Piscine orthoreovirus: Biology and distribution in farmed and wild fish

Piscine orthoreovirus (PRV) is a common and widely distributed virus of salmonids. Since its discovery in 2010, the virus has been detected in wild and farmed stocks from North America, South America, Europe and East Asia in both fresh and salt water environments. Phylogenetic analysis suggests three distinct genogroups of PRV with generally discrete host tropisms and/or regional patterns. PRV-1 is found mainly in Atlantic (Salmo salar), Chinook (Oncorhynchus tshawytscha) and Coho (Oncorhynchus kisutch) Salmon of Europe and the Americas; PRV-2 has only been detected in Coho Salmon of Japan; and PRV-3 has been reported primarily in Rainbow Trout (Oncorhynchus mykiss) in Europe. All three genotypes can establish high-load systemic infections by targeting red blood cells for principal replication. Each genotype has also demonstrated potential to cause circulatory disease. At the same time, high-load PRV infections occur in non-diseased salmon and trout, indicating a complexity for defining PRV's role in disease aetiology. Here, we summarize the current body of knowledge regarding PRV following 10 years of study.     

Patterns of fish movement at a desert river confluence

Quantifying fish movements in river networks helps identify critical habitat needs and how they change with environmental conditions. Some of the challenges in tracking fish movements can be overcome with the use of passive integrated transponder (PIT) tagging and antennas. We used PIT technology to test predictions of movement behaviour for four fish species at a mainstem–tributary confluence zone in an arid‐land river system. Specifically, we focused on the McElmo Creek tributary confluence with the San Juan River in south‐western Utah, USA. We quantified variation in species occurrences at this confluence zone from May 2012 to December 2015 relative to temporal and environmental conditions. We considered occurrences among species relative to tagging origins (tributary versus mainstem), season and time of day. Generally, fishes tagged in the focal tributary were more likely to be detected compared to fish tagged in the mainstem river or other tributaries. Additionally, adults were most likely to be detected across multiple years compared to subadults. Based on a Random Forests model, the best performing environmental variables for predicting seasonal detections included mainstem discharge during run‐off season (razorback sucker Xyrauchen texanus), tributary discharge during monsoon season (Colorado pikeminnow Ptychocheilus lucius) and mainstem water temperature (flannelmouth sucker Catostomus latipinnis and channel catfish Ictalurus punctatus). The variable responses by endemic and introduced fishes indicate tributary habitats provide several key functions within a fish community including spawning, rearing, foraging and refuge.     

Thermal performance curves based on field movements reveal context-dependence of thermal traits in a desert ectotherm

Landscape Ecology - Thermal traits likely mediate organismal responses to changing thermal environments. As temperatures increase, predicting species responses will depend on understanding how...     

Grassland fragmentation affects declining tallgrass prairie birds most where large amounts of grassland remain

Landscape Ecology - Habitat fragmentation can exacerbate the negative effects of habitat loss for some species. Mitigating fragmentation is difficult, however, because population responses depend...     

First evidence of spawning migration by goldfish (Carassius auratus); implications for control of a globally invasive species

Goldfish (Carassius auratus) was one of the first fishes to be domesticated and has been widely introduced across the globe, but is now considered one of the world's worst invasive aquatic species. Surprisingly, there is a dearth of information on its spatial and temporal movement patterns, which hampers the development of effective control programmes. We examined the movement patterns of an introduced population of C. auratus in a south‐western Australian river using passive acoustic telemetry. The study population had a high residency index within the array (i.e. proportion of all days at liberty that, on average, each fish was detected by a receiver) with fish being detected on 64% of days. The individuals were also reasonably mobile, travelling a mean of 0.30 km (linear river kilometres).day^‐1 within the array, and one fish moved 231.3 km over the 365‐day study period (including 5.4 km in a 24 hr period). Importantly, C. auratus displayed significant seasonal movement patterns including a clear shift in habitats during its breeding period with most mature individuals being detected in an off‐channel wetland during that time. The results of this study strongly suggest that C. auratus undertook a spawning migration into a lentic habitat. These results have important implications for developing control programmes for the species, such as targeting connections to off‐channel lentic systems during its breeding period.     

Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications

Background

Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit “sweet spot” for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice.

Results

Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina’s production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material.

Conclusions

The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.

     

Changes in phosphorus fractions in three tropical soils amended with corn cob and rice husk biochars

ABSTRACT

The formation of phosphorus (P) compounds including iron-P, aluminum-P and calcium-P in highly weathered tropical soils can be altered upon biochar addition. We investigated the effect of corn cob biochar (CC) and rice husk biochar (RH) pyrolyzed at three temperatures (300°C, 450°C and 650°C) on phosphorus (P) fractions of three contrasting soils. A 90d incubation study was conducted by mixing biochar with soil at a rate of 1% w/w and at 70% field capacity. Sequential P fraction was performed on biochar, soil and soil-biochar mixtures. Increase in most labile P (resin-P_i, NaHCO₃-P_i) and organic P fraction (NaHCO₃-P_o + NaOH-P_o) in CC and RH biochars were inversely related to increasing temperature. HCl-P_i and residual P increased with increasing temperature. Interaction of CC and RH with soils resulted in an increase in most labile P as well as moderately labile P (NaOH-P_i) fractions in the soils. CC increased most labile P in the soils more than RH. The increase in most labile P fraction in soils was more significant at relatively lower temperatures (300°C and 450°C) than 650°C. However, the increase in HCl-P_i and residual P of the soils was more predominant at high temperature (650°C). The study suggested that biochar pyrolyzed at 300–450°C could be used to increase P bioavailability in tropical soils.     

Survival and behavioural responses of cool and warm water fish sedated with AQUI‐S®20E (10% eugenol) at high loading densities

This study evaluated the effects of AQUI‐S^®20E (10% eugenol) sedation on the survival and behaviour of yellow perch Perca flavescens (Mitchill) and Nile tilapia Oreochromis niloticus L. held in high loading densities. Fish were held in 0–300 mg L^?1 AQUI‐S^®20E (0–30 mg L^?1 eugenol) for up to 10 h in static tanks. At 17°C, yellow perch held in 200 and 300 mg L^?1 AQUI‐S^®20E were lightly sedated for up to 7 h. Yellow perch at 200 and 300 mg L^?1 AQUI‐S^®20E also had >95% mean survival 7‐days post exposure using loading densities up to 360 g L^?1. Nile tilapia were only sedated for ≤3 h in concentrations up to 300 mg L^?1 at 22°C and had >90% mean survival at loading densities ≤480 g L^?1. Ammonia in tanks increased significantly as loading density increased, but treatment with AQUI–S^®20E did not reduce ammonia accumulation. Results suggest that AQUI–S^®20E was effective to sedate yellow perch and Nile tilapia at high loading densities, but sedation varied with loading density and species.