koi had large total linear ranges (mean, 39 km), and most fish (74%) monitored for more than 250 d traveled between the Waikato River and lateral habitat. Differences in total linear range and mean daily movement between years suggest a behavioral response associated with reduced habitat availability during periods of low flow. The movements of koi were highly variable and infrequent, suggesting that important long-range movements are missed in short-term studies (

The threat status of 74 freshwater and estuarine fish present in New Zealand was determined. Fifty-one native taxa were ranked of which 67% were considered Threatened or At Risk. A single species was classified as Extinct, the New Zealand grayling, which has not been observed since the 1920s. Four taxa were classified in the highest threat category, Nationally Critical, and a further 10 taxa as Threatened (Nationally Endangered or Nationally Vulnerable). Twenty taxa were ranked in the At Risk group with the majority ranked as Declining. Endemic galaxiids (Galaxiidae) dominated the Threatened and At Risk taxa. The majority (68%) belonged to the Galaxias genus, comprising 81% of recognised taxa in this genus and all five species in the genus Neochanna were also ranked as Threatened or At Risk. In addition to 51 native taxa, a further three fish species were considered colonists and 20 introduced species were classified as naturalised, although two of these are considered rare. The majority of the T...

The New Zealand fish fauna contains species that are affected not only by river system connectivity, but also by catchment and local-scale changes in landcover, water quality and habitat quality. Consequently, native fish have potential as multi-scale bioindicators of human pressure on stream ecosystems, yet no standardised, repeatable and scientifically defensible methods currently exist for effectively quantifying their abundance or diversity in New Zealand stream reaches. Here we report on the testing of a back-pack electrofishing method, modified from that used by the United States Environmental Protection Agency, on a wide variety of wadeable stream reaches throughout New Zealand. Seventy-three first- to third-order stream reaches were fished with a single pass over 150–345 m length. Time taken to sample a reach using single-pass electrofishing ranged from 1–8 h. Species accumulation curves indicated that, irrespective of location, continuous sampling of 150 stream metres is required to accu...

The use of mussel spat ropes to enable the passage of banded kokopu (Galaxias fasciatus) past perched culverts was tested under laboratory conditions. A 0.5 m high simulated perched culvert was fitted with one of two UV stabilised polypropylene rope types: “Russet Loop” and “Super Xmas Tree”. Four randomised replicate trials using each rope type were conducted to test their respective abilities to provide passage for “fresh‐run” banded kokopu whitebait (migrating post‐larval juveniles). There was no statistical difference in performance between the two rope types, with both performing equally well over each 3 h trial. A high proportion of fish used the ropes to successfully negotiate the structure (mean >85% individuals per trial irrespective of rope type). The high rate of successful passage over a short time period suggests that these ropes may be an effective, affordable and potentially easy retrofit to perched culverts, particularly for native species with similar climbing capabilities to ban...

The small, transparent gobioid Gobiopterus semivestitus is recorded for the first time from New Zealand, from a tributary of Ngunguru River, near Whangarei, Northland. Distinctive features of its sexual dimorphism are reported, in particular enlarged fins and greatly enlarged jaw dentition in the male. The origins of this species in New Zealand waters are uncertain: it could have been here for some time, unobserved; it could have dispersed recently to New Zealand across the Tasman Sea from Australia; or it could have arrived in ships’ ballast water.

Dominance hierarchies among pool-dwelling drift-feeding fish can determine spatial and temporal segregation of feeding territories. We tested the hypothesis that primarily nocturnal, dominant giant kokopu, Galaxias argenteus, force smaller, primarily diurnal, subordinate giant kokopu to feed by day. To test whether subordinate fish would become more nocturnal in the absence of dominant fish, we temporarily removed dominant fish from stream pools in which stable dominance hierarchies operated. Removal of the dominant fish resulted in a significant increase in the number of smaller giant kokopu active in stream pools at night; however, no change in activity was detected by day. The results indicate that large dominant fish control diel activity of subordinate fish, excluding them from stream pools at times (night) when invertebrate drift densities are at their highest.

Summary 1. Seasonal variation in microhabitat use and activity of 14 giant kokopu Galaxias argenteus, a drift-feeding galaxiid fish, was compared using radiotelemetry. 2. During winter giant kokopu predominantly used low velocities and intermediate depths by night and day. Activity recorded during 24 and 72 h periods indicated that fish were consistently active at night and inactive during the day. Activity data corresponded with point-in-time habitat use data, both of which indicated that fish were concealed amongst cover during the day and used open water habitats at night. 3. During summer, giant kokopu used higher water velocities, shallower depths and coarser substrata, particularly at night but also occasionally during the day relative to winter. Giant kokopu were active by both day and night in summer, although periods of activity were less defined and less predictable than during winter. 4. Adults used predictable home reaches at base-flow, with most individuals repeatedly using of one or two cover locations within their ‘home’ reach. Reaches used by fish were relatively short (rarely exceeding 26 m) irrespective of season and always included a single pool-riffle sequence. 5. Diel and seasonal behaviour of giant kokopu was generally comparable with that exhibited by other drift feeding fish species in small temperate streams. However, the nocturnal activity of giant kokopu contrasts with activity patterns in various salmonids, indicating that the impact of predation by different drift feeding fish may vary considerably.

The spatial organisation and behavioural interactions between giant kokopu (Galaxias argenteus) of varying sizes were investigated in two stream pools which varied in fish density. The spatial distributions offish in Pool A were more exclusive, exhibited less overlap, and appeared to be more stable than those for fish in Pool B. The distinct difference observed between the two pools may have been influenced by fish density which was lower in Pool A (0.27 fish/m2) than in Pool B (0.51 fish/m2). A linear, size (weight) related dominance hierarchy appeared to exist within both pools whereby the heaviest individual was the most dominant. Though primarily nocturnal in habit, the social structure and behaviour of giant kokopu (when active during the day) was comparable to that exhibited by other drift‐feeding fish in the Northern Hemisphere.

Nocturnal microhabitat selection in relation to size was examined for a New Zealand drift-feeding freshwater fish, the giant kokopu Galaxias argenteus in three coastal Otago streams. Evidence for ontogenetic shifts in microhabitat selection were observed, particularly with respect to water velocity and depth. Small (

The distribution of fish within eight small streams feeding into the lower Taieri and Waipori Rivers on the east coast of New Zealand's South Island was examined. A total of eight native and two introduced species were recorded. Eels (Anguilla spp.) and giant kokopu (Galaxias argenteus Gmelin) were the most widely distributed species being located in all streams surveyed. Common bullies (Gobiomorphus cotidianus McDowall) and brown trout (Salmo trutta Linnaeus) were also widely distributed being detected in seven and six of the streams respectively. Three streams of potential conservation significance were identified. These were Picnic Gully Creek which contained a significant population of banded kokopu (Galaxias fasciatus Gray), a Category C threatened species, and Cullens and Alex Creeks which contained significant populations of giant kokopu, a Category B threatened species. The population of giant kokopu in Cullens and Alex Creeks currently represents the largest known population of this spec...

The movements of giant kokopu Galaxias argenteus were recorded before, during, and after high-discharge events in two small streams using radiotelemetry. Giant kokopu remained within defined stream reaches during base flow conditions. During high-discharge events, individuals either stayed within their home reach, moved and settled elsewhere, or moved and returned to their home reach as flows subsided. The variable behavior exhibited by individual giant kokopu suggested that reasons for moving during floods are complex. Reasons that may have influenced movement during floods included reproduction and mate searching, lack of adequate refugia, or some combination of these. In many instances, individual giant kokopu appeared to exhibit adaptive behaviors in response to high discharges. Behaviors supporting this view included fish not moving during the highest floods, fish moving upstream during the peak discharge period, and fish making purposeful “micromovements” (movements

Signal strength received by a fixed antenna increased as a transmitter was positioned closer to it and decreased as the transmitter was positioned further away. Depth and transmitter orientation also influenced signal strength, but these were less pronounced than the effect of distance. The variations in signal strength recorded from fixed distances, depths or orientations were low, suggesting that variation in signal strength only occurs if the transmitter is moved. The use of signal strength variation as a measure of fish activity over a 24 h period was compared with observed patterns of point habitat use of a live fish. Close correspondence of assessments of activity using signal strength variation and habitat use was observed. This study demonstrated the potential utility of radiotelemetry in association with point-in-time habitat use data to determine home-range and diel and seasonal patterns of fish activity over 24 h periods.

Understanding migratory life histories is critical for the effective management and conservation of migratory species. However, amphidromous migrations (fish hatch in streams, immediately migrate to the sea for a feeding period and return to fresh water as juveniles) remain understudied owing to the difficulties of tracking tiny larval fish. Despite this, it has widely been assumed that amphidromous fish have open, resilient populations, with marine-rearing larvae dispersing widely during their pelagic phase. In the present study we tested the hypothesis that when an alternative freshwater pelagic habitat is available, non-diadromous recruitment will be the dominant process in sustaining amphidromous fish populations, with implications for their connectivity and resilience. Otolith microchemical analyses of five species (three Galaxias (Galaxiidae), two Gobiomorphus (Eleotridae)) from paired systems on the South Island of New Zealand indicated that when a suitable freshwater pelagic habitat existed downstream, non-diadromous recruitment was the primary population-sustaining process, typically contributing >90% of recruits. In addition, not all species recruited from all lakes, indicating the importance of the largely unstudied role of species-specific amphidromous larval requirements. The results of the present study emphasise the need to better understand the dynamics of individual populations of amphidromous fish, and highlight the importance of understanding species-specific early life history requirements to fully understand their distributions and management needs.

Worldwide, human-mediated disruption of river networks by artificial structures negatively affects migratory fish species. To creatively solve part of this problem, we assessed the effectiveness of mussel spat ropes for improving fish passage past perched culvert structures. We used a before–after–control–treatment design to test our hypothesis that relative abundances of ‘young-of-the-year’ migratory fish species would increase following rope installation in a New Zealand stream. Results following remediation indicated a significant three- to four-fold increase in fish abundance relative to a control stream. Although four species (banded kokopu (Galaxias fasciatus), redfin bullies (Gobiomorphus huttoni), longfin eels (Anguilla dieffenbachii) and shortfin eels (Anguilla australis)) were present at both the treatment and control stream sites, the increased fish relative abundance at the treatment site was driven primarily by an increase in ‘young-of-the-year’ banded kokopu. The present study has shown that mussel spat ropes can significantly improve fish relative abundances above severely perched culverts, but may not be effective for all species present. Future use of ropes for evaluating passage efficacy for other species, and for a wider range of barrier situations globally, may greatly extend the application of this cost-effective tool.

Common carp (Cyprinus carpio) are notoriously difficult to monitor in water temperatures above 20°C using telemetry owing to transmitter expulsion. To reduce transmitter loss, radio transmitters were anchored to the pelvic girdle and a polymer coating was applied to acoustic transmitters to reduce tissue irritation in two tank trials. Ten dummy transmitters were surgically implanted in each of four groups of adult koi carp, a highly coloured strain of C. carpio. Water temperatures ranged between 7 and 24°C. After 365 days, the control and test groups of each trial had similar expulsion rates (P ≥ 0.30; two-tailed Fisher’s exact probability test). Expulsion rates for uncoated acoustic transmitters were 60% (n = 6), coated acoustic transmitters 50% (n = 5), unanchored radio transmitters 60% (n = 6) and anchored radio transmitters 90% (n = 9). Expulsions occurred 15–362 days after implantation as a result of ulcers at or near the surgical wound. Bacterial infection of the wound appears to be the primary mechanism for transmitter expulsion.