Metagenomic analysis of coastal RNA virus communities

RNA viruses infect marine organisms from bacteria to whales, but RNA virus communities in the sea remain essentially unknown. Reverse-transcribed whole-genome shotgun sequencing was used to characterize the diversity of uncultivated marine RNA virus assemblages. A diverse assemblage of RNA viruses, including a broad group of marine picorna-like viruses, and distant relatives of viruses infecting arthropods and higher plants were found. Communities were dominated by distinct genotypes with small genome sizes, and we completely assembled the genomes of several hitherto undiscovered viruses. Our results show that the oceans are a reservoir of previously unknown RNA viruses.     

The effect of substrate particle size on the production of mucus in Haliotis tuberculata L. and the importance of this in a culture system

Haliotis tuberculata, the ormer, produces mucus from secretory cells in its foot. A relationship between substrate particle size and production of mucus is demonstrated. The results are also related to the energy budget of the ormer and considered in the light of the possible culture of the organism.     

Molting,Mortality, and the Effects of Density in a Soft-Shell Crawfish Culture System 1

The molting and mortality patterns at a crawfish density recommended for commercial-scale soft-shell crawfish culture systems showed that, over a 116 day period, 74% of the crawfish molted, 22% died, and 4% remained in the system at the end of the study. Approximately three weeks of adaption to the system were required before molting rates of the crawfish began to increase. By the sixth week, the number of malted crawfish per day exceeded the overall mean and remained at this level until 10 days before moltable crawfish were depleted. In a second study, three density levels (3.7,4.9, and 6.1 kg crawfish/m²) were tested for 60 days. The lowest density produced significantly fewer (P < 0.05) molted crawfish. Mortality was significantly greater (P < 0.05) at the highest density compared with the lowest density. The highest density (6.1 kg crawfish/m²) showed a higher molting rate than the lower densities, but it was not significantly different (P < 0.05) from the molting rate of 4.9 kg/m².     

Effect of two types of light on survival,growth and ovary development of Rana catesbeiana

The survival, growth and ovary development of post-metamorphic, juvenile and young adult bullfrogs (Rana catesbeiana) raised under two different types of light were measured. There was no significant difference in growth or mortality between bullfrogs raised under standard or “growlight” fluorescent light. No significant differences due to treatment were found in the development of the ovary. Most females reached ovarian maturity 12 months after metamorphosis.     

Case studies and reviews. Working towards a marine nature reserve in Jersey

• 1. A biological inventory is described for Portelet Bay, on the south coast of Jersey in the Channel Islands, which has been selected for the Island's first marine nature reserve.
• 2. The application of site assessment criteria in justifying the selection of the site is discussed.
• 3. Conclusions are drawn on the process by which marine reserve status might be achieved.

     

Environmental genomics reveals a single-species ecosystem deep within Earth

DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, composes >99.9% of the microorganisms inhabiting the fluid phase of this particular fracture. Its genome indicates a motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon by using machinery shared with archaea. Candidatus Desulforudis audaxviator is capable of an independent life-style well suited to long-term isolation from the photosphere deep within Earth's crust and offers an example of a natural ecosystem that appears to have its biological component entirely encoded within a single genome.     

Inferred origin of several Native American potatoes from the Pacific Northwest and Southeast Alaska using SSR markers

Certain Native Americans from the Pacific Northwest and Alaska of the USA have grown potatoes in their gardens for many generations. In this study, the origin of several potatoes collected from Native gardens was investigated. Fourteen SSR markers covering the 12 potato homologs yielding a total of 199 alleles were amplified and scored in Solanum tuberosum Group Andigena (52 accessions), S. tuberosum Group. Tuberosum (39 accessions) and wild species (6 accessions). “Ozette” from the Makah Nation on the Olympic Peninsula in Washington State was closely related to “Maria’s” and “Kasaan” potatoes collected from Native Alaskan gardens in Southeast Alaska. These three potatoes were more closely related to either two Mexican and one Peruvian andigena accessions or three Chilean Group Tuberosum accessions, while being relatively less related to the old European or modern varieties and most distantly related to Group Andigenum. “To-Le-Ak” was closely related to two Chilean tuberosum accessions and one old European variety. All Native potatoes harbored T-type chloroplast genome indicating that their maternal lineage is shared with Chilean Group Tuberosum. Using genetic relationship as a guide to origin it appears plausible that the Native American/Alaskan cultivars are either directly or indirectly from Mexico and Chile. These Native potato cultivars present a possible second route of diffusion distinct from the South America to Europe transfer which has been assumed to the sole means by which potato was spread out of South America.     

Fatty Acid Composition of Muscle, Liver, and Depot Fat of Wild and Cultured Common Snapping Turtles Chelydra serpentina

Abstract This study was conducted to compare the fatty acid composition of muscle, liver, and depot fat of common snapping turtles Chelydra serpentina from the wild with those of captive common snapping turtles fed a diet of known fatty acid composition. Total lipid from each tissue was separated by thin-layer chromotography, methylated, and analyzed by gas chromatography/mass spectrometry. The fatty acid composition of total lipid, polar lipid, and nonpolar lipid in muscle and depot fat of wild and captive turtles exhibited greater variability than liver polar lipid. Cultured turtles contained significantly lower levels of linolenic and arachidonic acids in liver polar lipid than wild turtles. Total n-9 fatty acids were significantly higher in whole-lipid and nonpolar fractions of muscle, liver, and depot fat of cultured turtles indicating de novo synthesis. Total polyunsaturated fatty acids were significantly lower in total lipid of muscle tissue from cultured turtles. Total polyunsaturated fatty acids were significantly lower in both depot fat and liver nonpolar lipid of cultured turtles, but did not differ (P > 0.05) in the polar lipid fractions of cultured and wild turtles.