Murray Cod Research Articles (Page 5)

The allocation of time and energy to different behaviours can impact survival and fitness, and ultimately influence population dynamics. Intrinsically, the rate at which animals expend energy is a key component in understanding how they interact with surrounding environments. Activity, derived through locomotion and basic metabolism, represents the principal energy cost for most animals, although it is rarely quantified in the field. We examined some abiotic drivers of variability in locomotor activity of a free-ranging freshwater predatory fish, Murray cod (Maccullochella peelii), for six months using tri-axial accelerometers. Murray cod (n = 20) occupied discrete river reaches and generally exhibited small-scale movements (<5 km). Activity was highest during crepuscular and nocturnal periods when water temperatures were warmest (19–30°C; January–March). As water temperatures cooled (9–21°C; April–June) Murray cod were active throughout the full diel cycle and dormant periods were rarely observed. Light level, water temperature and river discharge all had a significant, non-linear effect on activity. Activity peaked during low light levels, at water temperatures of ~20°C, and at discharge rates of ~400 ML d-1. The temporal changes observed in the behaviour of Murray cod likely reflect the complex interactions between physiological requirements and prey resource behaviour and availability in driving activity, and highlight the importance of empirical field data to inform bioenergetics models.

Making culverts great again. Efficacy of a common culvert remediation strategy across sympatric fish species

ABSTRACTThis article enacts Deleuze and Guattari's (1987) concept assemblage to craft a riverScape pedagogy that is informed by, and responsive to, the Murray Cod, the river, and its circumstances. The Murray Cod, the largest fish species in Australia's Murray-Darling Basin, has diverse cultural meanings. Cod are at once a creation being of Indigenous people, a migratory predator that breeds in response to warm floodwaters, and a fish suffering significant ecological decline as a result of changes to land and water use in its habitat. Murray Cod assemblage weaves these elements together to re/create a bioegalitarian pedagogy, part thought experiment and part teaching strategy.

A taxonomic study was carried out on strain LW15T, which was isolated from the external lesions of diseased farmed Murray cod (Maccullochella peelii peelii) from an intensive culture pond. Cells of strain LW15T were Gram-negative, facultative-anaerobic, non-motile, and both coccobacillus- and bacillus-shaped. Growth was observed at NaCl concentrations of 0-2 % (w/v) (optimum, 0 %), 4-32 °C (optimum, 25-28 °C) and pH 5.0-9.0 (optimum, 7.0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LW15T was affiliated to the genus Acinetobacter, showing the highest similarity to Acinetobacter guillouiae CIP 63.46T (97.7 %) and other Acinetobacter species with validly published names (93.5-97.6 %). Whole-genome sequencing and phylogeny reconstruction based on a core set of 1061 Acinetobacter genes indicated that strain LW15T was most closely related to the clade formed by A. guillouiae CIP 63.46T and Acinetobacter bereziniae CIP 70.12T and distantly related to any of the described species of genus Acinetobacter. Furthermore, strain LW15T could be distinguished from all known Acinetobacter species by its ability to assimilate β-alanine and l-arginine, but not d-glucose. The principal fatty acids were C18 : 1ω9c, C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. The major respiratory quinone was Q-9. Polar lipids of strain LW15T comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, four phospholipids, aminolipid and two unknown lipids. Based on its phenotypic and genotypic data, strain LW15T represents a novel species of the genus Acinetobacter, for which the name Acinetobacterpiscicola sp. nov. is proposed. The type strain is LW15T (=MCCC 1K03337T=CICC 24241T=KCTC 62134T=JCM 32101T).

Per- and poly-fluoroalkyl substances (PFASs) are persistent organic pollutants that have been extensively used in commercial and industrial applications, such as aqueous film-forming foam (AFFF) formulations. Widespread use of AFFFs has led to an increasing number of reports documenting PFAS contamination around civilian and military airports. However, research on the presence and distribution of PFASs in Australia is lacking. This study presents the first report of PFASs in Australian native and introduced freshwater species, sampled from a watercourse adjacent to the regional airport and colocated fire training ground near Tamworth, New South Wales, Australia. Perfluorooctane sulfonate was the most abundant PFAS compound in biota samples from this area, and both introduced common carp Cyprinus carpio and native Murray cod Maccullochella peelii had average concentrations higher than the Australian trigger value of 5.2μgkg–1. Common yabby Cherax destructor and golden perch Macquaria ambigua carried low concentrations, and common yabby also had low concentrations of perfluorohexane sulfonate. Differences in foraging habits provided some potential explanations of the differences observed among species. There is a clear and pressing need to better understand potential toxicological and reproductive effects of PFASs on Australian freshwater species.

Adaptive differences across species' ranges can have important implications for population persistence and conservation management decisions. Despite advances in genomic technologies, detecting adaptive variation in natural populations remains challenging. Key challenges in gene-environment association studies involve distinguishing the effects of drift from those of selection and identifying subtle signatures of polygenic adaptation. We used paired-end restriction site-associated DNA sequencing data (6,605 biallelic single nucleotide polymorphisms; SNPs) to examine population structure and test for signatures of adaptation across the geographic range of an iconic Australian endemic freshwater fish species, the Murray cod Maccullochella peelii. Two univariate gene-association methods identified 61 genomic regions associated with climate variation. We also tested for subtle signatures of polygenic adaptation using a multivariate method (redundancy analysis; RDA). The RDA analysis suggested that climate (temperature- and precipitation-related variables) and geography had similar magnitudes of effect in shaping the distribution of SNP genotypes across the sampled range of Murray cod. Although there was poor agreement among the candidate SNPs identified by the univariate methods, the top 5% of SNPs contributing to significant RDA axes included 67% of the SNPs identified by univariate methods. We discuss the potential implications of our findings for the management of Murray cod and other species generally, particularly in relation to informing conservation actions such as translocations to improve evolutionary resilience of natural populations. Our results highlight the value of using a combination of different approaches, including polygenic methods, when testing for signatures of adaptation in landscape genomic studies.

Abstract The serial discontinuity concept (SDC) proposes that hypolimnetic‐releasing impoundments cause major disruptions to the naturally occurring physical, chemical and biological gradients of rivers but that this impact diminishes with distance downstream. Such a gradient in discharge, flow velocity and temperature regime occurs below a large hypolimnetic‐releasing impoundment, the Hume Dam, on the River Murray in south‐eastern Australia. To examine the effects of this disturbance gradient on a warm‐water large‐bodied freshwater fish, the Murray cod (Maccullochella peelii), a bioenergetics model was developed and calibrated to explore energy expended under differing water velocities and temperature regimes. Model simulations predicted negative growth of juveniles directly downstream of the impoundment, due largely to the energetic costs associated with active and, to a lesser extent, standard metabolism outweighing the achievable energetic gains through food consumption. As flow velocity and temperature regimes became more favourable downstream, so did the simulated growth of the species. It was not until +239 km downstream of the impoundment that the model predicted that flow velocity and temperature regimes were suitable for greater weight gains. The modelled growth responses of juvenile Murray cod are consistent with the predictions of the SDC, emphasising that changes in the bioenergetics of individuals are likely to be reflected in reduced growth rates under the changed flow velocity and temperature regimes imposed by disturbance gradients. This research represents a valuable step in the biological understanding of Murray cod within variable riverine environments and emphasises the urgency required to mitigate impacts associated with hypolimnetic impoundments.

One of the most iconic Australian fish is the Murray cod, Maccullochella peelii (Mitchell 1838), a freshwater species that can grow to ∼1.8 metres in length and live to age ≥48 years. The Murray cod is of a conservation concern as a result of strong population contractions, but it is also popular for recreational fishing and is of growing aquaculture interest. In this study, we report the whole genome sequence of the Murray cod to support ongoing population genetics, conservation, and management research, as well as to better understand the evolutionary ecology and history of the species. A draft Murray cod genome of 633 Mbp (N50 = 109 974bp; BUSCO and CEGMA completeness of 94.2% and 91.9%, respectively) with an estimated 148 Mbp of putative repetitive sequences was assembled from the combined sequencing data of 2 fish individuals with an identical maternal lineage; 47.2 Gb of Illumina HiSeq data and 804 Mb of Nanopore data were generated from the first individual while 23.2 Gb of Illumina MiSeq data were generated from the second individual. The inclusion of Nanopore reads for scaffolding followed by subsequent gap-closing using Illumina data led to a 29% reduction in the number of scaffolds and a 55% and 54% increase in the scaffold and contig N50, respectively. We also report the first transcriptome of Murray cod that was subsequently used to annotate the Murray cod genome, leading to the identification of 26 539 protein-coding genes. We present the whole genome of the Murray cod and anticipate this will be a catalyst for a range of genetic, genomic, and phylogenetic studies of the Murray cod and more generally other fish species of the Percichthydae family.

Accounting for false mortality in telemetry tag applications

Evidence of multiple species of Chilodonella (Protozoa, Ciliophora) infecting Australian farmed freshwater fishes

Rates of hybridization and introgression are increasing dramatically worldwide because of translocations, restocking of organisms and habitat modifications; thus, determining whether hybridization is occuring after reintroducing extirpated congeneric species is commensurately important for conservation. Restocking programs are sometimes criticized because of the genetic consequences of hatchery-bred fish breeding with wild populations. These concerns are important to conservation restocking programs, including those from the Australian freshwater fish family, Percichthyidae. Two of the better known Australian Percichthyidae are the Murray Cod, Maccullochella peelii and Trout Cod, Maccullochella macquariensis which were formerly widespread over the Murray Darling Basin. In much of the Murrumbidgee River, Trout Cod and Murray Cod were sympatric until the late 1970s when Trout Cod were extirpated. Here we use genetic single nucleotide polymorphism (SNP) data together with mitochondrial sequences to examine hybridization and introgression between Murray Cod and Trout Cod in the upper Murrumbidgee River and consider implications for restocking programs. We have confirmed restocked riverine Trout Cod reproducing, but only as inter-specific matings, in the wild. We detected hybrid Trout Cod–Murray Cod in the Upper Murrumbidgee, recording the first hybrid larvae in the wild. Although hybrid larvae, juveniles and adults have been recorded in hatcheries and impoundments, and hybrid adults have been recorded in rivers previously, this is the first time fertile F1 have been recorded in a wild riverine population. The F1 backcrosses with Murray cod have also been found to be fertile. All backcrosses noted were with pure Murray Cod. Such introgression has not been recorded previously in these two species, and the imbalance in hybridization direction may have important implications for restocking programs.

Abstract Localized catastrophic events can dramatically affect fish populations. Management interventions, such as stocking, are often undertaken to re‐establish populations that have experienced such events. Evaluations of the effectiveness of these interventions are required to inform future management actions. Multiple hypoxic blackwater events in 2010–2011 substantially reduced fish communities in the Edward‐Wakool river system in the southern Murray‐Darling Basin, New South Wales, Australia. These events led to extensive fish kills across large sections of the entire system following a period of prolonged drought. To expedite recovery efforts, 119 661 golden perch Macquaria ambigua and 59 088 Murray cod Maccullochella peelii fingerlings were stocked at five locations over 3 years. All fish stocked were chemically marked with calcein to enable retrospective evaluation of wild or hatchery origin. Targeted collections were undertaken 3 years post‐stocking to investigate the relative contribution of stocking efforts and recovery via natural recruitment in the system. Of the golden perch retained for annual ageing (n = 93) only nine were of an age that could have coincided with stocking activities. Of those, six were stocked. The dominant year‐class of golden perch were spawned in 2009; before the stocking programme began and prior to blackwater events. All Murray cod retained (n = 136) were of an age that coincided with stocking activities, although only eight were stocked. Among the Murray cod captured, the dominant year‐class was spawned in 2011, after the blackwater events occurred. The results from this study provide first evidence that natural spawning and recruitment, and possibly immigration, were the main drivers of golden perch and Murray cod recovery following catastrophic fish kills. Interpreted in the context of other recent examples, the collective results indicate limited benefit of stocking to existing connected populations already naturally recruiting in riverine systems.

Megalocytiviruses cause high mortality diseases that have seriously impacted aquaculture, with the most frequent outbreaks occurring in East and South-East Asia. The international trade of juvenile fish for food and ornamental aquaculture has aided the spread of these viruses, which have spread to Europe and Australia and other regions. Australian freshwater fishes were examined for susceptibility to infection with the exotic megalocytivirus, dwarf gourami iridovirus (DGIV), which belongs to a group with the type species, Infectious spleen and kidney necrosis virus (ISKNV). Fish were held at 23±1°C and challenged by intraperitoneal (IP) injection or by cohabitation with Murray cod, Maccullochella peelii (Mitchell) infected with DGIV. A species was deemed to be susceptible to DGIV based on evidence of viral replication, as determined by qPCR, and megalocytic inclusion bodies observed histologically. Horizontal transmission occurred between infected Murray cod and golden perch, Macquaria ambigua (Richardson), Macquarie perch, Macquaria australasica (Cuvier) and Murray cod. This indicated that DGIV shed from infected fish held at 23°C can survive in fresh water and subsequently infect these naïve fish. Further, DGIV administered IP was highly pathogenic to golden perch, Macquarie perch and Murray cod. Compared to these species, the susceptibility of southern pygmy perch, Nannoperca australis (Gunther) was lower. Freshwater catfish (dewfish), Tandanus tandanus (Mitchell), were not susceptible under the experimental conditions based on the absence of clinical disease, mortality and virus replication. This study showed the potential risks associated with naïve and DGIV-infected fish sharing a common water source.

Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution).

A piecewise regression approach was used to objectively quantify barotrauma injury thresholds in two physoclistous species, Murray cod Maccullochella peelii and silver perch Bidyanus bidyanus, following simulated infrastructure passage in a barometric chamber. The probability of injuries such as swimbladder rupture, exophthalmia and haemorrhage, and emphysema in various organs increased as the ratio between the lowest exposure pressure and the acclimation pressure (ratio of pressure change, R(NE:A) ) reduced. The relationship was typically non-linear and piecewise regression was able to quantify thresholds in R(NE:A) that once exceeded resulted in a substantial increase in barotrauma injury. Thresholds differed among injury types and between species but by applying a multispecies precautionary principle, the maintenance of exposure pressures at river infrastructure above 70% of acclimation pressure (R(NE:A) of 0·7) should protect downstream migrating juveniles of these two physoclistous species sufficiently. These findings have important implications for determining the risk posed by current infrastructures and informing the design and operation of new ones.

Modelling population responses to flow: The development of a generic fish population model

Tail rot disease is the cause of significant economic damage in freshwater farmed Murray cod Maccullochella peelii. Only scarce information is available on Aeromonas hydrophila as a possible causal agent for this disease. In this study, a virulent strain, temporarily named XY3, was isolated from diseased codfish suffering from tail rot disease, and identified as A. hydrophila through phylogenetic analysis and phenotypic characteristics. A. hydrophila possesses multiple virulence genes including aerA, ahpA, alt, ast and hlyA genes. In addition, it appears that isolate XY3 has developed multiple resistances to cephalosporin, chloromycetin, glycopeptides, macrolides, nitrofuran, and penicillin drugs, as well as to aminoglycosides, sulfonamides, and tetracyclines antibiotics for veterinary uses in aquaculture as revealed when screened against a range of common antibiotics. To the best of our knowledge, this is the first report of tail rot disease caused by A. hydrophila in freshwater farmed codfish.

Many freshwater fish worldwide have been shown to use Structural Woody Habitat (SWH) for a variety of reasons. The mid reaches of the Murray River, a large lowland river in south-eastern Australia, was surveyed by boat electrofishing, to investigate the use of SWH type (hollows, rootmass and solids), SWH distance to bank (near bank, intermediate to bank and mid-channel) and the interaction between SWH type and distance to bank. The study found that Murray cod catch per unit effort (CPUE) increased in near-bank areas when hollows were a component of the SWH. The CPUE of trout cod was higher when hollows were present. However, the interactions between distance to bank and hollow SWH were complex and dependent on presence or absence of rootmass. The species-specific interactions between SWH microhabitat and distance to bank found within this study has important relevance for stream managers. The common practice of realigning SWH favours Murray cod over trout cod, which could have negative consequences for the endangered trout cod. More broadly, managers may need to consider a balance of SWH type and where it is placed in the river for the species they are targeting when rehabilitating rivers via the introduction of SWH.

Abstract The Murray Cod Maccullochella peelii and Golden Perch Macquaria ambigua are important recreational species in Australia's Murray–Darling Basin (MDB); both species have declined substantially, but recovery is evident in some areas. Minimum length limits (MLLs)—implemented to ensure fish could spawn at least once prior to harvest eligibility—have increased three times in the past decade. We quantified variation in length at 50% maturity (LM50), age at 50% maturity (AM50), and von Bertalanffy growth parameters (k = Brody growth coefficient; L∞ = asymptotic length; t0 = theoretical age at zero length) of these species within two rivers and two reservoirs of the MDB; to investigate whether fish length is a suitable surrogate for AM50 in setting MLLs. Between 2006 and 2013, we collected 1,118 Murray Cod and 1,742 Golden Perch by electrofishing and gillnetting. Values of k and L∞ were greater for reservoir fish than for riverine fish. For both species, AM50 was generally greater in rivers than in reservoirs; for Murray Cod, LM50 was greater in reservoirs than in rivers. A yield-per-recruit model demonstrated that smaller Murray Cod MLLs would be required for rivers and that an MLL at or below 600 mm (the existing MLL) across all populations could lead to overfishing in some systems. The differences in growth rate and the onset of reproductive maturation between riverine and reservoir populations suggest that system-specific regulations would be more effective at reducing the overfishing risk and meeting fishing quality objectives. Received August 18, 2014; accepted September 10, 2015

Stock enhancement is a management tool used for fishery recovery worldwide, yet the success of many stocking programs remains unquantified. Murray cod (Maccullochella peelii) and golden perch (Macquaria ambigua) are important Australian recreational target species that have experienced widespread decline. Stocking of these species has been undertaken for decades, with limited assessment of effectiveness. A batch marking and recapture approach was applied to assess stocked Murray cod and golden perch survival, contributions to wild fisheries, and condition in rivers and impoundments. Stocked fish were marked with calcein. Marked fish were detected during surveys undertaken 3 years and 10 months from initial marking, and it is probable that marks will persist beyond this time. The proportion of calcein marked fish in the population sub-sample whose age was equal to, or less than, the number of years since release, varied by 7–94% for Murray cod, and 9–98% for golden perch. Higher proportions of marked fish were found in impoundments than rivers. Marked Murray cod had significantly steeper length–weight relationships (i.e. higher weight at a given length) to unmarked fish. Our results show that application of methods for discriminating stocked and wild fish provides critical information for the development of adaptive, location-specific stocking strategies.