Genetic population structure of red snappers (Lutjanus malabaricus Bloch & Schneider, 1801 and Lutjanus erythropterus Bloch, 1790) in central and eastern Indonesia and northern Australia

The genetic population structure of red snapper Lutjanus malabaricus and Lutjanus erythropterus in eastern Indonesia and northern Australia was investigated by allozyme electrophoresis and sequence variation in the control region of mtDNA. Samples were collected from eight sites in Indonesia and four sites in northern Australia for both species. A total of 13 allozyme loci were scored. More variable loci were observed in L. malabaricus than in L. erythropterus. Sequence variation in the control region (left domain) of the mitochondrial genome was assessed by RFLP and direct sequencing. MtDNA haplotype diversity was high (L. erythropterus, 0.95 and L. malabaricus, 0.97), as was intraspecific sequence divergence, (L. erythropterus, 0.0-12.5% and L. malabaricus, 0.0-9.5%). The pattern of mtDNA haplotype frequencies grouped both species into two broad fisheries stocks with a genetic boundary either between Kupang and Sape (L. malabaricus) or between Kupang and Australian Timor Sea (L. erythropertus). The allozyme analyses revealed similar boundaries for L. erythropterus. Seven allozymes stocks compared to two mtDNA stocks of L. malabaricus including Ambon, which was not sampled with mtDNA, however, were reported. Possible reasons for differences in discrimination between the methods include: i) increased power of multiple allozyme loci over the single mtDNA locus, ii) insufficient gene sampling in the mtDNA control region and iii) relative evolutionary dynamics of nuclear (allozyme loci) and mitochondrial DNA in these taxa. Allozyme and haplotype data did not distinguish separate stocks among the four Australian locations nor the central Indonesian (Bali and Sape locations) for both L. malabaricus and L. erythropterus.

Henipavirus in Pteropus vampyrus Bats, Indonesia

The emergence of Nipah virus (NiV) in Malaysia in 1999 resulted in 265 known human infections (105 fatal), widespread infection in pigs (with >1 million culled to control the outbreak), and the collapse of the Malaysian pig export market. As with the closely related Hendra virus (HeV) that emerged in Australia in 1994 and caused fatal disease in horses and humans, bats of the genus Pteropus (commonly known as flying foxes) were identified as the major reservoir of Nipah virus in Malaysia. This report describes a serologic survey of Pteropus vampyrus in neighboring Indonesia.

Rice responses to soil management in a rice-based cropping system in the semi-arid tropics of southern Lombok, Eastern Indonesia

This paper is the first of a series that investigates whether new cropping systems with permanent raised beds (PRBs) or Flat land could be successfully used to increase farmers' incomes from rainfed crops in Lombok in Eastern Indonesia. This paper discusses the rice phase of the cropping system. Low grain yields of dry-seeded rice (Oryza sativa) grown on Flat land on Vertisols in the rainfed region of southern Lombok, Eastern Indonesia, are probably mainly due to (a) erratic rainfall (870-1220 mm/yr), with water often limiting at sensitive growth stages, (b) consistently high temperatures (average maximum - 31 C), and (c) low solar radiation. Farmers are therefore poor, and labour is hard and costly, as all operations are manual. Two replicated field experiments were run at Wakan (annual rainfall = 868 mm) and Kawo (1215 mm) for 3 years (2001/2002 to 2003/2004) on Vertisols in southern Lombok. Dry-seeded rice was grown in 4 treatments with or without manual tillage on (a) PRBs, 1.2 m wide, 200 mm high, separated by furrows 300 mm wide, 200 mill deep, with no rice sown in the well-graded furrows, and (b) well-graded Flat land. Excess surface water was harvested from each treatment and used for irrigation after the vegetative stage of the rice. All operations were manual. There were no differences between treatments in grain yield of rice (mean grain yield = 681 g/m(2)) which could be partly explained by total number of tillers/hill and mean panicle length, but not number of productive tillers/hill, plant height or weight of 1000 grains. When the data from both treatments on PRBs and from both treatments on Flat land, each year at each site were analysed, there were also no differences in grain yield of rice (g/m(2)). When rainfall in the wet season up to harvest was over 1000 mm (Year 2; Wakan, Kawo), or plants were water-stressed during crop establishment (Year 1; Wakan) or during grain-fill (Year 3: Kawo), there were significant differences in grain yield (g/1.5 m(2)) between treatments; generally the grain yield (g/1.5 m(2)) on PRBs with or without tillage was less than that on Flat land with or without tillage. However, when the data from both treatments on PRBs and from both treatments on Flat land, each year at each site, were analysed, the greater grain yield of dry-seeded rice on Flat land (mean yield 1 092 g/1.5 m(2)) than that on PRBs (mean 815 g/1.5 m(2)) was mainly because there were 25% more plants on Flat land. Overall when the data in the 2 outer rows and the 2 inner rows on PRBs were each combined, there was a higher number of productive tillers in the combined outer rows (mean 20.7 tillers/hill) compared with that in the combined inner rows on each PRB (mean 18.2 tillers/hill). However, there were no differences in grain yield between combined rows (mean 142 g/m row). Hence with a gap of 500 mm (the distance between the outer rows of plants on adjacent raised beds), plants did not compensate in grain yield for missing plants in furrows. This suggests that rice (a) also sown in furrows, or (b) sown in 7 rows with narrower row-spacing, or (c) sown in 6 rows with slightly wider row-spacing, and narrower gap between outer rows on adjacent beds, may further increase grain yield (g/1.5 m(2)) in this system of PRBs. The growth and the grain yield (y in g/m(2)) of rainfed rice (with rainfall on-site the only source of water for irrigation) depended mainly on the rainfall (x in mm) in the wet season up to harvest (due either to site or year) with y = 1. 1x -308; r(2) = 0.54; p < 0.005. However, 280 mm (i.e. 32%) of the rainfall was not directly used to produce grain (i.e. when y = 0 g/m(2)). Manual tillage did not affect growth and grain yield of rice (g/m(2); g/1.5 m(2)), either on PRB or on Flat land.

Scalloped Hammerhead microsatellite genotypes (eight loci) representing five regions on Australia's east coast and one location in central Indonesia.

Biodiversity of sharks in the tropical Indo-Pacific is high, but species-specific information to assist sustainable resource exploitation is scarce. The null hypothesis of population genetic homogeneity was tested for scalloped hammerhead shark (Sphyrna lewini, n=244) and the milkshark (Rhizoprionodon acutus, n=209) from northern and eastern Australia, using nuclear (S. lewini, eight microsatellite loci; R. acutus, six loci) and mitochondrial gene markers (873 base pairs of NADH dehydrogenase subunit 4). We were unable to reject genetic homogeneity for S. lewini, which was as expected based on previous studies of this species. Less expected were similar results for R. acutus, which is more benthic and less vagile than S. lewini. These features are probably driving the genetic break found between Australian and central Indonesian R. acutus (F-statistics; mtDNA, 0.751 to 0.903; microsatellite loci, 0.038 to 0.047). Our results support the spatially-homogeneous management plan for shark species in Queensland, but caution is advised for species yet to be studied.

Milkshark (Rhizoprionodon acutus) microsatellite genotype data (six loci) from samples collected from five locations in eastern Australia and central Indonesia.

Biodiversity of sharks in the tropical Indo-Pacific is high, but species-specific information to assist sustainable resource exploitation is scarce. The null hypothesis of population genetic homogeneity was tested for scalloped hammerhead shark (Sphyrna lewini, n=244) and the milkshark (Rhizoprionodon acutus, n=209) from northern and eastern Australia, using nuclear (S. lewini, eight microsatellite loci; R. acutus, six loci) and mitochondrial gene markers (873 base pairs of NADH dehydrogenase subunit 4). We were unable to reject genetic homogeneity for S. lewini, which was as expected based on previous studies of this species. Less expected were similar results for R. acutus, which is more benthic and less vagile than S. lewini. These features are probably driving the genetic break found between Australian and central Indonesian R. acutus (F-statistics; mtDNA, 0.751 to 0.903; microsatellite loci, 0.038 to 0.047). Our results support the spatially-homogeneous management plan for shark species in Queensland, but caution is advised for species yet to be studied.

Lobster aquaculture development in Indonesia, Vietnam and Australia

This project will support the sustainable development of lobster farming in Indonesia to meet global demand for tropical lobsters at high prices (>$US60 /kg). It will also address sustainability issues for the lobster farming industry in Vietnam and provide verification of lobster growout at commercial scale in Australia. The project will adapt technologies developed in Vietnam and apply them in Indonesia to establish a village-based industry for impoverished coastal communities. The Australian component will assess land-based growout systems to prepare for the likely availability of hatchery-reared lobster seed. Hatchery technology is currently being commercialised in Queensland through a partnership between DEEDI and Lobster Harvest Pty Ltd.

Improving production of cows and fattening cattle in Indonesia and north Australia

To increase numbers and reproduction in Ongole and Bali cows by as much as 60% in Indonesia requires use of rice straw for maintenance of cows and higher quality feed and crop by-products for growth and fattening of calves. These feedstuffs exist in large quantities. The project will couple feeding systems with management (controlled mating with a selected bull, weaning, compost production), previously developed by the project team, in village-based adaptive research across the main cattle regions of Indonesia, with emphasis on East Java. The project will link with research on nutrition interactions with reproduction of cows in indigenous pastoral systems in north Australia.

Spiny lobster aquaculture development in eastern Indonesia, Vietnam and Australia

The project was successful across all objectives, making demonstrable progress in support of establishing tropical lobster farming in Indonesia. The industry remains most active in Lombok where lobster seed resources are most abundant, and impact has been greatest there. Nevertheless, project activities have established activity and interest in lobster farming in other provinces and particularly Aceh and, South and Southeast Sulawesi. The project met all of its 23 milestones with the exception of publishing a production manual, which has been held over until 2017. For several milestone activities, further research will be required to build on the outcomes generated and reach practical commercial outputs. The research was instigated to address the opportunity to establish a significant small-holder based industry in Indonesia that could alleviate poverty in coastal communities. The premise was that such an industry – lobster farming, had been established in Vietnam, with ACIAR involvement, and it could be replicated in Indonesia where the availability of necessary basic requirements had been confirmed through a previous ACIAR project focussed in Vietnam (FIS/2001/058). The broad aim was to assess, develop and expand the resources of naturally settling lobster seed (puerulus), and develop grow out of those seed to meet export market demand. This was to be achieved by adapting and transferring to Indonesia technology from Vietnam, where lobster farming had become a successful industry producing 1,500 tonnes of export quality lobsters valued at $A100 million.

Sustainable productivity improvements in allium and solanaceous vegetable crops in Indonesia and sub-tropical Australia

The most important vegetable crops grown in Indonesia, and particularly lowland coastal production, are the true shallot and chilli. These crops are usually grown in rotation with rice but are far more valuable crops and are increasingly in high demand. They offer an opportunity for small farmers to generate extra income, increase farm profitability and shift away from subsistence production. However, the yield and profitability of shallot and chilli production is severely limited by a range of agronomic constraints. This project aims towards raising the productivity of allium (shallot and garlic) and chilli/capsicum cropping systems. The methodology will include a benchmarking survey and review of grower practices. This will be supplemented with physical surveys of crops for disease incidence and efficiency of fertiliser use. Once surveys are completed in Indonesia and the important pathogens identified, recommendations can be made for disease management. This will include review of chemical usage in Indonesia and Australia to provide best management guidelines for the application of insecticides, fungicides and other chemicals.

ACIAR Productivity and profitability enhancing tropical pulses in Indonesia and Australia

The project aims at improving the productivity and profitability of mung beans, soy beans and peanuts.

Liveweight gain and feed intake of weaned Bali cattle fed a range of diets in Central Sulawesi, Indonesia

Three experiments were conducted to determine liveweight (W) gain and feed and water intake of weaned Bali cattle offered a range of feed types. In each experiment, 18 weaned entire male Bali cattle were allocated to three treatment groups in a completely randomised block design, with six replicates (animals) per treatment. The dietary treatments were: Experiment 1, native grass fed ad libitum, native grass supplemented with rice bran at 10 g dry matter (DM)/kg W.day and native grass supplemented with a mixture of rice bran and copra meal in equal proportions fed at 10 g DM/kg W.day; Experiment 2, elephant grass hay fed ad libitum, elephant grass supplemented with gliricidia at 10 g DM/kg W.day, and gliricidia fed ad libitum; and Experiment 3, corn stover fed ad libitum, corn stover supplemented with gliricidia at 10 g DM/kg W.day, and corn stover supplemented with rice bran/copra meal in equal amounts (w/w) at 10 g DM/kg W.day. Each experiment was 10 weeks in duration, consisting of a 2-week preliminary period for adaptation to diets and an 8-week experimental period for the measurement of W change, feed and water intake and digestibility of the diet. Growth rates of 6-12-month-old, entire male Bali cattle fed a range of local diets ranged from 0.10 and 0.40 kg/day. Lowest growth rates occurred when the cattle were given the basal diets of native grass (0.104 kg/day), elephant grass (0.174 kg/day) and corn stover (0.232 kg/day). With the addition of supplements such as rice bran, rice bran/copra meal or gliricidia to these basal diets liveweight gains increased to between 0.225 and 0.402 kg/day. Forage DM intake was reduced with these supplements by on average 22.6% while total DM intake was increased by an average of 10.5%. The growth rate on gliricidia alone was 0.269 kg/day and feed DM intake was 28.0 g/kg W.day. Water intake was not affected by supplement type or intake. In conclusion, inclusion of small quantities of locally available, high quality feed supplements provide small-holder farmers with the potential to increase growth rates of Bali calves from 0.1 to 0.2 kg/day, under prevailing feeding scenarios, to over 0.4 kg/day.

Nipah Virus in the Fruit Bat Pteropus vampyrus in Sumatera, Indonesia

Nipah virus causes periodic livestock and human disease with high case fatality rate, and consequent major economic, social and psychological impacts. Fruit bats of the genus Pteropus are the natural reservoir. In this study, we used real time PCR to screen the saliva and urine of P. vampyrus from North Sumatera for Nipah virus genome. A conventional reverse transcriptase (RT-PCR) assay was used on provisionally positive samples to corroborate findings. This is the first report of Nipah virus detection in P. vampyrus in Sumatera, Indonesia.

Genera of the leaf-feeding Dendrothripinae of the world (Thysanoptera, Thripidae), with new species from Australia and Sulawesi, Indonesia

Character states used in distinguishing taxa within the Thripidae subfamily Dendrothripinae are discussed, and a key presented to the 11 genera recognized worldwide. Comments on each of these genera are provided, together with keys to the species from Australia of Dendrothrips, Ensiferothrips and Pseudodendrothrips. From Australia are described, four new species of Dendrothrips, one of Pseudodendrothrips, and a remarkable new species of Ensiferothrips that has required a re-diagnosis of that genus. Another new species of Ensiferothrips is described from Sulawesi, thus greatly extending the known geographical range of this previously Australian genus. © 2016 Magnolia Press.

Collecting banana diversity in eastern Indonesia

Major diseases, including Fusarium wilt tropical race 4, threaten banana production systems worldwide. New sources of genetic resistance are considered necessary in the fight against such diseases. The triangular region of Indonesia taking in Sulawesi, the Maluku Islands and Lesser Sunda Islands was prioritized by the Global Musa Genetic Resources Network, MusaNet for exploration and collecting. It is just east of the Wallace Line, which is recognized as a transition zone for flora in southeast Asia, and had been little explored. Bioversity International funded a team of scientists from Indonesia and Australia to make collecting missions in the triangle in October 2012 and February 2013. Suckers and seeds of 35 promising new accessions were collected. About 90% of these are either wild species or diploid cultivars of more direct use to breeding programs. These were morphologically characterized during the collecting missions and included a set of photographs recommended by Bioversitys Taxonomic Advisory Group. Cigar leaf samples were also collected and sent as fresh samples to the International Banana Genotyping Centre in the Czech Republic. Ploidy and DNA (SSR) genotyping determinations from these samples have been invaluable in quickly interpreting and better appreciating what has been discovered. The new accessions have been grown on at Solok field collection, West Sumatra and will be made available by Indonesia to the international community, including breeding programs, for evaluation and utilization. Information on wild Eumusa prompts a rethinking of the phytogeography of Musa acuminata. The variation within the Australimusa species M. lolodensis highlights the need for broader study of this Musa section. French Plantain-like edible AAs and prospects for the generation of African plantains in the region were identified. The mission indicated existence of local edible ABs in eastern Indonesia in association with balbisiana hybrids origins in the region. Further explorations in the region should add to Musa diversity knowledge.

Biodiversity of Australian smut fungi.

There are about 250 species of smut fungi known from Australia of which 95 are endemic. Fourteen of these endemic species were first collected in the period culminating with the publication of Daniel McAlpine's revision of Australian smut fungi in 1910. Of the 68 species treated by McAlpine, 10 were considered to be endemic to Australia at that time. Only 23 of the species treated by McAlpine have names that are currently accepted . During the following eighty years until 1990, a further 31 endemic species were collected and just 11 of these were named and described in that period. Since 1990, 50 further species of endemic smut fungi have been collected and named in Australia . There are 115 species that are restricted to either Australia or to Australia and the neighbouring countries of Indonesia, New Zealand, Papua New Guinea and the Philippines . These 115 endemic species occur in 24 genera, namely Anthracoidea (1 species), Bauerago (1), Cintractia (3), Dermatosorus (1), Entyloma (3), Farysporium (1), Fulvisporium (1), Heterotolyposporium (1), Lundquistia (1), Macalpinomyces (4), Microbotryum (2), Moreaua (20), Pseudotracya (1), Restiosporium (5), Sporisorium (26), Thecaphora (2), Tilletia (12), Tolyposporella (1), Tranzscheliella (1), Urocystis (2), Ustanciosporium (1), Ustilago (22), Websdanea (1) and Yelsemia (2). About a half of these local and regional endemic species occur on grasses and a quarter on sedges . The northern tropical savannah region of Australia offers most promise for the discovery of new endemic species . The agricultural, quarantine and environmental significance to Australia of some introduced species is discussed.