Leaf carbon chemistry effectively manipulated soil microbial profiles and induced metabolic adjustments under different revegetation types in the loess Plateau, China.

Microorganisms are essential components of underground life systems and drive elemental cycling between plants and soil. Yet, in the ecologically fragile Loess Plateau, scant attention has been paid to the response of microbial communities to organic carbon (C) chemistry of both leaves and soils under different revegetation conditions, as well as subsequent alternation in their C metabolic functions. Here, Fourier transform infrared (FTIR) spectrum, amplicon sequencing of 16S rRNA and ITS, and temporal incubation with Biolog-Eco 96 plates were combined to explore the vegetative heterogeneity of microbial community properties and metabolic functions, as well as their regulatory mechanisms in three typical revegetation types including Robinia pseudoacacia L. (RF), Caragana korshinskii KOM. (SL), and abandoned grassland (AG). We observed higher bacterial-to-fungal ratios (B: F = 270.18) and richer copiotrophic bacteria (Proteobacteria = 33.08%) in RF soil than those in AG soil, suggesting that microbes were dominated by r-strategists in soil under RF treatment, which is mainly related to long-term priming of highly bioavailable leaf C (higher proportion of aromatic and hydrophilic functional groups and lower hydrophobicity). Conversely, microbial taxa in AG soil, which was characterized by higher leaf organic C hydrophobicity (1.39), were dominated by relatively more abundant fungi (lower B: F ratio = 149.49) and oligotrophic bacteria (Actinobacteria = 29.30%). The co-occurrence network analysis showed that microbial interactive associations in RF and AG soil were more complex and connective than in SL soil. Furthermore, Biolog-Eco plate experiments revealed that microorganisms tended to utilize labile C compounds (carbohydrates and amino acids) in RF soil and resistant C compounds (polymers) in AG soil, which were consistent with the substrate adaptation strategies of predominant microbial trophic groups in different revegetation environments. Meanwhile, we observed greater microbial metabolic activity and diversity advantages in RF vegetation. Collectively, we suggest that besides the nutrient variables in the leaf-soil system, the long-term regulation of the microbial community by the C chemistry of the leaf sequentially alters the microbial metabolic profiles in a domino-like manner. RF afforestation is more conducive to restoring soil microbial fertility (including microbial abundance, diversity, interactive association, and metabolic capacity). Our study potentially paves the way for achieving well-managed soil health and accurate prediction of C pool dynamics in areas undergoing ecological restoration of the Loess Plateau.

Nitrogen and Microelements Co-Drive the Decomposition of Typical Grass Litter in the Loess Plateau, China.

In grassland ecosystems, the decomposition of litter serves as a vital conduit for nutrient transfer between plants and soil. The aim of this study was to depict the dynamic process of grass litter decomposition and explore its major driver. Three typical grasses [Stipa bungeana Trin (St. B), Artemisia sacrorun Ledeb (Ar. S), and Thymus mongolicus Ronniger (Th. M)] were selected for long-term litter decomposition. Experiments were conducted using three single litters, namely, St. B, Ar. S, and Th. M, and four different compositions of mixed litter: ML1 (55% St. B and 45% Th. M), ML2 (55% St. B and 45% Ar. S), ML3 (75% St. B and 25% Th. M), and ML4 (75% St. B and 25% Ar. S). The dynamic patterns of mass and microelements (Ca, Mg, Fe, Mn, Cu, and Zn) within different litter groups were analyzed. Our findings indicated that, after 1035 days of decomposition, the proportion of residual mass for the single litters was as follows: Th. M (60.6%) > St. B (47.3%) > Ar. S (44.3%), and for the mixed groups it was ML1 (48.0%) > ML3 (41.6%) > ML2 (40.9) > ML4 (38.4%). Mixed cultivation of the different litter groups accelerated the decomposition process, indicating that the mixture of litters had a synergistic effect on litter decomposition. The microelements of the litter exhibited an initial short-term increase followed by long-term decay. After 1035 days of decomposition, the microelements released from the litter were, in descending order, Mg > Ca > Fe > Cu > Mn > Zn. Compared to the separately decomposed St. B litter, mixing led to an inhibition of the release of Ca (antagonistic effect), while it promoted the release of Mg, Cu, and Zn (synergistic effect). For the single litter, the stepwise regression analysis showed that Ca was the dominant factor determining early litter decomposition. Mg, Mn, and Cu were the dominant factors regulating later litter decomposition. For the mixed litter groups, Ca, Mn, and Mg were the dominant factors closely related to early decomposition, and TN emerged as a key factor regulating the mass loss of mixtures during later decomposition. In summary, nitrogen and microelements co-drive the decomposition of typical grass litter. Our study underscores that, in the succession process of grassland, the presence of multiple co-existing species led to a faster loss of plant-derived materials (litter mass and internal elements), which was primarily modulated by species identity and uniformity.

[Effects of 24 Years Different Straw Return on Soil Carbon, Nitrogen, Phosphorus, and Extracellular Enzymatic Stoichiometry in Dryland of the Loess Plateau, China].

Exploring the biogeochemical cycle characteristics of soil carbon, nitrogen, and phosphorus in farmland in the dryland of the loess plateau can provide scientific basis and technical support for efficient crop production and sustainable land use. Here, based on a long-term (24 year) straw return field experiment in Shouyang, Shanxi province, the effects of different straw return regimes, i.e., straw mulching (SM), direct straw return (DS), animal-digested straw return (AS), and non-straw return (CK), on the stoichiometric ratio of soil elements and extracellular enzyme activities were studied. The vector angle and length were calculated to indicate the resource constraints faced by microorganisms. The vector angle was greater than 45° and less than 45°, indicating that microorganisms were limited by phosphorus and nitrogen, respectively. The greater the deviation from 45°, the greater the degree of limitation, and the longer the vector length, the more severely limited by carbon. The results showed that ① the soil C/N and C/P of long-term straw returning ranged from 9.81 to 14.28 and from 14.58 to 21.92, with the mean values of 12.36 and 17.51, respectively, which were 6.0% and 4.2% lower than that at the initial stage of the experiment. The soil N/P was distributed between 1.27 and 1.57, with an average of 1.42, which was 2.2% higher than that in the initial stage. The soil C/N and C/P ratios showed a trend of first decreasing and then increasing, the soil N/P ratio basically showed a flat trend, and there was no significant difference in soil element metering ratios between different straw returning treatments. ② Compared with the 24-year long-term non-straw return treatment, the activities of ß-1,4-glucosidase (BG) and ß-1,4-N-acetylglucosaminidase (NAG) in the soil of the long-term straw mulching treatment increased by 134.4% and 107.5% (P<0.05), the activities of BG and alkaline phosphatase (AP) in the soil of the long-term straw mulching treatment decreased by 59.3% and 59.5% (P<0.05), respectively, and the activities of NAG in the soil of the long-term straw mulching treatment increased by 102.8% (P<0.05). Under the long-term straw returning treatment, soil microorganisms were faced with carbon and phosphorus limitation as a whole. Long-term straw mulching aggravated microbial carbon limitation, and animal-digested straw return could alleviate the degree of carbon limitation. Compared with that in the 24-year long-term non-straw return treatment, soil EEAC/N could be significantly reduced by the animal-digested straw return treatment, and soil EEAC/P could be increased by the direct straw return treatment. The three straw returning methods had no significant indigenous effect on soil EEAN/P. The overall vector angle was greater than 45°, and the vector length increased by 3.8%-20.1% compared with that in the initial stage. ③ Correlation analysis showed that C and N inputs were significantly negatively correlated with BG activity; available nitrogen was significantly correlated with NAG activity, AP activity, and EEAC/N; C/P was significantly positively correlated with EEAC/N; there were significant correlations between N/P and NAG activity, AP activity, EEAC/N, and EEAC/P; and there was no significant correlation between EEAN/P and any environmental factors. In conclusion, the availability of soil nitrogen and phosphorus elements and N/P ratio had significant effects on soil extracellular enzyme activity and stoichiometric characteristics under different long-term straw returning treatments. In the future, more attention should be paid to the improvement of organic carbon and the promotion of nitrogen and phosphorus availability in farmland soil in soil-efficient cultivation and agricultural production activities.

A new inverse distance model to calculate the percentage contribution of various Pb sources.

Lead (Pb) isotopic composition analysis is a useful tool to accurately identify the origin of Pb in environmental media. The existing calculation method of the contribution of Pb sources from Pb isotope ratios greatly restricted the development of Pb contamination source apportionment. In the present study, a new distance model for calculating the mass proportion of Pb sources, which is based on the distance between the samples and the possible Pb sources in the Pb isotope ratios plot, was presented. The inverse distance model was applied to calculate the contribution proportion of two Pb sources in three previous studies. The average absolute differences between the proportions calculated by the conventional binary mixing equation and the inverse distance model were 0.21%, 1% and 1.9%, respectively, indicating that the new model agreeably calculated the contribution of two Pb sources. The anthropogenic sources proportion (52%) calculated by the inverse distance model of three Pb sources to park soil Pb in Shanghai was comparable to the result that was calculated by the conventional ternary mixing equation (53%), which showed the validity of the new model in calculating the contribution proportion of three Pb sources. Rational results were obtained by the inverse distance model in calculating the contribution of four Pb sources, illustrating that the new model has potential use in calculating the apportionment of four or more Pb sources. These results suggest that the inverse distance model is a simple and efficient approach for calculating the contribution proportion of various Pb contamination sources, and provides a prospective in the study of this field.

Insight into unique somitogenesis of yak (Bos grunniens) with one additional thoracic vertebra.

BACKGROUND: The yak is a species of livestock which is crucial for local communities of the Qinghai-Tibet Plateau and adjacent regions and naturally owns one more thoracic vertebra than cattle. Recently, a sub-population of yak termed as the Jinchuan yak has been identified with over half its members own a thoracolumbar vertebral formula of T15L5 instead of the natural T14L5 arrangement. The novel T15L5 positioning is a preferred genetic trait leading to enhanced meat and milk production. Selective breeding of this trait would have great agricultural value and exploration of the molecular mechanisms underlying this trait would both accelerate this process and provide us insight into the development and regulation of somitogenesis. RESULTS: Here we investigated the genetic background of the Jinchuan yak through resequencing fifteen individuals, comprising five T15L5 individuals and ten T14L5 individuals with an average sequencing depth of > 10X, whose thoracolumbar vertebral formulae were confirmed by anatomical observation. Principal component analysis, linkage disequilibrium analysis, phylogenetic analysis, and selective sweep analysis were carried out to explore Jinchuan yak's genetic background. Three hundred and thirty candidate markers were identified as associated with the additional thoracic vertebrae and target sequencing was used to validate seven carefully selected markers in an additional 51 Jinchuan yaks. The accuracies of predicting 15 thoracic vertebrae and 20 thoracolumbar vertebrae with these 7 markers were 100.00 and 33.33% despite they both could only represent 20% of all possible genetic diversity. Two genes, PPP2R2B and TBLR1, were found to harbour the most candidate markers associated with the trait and likely contribute to the unique somitic number and identity according to their reported roles in the mechanism of somitogenesis. CONCLUSIONS: Our findings provide a clear depiction of the Jinchuan yak's genetic background and a solid foundation for marker-assistant selection. Further exploitation of this unique population and trait could be promoted with the aid of our genomic resource.

Transcriptomic profiles of Dunaliella salina in response to hypersaline stress.

BACKGROUND: Dunaliella salina is a good model organism for studying salt stress. In order to have a global understanding of the expression profiles of Dunaliella salina in response to hypersaline stress, we performed quantitative transcriptomic analysis of Dunaliella salina under hypersaline stress (2.5 M NaCl) of different time duration by the second and third generation sequencing method. RESULTS: Functional enrichment of the up-regulated genes was used to analyze the expression profiles. The enrichment of photosynthesis was observed, accompanied by enrichments of carbon fixation, pigment biosynthetic process and heme biosynthetic process, which also imply the enhancement of photosynthesis. Genes responsible for starch hydrolysis and glycerol synthesis were significantly up-regulated. The enrichment of biosynthesis of unsaturated fatty acids implies the plasma membrane undergoes changes in desaturation pattern. The enrichment of endocytosis implies the degradation of plasma membrane and might help the synthesis of new glycerophospholipid with unsaturated fatty acids. Co-enrichments of protein synthesis and degradation imply a higher protein turnover rate. The enrichments of spliceosome and protein processing in endoplasmic reticulum imply the enhancement of regulations at post-transcriptional and post-translational level. No up-regulation of any Na+ or Cl- channels or transporters was detected, which implies that the extra exclusion of the ions by membrane transporters is possibly not needed. Voltage gated Na+ and Cl- channels, mechanosensitive ion channel are possible signal receptors of salt stress, and Ca2+ and MAP kinase pathways might play a role in signal transduction. CONCLUSION: At global transcriptomic level, the response of Dunaliella salina to hypersaline stress is a systematic work, possibly involving enhancements of photosynthesis, carbon fixation, and heme biosynthetic process, acceleration of protein turnover, spliceosome, protein processing in endoplasmic reticulum, and endocytosis, as well as degradation of starch, synthesis of glycerol, membrane lipid desaturation. Altogether, the changes of these biological processes occurred at trancriptomic level will help understand how a new intracellular balance achieved in Dunaliella salina to adapt to hypersaline environment, which are worth being confirmed at the physiological levels.

δ-Quench Measurement of a Pure Quantum-State Wave Function.

The measurement of a quantum state wave function not only acts as a fundamental part in quantum physics but also plays an important role in developing practical quantum technologies. Conventional quantum state tomography has been widely used to estimate quantum wave functions, which usually requires complicated measurement techniques. The recent weak-value-based quantum measurement circumvents this resource issue but relies on an extra pointer space. Here, we theoretically propose and then experimentally demonstrate a direct and efficient measurement strategy based on a δ-quench probe: by quenching its complex probability amplitude one by one (δ quench) in the given basis, we can directly obtain the quantum wave function of a pure ensemble by projecting the quenched state onto a postselection state. We confirm its power by experimentally measuring photonic complex temporal wave functions. This new method is versatile and can find applications in quantum information science and engineering.

Impact of agricultural fertilization practices on organo-mineral associations in four long-term field experiments: Implications for soil C sequestration.

Soil organic carbon (SOC) associated with minerals is considered to be one of the most fundamental long-term SOC storage strategies, but little research has integrated the organo-mineral complexes regulated by long-term fertilization. Here, soil samples under three fertilization treatments (Control, no fertilization; NPK, chemical nitrogen, phosphorus and potassium fertilization; NPKM, NPK plus manure) from four 23-34 years long-term field experiment sites across China were examined. Chemical analyses indicated that vigorous iron (Fe) mobilization could be regulated by long-term fertilization regimes. Meanwhile, Fe K-edge X-ray absorption near-edge fine structure (XANES) demonstrated that compared to NPK treated soils, NPKM treated soils contained significantly higher concentration of poorly crystalline ferrihydrite. Results from both the Fourier transform infrared combined with two-dimensional correlation spectroscopy analyses (FTIR-2DCOS) and C 1 s X-ray photoelectron spectroscopy (XPS) revealed that aliphatic carbohydrate might play an important role in binding exogenous Fe(III) in all tested four soils. In addition, greater amounts of aromatic C (the most resistant soil C fraction) were under long-term treated NPKM than NPK soils. Furthermore, multiple regression analyses showed a significantly positive relationship between poorly crystalline Fe minerals and SOC or aromatic C. Such relationships indicated that aromatic functional groups had been attached to the poorly crystalline Fe minerals, which could also be protected from being transformed to the crystalline counterpart. In conclusion, results from our integrated spectroscopic analyses have evidenced greater improvement of both poorly crystalline Fe minerals and aromatic C in organically fertilized than in chemically fertilized soils.

Multiplex Assay for Identifying Animal Species Found in the Tibetan Area Using the Mitochondrial 12S rRNA Gene.

Southwestern China has an area with unique natural conditions located in alpine regions at altitudes from 2000 to 5000 m; this area is referred to as the Qinghai-Tibetan plateau (QTP). Unique animals, such as yaks (Bos grunniens), are found extensively on the plateau of Southwestern China due to its unique environment. In recent years, the prevalence of fake meat products such as fake jerky has increased in this area. This research was conducted as an attempt to develop a reliable multiplex polymerase chain reaction (mPCR) detection method for identifying nine animal species found in QTP. We developed the mPCR method using the specific sites found in 12S rRNA region of these nine species, which was effective in discriminating between the nine species and was successful in terms of validated reproducibility, detection limit (<6 pg total DNA), discrimination of mixed samples, and specificity (approximately 99%) using real meat samples. Our results show that the mPCR detection method can overcome the limitations of prior detection methods, such as restriction fragment length polymorphism or high-resolution melting analysis methods.

In situ visualisation and characterisation of the capacity of highly reactive minerals to preserve soil organic matter (SOM) in colloids at submicron scale.

Mineral-organo associations (MOAs) are a mixture of identifiable biopolymers associated with highly reactive minerals and microorganisms. However, the in situ characterization and correlation between soil organic matter (SOM) and highly reactive Al and Fe minerals are still unclear for the lack of technologies, particularly in the long-term agricultural soil colloids at submicron scale. We combined several novel techniques, including nano-scale secondary ion mass spectrometry (NanoSIMS), X-ray absorption near edge structure (XANES) and confocal laser scanning microscopy (CLSM) to characterise the capacity of highly reactive Al and Fe minerals to preserve SOM in Ferralic Cambisol in south China. Our results demonstrated that: (1) highly reactive minerals were strongly related to SOM preservation, while SOM had a more significant line correlation with the highly reactive Al minerals than the highly reactive Fe minerals, according to the regions of interest correlation analyses using NanoSIMS; (2) allophane and ferrihydrite were the potential mineral species to determine the SOM preservation capability, which was evaluated by the X-ray photoelectron spectroscopy (XPS) and Fe K-edge XANES spectroscopy techniques; and (3) soil organic biopolymers with dominant compounds, such as proteins, polysaccharides and lipids, were distributed at the rough and clustered surface of MOAs with high chemical and spatial heterogeneity according to the CLSM observation. Our results also promoted the understanding of the roles played by the highly reactive Al and Fe minerals in the spatial distribution of soil organic biopolymers and SOM sequestration.

Insights into complexation of dissolved organic matter and Al(III) and nanominerals formation in soils under contrasting fertilizations using two-dimensional correlation spectroscopy and high resolution-transmission electron microscopy techniques.

Understanding the organomineral associations in soils is of great importance. Using two-dimensional correlation spectroscopy (2DCOS) and high resolution-transmission electron microscopy (HRTEM) techniques, this study compared the binding characteristics of organic ligands to Al(III) in dissolved organic matter (DOM) from soils under short-term (3-years) and long-term (22-years) fertilizations. Three fertilization treatments were examined: (i) no fertilization (Control), (ii) chemical nitrogen, phosphorus and potassium (NPK), and (iii) NPK plus swine manure (NPKM). Soil spectra detected by the 2DCOS Fourier transform infrared (FTIR) spectroscopy showed that fertilization modified the binding characteristics of organic ligands to Al(III) in soil DOM at both short- and long- term location sites. The CH deformations in aliphatic groups played an important role in binding to Al(III) but with minor differences among the Control, NPK and NPKM at the short-term site. While at the long-term site both C-O stretching of polysaccharides or polysaccharide-like substances and aliphatic O-H were bound to Al(III) under the Control, whereas only aliphatic O-H, and only polysaccharides and silicates, were bound to Al(III) under NPK and NPKM, respectively. Images from HRTEM demonstrated that crystalline nanominerals, composed of Fe and O, were predominant in soil DOM under NPK, while amorphous nanominerals, predominant in Al, Si, and O, were dominant in soil DOM under Control and NPKM. In conclusion, fertilization strategies, especially under long-term, could affect the binding of organic ligands to Al(III) in soil DOM, which resulted in alterations in the turnover, reactivity, and bioavailability of soil organic matter. Our results demonstrated that the FTIR-2DCOS combined with HRTEM techniques could enhance our understanding in the binding characteristics of DOM to Al(III) and the resulted nanominerals in soils.

Rapid and accurate evaluation of the quality of commercial organic fertilizers using near infrared spectroscopy.

The composting industry has been growing rapidly in China because of a boom in the animal industry. Therefore, a rapid and accurate assessment of the quality of commercial organic fertilizers is of the utmost importance. In this study, a novel technique that combines near infrared (NIR) spectroscopy with partial least squares (PLS) analysis is developed for rapidly and accurately assessing commercial organic fertilizers quality. A total of 104 commercial organic fertilizers were collected from full-scale compost factories in Jiangsu Province, east China. In general, the NIR-PLS technique showed accurate predictions of the total organic matter, water soluble organic nitrogen, pH, and germination index; less accurate results of the moisture, total nitrogen, and electrical conductivity; and the least accurate results for water soluble organic carbon. Our results suggested the combined NIR-PLS technique could be applied as a valuable tool to rapidly and accurately assess the quality of commercial organic fertilizers.

Maternal phylogeny of a newly-found yak population in china.

The Jinchuan yak is a new yak population identified in Sichuan, China. This population has a special anatomical characteristic: an additional pair of ribs compared with other yak breeds. The genetic structure of this population is unknown. In the present study, we investigated the maternal phylogeny of this special yak population using the mitochondrial DNA variation. A total of 23 Jinchuan yaks were sequenced for a 823-bp fragment of D-loop control region and three individuals were sequenced for the whole mtDNA genome with a length of 16,371-bp. To compare with the data from other yaks, we extracted sequence data from Genebank, including D-loop of 398 yaks (from 12 breeds) and 55 wild yaks, and whole mitochondrial genomes of 53 yaks (from 12 breeds) and 21 wild yaks. A total of 127 haplotypes were defined, based on the D-loop data. Thirteen haplotypes were defined from 23 mtDNA D-loop sequences of Jinchuan yaks, six of which were shared only by Jinchuan, and one was shared by Jinchuan and wild yaks. The Jinquan yaks were found to carry clades A and B from lineage I and clade C of lineage II, respectively. It was also suggested that the Jinchuan population has no distinct different phylogenetic relationship in maternal inheritance with other breeds of yak. The highly haplotype diversity of the Pali breed, Jinchuan population, Maiwa breed and Jiulong breed suggested that the yak was first domesticated from wild yaks in the middle Himalayan region and the northern Hengduan Mountains. The special anatomic characteristic that we found in the Jinchuan population needs further studies based on nuclear data.

Yak (Bos grunniens) stomach lysozyme: molecular cloning, expression and its antibacterial activities.

The cDNA coding for stomach lysozyme in yak was cloned. The cloned cDNA contains a 432 bp open reading frame and encodes 143 amino acids (16.24 KDa) with a signal peptide of 18 amino acids. Further analysis revealed that its amino acid sequence shares many common properties with cow milk lysozyme. Expression of this gene was also detected in mammary gland tissue by RT-PCR. Phylogenetic relationships among yak stomach lysozyme and 8 cow lysozymes indicated that the yak enzyme is more closely related to both cow milk lysozyme and the pseudogene PsiNS4 than cow stomach lysozyme. Recombinant yak lysozyme purified by Ni(2+)-column showed a molecular weight of 33.78 kDa and exhibited lytic activity against Staphylococcus aureus, providing evidence of its antibacterial activities.