Carbon Inputs from <Emphasis Type="Italic">Miscanthus</Emphasis> Displace Older Soil Organic Carbon Without Inducing Priming

The carbon (C) dynamics of a bioenergy system are key to correctly defining its viability as a sustainable alternative to conventional fossil fuel energy sources. Recent studies have quantified the greenhouse gas mitigation potential of these bioenergy crops, often concluding that C sequestration in soils plays a primary role in offsetting emissions through energy generation. Miscanthus is a particularly promising bioenergy crop and research has shown that soil C stocks can increase by more than 2 t C ha^?1 yr^?1. In this study, we use a stable isotope (¹³C) technique to trace the inputs and outputs from soils below a commercial Miscanthus plantation in Lincolnshire, UK, over the first 7 years of growth after conversion from a conventional arable crop. Results suggest that an unchanging total topsoil (0–30 cm) C stock is caused by Miscanthus additions displacing older soil organic matter. Further, using a comparison between bare soil plots (no new Miscanthus inputs) and undisturbed Miscanthus controls, soil respiration was seen to be unaffected through priming by fresh inputs or rhizosphere. The temperature sensitivity of old soil C was also seen to be very similar with and without the presence of live root biomass. Total soil respiration from control plots was dominated by Miscanthus-derived emissions with autotrophic respiration alone accounting for ～50 % of CO₂. Although total soil C stocks did not change significantly over time, the Miscanthus-derived soil C accumulated at a rate of 860 kg C ha^?1 yr^?1 over the top 30 cm. Ultimately, the results from this study indicate that soil C stocks below Miscanthus plantations do not necessarily increase during the first 7 years.     

Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand

We examined bacterial diversity of three geothermal soils in the Taupo Volcanic Zone of New Zealand. Phylogenetic analysis of 16S rRNA genes recovered directly from soils indicated that the bacterial communities differed in composition and richness, and were dominated by previously uncultured species of the phyla Actinobacteria , Acidobacteria , Chloroflexi , Proteobacteria and candidate division OP10. Aerobic, thermophilic, organotrophic bacteria were isolated using cultivation protocols that involved extended incubation times, low-pH media and gellan as a replacement gelling agent to agar. Isolates represented previously uncultured species, genera, classes, and even a new phylum of bacteria. They included members of the commonly cultivated phyla Proteobacteria , Firmicutes , Thermus/Deinococcus , Actinobacteria and Bacteroidetes , as well as more-difficult-to-cultivate groups. Isolates possessing < 85% 16S rRNA gene sequence identity to any cultivated species were obtained from the phyla Acidobacteria , Chloroflexi and the previously uncultured candidate division OP10. Several isolates were prevalent in 16S rRNA gene clone libraries constructed directly from the soils. A key factor facilitating isolation was the use of gellan-solidified plates, where the gellan itself served as an energy source for certain bacteria. The results indicate that geothermal soils are a rich potential source of novel bacteria, and that relatively simple cultivation techniques are practical for isolating bacteria from these habitats.     

Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1

Background

Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life.

Results

We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres.

Conclusions

Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.     

Myeloid and lymphoid contribution to non-haematopoietic lineages through irradiation-induced heterotypic cell fusion

Recent studies have suggested that regeneration of non-haematopoietic cell lineages can occur through heterotypic cell fusion with haematopoietic cells of the myeloid lineage. Here we show that lymphocytes also form heterotypic-fusion hybrids with cardiomyocytes, skeletal muscle, hepatocytes and Purkinje neurons. However, through lineage fate-mapping we demonstrate that such in vivo fusion of lymphoid and myeloid blood cells does not occur to an appreciable extent in steady-state adult tissues or during normal development. Rather, fusion of blood cells with different non-haematopoietic cell types is induced by organ-specific injuries or whole-body irradiation, which has been used in previous studies to condition recipients of bone marrow transplants. Our findings demonstrate that blood cells of the lymphoid and myeloid lineages contribute to various non-haematopoietic tissues by forming rare fusion hybrids, but almost exclusively in response to injuries or inflammation.     

Extended polypeptide linkers establish the spatial architecture of a pyruvate dehydrogenase multienzyme complex

Icosahedral pyruvate dehydrogenase (PDH) enzyme complexes are molecular machines consisting of a central E2 core decorated by a shell of peripheral enzymes (E1 and E3) found localized at a distance of approximately 75-90 A from the core. Using a combination of biochemical, biophysical, and cryo-electron microscopic techniques, we show here that the gap between the E2 core and the shell of peripheral enzymes is maintained by the flexible but extended conformation adopted by 60 linker polypeptides that radiate outwards from the inner E2 core, irrespective of the E1 or E3 occupancy. The constancy of the gap is thus not due to protein-protein interactions in the outer protein shell. The extended nature of the E2 inner-linker regions thereby creates the restricted annular space in which the lipoyl domains of E2 that carry catalytic intermediates shuttle between E1, E2, and E3 active sites, while their conformational flexibility facilitates productive encounters.     

Mixing gilts in early pregnancy does not affect embryo survival

There is general acceptance that mixing sows during the first 3 weeks of gestation is detrimental to embryo development and survival. However, there is a paucity of data describing the influence of group housing and remixing during the first 14 days of gestation on pregnancy outcomes. Using 96 purebred maternal (Large White)/terminal (Duroc) line gilts, the current study determined the effects of regrouping, and the timing of regrouping, during the pre-implantation period on embryo mortality. The study was conducted in 2 blocks, with 12 gilts allocated to each of 4 treatments in each block. At 175 days of age, the combination of PG600 and 20 min of daily physical boar contact was used to stimulate puberty, with boar contact resuming 12 days after first detection of oestrus and gilts receiving two artificial inseminations (AIs), 24 h apart, at their second oestrus. After their first AI gilts were allocated to one of four treatment groups (n=12 gilts/treatment). Gilts in one treatment group were housed individually in stalls (STALL). The remaining gilts continued to be housed in their pre-AI groups and were either not remixed (NOMIX), or remixed to form new groups on day 3/4 (RMIXD3/4) or day 8/9 (RMIXD8/9) of gestation (day 0=day of first detection of second oestrus and first insemination). Group-housed gilts were housed in groups of 6, with a space allowance of 2.4 m2/gilt. All gilts were fed once a day (2.2 kg/gilt). Reproductive tracts were collected on day 26.6+/-0.13 of gestation, and the number of corpora lutea (CL) and viable embryos counted. Pregnancy rate was similar across all treatments, averaging 94.5% across the four treatment groups. The number of embryos present on day 26 of gestation was unaffected by housing treatments (P>0.05); gilts in the STALL, NOMIX, RMIXD3/4 and RMIXD8/9 groups possessed 13.2+/-0.67, 12.9+/-0.66, 14.1+/-0.46 and 13.8+/-0.57 embryos, respectively. Similarly, embryo survival rates were 0.91+/-0.04, 0.85+/-0.04, 0.91+/-0.02 and 0.87+/-0.05 for the STALL, NOMIX, RMIXD3.4 and RMIXD8/9 groups, respectively (P>0.05). In conclusion, the current data indicate that individually housing gilts immediately after their first AI does not improve embryo survival. There also appear to be no adverse effects on embryo development or survival when group-housed, mated gilts are remixed during the first 10 days of gestation.     

The effects of PG600 and boar exposure on oestrus detection and potential litter size following mating at either the induced (pubertal) or second oestrus

Within gilt pools, incidences of delayed puberty attainment, failure to exhibit regular oestrous cycles and low first litter size are often high. Boar exposure is an effective method of accelerating puberty; however, the timing of gilt response can vary greatly. Although, PG600 (400 IU of PMSG and 200 IU of hCG; Intervet) can induce a rapid and synchronous ovulatory response, thus providing an alternative to boar contact, the quality of the response is often variable. This study compared the effect of PG600, either alone (NBC) or in conjunction with boar exposure (BC), on puberty attainment and maintenance of oestrous cyclicity. The effects of first mating these gilts at the hormonally induced (pubertal) or second oestrus on ovulation rate and early embryo survival were also studied. Eighty Large White cross terminal (Duroc) line gilts were used in this study. The study was conducted in two blocks, with 10 gilts allocated to each of the four treatments in each block. Gilts were artificially inseminated at the allocated oestrus, with the reproductive tracts collected at 26.5+/-0.29 days after first mating (mean+/-S.E.M.), and the number of corpora lutea and viable embryos recorded. Mean days-to-puberty was significantly reduced (P<0.05) when gilts received both PG600 and boar exposure as opposed to PG600 alone (5.7+/-0.15 versus 6.9+/-0.37 days; P<0.01). The proportion of gilts exhibiting an ovulatory response to PG600 was similar for the BC and NBC treatment groups (0.88 and 0.84); however, the proportion of gilts exhibiting visible signs of oestrus in response to PG600 was significantly higher for the BC compared to the NBC treatment groups (0.81 versus 0.49; P<0.05). Boar contact resulted in a numerical, but not significant, increase in the proportion of gilts exhibited a second oestrus (1.00 versus 0.76). There was no significant effect of boar contact on ovulation rate, embryo number or survival. Although ovulation rate was unaffected by oestrus at mating, embryo number was significantly increased (P<0.05) following mating at the second compared to the first oestrus (11.2+/-0.96 versus 7.8+/-1.17). In conclusion, the current data indicate that the timing of puberty attainment and oestrus detection are significantly improved when PG600 treated gilts receive full boar contact. Further, it is evident that mating gilts at their second as opposed to the hormonally induced oestrus significantly increases embryo number at day 26 post-mating.     

Multiple spatial-scale resource selection function models in relation to human disturbance for moose in northeastern China

The moose (Alces alces cameloides) population in northeastern China is on the southernmost edge of its distribution in Asia. A survey was conducted to determine moose resource selection and the effects of human disturbance on moose in a study area of 20,661 ha located on the northwestern slope of the Lesser Khingan Mountains, located in northeastern China. Predictive models of resource selection were developed using logistic and autologistic regression. All models considered resource variable selection at two spatial scales, patch and landscape. At the patch scale, moose preferred larger birch (Betula platyphylla) patches, but avoided larger tamarack (Larix gmelinii) patches. At the landscape scale, moose preferred higher densities of tamarack patches, i.e., heterogeneity of tamarack stands, selected areas with more abundant annual shoots, terrain conducive to better concealment, higher altitudes and areas saturated with soil moisture. Roads and forest harvest intervals were identified as important human disturbance factors. This is the first time that moose have been reported to avoid roads, and the avoidance distance was nearly 3 km. We believe that in this region moose under the influence of roads are behaviorally plastic, compared with the indifference of moose to the presence of roads in other regions. Moose avoided forest areas logged more than 3 years previously and preferred areas logged 1–2 years previously. In addition, it may be necessary to monitor the effect of the dynamic of density of roe deer on the spatial distribution of the moose population.