Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI565

Rhizobium leguminosarum bv. trifolii SRDI565 (syn. N8-J) is an aerobic,motile, Gram-negative, non-spore-forming rod. SRDI565 was isolated from anodule recovered from the roots of the annual clover Trifolium subterraneum subsp. subterraneum grown in thegreenhouse and inoculated with soil collected from New South Wales, Australia. SRDI565has a broad host range for nodulation within the clover genus, however N2-fixationis sub-optimal with some Trifoliumspecies and ineffective with others. Here we describe the features of R. leguminosarum bv. trifolii strain SRDI565, together with genomesequence information and annotation. The 6,905,599 bp high-quality-draft genomeis arranged into 7 scaffolds of 7 contigs, contains 6,750 protein-coding genesand 86 RNA-only encoding genes, and is one of 100 rhizobial genomes sequencedas part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia forBacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

Complete genome sequence of Rhizobium leguminosarum bv trifolii strain WSM2304, an effective microsymbiont of the South American clover Trifolium polymorphum

Rhizobium leguminosarum bv. trifolii is the effective nitrogen fixing microsymbiont of a diverse range of annual and perennial Trifolium (clover) species. Strain WSM2304 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from Trifolium polymorphum in Uruguay in 1998. This microsymbiont predominated in the perennial grasslands of Glencoe Research Station, in Uruguay, to competitively nodulate its host, and fix atmospheric nitrogen. Here we describe the basic features of WSM2304, together with the complete genome sequence, and annotation. This is the first completed genome sequence for a nitrogen fixing microsymbiont of a clover species from the American centre of origin. We reveal that its genome size is 6,872,702 bp encoding 6,643 protein-coding genes and 62 RNA only encoding genes. This multipartite genome was found to contain 5 distinct replicons; a chromosome of size 4,537,948 bp and four circular plasmids of size 4,537,948, 1,266,105, 501,946, 308,747 and 257,956 bp.

Production of Australian freshwater crayfish in earthen-based systems using pelleted diets and forage crops as food

Juvenile Cherax destructor (commonly called theyabby) were cultured in earthen-based ponds and tanks for 70–105d, and were fed pellets and/or a forage crop of the perennialwhiteclover, Trifolium repens. Three supplementary feedingstrategies were evaluated. Yabby growth on pellets consistently exceeded (by67–159%) that obtained on clover. Base-line yields for extensiveproduction systems are around 400 kg ha^–1. Thesupplementary addition of T. repens produced yields of 635kg ha^–1 (in ponds) to 1086 kgha^–1 (in tanks). The sequential addition of cut-cloverto tanks stimulated growth to levels approaching those achieved on pellets.Yabbies stocked into ponds at 17 m^–2 and fed 33%protein pellets for 100 d, resulted in a yield of 1117 kgha^–1.Pellet inputs at a rate of 129–249 g m^–2(dry matter) and 38–83 g m^–2 (protein) over70–100 d resulted in acceptable growth and feed utilisationindices. Clover inputs of 534–682 g m–2 (asdry matter) or 84–177 g m^–2 (as protein)produced reasonable growth rates but poor feed utilisation indices. Aconsiderable quantity of the dry matter and protein content of clover waseitherinefficiently utilised or directed into other production pathways. In tanks,clover inputs from 113–296 g m^–2 (drymatter) and 24–54 g m^–2 (protein) weresufficient to maintain high growth rates for 4 weeks, while in ponds, inputs of21 g m^–2 (dry matter) and 4.3 gm^–2 (protein) were sufficient for 3 weeks. During theearly weeks of production no growth advantage was gained by providing pelletstoanimals cultured in forage-based systems. Forage depletion occurred after3–4 weeks and was probably a major growth limiting factor.

Nutrition, growth and production of Cherax Destructor Clark, 1936 (Decapoda, Parastacidae)

In this study the nutrition, growth and production of C. destructor was examined. Selected nutritional requirements of juvenile animals were determined under controlled conditions with the aim of developing a pelleted diet for use in hatcheries, nurseries and growout situations. The best developed diet was assessed for its potential as a supplementary feed for animals cultured in earthen environments. The protein requirements were first determined simultaneously with an evaluation of the effect of replacing animal protein (fishmeal) by soybean meal. Juveniles were reared communally for 59 d on isoenergetic diets containing 15-30% protein and graded levels of soybean meal (0-60%, of protein). When soybean meal was included at a level of 40-60%, growth was reduced relative to that achieved with control diets containing 15% and 20% protein, but this was not the case at a 20% soybean meal substitution level. A two-way interaction occurred between dietary protein and soybean meal content. Higher protein feeds enabled higher soybean meal inclusion levels without significantly affecting growth. Protein increases of 5% produced better growth at the 40% and 60% soybean meal substitution levels. This effect was less pronounced in the control and the 20% soybean meal diets. Carcass %protein increased and %lipid decreased as dietary protein increased. A similar effect occurred by increasing the soybean meal level to 60%. No obvious trend in carcass moisture, energy, and ash occurred. A protein requirement of 30% was apparent when fish meal and soybean meal were included in diets at levels of 20% and 24% (dry matter) respectively. Alternative protein sources to soybean meal were subsequently identified. Juveniles were maintained for 12 weeks on isoenergetic diets containing 30% protein and differing in the primary source of protein used, with meat, snail, soybean, yabby, and zooplankton meals comprising the major protein ingredient. No significant difference occurred in mean weight (MW), percentage weight gain (%WG), SGR or survival among diets. Food conversion ratios (FCR) were low, with a minimum value of 0.95 for the snail-based diet. The apparent net protein utilisation (ANPU) varied from 29.6% (zooplankton-based diet) to 41.2% (snail-based diet). Carcass composition varied with diet, with the greatest difference occurring in carapace colour. Animals fed the zooplankton-based diet developed the strongest, most natural pigmentation. A new combination of previously used protein-based ingredients was subsequently tested with reference to two yabby species, Cherax albidus and Cherax destructor, that were grown simultaneously in identical conditions. Juvenile male animals were reared individually for 20 weeks on isoenergetic diets containing 15% or 30% protein with fish meal, soybean meal, yabby meal and wheat products forming the basis of the diets. C albidus grew the fastest and utilised the food the most effectively. Carcass composition was influenced by diet with the 30% protein diet resulting in an increase in carcass protein and ash and a decrease in carcass lipid and energy relative to the low protein diet. Carcass moisture and calcium were not affected by diet. The intermoult period (IP) was highly dependent on the premoult weight (W) but the mean moult increment (WI, as weight) was independent of the PM. The orbital carapace length (OCL) and the abdominal length (ABL) %moult increments generally declined with an increase in PM whereas the propus length (PL) %moult increment generally increased. The IP, WI, %OCL, %ABL, and %PL moult increments varied according to diet and to species. Elevated dietary protein caused a reduction to the IP (for similar sized animals) by 11 d and 7 d and an increase to the WI by 85% and 81% in C. albidus and C destructor respectively. Dietary induced morphological changes also occurred. Animals of a standard OCL (both species) had significantly larger abdomens when fed the higher protein diet. Growth on the best developed diet was compared to the growth obtained on a natural diet of freshwater zooplankton. Juveniles were reared individually for 12 weeks on the two diets. The MW, %WG and SGR were higher for the zooplankton diet. Carcass composition was influenced by diet and the zooplankton fed animals had a higher carcass %protein, %lipid, %ash and %fibre content and were more richly pigmented than animals fed pellets. The IP and the WI were highly dependent on the PM and varied according to diet; feeding with zooplankton reduced the IP by 1.2 days and increased the WI by 13.7% compared to pellets. Nutrient digestibility was determined for the pelleted diets evaluated in the growth trials. Protein digestibility (PD) and dry matter digestibility (DMD), using chromic oxide (Cr2O3) as an exogenous marker, were high for all diets, at around 93% and 83% respectively. Ash digestibility varied considerably from 17% to 73% for the snail and yabby meal diets respectively. Crude fibre digestibility was around 50% and probably indicates cellulase activity. Alternative markers to Cr2O3 were evaluated. Ash was considered to be the most suitable alternative to Cr2O3, providing a reasonable, albeit lower, estimate of nutrient digestibility. Cr2O3 and ash were preferentially excreted whereas fibre was retained in the digestive system for a longer period, consequently, the collection of a particular fraction of the deposited faeces (late or early) substantially affected the digestibility coefficients. In earthen-based environments, animals fed the best developed diet were compared to animals cultured using a forage crop of clover (Trifolium repens). Three supplementary feeding strategies representing varying levels of management intensity were evaluated in a series of trials conducted in ponds and pond microcosms. Growth on pellets consistently exceeded that obtained with the forage crop, with final MW being 67-159% higher than that using clover and appeared to be the result of direct pellet consumption and from a pellet fertiliser effect (on the sediment). Within-pond DMD and PD were high and similar for each treatment (DMD = 51-58%; PD = 89-92%). In the control pond, DMD and PD increased with each successive flood. The faecal egestion rate (PER) decreased with each successive flood in all ponds, and is negatively related to animal weight and to foregut fullness (FF) according to power curves. FF was consistently lowest in the control pond. Mean FF was 48.5%, 62.3%, and 26.7% for the pellet, crop and control ponds respectively. FF increased to the third flood in each pond. The foregut protein content was high in all samples and the mean values were 33.9%, 32.7% and 35.6% for the pellet, crop and control ponds respectively. Foregut ash was highly variable within each pond and is inversely related to the foregut protein content. In the control and pellet ponds the highest foregut ash content occurred during flood 1. The culture system (aquaria or pond) strongly influenced the composition of the foregut content. The foregut of animals fed the manufactured diet (B2) in ponds contained approximately 176% more ash and 5% more protein than the foregut of animals fed in bare-bottom tanks. The FF of the tank fed animals was approximately 45% higher than the FF of pond fed animals after a similar feeding period. Base-line yields for extensive production systems appeared to be around 400kg ha-1. The supplementary addition of T. repens produced yields of approximately 635kg ha-1 (in ponds) to around 1086kg ha-1 (in tanks). The sequential addition of cut-clover to tanks stimulated growth to levels approaching those achieved on pellets. Yabbies stocked into ponds at 15-20 m-2 with a mean weight of 2.67g and fed a 30% protein pelleted diet for 100 d, resulted in a yield of approximately 1117kg ha-1, but only 2% of the population were above a marketable size of 50g. The feed utilisation indices were better for animals reared on pellets in bare-bottom tanks than in earthen environments, indicating some degree of pellet wastage when natural feeds are simultaneously present. High apparent food conversion ratios and low protein efficiency ratios occurred when the forage crop was provided. A considerable quantity of the dry matter and protein content of the forage crop was either inefficiently utilised or directed into other production pathways. Sowing a forage crop into pond microcosms to which a pelleted diet was also provided, did not enhance growth performance. Pelleted feed inputs at a rate of approximately 129g m-2 to 198g m-2 (dry matter) and 38g -2 to 64g m-2 (protein) over 70-100 d resulted in acceptable growth and feed utilisation indices for animals reared in ponds and pond microcosms. Forage crop inputs of approximately 533g m-2 to 680g m-2 (as dry matter) or 84g m-2 to 177g m-2 (as protein) over a 70-100 d period produced reasonable growth rates but poor feed utilisation indices. Low inputs of dry matter (from 113-296g m-2) and protein (from 24-54g m-2) from clover were sufficient to maintain high growth rates in pond microcosms for around 28 d. In ponds, a very low level of 21g m-2 (dry matter) and 4.3g m-2 (protein) was sufficient for around 3 weeks. Forage depletion appeared to occur beyond week 3-4 and was probably a major growth limiting factor. The mean hepatosomatic index (HSI) was 9.44, 7.68, and 6.79 for the pellet, crop, and control ponds respectively. The relationship between hepatopancreas weight and overall animal weight was significantly different between treatments. The hepatopancreas of pellet-fed animals had the highest %lipid and lowest %ash, %protein, %carbohydrate and %moisture content. In terms of absolute quantities, the only major difference in hepatopancreas composition between treatments occurred for lipid and dry matter content. The hepatopancreas of the pellet-fed animals was a cream/cream-yellow colour and was very fragile, whereas in the other ponds it was a more ‘natural’ bright yellow colour and was structurally more robust. C. destructor has a capacious foregut, being approximately 5 times the volume of similar sized Penaeids. The foregut volume (V, ml) of the yabby is related to animal weight (W, g) according to V = 0.048 W0.9543. Animals that were starved for 96 h and then fed diet B2 were almost completely foil after 30 min. The ‘apparent enzymatic response’ of animals fed various natural and artificial diets in tanks was evaluated. Nutrient processing time and the enzymatic response following ingestion appeared to be regulated by the chemical and physical properties of the diet. For the natural feeds, foregut protein was 1.2% higher (for zooplankton) and up to 300% higher (for detritus) than dietary protein, whereas ash was 7.5% higher (zooplankton) and 46-63% lower (detritus) than dietary ash. For animals fed diet B2 after 48 h without food, FF was approximately half that of 96 h starved animals after a similar feeding period but foregut protein and ash contents were similar. Finally, the physiological and morphological attributes elucidated in this study are discussed with reference to the ecology of the yabby. High growth rates, excellent feed utilisation indices and high digestibility coefficients for a wide range of diet-types illustrate nutritional flexibility. A capacious foregut, a large hepatopancreas with a high energy storage capacity, the ability to partition and preferentially excrete the low nutrient value inorganic component of the diet, the capacity to alter body form, nutrient processing time and enzymatic secretions in relation to diet-type, and modified behaviour according to feed availability also demonstrate plasticity/adaptability/flexibility. The combined effect of these important characteristics ensures survival in environments that may be adverse and highly variable in terms of nutrient availability. Collectively the morphological and digestive traits elucidated in this study reflect the generalist-type nature of C destructor and indicate that a polytrophic classification still seems appropriate. Several priority areas for further nutrition research are identified and recommendations are made regarding the best-practices to use in the commercial culture of the yabby. Of paramount importance is the further clarification of the nutritional requirements and feeding preferences of animals in various phases of development.

Complete genome sequence of rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers

Rhizobium leguminosarum bv trifolii is a soil-inhabiting bacterium that that has the capacity to be an effective nitrogen fixing microsymbiont of a diverse range of annual Trifolium (clover) species. Strain WSM1325 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from root nodules collected in 1993 from the Greek Island of Serifos. WSM1325 is manufactured commercially in Australia as an inoculant for a broad range of annual clovers of Mediterranean origin due to its superior attributes of saprophytic competence, nitrogen fixation and acid-tolerance. Here we describe the basic features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence for a microsymbiont of annual clovers. We reveal that its genome size is 7,418,122 bp encoding 7,232 protein-coding genes and 61 RNA-only encoding genes. This multipartite genome contains 6 distinct replicons; a chromosome of size 4,767,043 bp and 5 plasmids of size 828,924, 660,973, 516,088, 350,312 and 294,782 bp.

Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943

Rhizobium leguminosarum bv. trifolii SRDI943(syn. V2-2) is an aerobic, motile, Gram-negative, non-spore-forming rod. SRDI943was isolated from a nodule recovered from the roots of the annual clover Trifoliummichelianum savi cv. paradanathat had been inoculated with a soil collected from a mixed pasture in Victoria, Australia. SRDI943 has a broadhost range for nodulation within the clover genus, however N2-fixationis sub-optimal (20-54% of reference strain WSM1325) on T. subterraneum spp.Here we describe the features of R. leguminosarum bv. trifolii strain SRDI943, together with genomesequence information and annotation. The 7,412,387 bp high-quality-draft genomeis arranged into 5 scaffolds of 5 contigs, contains 7,317 protein-coding genesand 89 RNA-only encoding genes, and is one of 100 rhizobial genomes sequencedas part of the DOE Joint Genome Institute 2010 Genomic Encylopedia for Bacteriaand Archaea-Root Nodule Bacteria (GEBA-RNB) project.

Genome sequence of Ensifer arboris strain LMG 14919T, a microsymbiont of the legume Prosopis chilensis growing in Kosti, Sudan

Ensifer arboris LMG 14919T is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of several species of legume trees. LMG 14919T was isolated in 1987 from a nodule recovered from the roots of the tree Prosopis chilensis growing in Kosti, Sudan. LMG 14919T is highly effective at fixing nitrogen with P. chilensis (Chilean mesquite) and Acacia senegal (gum Arabic tree or gum acacia). LMG 14919T does not nodulate the tree Leucena leucocephala, nor the herbaceous species Macroptilium atropurpureum, Trifolium pratense, Medicago sativa, Lotus corniculatus and Galega orientalis. Here we describe the features of E. arboris LMG 14919T, together with genome sequence information and its annotation. The 6,850,303 bp high-quality-draft genome is arranged into 7 scaffolds of 12 contigs containing 6,461 protein-coding genes and 84 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.