RNA-Seq Analysis of the Key Long Noncoding RNAs and mRNAs Related to the Regulation of Acute Heat Stress in Rainbow Trout.

As the global climate warms, more creatures are threatened by high temperatures, especially cold-water fish such as rainbow trout. Evidence has demonstrated that long noncoding RNAs (lncRNAs) play a pivotal role in regulating heat stress in animals, but we have little understanding of this regulatory mechanism. The present study aimed to identify potential key lncRNAs involved in regulating acute heat stress in rainbow trout. lncRNA and mRNA expression profiles of rainbow trout head kidney were analyzed via high-throughput RNA sequencing, which exhibited that 1256 lncRNAs (802 up-regulation, 454 down-regulation) and 604 mRNAs (353 up-regulation, 251 down-regulation) were differentially expressed. These differentially expressed genes were confirmed to be primarily associated with immune regulation, apoptosis, and metabolic process signaling pathways through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis and coding-noncoding co-expression network analysis. These results suggested that 18 key lncRNA-mRNA pairs are essential in regulating acute heat stress in rainbow trout. Overall, these analyses showed the effects of heat stress on various physiological functions in rainbow trout at the transcriptome level, providing a theoretical basis for improving the production and breeding of rainbow trout and the selection of new heat-resistant varieties.

Characterization of natural co-cultures of Piromyces with Methanobrevibacter ruminantium from yaks grazing on the Qinghai-Tibetan Plateau: a microbial consortium with high potential in plant biomass degradation.

Anaerobic fungi reside in the gut of herbivore and synergize with associated methanogenic archaea to decompose ingested plant biomass. Despite their potential for use in bioconversion industry, only a few natural fungus-methanogen co-cultures have been isolated and characterized. In this study we identified three co-cultures of Piromyces with Methanobrevibacter ruminantium from the rumen of yaks grazing on the Qinghai Tibetan Plateau. The representative co-culture, namely (Piromyces + M. ruminantium) Yak-G18, showed remarkable polysaccharide hydrolase production, especially xylanase. Consequently, it was able to degrade various lignocellulose substrates with a biodegrading capability superior to most previously identified fungus or fungus-methanogen co-culture isolates. End-product profiling analysis validated the beneficial metabolic impact of associated methanogen on fungus as revealed by high-yield production of methane and acetate and sustained growth on lignocellulose. Together, our data demonstrated a great potential of (Piromyces + M. ruminantium) Yak-G18 co-culture for use in industrial bioconversion of lignocellulosic biomass.

Pyrolysis of attapulgite clay blended with yak dung enhances pasture growth and soil health: Characterization and initial field trials.

Recent studies have shown that the pyrolysis of biomass combined with clay can result in both lower cost and increase in plant yields. One of the major sources of nutrients for pasture growth, as well as fuel and building materials in Tibet is yak dung. This paper reports on the initial field testing in a pasture setting in Tibet using yak dung, biochar, and attapulgite clay/yak dung biochars produced at ratios of 10/90 and 50/50 clay to dung. We found that the treatment with attapulgite clay/yak dung (50/50) biochar resulted in the highest pasture yields and grass nutrition quality. We also measured the properties and yields of mixtures of clay/yak dung biochar used in the field trials produced at 400°C and 500°C to help determine a possible optimum final pyrolysis temperature and dung/clay ratio. It was observed that increasing clay content increased carbon stability, overall biochar yield, pore size, carboxyl and ketone/aldehyde functional groups, hematite and ferrous/ferric sulphate/thiosulphate concentration, surface area and magnetic moment. Decreasing clay content resulted in higher pH, CEC, N content and an enhanced ability to accept and donate electrons. The resulting properties were a complex function of both processing temperature and the percentage of clay for the biochars processed at both 400°C and 500°C. It is possible that the increase in yield and nutrient uptake in the field trial is related to the higher concentration of C/O functional groups, higher surface area and pore volume and higher content of Fe/O/S nanoparticles of multiple oxidation state in the 50/50 clay/dung. These properties have been found to significantly increase the abundance of beneficial microorganisms and hence improve the nutrient cycling and availability in soil. Further field trials are required to determine the optimum pyrolysis production conditions and application rate on the abundance of beneficial microorganisms, yields and nutrient quality.

Fiber degradation potential of natural co-cultures of Neocallimastix frontalis and Methanobrevibacter ruminantium isolated from yaks (Bos grunniens) grazing on the Qinghai Tibetan Plateau.

Several natural anaerobic fungus-methanogen co-cultures have been isolated from rumen and feces source of herbivores with strong fiber degrading ability. In this study, we isolated 7 Neocallimastix with methanogen co-cultures from the rumen of yaks grazing on the Qinghai Tibetan Plateau. Based on morphological characteristics and internal transcribed spacer 1 sequences (ITS1), all the fungi were identified as Neocallimastix frontalis. The co-cultures were confirmed as the one fungus - one methanogen pattern by the PCR-denatured gradient gel electrophoresis (DGGE) assay. All the methanogens were identified as Methanobrevibacter ruminantium by 16s rRNA gene sequencing. We investigated the biodegrading capacity of the co-culture (N. frontalis + M. ruminantium) Yaktz1 on wheat straw, corn stalk and rice straw in a 7 days-incubation. The in vitro dry matter digestibility (IVDMD), acid detergent fiber digestibility (ADFD) and neural detergent fiber digestibility (NDFD) values of the substrates in the co-culture were significantly higher than those in the mono-culture N. frontalis Yaktz1. The co-culture exhibited high polysaccharide hydrolase (xylanase and FPase) and esterase activities. The xylanase in the co-culture reached the highest activity of 12500 mU/ml on wheat straw at the day 3 of the incubation. At the end of the incubation, 3.00 mmol-3.29 mmol/g dry matter of methane were produced by the co-culture. The co-culture also produced high level of acetate (40.00 mM-45.98 mM) as the end-product during the biodegradation. Interestingly, the N. frontalis Yaktz1 mono-culture produced large amount of lactate (8.27 mM-11.60 mM) and ethanol (163.11 mM-242.14 mM), many times more than those recorded in the previously reported anaerobic fungi. Our data suggests that the (N. frontalis + M. ruminantium) Yaktz1 co-culture and the N. frontalis Yaktz1 mono-culture both have great potentials for different industrial use.

Seed rain and its relationship with above-ground vegetation of degraded Kobresia meadows.

Seed rain is a crucial element in vegetation regeneration, but has been rarely studied in high altitude regions, particularly degraded Kobresia meadow. Weed infestation is a distinctive feature of pasture degradation in Kobresia meadows on the Tibetan plateau, the ecological mechanism of which is closely related with vegetation's seed rain. In this paper we assess the effect of vegetation degradation on seed rain and consider its implication for restoration of degraded Kobresia meadows in the headwater area of Yellow river, through analysis of seed species composition, number of seeds landing per m(2) of soil surface, and their relationship with above ground vegetation. Vegetation degradation had an impact on the species composition and numbers of seeds in seed rain and their relationship with above-ground vegetation. Within the un-degraded meadow, which provided a closed vegetation cover, 35 % of the seed rain was of sedge and gramineae species. However, within the degraded meadows, as the extent of degradation increased, so the total number of seeds m(-2) increased, with those derived from sedge and gramineae species forming a declining proportion of the total. Degradation of Kobresia meadow on the Tibetan plateau is exacerbated by the seed input of weed species (such as Oxytropis ochrocephala, Carum carvi, Aconitum pendulum, Pedicularis kansuensis in this study). Therefore, a major priority for the restoration of such degraded meadows should be the elimination of these weeds from the above ground vegetation by human intervention.

[Soil quality assessment of alpine meadow in Haibei State of Qinghai Province].

Taking the typical alpine meadows Potentilla froticosa shrub meadow, Kobresia humilis meadow, and K. pygmaea meadow in the Haibei State of Qinghai Province as the research objects, a comprehensive assessment of soil quality was conducted by principal component analysis (PCA), with seven indices of soil microbial activities and ten indices of soil chemical properties. The soil quality of the alpine meadow could be characterized by three principal components (PC). In the first component (PC1), 13 indices had high factorial loads; in the second component (PC2), 3 indices had high factorial loads; in the third component (PC3), only one index, total phosphors, had high factorial load. In combining with Norm values, eleven indices including microbial biomass carbon (MBC), urease, alkaline phosphatase, protease, organic matter, total N, available N, available P, available K, bulk density, and CEC were selected to establish minimum data set (MDS) for the comprehensive assessment of soil quality of alpine meadow in Haibei. The PCA and corresponding weight coefficient analysis showed that the soil quality (0-10 cm and 10-20 cm layers) of the three kind meadows was in the order of K. humilis meadow > P. froticosa shrub meadow > K. pygmaea meadow, and P. froticosa shrub meadow > K. pygmaea meadow > K. humilis meadow, respectively.

[Measurement of methane and carbon dioxide emissions from ruminants based on the NDIR technique].

Methane (CH4) production in the rumen represents a loss of energy for the host animal; in addition, methane eructated by ruminants may contribute to a greenhouse effect or global warming. The dinumal CH4 and carbon dioxide (CO2) emissions from sheep were continuously recorded using the flow-through chamber method. A type new type of non-disperse infrared (NDIR) gas sensors based on pulse IR source was introduced, and by using the high performance pyroelectric IR sensor with built in interference filter and the "single light and two wavelengths" technology, CH4 and CO2 measurement from ruminants was achieved. Animals were given dry oat hay as the basic diet and supplemented concentrate with the ratio of 7 : 3. The results showed that the recovery was 96.7% and 96.2% for CH4 and CO2, respectively. Methane and carbon dioxide output from sheep respectively averaged 15.6 g per day and 184.7 g per day, equivalent to 6.8 and 71.1 kg per animal. Diurnal fluctuations in hourly rates of CH4 and CO2 production in hourly of methane increased during day light to reach a peak at or near sunset and then declined towards sunrise, and consideration was given to the dry matter intake of the animals used in these studies and its possible effects on CH4 production.

[Determination of inorganic elements in the soil-grass-animal system by sealed microwave digestion ICP-AES].

The contents of inorganic elements including K, Ca, Na, Mg, P, S, Fe, Cu, Mn, Zn, Mo, and Co in the soil-grass-animal mineral system from Qinghai Tibetan Plateau were determined by ICP-AES using high pressure system-sealed microwave digestion. The sample of soil was digested with HNO3-HF-H2O2 acids system, but others including pasture, animal fur, liver, and serum were digested with HNO3-H2O2 acids system. The operation would be simplified and the blank value would be decreased with the above acids systems. The results were proved to be reliable with the relative standard deviation being 0.271%-2.633% for Ca, 2.971%-4.854% for Co, 0.372%-2.874% for Cu, 0.600%-3.683% for Fe, 0.347%-2.829% for K, 0.626%-2.593% for Mg, 0.705%-4.828% for Mn, 2.946%-4.622% for Mo, 0.689%-3.621% for Na, 0.422%-3.890% for P, and 0.143%-4.622% for S, 0.166%-2.399% for Zn, and all of them were less than 5% for all the elements, and the recovery being 97.1%-101.4% for Ca, 93.5%-112.5% for Co, 95.2%-104.0% for Cu, 96.9%-104.2% for Fe, 96.1%-105.6% for K, 96.2%-102.8% for Mg, 91.5%-108.9% for Mn, 95.0%-113.5% for Mo, 95.2%-101.8% for Na, 94.7%-100.7% for P, 98.3%-108.4% for S, and 97.5%-102.0% for Zn by adding standard recovery experiment. The results of determination were proved that the method of sealed microwave digestion ICP-AES was sensitive, precise, easy to operate and rapid for the determination of inorganic elements in the soil-grass-animal mineral system, and could satisfy the sample examination request. The methods and results were meaningful to research on the soil-pasture-animal mineral system including the contents of mineral elements, the circulation of mineral elements, the interaction, and the application of mineral additive.

[Progress in application of near infrared reflectance spectroscopy to the study of ruminant nutrition].

The near infrared reflectance spectroscopy (NIRS) technique has been widely used in the study of ruminant nutrition with many of its operational merits such as facility, shortcut and accuracy, etc. Study suggested that the standard error of cross-validation (SECV) ranges from 1.6% to 2.8% in predicting organic matter digestion of ruminant diet by using the NIRS technique; the chemical and biological compositions and the microbial protein proportion in the duodenal digesta can be predicted accurately using the NIRS. However, the kinetic parameters of degradation are not well predicted; The prediction of intake of stall feeding animals by using NIRS is similar to the determination of in vivo method, but the standard error of prediction is about 14% when using the NIRS to predict intake of grazing animals. All of the studies suggest that big progress has been made in using NIRS technique to predict feed digestion and evaluate the diet quality and intake of ruminant animals, which also suggest that the NIRS technique has a wide prospect in the study of ruminant nutrition.

[Spectroscopy technique and ruminant methane emissions accurate inspecting].

The increase in atmospheric CH4 concentration, on the one hand through the radiation process, will directly cause climate change, and on the other hand, cause a lot of changes in atmospheric chemical processes, indirectly causing climate change. The rapid growth of atmospheric methane has gained attention of governments and scientists. All countries in the world now deal with global climate change as an important task of reducing emissions of greenhouse gases, but the need for monitoring the concentration of methane gas, in particular precision monitoring, can be scientifically formulated to provide a scientific basis for emission reduction measures. So far, CH4 gas emissions of different animal production systems have received extensive research. The methane emission by ruminant reported in the literature is only estimation. This is due to the various factors that affect the methane production in ruminant, there are various variables associated with the techniques for measuring methane production, the techniques currently developed to measure methane are unable to accurately determine the dynamics of methane emission by ruminant, and therefore there is an urgent need to develop an accurate method for this purpose. Currently, spectroscopy technique has been used and is relatively a more accurate and reliable method. Various spectroscopy techniques such as modified infrared spectroscopy methane measuring system, laser and near-infrared sensory system are able to achieve the objective of determining the dynamic methane emission by both domestic and grazing ruminant. Therefore spectroscopy technique is an important methane measuring technique, and contributes to proposing reduction methods of methane.

[Changes of plant community structure and species diversity in degradation process of Shouqu wetland of Yellow River].

Shouqu wetland of Yellow River plays important roles in the ecological security of the lower reaches of Yellow River. By the method of replacing time series with spatial sequence, an investigation was made on the changes of plant species diversity in the process of the natural degradation of the wetland. A comparison was also made to study the effects of artificial drainage on the plant species diversity. The results indicated that in the degradation process of Shouqu wetland, i.e., from swamp to swamp meadow, to alpine meadow, and to steppe meadow, the dominant plants followed the pattern of hygrophytes being gradually replaced by mesophytes and xerophytes, richness index and diversity index were increasing while dominance index was decreasing, and evenness index decreased first and increased then. The species diversity had an overall increasing trend. After artificial drainage, the proportion of poisonous weeds in the plant community increased, resulting in the increase of richness index and diversity index, slight decrease of evenness index and dominance index, and gradual decrease of Sorensen index. Artificial drainage made the habitat drying, which provided a chance for some mesophytes to invade, resulting in the increase of diversity index and richness index and the decrease of evenness index. On the whole, artificial drainage increased the plant diversity in the community, but the increase accompanied with increasing poisonous weeds, and thus, led the Shouqu wetland degraded into weed type wetland.

[Changes in plant communities and soil microbial physiological groups of artificial grasslands established for different years in headwater region of Yangtze River and Yellow River].

An investigation was made on the plant communities of artificial grasslands established for different years in headwater region of Yangtze River and Yellow River, and the related soil physical and chemical properties and soil microbial physiological groups were analyzed. With the increase of establishment years, most of plant communities on the grasslands showed a "V" type change trend in their quantities, i.e., high-low-high, but the forbs biomass had a "A" type change trend and the sedge biomass increased gradually. Soil nutrients presented a "V" type but soil bulk density presented a "A" type change trend, while soil pH presented a decreasing trend. Most of soil microbial physiological groups and microbial biomass carbon showed a "V" type change trend, phosphorus-dissolving bacteria showed a "A" type change trend, denitrifying bacteria decreased gradually, while cellulose-decomposing bacteria showed an increasing trend. The numbers of soil microbes had a close relationship with tested soil factors, and the soil microbial physiological groups were directly or indirectly affected by the soil factors. All the results indicated that the establishment of artificial grassland and the positive succession of vegetation could effectively improve soil physical and chemical properties, which benefit for the beneficial microbes to settle down and propagation, while proliferation of the non-beneficial microbes was inhibited.

Growing season ecosystem respirations and associated component fluxes in two alpine meadows on the Tibetan Plateau.

From 30 June to 24 September in 2003 ecosystem respiration (Re) in two alpine meadows on the Tibetan Plateau were measured using static chamber- and gas chromatography- (GC) based techniques. Simultaneously, plant removal treatments were set to partition Re into plant autotrophic respiration (Ra) and microbial heterotrophic respiration (Rh). Results indicated that Re had clear diurnal and seasonal variation patterns in both of the meadows. The seasonal variability of Re at both meadow sites was caused mainly by changes in Ra, rather than Rh. Moreover, at the Kobresia humilis meadow site (K_site), Ra and Rh accounted for 54% and 46% of Re, respectively. While at the Potentilla fruticosa scrub meadow (P_site), the counterparts accounted for 61% and 39%, respectively. T test showed that there was significant difference in Re rates between the two meadows (t = 2.387, P = 0.022). However, no significant difference was found in Rh rates, whereas a significant difference was observed in Ra rates between the two meadows. Thus, the difference in Re rate between the two meadows was mainly attributed to plant autotrophic respirations. During the growing season, the two meadows showed relatively low Q10 values, suggesting that Re, especially Rh was not sensitive to temperature variation in the growing season. Additionally, Re and Rh at the K_site, as well as Rh at the P_site was negatively correlated with soil moisture, indicating that soil moisture would also play an important role in respirations.

The cooperative relation between non-hydraulic root signals and osmotic adjustment under water stress improves grain formation for spring wheat varieties.

Non-hydraulic root signals (nHRS) and osmotic adjustment (OA) are two important adaptive responses of plants to water stress. There is little understanding of their relationships during water stress. The threshold range of soil water potential to occurrence of nHRS, the capacity for OA, grain yield and water use efficiency (WUE) were examined in three spring wheat (Triticum aestivum L.) varieties (two bred after 1975 and one bred before 1900) under water stress conditions. The threshold range of nHRS was significantly correlated with the maintenance rate of grain yield (MRGY) (r = 0.99, P < 0.05) under moderate drought (-0.49 to -0.55 MPa) but not under severe drought (-0.70 to -0.76 MPa). There were similar correlations between OA and the MRGY. However, regulation of nHRS precedes OA during gradual water stress. The threshold range of nHRS and OA was positively correlated (r = 0.93, P < 0.05), suggesting a mechanism for adapting to drought. WUE was higher for modern than for old varieties and was correlated with the root efficiency (full biomass weight including root per root weight, r = 0.78, P < 0.05) and the root water uptake efficiency (water consumption per root weight, r = 0.72, P < 0.05). However, there was a significant negative correlation between WUE and root weight (r = -0.84, P < 0.01). The cooperative relationship between the threshold range of nHRS and OA under water stress was beneficial for improving grain formation for spring wheat varieties.

[Characteristics of artificial grassland plant communities with different establishment duration and their relationships with soil properties in the source region of three rivers in China].

This paper studied the biomass, species composition, and diversity index of artificial grassland plant communities with different establishment duration in the source region of the Three Rivers, and examined the relationships of soil physical and chemical properties with the changes of the plant community biomass and species diversity. The results showed that the species composition, functional group composition, and quantitative characters of the plant communities varied greatly. Soil moisture content increased with increasing species diversity, while soil bulk density was in adverse. Soil microbial biomass carbon significantly positively correlated with soil moisture and organic matter contents, but negatively correlated with soil bulk density. Soil organic carbon content had a "V" type change, which was consistent with the change pattern of soil moisture content, and decreased with increasing soil bulk density. Plant community biomass had significant positive correlations with the contents of soil nutrients and moisture, and the increase of the above- and below-ground biomass of plant communities promoted the increase of soil nutrient contents.

[Effects of exogenous nitric oxide, salicylic acid and hydrogen peroxide on free amino acid and soluble protein contents in tobacco leaves].

The work focused on the effects of signal molecules of nitric oxide (NO), salicylic acid (SA) and hydrogen peroxide (H(2)O(2)) on compounds of nitric metabolites of free amino acid, soluble protein and proline in tobacco. The results indicated that NO, SA and H(2)O(2) were able to regulate the proline, free amino acid and soluble protein content in tobacco. Lower concentration of NO and H(2)O(2) raised the level of proline; while higher concentration of NO and H(2)O(2) lowered the proline, free amino acid content in tobacco. The above three signal molecules also showed similar effects on proline, free amino acid and soluble protein content in tobacco.