Survival of bacterial DNA and culturable bacteria in archived soils from the Rothamsted Broadbalk experiment

Dried soil samples from many sources have been stored in archives world-wide over the years, but there has been little research on their value for studying microbial populations. Samples collected since 1843 from the Broadbalk field experiment on crop nutrition at Rothamsted have been used to document changes in the structure and composition of soils as agricultural practices evolve, also offering an invaluable record of environmental changes from the pre- to post-industrial era in the UK. To date, the microbial communities of these soils have not been studied, in part due to the well-documented drop in bacterial culturability in dried soils. However, modern molecular methods based on PCR amplification of DNA extracted directly from soil do not require bacterial cells to be viable or intact and may allow investigations into the legacy of bacteria that were present at the time of sample collection.

In a preliminary study, to establish if dried soils can provide a historical record of bacterial communities, samples from the Broadbalk soil archive dating back to 1868 were investigated and plots treated with either farmyard manure (FYM) or inorganic fertilizer (NPK) were compared. As anticipated, the processes of air-drying and milling greatly reduced bacterial viability whilst DNA yields declined less and may be preserved by desiccation. A higher proportion of culturable bacteria survived the archiving process in the FYM soil, possibly protected by the increased soil organic matter. The majority of surviving bacteria were firmicutes, whether collected in 2003 or in 1914, but a wide range of genera was detected in DNA extracted from the samples using PCR and DGGE of 16S rRNA genes. Analysis of DGGE band profiles indicated that the two plots maintained divergent populations. Sequence analysis of bands excised from DGGE gels, from a sample collected in 1914, revealed DNA from - and β-proteobacteria as well as firmicutes. PCR using primers specific for ammonia oxidizing bacteria showed similar band profiles across the two treatments in recently collected samples, however older samples from the NPK plot showed greater divergence. Primers specific for the genus Pseudomonas were designed and used in real-time quantitative PCR to indicate that archived soil collected in 1868 contained 10-fold less pseudomonad DNA than fresh soil, representing around 10⁵ genomes g⁻¹ soil. Prior to milling, dramatically less pseudomonad DNA was extracted from recently collected air-dried soil from the NPK compared to the FYM plot; otherwise, the two plots followed similar trends. Overall bacterial abundance, diversity and survival during the archiving process differed in the two soils, possibly due to differences in clay and soil organic matter content. Nevertheless, the results demonstrate that air-dried soils can protect microbial DNA for more than 150 years and offer an invaluable resource for future research.     

Management strategies for forage rape (Brassica napus L. cv Goliath): Impact on dry-matter yield,plant reserves,morphology and nutritive value

Limited information is available on the grazing management principles of forage rape (Brassica napus L.), particularly in relation to grazing height and intensity and the impact of these on dry-matter (DM) yield and nutritive value. A glasshouse study was undertaken to investigate the effect of three defoliation heights (plant height at harvest; DH: 40, 70 and 90 cm; L, M and H DH respectively) and three defoliation intensities (height at which plants were cut; DI: 5, 20 and 35 cm of residual height; H, M and L DI respectively) on forage rape (cv Goliath) yield and nutritive value at two harvests (harvest 1, H1 and harvest 2, H2), and the impact of nitrogen (N) and water soluble carbohydrate (WSC) reserves on regrowth. Increasing DH from L to H increased estimated total DM yield (H1 plus H2) from 0.5 to 4.6 t DM/ha but DI did not affect yield. Dry-matter yield was optimized at 90 cm DH, but greater nutritive value was achieved by harvesting at lower levels of DH. Despite high in vitro DM digestibility (IVDMD; 852–889 g/kg), harvesting at 90 cm DH could not meet the protein requirement of lactating dairy cows and harvesting at lower levels risks nitrate poisoning. Our results indicate the optimum DH may be between 70 and 90 cm DH, and 20 and 35 cm DI, which requires further studies.     

Litopenaeus vannamei (Boone) post-larval survival related to age, temperature, pH and ammonium concentration

Transport of post‐larvae shrimp used in aquaculture is an important element of successful cultivation because of the potential for stress during stocking procedures. To find optimum transport conditions, several bioassays were performed in the laboratory to evaluate survival of whiteleg shrimp Litopenaeus vannamei 5–30‐day‐old postlarvae under conditions similar to those encountered during transport from the hatchery to nursery and shrimp ponds. Postlarvae were exposed for 4 h to different temperatures and pH levels ammonia concentrations. Survival was significantly reduced after a 4 h exposure to pH 9 and was inversely related to temperature with or without 7 mg L^?1 of ammonia. The 15‐ and 20‐day‐old postlarvae had higher survival rates than other ages. The lowest survival occurred in alkali conditions (pH 9), with 7 mg L^?1ammonia at 30 and 32°C. To assure optimal survival of postlarvae during transfer from the hatchery to the nursery and shrimp ponds, we recommend temperatures below 28°C, pH no higher than 8, no ammonia and post‐larval age at least 15 days.