Seasonal variation in N2O emissions from urine patches: Effects of urine concentration, soil compaction and dung

Urine patches in pastures rank among the highest sources of the greenhouse gas nitrous oxide (N₂O) from animal production systems. Previous laboratory studies indicate that N₂O emissions for urine-N in pastures may increase with a factor five or eight in combination with soil compaction and dung, respectively. These combinations of urine, compaction and dung occur regularly in pastures, especially in so-called camping areas. The aims of this study were (i) to experimentally quantify the effect of compaction and dung on emission factors of N₂O from urine patches under field conditions; (ii) to detect any seasonal changes in emission from urine patches; and (iii) to quantify possible effects of urine concentration and -volume. A series of experiments on the effects of compaction, dung, urine-N concentration and urine volume was set up at a pasture on a sandy soil (typic Endoaquoll) in Wageningen, the Netherlands. Artificial urine was applied 8 times in the period August 2000–November 2001, and N₂O emissions were monitored for a minimum of 1 month after each application. The average emission factor for urine-only treatments was 1.55%. Over the whole period, only soil compaction had a clear significant effect, raising the average N₂O emissions from urine patches from 1.30% to 2.92% of the applied N. Dung had no consistent effect; although it increased the average emissions from 1.60% to 2.82%, this was clearly significant (P< 0.01) for only one application date and marginally significant (P=0.054) for the whole experiment. Both compaction and dung increased water-filled pore space (WFPS) of the topsoil for a more prolonged time than high urine volumes. No effect of amount of urine-N or urine volume on N₂O emissions relative to added N was detected for the whole experiment. There were clear differences between application dates, with highest emissions for urine-only treatments of 4.25% in October, 2000, and lowest of –0.11% in June, 2001. Emissions peaked at 60–70% WFPS, and decreased rapidly with both higher and lower WFPS. We conclude that compaction leads to a considerable increase in the N₂O emissions under field conditions, mainly through higher WFPS. Dung addition may have the same effect, although this was not consistent throughout our experiment. Seasonal variations seemed mainly driven by differences in WFPS. Based on this study, mitigation strategies should focus on minimizing the grazing period with wet conditions leading to WFPS > 50%, avoiding camping areas in pastures, and on avoiding grazing under moist soil conditions. Greenhouse gas budgets for grazing conditions should include the effects of soil compaction and dung to represent actual emissions.     

The impact of the Mid-Pleistocene Transition on the composition of submerged reefs of the Maui Nui Complex,Hawaii

The submarine reef terraces (L1–L12) of the Maui Nui Complex (MNC—the islands of Lanai, Molokai, Maui and Kahoolawe) in Hawaii provide a unique opportunity to investigate the impact of climate and sea level change on coral reef growth by examining changes in reef development through the Mid-Pleistocene Transition (900–800 ka). We present an analysis of the biological and sedimentary composition of the reefs that builds directly on recently published chronological and morphological data. We define nine distinct limestone facies and place them in a spatial and stratigraphic context within 12 reef terraces using ROV and submersible observations. These include oolitic, two coral reef, two coralline algal nodule, algal crust, hemi-pelagic mud, bioclastic and peloidal mud facies. These facies characterise environments from high energy shallow water coral reef crests to low energy non-reefal deep-water settings. Combining the bottom observations and sedimentary facies data, we report a shift in the observed sedimentary facies across the submerged reefs of the MNC from dominant shallow coral reef facies on the deep reefs to coralline algae dominated exposed outcrop morphology on the shallower reefs. We argue that this shift is a reflection of the change in period and amplitude of glacioeustatic sea level cycles (41 kyr and 60–70 m to 100 kyr and 120 m) during the Mid-Pleistocene Transition (MPT, ~ 800 ka), coupled with a slowing in the subsidence rate of the complex. The growth of stratigraphically thick coral reef units on the deep Pre-MPT reefs was due to the rapid subsidence of the substrate and the shorter, smaller amplitude sea level cycles allowing re-occupation and coral growth on successive cycle low-stands. Longer, larger amplitude sea level cycles after the MPT combined with greater vertical stability at this time produced conditions conducive to deep-water coralline algae growth which veneered the shallower terraces. Additionally, we compare reef development both within the MNC, and between the MNC and Hawaii. Finally we suggest that climatic forcings such as sea-surface temperature and oceanographic currents may also have influenced the distribution of coral species within the sample suite, e.g., the disappearance of the Acropora genus from the Maui Nui Complex in the Middle Pleistocene.     

Ribosomal protein genes of yeast contain intervening sequences

From a colony bank of HindIII-generated yeast DNA fragments we have isolated a number of recombinant DNAs carrying genes for ribosomal proteins (e.g., S10, S16A, S20, S24, S31, S33, L16, L25 and L34) of the yeast Saccharomyces carlsbergensis. By electron microscopic analysis of the R-loops formed between various DNA fragments and yeast mRNA, we could locate the ribosomal protein genes on the physical maps of the cloned DNA fragments. The R-loop structures observed indicate that a number of the ribosomal protein genes contain an intervening sequence.     

Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model

A genome-scale metabolic model of the lactic acid bacterium Lactobacillus plantarum WCFS1 was constructed based on genomic content and experimental data. The complete model includes 721 genes, 643 reactions, and 531 metabolites. Different stoichiometric modeling techniques were used for interpretation of complex fermentation data, as L. plantarum is adapted to nutrient-rich environments and only grows in media supplemented with vitamins and amino acids. (i) Based on experimental input and output fluxes, maximal ATP production was estimated and related to growth rate. (ii) Optimization of ATP production further identified amino acid catabolic pathways that were not previously associated with free-energy metabolism. (iii) Genome-scale elementary flux mode analysis identified 28 potential futile cycles. (iv) Flux variability analysis supplemented the elementary mode analysis in identifying parallel pathways, e.g. pathways with identical end products but different co-factor usage. Strongly increased flexibility in the metabolic network was observed when strict coupling between catabolic ATP production and anabolic consumption was relaxed. These results illustrate how a genome-scale metabolic model and associated constraint-based modeling techniques can be used to analyze the physiology of growth on a complex medium rather than a minimal salts medium. However, optimization of biomass formation using the Flux Balance Analysis approach, reported to successfully predict growth rate and by product formation in Escherichia coli and Saccharomyces cerevisiae, predicted too high biomass yields that were incompatible with the observed lactate production. The reason is that this approach assumes optimal efficiency of substrate to biomass conversion, and can therefore not predict the metabolically inefficient lactate formation.     

Distribution and characterization of plasmid-related sequences in the chromosomal DNA of different thermophilic Methanobacterium strains

The genomes of several thermophilic members of the genus Methanobacterium were analyzed for homology to the related restriction-modification plasmids pFVI and pFZ1 from M. thermoformicicum strains THF and Z-245, respectively. Two plasmid regions, designated FR-I and FR-II, could be identified with chromosomal counterparts in six Methanobacterium strains. Multiple copies of the pFVI-specific element FR-I were detected in the M. thermoformicicum strains CSM3, FF1, FF3 and M. thermoautotrophicum ΔH. Sequence analysis showed that one FR-I element had been integrated in almost identical sequence contexts into the chromosomes of the strains CSM3 and AH. Comparison of the FR-I elements from these strains with that from pFVI revealed that they consisted of two subfragments, boxI (1118 bp) and boxII (383 bp), the order of which is variable. Each subfragment was identical on the sequence level with the corresponding plasmid-borne element and was flanked by terminal direct repeats with the consensus sequence A(A/T)ATTT. These results suggest that FR-I represents a mobile element. FR-II was located on both plasmids pFVI and pFZI, and on the chromosome of M. thermoformicicum strains THF, CSM3 and HN4. Comparison of the nucleotide sequences of the two plasmid FR-II copies and that from the chromosome of strain CSM3 showed that the FR-II segments were approximately 2.5–3.0 kb in size and contained large open reading frames (ORFs) that may encode highly related proteins with an as yet unknown function.     

Fecal progestagen evaluations to monitor the estrous cycle and pregnancy in the okapi (Okapia johnstoni)

The present study was conducted to establish a noninvasive method of reproductive monitoring in the okapi (Okapia johnstoni). Fecal samples were collected three times a week from nonpregnant okapis (n = 3) for periods of 2, 9, and 23 months, respectively, and for 2 months each from pregnant okapis (n = 4) at different stages of gestation. Samples were analyzed with an enzyme-immunoas-say (EIA), using an antibody against pregnanediol, and the results are considered as measurements of unconjugated total immunoreactive progestagens (Pd-Pgs). Mean values of Pd-Pgs during the follicular (FP) and the luteal phases (LP) of the estrous cycles were 0.6 ± 0.1 μg/g and 6.1 ?0.3 μg/g feces, respectively. Matings occurred at the terminations of the LP. By dividing the number of entire LPs into the time over which samples were available, average estrous cycle lengths in two okapis were estimated to be 15.5 (n = 11 LP) and 15.8 (n = 36 LP) days, respectively. In three animals, gestation lengths of 423, 424, and 431 days were calculated by observed matings. During days -280 to -220 before parturition, the fecal Pd-Pgs constantly increased from about 20--60 μg/g fecès. Values were 100--350 μg/g during the last third of gestation. Values decreased in the week before parturition, and a continuous decline to FP values was observed within 3--4 days postpartum. During the 2 months postpartum investigated in one animal, the Pd-Pgs were in the FP range except one LP 3 weeks postpartum. It was concluded that fecal Pd-Pgs in female okapis are present in a ratio of ～1: 10:>100 during FP, LP, and late pregnancy, respectively. Their measurement by EIA enables noninvasive monitoring of the estrous cycle and pregnancy diagnosis. © 1993 Wiley-Liss, Inc.