Rapid Fishery Assessment by Market Survey (RFAMS) – An Improved Rapid-Assessment Approach to Characterising Fish Landings in Developing Countries

The complex multi-gear, multi-species tropical fisheries in developing countries are poorly understood and characterising the landings from these fisheries is often impossible using conventional approaches. A rapid assessment method for characterising landings at fish markets, using an index of abundance and estimated weight within taxonomic groups, is described. This approach was developed for contexts where there are no detailed data collection protocols, and where consistent data collection across a wide range of fisheries types and geographic areas is required, regardless of the size of the site and scale of the landings. This methodology, which was demonstrated at seven fish landing sites/fish markets in southern Indonesia between July 2008 and January 2011, provides a rapid assessment of the abundance and diversity in the wild catch over a wide variety of taxonomic groups. The approach has wider application for species-rich fisheries in developing countries where there is an urgent need for better data collection protocols, monitoring future changes in market demographics, and evaluating health of fisheries.     

Species composition and aspects of the biology of Orectolobiformes from Indonesian waters

The biological aspects of members of the order Orectolobiformes exploited in Indonesian waters are given. Seven species belonging to five families were recorded in the catches at various landing sites in southern Indonesia. Of these, Chiloscyllium punctatum was the most abundant species landed, contributing >50% of the number of orectolobiforms recorded. The biological data obtained varied greatly between the species listed. The total length (L_T) at maturity for some species, e.g. C. punctatum and Nebrius ferrugineus, varied from that which has been previously recorded for those species in other regions. This highlights the need for regional‐specific biological data for fisheries managers and conservation assessors.     

A new model for the anaerobic fermentation of glycerol in enteric bacteria: trunk and auxiliary pathways in Escherichia coli

Anaerobic fermentation of glycerol in the Enterobacteriaceae family has long been considered a unique property of species that synthesize 1,3-propanediol (1,3-PDO). However, we have discovered that Escherichia coli can ferment glycerol in a 1,3-PDO-independent manner. We identified 1,2-propanediol (1,2-PDO) as a fermentation product and established the pathway that mediates its synthesis as well as its role in the metabolism of glycerol. We also showed that the trunk pathway responsible for the conversion of glycerol into glycolytic intermediates is composed of two enzymes: a type II glycerol dehydrogenase (glyDH-II) and a dihydroxyacetone kinase (DHAK), the former of previously unknown physiological role. Based on our findings, we propose a new model for glycerol fermentation in enteric bacteria in which: (i) the production of 1,2-PDO provides a means to consume reducing equivalents generated in the synthesis of cell mass, thus facilitating redox balance, and (ii) the conversion of glycerol to ethanol, through a redox-balanced pathway, fulfills energy requirements by generating ATP via substrate-level phosphorylation. The activity of the formate hydrogen-lyase and F(0)F(1)-ATPase systems were also found to facilitate the fermentative metabolism of glycerol, and along with the ethanol and 1,2-PDO pathways, were considered auxiliary or enabling. We demonstrated that glycerol fermentation in E. coli was not previously observed due to the use of medium formulations and culture conditions that impair the aforementioned pathways. These include high concentrations of potassium and phosphate, low concentrations of glycerol, alkaline pH, and closed cultivation systems that promote the accumulation of hydrogen gas.     

Anaerobic fermentation of glycerol by Escherichia coli: a new platform for metabolic engineering

The worldwide surplus of glycerol generated as inevitable byproduct of biodiesel fuel and oleochemical production is resulting in the shutdown of traditional glycerol-producing/refining plants and new applications are needed for this now abundant carbon source. In this article we report our finding that Escherichia coli can ferment glycerol in a pH-dependent manner. We hypothesize that glycerol fermentation is linked to the availability of CO(2), which under acidic conditions is produced by the oxidation of formate by the enzyme formate hydrogen lyase (FHL). In agreement with this hypothesis, glycerol fermentation was severely impaired by blocking the activity of FHL. We demonstrated that, unlike CO(2), hydrogen (the other product of FHL-mediated formate oxidation) had a negative impact on cell growth and glycerol fermentation. In addition, supplementation of the medium with CO(2) partially restored the ability of an FHL-deficient strain to ferment glycerol. High pH resulted in low CO(2) generation (low activity of FHL) and availability (most CO(2) is converted to bicarbonate), and consequently very inefficient fermentation of glycerol. Most of the fermented glycerol was recovered in the reduced compounds ethanol and succinate (93% of the product mixture), which reflects the highly reduced state of glycerol and confirms the fermentative nature of this process. Since glycerol is a cheap, abundant, and highly reduced carbon source, our findings should enable the development of an E. coli-based platform for the anaerobic production of reduced chemicals from glycerol at yields higher than those obtained from common sugars, such as glucose.     

Fermentative Utilization of Glycerol by Escherichia coli and Its Implications for the Production of Fuels and Chemicals

Availability, low prices, and a high degree of reduction make glycerol an ideal feedstock to produce reduced chemicals and fuels via anaerobic fermentation. Although glycerol metabolism in Escherichia coli had been thought to be restricted to respiratory conditions, we report here the utilization of this carbon source in the absence of electron acceptors. Cells grew fermentatively on glycerol and exhibited exponential growth at a maximum specific growth rate of 0.040 ± 0.003 h⁻¹. The fermentative nature of glycerol metabolism was demonstrated through studies in which cell growth and glycerol utilization were observed despite blocking several respiratory processes. The incorporation of glycerol in cellular biomass was also investigated via nuclear magnetic resonance analysis of cultures in which either 50% U-¹³C-labeled or 100% unlabeled glycerol was used. These studies demonstrated that about 20% of the carbon incorporated into the protein fraction of biomass originated from glycerol. The use of U-¹³C-labeled glycerol also allowed the unambiguous identification of ethanol and succinic, acetic, and formic acids as the products of glycerol fermentation. The synthesis of ethanol was identified as a metabolic determinant of glycerol fermentation; this pathway fulfills energy requirements by generating, in a redox-balanced manner, 1 mol of ATP per mol of glycerol converted to ethanol. A fermentation balance analysis revealed an excellent closure of both carbon (~95%) and redox (~96%) balances. On the other hand, cultivation conditions that prevent H₂ accumulation were shown to be an environmental determinant of glycerol fermentation. The negative effect of H₂ is related to its metabolic recycling, which in turn generates an unfavorable internal redox state. The implications of our findings for the production of reduced chemicals and fuels were illustrated by coproducing ethanol plus formic acid and ethanol plus hydrogen from glycerol at yields approaching their theoretical maximum.     

Species and size compositions and reproductive biology of rays (Chondrichthyes, Batoidea) caught in target and non-target fisheries in eastern Indonesia

Extensive surveys of various fish landing sites in eastern Indonesia, conducted between April 2001 and March 2006, recorded a total of 54 species of batoid rays belonging to 12 families. The Dasyatidae was by far the most speciose family, comprising half of the recorded species, and was also the most abundant, contributing 89 and 44% to the total numbers and total estimated biomass of batoids, respectively. The size and sex compositions of 23 species of rays are described and an accurate size at maturity of males, i.e. with 95% CI, was determined for 13 of these species. The sex ratios were found to be close to parity in the majority of species, however, the landings of the whitespotted guitarfish Rhynchobatus australiae consisted of significantly more females than males, a situation also recorded for this species in the by-catch of the northern Australian prawn fishery. Data on aspects of the reproductive biology of three dasyatid species ( Dasyatis cf. kuhlii , Dasyatis zugei and Himantura walga ), which form a substantial component of the by-catch of the bottom trawl fisheries in the region, were collected on most sampling occasions. These small rays, i.e. maximum sizes 243–379 mm disc width, were found to have no distinct seasonal reproductive cycle and small litter sizes, i.e. less than four embryos. Opportunistic reproductive data, e.g. litter size and embryo sizes, were also collected from various other species. The litter sizes of the rhynchobatid and rhinobatid species examined were found to be larger than those of the gymnurid and dasyatid species examined, i.e. seven to 19 and two to 13 v. one to four, respectively. The data presented in this paper for the numerous species of rays which are landed by target and non-target fisheries in Indonesia represent the first such data for the vast majority of these species.     

Age,growth and maturity of the pelagic thresher Alopias pelagicus and the scalloped hammerhead Sphyrna lewini

Indonesia has the greatest reported chondrichthyan catches worldwide, with c.110,000 t caught annually. The pelagic thresher (Alopias pelagicus) and scalloped hammerhead (Sphryna lewini) together comprise about 25% of the total catches of sharks landed in Indonesia. Age and growth parameters were estimated for A. pelagicus and S. lewini from growth‐band counts of thin‐cut vertebral sections. Alopias pelagicus (n = 158) and S. lewini (n = 157) vertebrae were collected from three Indonesian fish markets over a 5 year period. A multi‐model analysis was used to estimate growth parameters for both species. The models of best fit for males and females for A. pelagicus was the three‐parameter logistic (L_∞ = 3169 mm L_T, k = 0·2) and the two‐parameter von Bertalanffy models (L_∞ = 3281 mm L_T, k = 0·12). Age at maturity was calculated to be 10·4 and 13·2 years for males and females, respectively, and these are the oldest estimated for this species. The samples of S. lewini were heavily biased towards females, and the model of best fit for males and females was the three‐parameter Gompertz (L_∞ = 2598 mm L_T, k = 0·15) and the two‐parameter Gompertz (L_∞ = 2896 mm L_T, k= 0·16). Age at maturity was calculated to be 8·9 and 13·2 years for males and females, respectively. Although numerous age and growth studies have previously been undertaken on S. lewini, few studies have been able to obtain adequate samples from all components of the population because adult females, adult males and juveniles often reside in different areas. For the first time, sex bias in this study was towards sexually mature females, which are commonly lacking in previous biological studies on S. lewini. Additionally, some of the oldest aged specimens and highest age at maturity for both species were observed in this study. Both species exhibit slow rates of growth and late age at maturity, highlighting the need for a re‐assessment of the relative resilience of these two globally threatened sharks at current high levels of fishing mortality throughout the eastern Indian Ocean.     

High-throughput,cost-effective verification of structural DNA assembly

DNA ‘assembly’ from ‘building blocks’ remains a cornerstone in synthetic biology, whether it be for gene synthesis (∼1 kb), pathway engineering (∼10 kb) or synthetic genomes (>100 kb). Despite numerous advances in the techniques used for DNA assembly, verification of the assembly is still a necessity, which becomes cost-prohibitive and a logistical challenge with increasing scale. Here we describe for the first time a comprehensive, high-throughput solution for structural DNA assembly verification by restriction digest using exhaustive in silico enzyme screening, rolling circle amplification of plasmid DNA, capillary electrophoresis and automated digest pattern recognition. This low-cost and robust methodology has been successfully used to screen over 31 000 clones of DNA constructs at <$1 per sample.     

Elasmobranchs in southern Indonesian fisheries: the fisheries, the status of the stocks and management options

The biology of elasmobranchs makes them very vulnerable to fishing pressure and there is increasing international concern over their exploitation. In northern Australia the stocks of some species may be shared with those in southern Indonesia. Indonesia has the highest landings of elasmobranchs worldwide (>100,000 t p.a.) and millions of Indonesian artisanal fishers rely heavily on elasmobranchs taken in target fisheries. They are also taken by industrial trawlers and as bycatch in pelagic tuna fisheries. This paper, resulting from a collaborative project between Australia and Indonesia, summarises the elasmobranch fisheries; the characteristics of the fisheries are outlined, the status of the stocks are assessed, and management options described and discussed. The project focussed on representative markets and fish landing sites in southern Indonesia from 2001 to 2005. Data were from market surveys, the records of the Indonesian Directorate General of Capture Fisheries, and from research cruises. Data from the ongoing tuna monitoring programme showed that shark bycatch from the tuna fleets forms about 11% of shark landings in Indonesia. Yield per recruit and related analyses were used to integrate biological information to indicate the productivity of each species to allow for management policy options and constraints. Research cruise data show that catch rates of elasmobranchs in the Java Sea declined by at least one order of magnitude between 1976 and 1997. The results indicate strongly that many of the shark and ray species in Indonesia are overfished and that the most effective management strategy may need to involve capacity control, such as licencing, gear restrictions and catch limits, together with controls on the fin trade.