Effect of biogas digested slurry based-biochar and digested liquid on N2O,CO2 flux and crop yield for three continuous cropping cycles of komatsuna (Brassica rapa var. perviridis)

Biogas production generates digested slurry, as a byproduct, which can be used as fertilizer after its conversion into digested liquid and biochar. A microcosm-based study was conducted to evaluate the effects of chemical fertilizer (CF), digested liquid (DL) and varying concentrations of biogas digested slurry based-biochar along with DL on N₂O flux, CO₂ flux, soil chemical properties and crop yield for three continuous cropping cycles of komatsuna (Brassica rapa var. perviridis) from April to July 2013. Analyses revealed that DL-treated soils released almost equal cumulative amounts of N₂O and CO₂ as soils treated with CF. The soil mineral-N contents were also similar for the DL- and CF-treated soils while DL application increased the soluble organic carbon (SOC) content of the soil compared to CF treatment. The application of slurry-based biochar increased N₂O and CO₂ flux, which, in turn, appeared to depend upon biochar concentration. The application of biochar probably increased the nitrification rate as biochar-treated soils had higher values of NO₃ ^?-N and lower values of NH₄ ⁺-N compared to soils not treated with biochar at most of the observations. The SOC content was also the highest in biochar-treated soils. The overall crop yield for three cropping cycles was the highest in DL and biochar at low application rate (BL), and it was lower in CF, biochar at medium (BM) and high (BH) application rate. This study indicates that the application of DL could be an effective strategy to minimize the use of CF, without affecting N₂O flux, CO₂ flux, soil mineral N, and increasing crop productivity. The effects of slurry-based biochar on greenhouse gases flux and crop yield depends on the application rate of biochar.     

Compositional characterization of soil organic matter and hot-water-extractable organic matter in organic horizons using a molecular mixing model

Purpose

Microbial decomposition of soil organic matter (SOM) is generally believed to be heterogeneous, resulting in the preferential loss of labile compounds such as carbohydrates and proteins and the accumulation of recalcitrant compounds such as lipids and lignin. However, these fractions are difficult to measure directly in soils. We examined patterns in the biomolecular composition of SOM and hot-water-extractable organic matter (HWEOM) by using a molecular mixing model (MMM) to estimate the content of carbohydrates, protein, lipids, and lignin.

Materials and methods

Organic-horizon soils from Spodosols at the Hubbard Brook Experimental Forest in NH, USA were analyzed for this study. The MMM uses data from elemental analysis (C, H, and N) and ¹³C nuclear magnetic resonance spectroscopy with cross-polarization and magic-angle spinning to estimate the percentage of total C in the various classes of biomolecules.

Results and discussion

Carbohydrate content decreased from about 50 % of the C in recent litter to approximately 35 % in the bottom of the humus layer. Lipids accounted for about 18 % of C in recent litter and increased to 40 % in the lower humus layers. The HWEOM fraction of SOM was dominated by carbohydrates (40–70 % of C). Carbohydrates and lipids in HWEOM exhibited depth patterns that were the opposite of the SOM. The results from the MMM confirmed the selective decomposition of carbohydrates and the relative accumulation of lipids during humus formation. The depth patterns in HWEOM suggest that the solubility of carbohydrates increases during decomposition, while the solubility of the lipid fraction decreases. The MMM was able to reproduce the spectral properties of SOM and HWEOM very accurately, although there were some discrepancies between the predicted and measured H/C and O/C ratios.

Conclusions

The MMM approach is an accurate and cost-effective alternative to wet-chemical methods. Together, carbohydrates and proteins account for up to 85 % of the C in HWEOM, indicating that the HWEOM fraction represents a labile source of C for microbes. Humification resulted in a decrease in carbohydrate content and an increase in lipids in SOM, consistent with investigations carried out in diverse soil environments.     

Comparison the effects of 5-Aza-2′-deoxycytidine and zebularine on the in vitro development,blastocyst quality,methylation pattern and conception rate on handmade cloned buffalo embryos

In this study we treated the handmade cloned (HMC) buffalo embryos with the DNA methylation inhibitors; 5-aza-2′-deoxycytidine (AzadC) or Zebularine individually after post-fusion and during in vitro culture till eighth day. The blastocysts production rate significantly improved (p < .01) after treating embryos independently with 5 nM AzadC and 5 nM zebularine compared with 2 and 10 nM AzadC or zebularine groups, respectively. The highest cleavage rates were obtained for 5 nM treatment of AzadC and zebularine compared with other treatments and untreated control group. Quality of blastocysts were evaluated using total cell number (TCN) and the ratio of number of inner cell mass (ICM) cells/total cell number (ICM/TCN). Zebularine treatments (2/5/10 nM) significantly improved both TCN and ICM/TCN ratio compared with AzadC treatments (2/5/10 nM); however, control group TCN and ICM/TCN ratio was found lower. The methylation percentage of pDS4.1 and B. bubalis satellite DNA were comparatively more attenuated with 5 nM zebularine than 5 nM AzadC treatment. The increased in vitro development rates of the treated embryos were correlated with the decreased level of DNA methylation and the improved blastocyst quality. Following transfer of 5 nM zebularine treated embryos to 6 recipients, 4 were found to be pregnant, though the pregnancies were not carried to full term.     

Complete genome sequence analysis of chicken astrovirus isolate from India

Objective

Chicken astroviruses have been known to cause severe disease in chickens leading to increased mortality and “white chicks” condition. Here we aim to characterize the causative agent of visceral gout suspected for astrovirus infection in broiler breeder chickens.

Methods

Total RNA isolated from allantoic fluid of SPF embryo passaged with infected chicken sample was sequenced by whole genome shotgun sequencing using ion-torrent PGM platform. The sequence was analysed for the presence of coding and non-coding features, its similarity with reported isolates and epitope analysis of capsid structural protein.

Results

The consensus length of 7513 bp genome sequence of Indian isolate of chicken astrovirus was obtained after assembly of 14,121 high quality reads. The genome was comprised of 13 bp 5′-UTR, three open reading frames (ORFs) including ORF1a encoding serine protease, ORF1b encoding RNA dependent RNA polymerase (RdRp) and ORF2 encoding capsid protein, and 298 bp of 3′-UTR which harboured two corona virus stem loop II like “s2m” motifs and a poly A stretch of 19 nucleotides. The genetic analysis of CAstV/INDIA/ANAND/2016 suggested highest sequence similarity of 86.94% with the chicken astrovirus isolate CAstV/GA2011 followed by 84.76% with CAstV/4175 and 74.48%% with CAstV/Poland/G059/2014 isolates. The capsid structural protein of CAstV/INDIA/ANAND/2016 showed 84.67% similarity with chicken astrovirus isolate CAstV/GA2011, 81.06% with CAstV/4175 and 41.18% with CAstV/Poland/G059/2014 isolates. However, the capsid protein sequence showed high degree of sequence identity at nucleotide level (98.64-99.32%) and at amino acids level (97.74–98.69%) with reported sequences of Indian isolates suggesting their common origin and limited sequence divergence. The epitope analysis by SVMTriP identified two unique epitopes in our isolate, seven shared epitopes among Indian isolates and two shared epitopes among all isolates except Poland isolate which carried all distinct epitopes.

     

Surface Treated Jute Fiber Induced Foam Microstructure Development in Poly(lactic acid)/Jute Fiber Biocomposites and their Biodegradation Behavior

Poly(lactic acid) (PLA)/jute fiber biocomposites with: i) untreated jute fiber, ii) NaOH treated jute fiber, and iii) (NaOH+silane) treated jute fibers were prepared by melt extrusion process. Microcellular foaming of the injection molded samples was carried out by using single stage batch process. The effects of jute fiber content as well as that of matrix-fiber phase adhesion, in composites with surface treated jute fibers, on the foam microstructure were studied. Further, water absorption, thickness swelling, and biodegradation behavior of the foamed biocomposites were studied and correlated with their foam microstructures. It was observed that on increasing jute fiber content in PLA/JFU biocomposites, cell density increased from 6.5×10⁷ to 8.1×10⁷, while the cell size and expansion ratio decreased from 40 to 23 μm and 2.41 to 1.45, respectively. Again, on increasing the extent of the jute fiber surface treatment in the biocomposites, cell size and expansion ratio increased from 40 to 78 μm and 2.41 to 2.80 respectively. This study also revealed that the rate of biodegradation accelerated with increase in the jute fiber content in the biocomposites while the same retarded with increase in the extent of jute fiber surface treatment.     

m‐carboxycinnamic acid bishydroxamide improves developmental competence,reduces apoptosis and alters epigenetic status and gene expression pattern in cloned buffalo (Bubalus bubalis) embryos

Incomplete or aberrant reprogramming of nuclear genome is one of the major problems in somatic cell nuclear transfer. In this study, we studied the effect of histone deacetylase inhibitor m‐carboxycinnamic acid bishydroxamide (CBHA) on in vitro development of buffalo embryos produced by Hand‐made cloning. Cloned embryos were treated with CBHA (0, 5, 10, 20 or 50 μM) for 10 hr from the start of reconstruction till activation. At 10 μM, but not at other concentrations examined, CBHA increased (p < .05) the blastocyst rate (63.77 ± 3.97% vs 48.63 ± 3.55%) and reduced (p < .05) the apoptotic index of the cloned blastocysts (8.91 ± 1.94 vs 4.36 ± 1.08) compared to untreated controls, to levels similar to those in IVF blastocysts (4.78 ± 0.74). CBHA treatment, at all the concentrations examined, increased (p < .05) the global level of H3K9ac in cloned blastocysts than in untreated controls to that observed in IVF blastocysts. Treatment with CBHA (10 μM) decreased (p < .05) the global level of H3K27me3 in cloned blastocysts than in untreated controls but it was still higher (p < .05) than in IVF blastocysts. CBHA (10 μM) treatment increased (p < .05) the relative expression level of pluripotency‐related genes OCT‐4 and NANOG, and anti‐apoptotic gene BCL‐XL, and decreased (p < .05) that of pro‐apoptotic gene BAX than in untreated controls but did not affect the relative expression level of apoptosis‐related genes p53 and CASPASE3 and epigenetics‐related genes DNMT1, DNMT3a and HDAC1. These results suggest that treatment of cloned embryos with 10 μM CBHA improves the blastocyst rate, reduces the level of apoptosis and alters the epigenetic status and gene expression pattern.     

Effect of TGF‐β1 Superfamily Members on Survival of Buffalo (Bubalus bubalis) Embryonic Stem‐like Cells

This study examined the effects of supplementation of ES‐like cell culture medium with bone morphogenetic protein (BMP)‐4 (0, 10, 20 or 100 ng/ml) or Noggin (250, 500 or 750 ng/ml) or TGF‐β1 (0, 0.1, 1 or 10 ng/ml) or SB431542 (0, 10, 25 or 50 μm ), an inhibitor of TGF‐β1 signalling, on survival, colony area and expression level of pluripotency genes in buffalo ES‐like cells at passage 40–80, under different culture conditions. BMP‐4 supplementation significantly reduced (p < 0.05) colony survival rate, percentage increase in colony area and relative mRNA abundance of OCT4, whereas that of NANOG and SOX‐2 was increased significantly (p < 0.05). Noggin supplementation did not affect the colony survival rate and percentage increase in colony area in the presence of FGF‐2 and LIF. In the presence of FGF‐2 alone, it significantly reduced (p < 0.05) the relative mRNA abundance of OCT4 and SOX‐2 and increased (p < 0.05) that of NANOG. Supplementation with TGF‐β1 at 1.0 ng/ml but not at other concentrations increased colony survival rate but had no effect on percentage increase in colony area at any concentration. Supplementation with SB‐431542 decreased (p < 0.05) colony survival rate at 50 μm but not at other concentrations. The percentage increase in colony area was lower (p < 0.05) with 10 μm SB‐431542 than that in the controls, whereas at higher concentrations of 25 or 50 μm , SB‐431542 decreased (p < 0.05) the colony size instead of increasing it. In conclusion, these results suggest that BMP‐4 induces differentiation in buffalo ES‐like cells, whereas TGF‐β/activin/nodal pathway may not be playing a crucial role in maintaining pluripotency in these cells.     

Nitrous oxide flux from komatsuna (Brassica rapa) vegetated soil: a comparison between biogas digested liquid and chemical fertilizer

Biogas production generates digested slurry as a by-product. It can be used as fertilizer especially after its conversion into digested liquid. A microcosm-based study was conducted in order to compare the effects of single application of digested liquid or chemical fertilizer on N₂O flux and crop yield of komatsuna vegetable. Analysis revealed that digested liquid-treated soils released almost equal cumulative N₂O (0.43 g?N m^?2) compared to chemical fertilizer (0.39 g?N m^?2). The uncropped soils treated with the digested liquid and chemical fertilizer released more N₂O compared to corresponding cropped soils. The N₂O emission factor and soil mineral N contents were similar for the digested liquid and chemical fertilizer-treated soils. Plant biomass in the first crop after digested liquid application was significantly higher (5.59 g plant^?1) than that after applied chemical fertilizer (4.78 g plant^?1); but there was no significant difference for the second crop. Nitrogen agronomic efficiency was improved by the digested liquid compared to chemical fertilizer. This study indicates that cumulative N₂O flux was similar after application of the digested liquid and chemical fertilizer, while the overall yield from both croppings was increased in the digested liquid-treated soil compared to chemical fertilizer-treated soil.     

Cleavage capability of water buffalo follicular oocytes classified by cumulus cells and fertilized in vitro.

Water buffalo (Murrah) oocytes were collected from ovaries obtained from the slaughter house. They were classified according to the character of the cumulus cells under a stereomicroscope, and cultured in 25 mM Hepes buffered Tissue Culture Medium-199 (TCM-199) supplemented with 5% estrous water buffalo serum in an atmosphere containing 5% CO2 in air at 39 degrees C. After 20-24 hr of in vitro maturation, the oocytes were fertilized using capacitated sperm obtained from 4 different bulls. For cleavage the oocytes were cultured at 39 degrees C in TCM-199 supplemented with 1% estrous water buffalo serum and in an atmosphere containing 5% CO2 in air. The good oocytes, with compact and dense cumulus cells cleaved significantly higher (p less than 0.01, 67.3%), than those of fair. partially naked oocytes with thin cumulus layers (27.5%, 25/91) or small remnants of cumulus cells and poor naked oocytes (3/100). A substantial variation cumulus layers (27.5% 25/91) or small remnants of cumulus cells and poor naked oocytes (3/100). A substantial variation in fertilization and developmental rates (16.0% to 43.8%) was observed among 4 different bulls. Late non-surgically into 14 buffalo recipients on day 6 or 7 of their estrous cycle. One recipient was diagnosed to be pregnant by rectal palpation on day 60 and confirmed to be so on day 90 post-estrus.