An efficient peptide ligase engineered from a bamboo asparaginyl endopeptidase.

In recent years, a few asparaginyl endopeptidases (AEPs) from certain higher plants have been identified as efficient peptide ligases with wide applications in protein labeling and cyclic peptide synthesis. Recently, we developed a NanoLuc Binary Technology (NanoBiT)-based peptide ligase activity assay to identify more AEP-type peptide ligases. Herein, we screened 61 bamboo species from 16 genera using this assay and detected AEP-type peptide ligase activity in the crude extract of all tested bamboo leaves. From a popular bamboo species, Bambusa multiplex, we identified a full-length AEP-type peptide ligase candidate (BmAEP1) via transcriptomic sequencing. After its zymogen was overexpressed in Escherichia coli and self-activated in vitro, BmAEP1 displayed high peptide ligase activity, but with considerable hydrolytic activity. After site-directed mutagenesis of its ligase activity determinants, the mutant zymogen of [G238V]BmAEP1 was normally overexpressed in E. coli, but failed to activate itself. To resolve this problem, we developed a novel protease-assisted activation approach in which trypsin was used to cleave the mutant zymogen and was then conveniently removed via ion-exchange chromatography. After the noncovalently bound cap domain was dissociated from the catalytic core domain under acidic conditions, the recombinant [G238V]BmAEP1 displayed high peptide ligase activity with much lower hydrolytic activity and could efficiently catalyze inter-molecular protein ligation and intramolecular peptide cyclization. Thus, the engineered bamboo-derived peptide ligase represents a novel tool for protein labeling and cyclic peptide synthesis.

Dynamics of rhizosphere microbial structure and function associated with the biennial bearing of moso bamboo.

Moso bamboo (Phyllostachys edulis) is a valuable nontimber forestry product with a biennial cycle, producing abundant bamboo shoots within one year (on-year) and few shoots within the following year (off-year). Moso bamboo plants undergo clonal reproduction, resulting in similar genetic backgrounds. However, the number of moso bamboo shoots produced each year varies. Despite this variation, the impact of soil nutrients and the root microbiome on the biennial bearing of moso bamboo is poorly understood. We collected 139 soil samples and determined 14 major physicochemical properties of the rhizosphere, rhizoplane, and bulk soil in different seasons (i.e., the growing and deciduous seasons) and different years (i.e., on- and off-years). Based on 16S rRNA and metagenomic sequencing, major variations were found in the rhizospheric microbial composition during different seasons and years in the moso bamboo forest. Environmental driver analysis revealed that essential nutrients (i.e., SOC, TOC, TN, P, and NH4+) were the main drivers of the soil microbial community composition and were correlated with the on- and off-year cycles. Moreover, 19 MAGs were identified as important biomarkers that could distinguish on- and off-years. We found that both season and year influenced both the microbial community structure and functional pathways through the biosynthesis of nutrients that potentially interact with the moso bamboo growth rhythm, especially the on-year root-associated microbiome, which had a greater abundance of specific nutrients such as gibberellins and vitamin B6. This work provides a dynamic perspective of the differential responses of various on- and off-year microbial communities and enhances our understanding of bamboo soil microbiome biodiversity and stability.

Effects of physiological integration on nitrogen use efficiency of moso bamboo in homogeneous and heterogeneous environments.

Introduction: Moso bamboo is one of the important clonal plants with complex underground rhizome-root system. Ramets connected by rhizome can translocate and share nitrogen (N), which may affect the nitrogen use efficiency (NUE) of moso bamboo. The aims of this study were to investigate the mechanisms of N physiological integration and its relationship with NUE of moso bamboo. Methods: A pot experiment was conducted to trace the movement of 15N between the connected ramets of moso bamboo in both homogeneous and heterogeneous N environments. Results: Results showed that N translocation within clonal fragments of moso bamboo was detected in both homogeneous and heterogeneous environments. The intensity of physiological integration (IPI) was significantly lower in homogeneous environments than that in heterogeneous environments. 15N translocation between the connected ramtes of moso bamboo was determined by the source-sink relationship in heterogeneous environments, and the 15N allocation of the fertilized ramet was higher than that of the connected unfertilized ramet. The NUE of connected treatment was significantly higher than that of severed treatment, which suggested that physiological integration significantly improved the NUE of moso bamboo. In addition, the NUE of moso bamboo was significantly higher in heterogeneous environments than that in homogeneous environments. The contribution rate of physiological integration (CPI) on NUE in heterogeneous environments was significantly higher than that in homogenous environments. Discussion: These results will provide theoretical basis for precision fertilization in moso bamboo forests.

Controls and variability of soil respiration temperature sensitivity across China.

Understanding the temperature sensitivity (Q10) of soil respiration is critical for benchmarking the potential intensity of regional and global terrestrial soil carbon fluxes-climate feedbacks. Although field observations have demonstrated the strong spatial heterogeneity of Q10, a significant knowledge gap still exists regarding to the factors driving spatial and temporal variabilities of Q10 at regional scales. Therefore, we used a machine learning approach to predict Q10 from 1994 to 2016 with a spatial resolution of 1 km across China from 515 field observations at 5 cm soil depth using climate, soil and vegetation variables. Predicted Q10 varied from 1.54 to 4.17, with an area-weighted average of 2.52. There was no significant temporal trend for Q10 (p = 0.32), but annual vegetation production (indicated by normalized difference vegetation index, NDVI) was positively correlated to it (p < 0.01). Spatially, soil organic carbon (SOC) was the most important driving factor in 62 % of the land area across China, and varied greatly, demonstrating soil controls on the spatial pattern of Q10. These findings highlighted different environmental controls on the spatial and temporal pattern of soil respiration Q10, which should be considered to improve global biogeochemical models used to predict the spatial and temporal patterns of soil carbon fluxes to ongoing climate change.

Soil meso- and micro-fauna community in response to bamboo-fungus agroforestry management.

Bamboo-fungus agroforestry management is an ecological model of sustainable production of moso bamboo forest, and Stropharia rugosoannulata has been widely planted in moso bamboo forest. However, little attention has been paid to soil fauna community in bamboo-fungus agroforestry system. Thus, the aim of this study was to investigate the response of soil fauna communities to agroforestry management, and to explore the relationships between soil fauna communities and soil properties. An experiment with 0, 1, 2 and 3 years of planting was carried out in an existing moso bamboo forest. The community composition of soil meso- and micro-fauna was investigated, and the soil properties were determined. Results showed that a total of 2968 individuals of soil meso- and micro-fauna, belonging to 8 classes and 13 groups were detected. The group number and density of soil fauna was highest right and then decreased. Planting Stropharia rugosoannulata in moso bamboo forest increased the density of dominant groups, but did not change its composition. Shannon-Weiner diversity index (H), Margalef richness index (D) and Density-Group diversity index (DG) were the highest one year after planting the fungus, while Simpson dominance index (C) was the lowest in the meantime. Contents of soil moisture (SMC), organic matter (SOM), total nitrogen (TN), total phosphorus (TP) and total potassium (TK) increased first and then decreased with the increase of planting years, peaking at 1 year after planting, while the pH value continued to increase. Responses of soil fauna community were associated with soil physicochemical properties. Redundancy analysis (RDA) showed that SOM was the main environmental factor driving the variation of soil fauna community, followed by TP and TN. In conclusion, planting Stropharia rugosoannulata in moso bamboo increased the diversity and abundance of soil fauna communities due to its contribution to abundance of organic matter and supply of nutrients.

Discussing on "source-sink" landscape theory and phytoremediation for non-point source pollution control in China.

Water pollution is exacerbated due to irrational human activities in China. Restoring and rebuilding river basin ecosystems are major ecological strategies at present. Controlling the non-point source pollution (NPSP) by reasonable management of land use in the basin and phytoremediation of contaminated waters is the optimum approach. Thus, it is significant to study on the relationship that between landscape change and the aquatic environment, as well as further to analyze on the combined effect of the landscape and water quality. This paper describes the application and development of the "source-sink" landscape theory in China, and the role of the theory in controlling NPSP. From this perspective, a landscape capable of generating NPSP would be a "source" landscape, such as farmland, while another capable of preventing NPSP would be a "sink" landscape, such as forests and wetland. Applying the source-sink landscape theory, it is possible to exert the ecological benefits of the landscape while playing the esthetic value of the landscape. Also, the purification mechanism of plants in contaminated water is discussed. Besides, it is vital that research on water body restoration should focus not only on single discipline but also on integration and coordination between various ones such as ecology, environmental science, and geography to jointly push up researches related to water body phytoremediation. Hopefully, this paper could help to control water pollution from a new perspective, also to improve water environment and benefit human lives.

Coupling of non-point source pollution and soil characteristics covered by Phyllostachys edulis stands in hilly water source area.

The non-point source pollution of drinking water source areas is a global issue which is mainly caused by unreasonable management of the commercial forests growing in the upstream areas. However the occurrence and specific mechanism of runoff pollution in these areas have not been approached. In order to clarify the factors influencing the non-point source pollution in the area, the test plot in Fushi Reservoir watershed covered by Phyllostachys edulis plantations with pure and modified stands was chosen, and the characteristics of soil chemical properties, enzyme activities and the coupling between soil factors and surface runoff of were initially analyzed, the relationship between soil factors and surface runoff pollutants was examined using redundancy analysis. The results showed that pH, soil nitrate reductase (S-NR) and catalase (S-CAT) were the key factors affecting the differentiation of water quality in surface runoff. The total nitrogen (TN) concentration in surface runoff was positively correlated with S-NR but negatively correlated with pH, TN and alkali-hydrolyzed nitrogen (AN) concentrations in soil. The total phosphorus (TP) concentration was negative correlation with soil pH and TP. In addition, the permanganate index (CODMn) concentration has positive correlation with urease (S-UE), acid phosphatase (S-ACP) and organic matter (SOM) in soil. These results suggest that soil enzyme activities are more sensitive than soil nutrient status, and could be used as indicators of non-point source pollution assessing. Moreover, pollution in this area could be effectively controlled by enhancing vegetation coverage and ameliorating soil environment.

Effects of Rhizome Integration on the Water Physiology of Phyllostachys edulis Clones Under Heterogeneous Water Stress.

Water is crucial to plant growth and development. Under heterogeneous environmental water deficiency, physiological integration of the rhizomatous clonal plant triggers a series of physiological cascades, which induces both signaling and physiological responses. It is known that the rhizome of Phyllostachys edulis, which connects associated clonal ramets, has important significance in this physiological integration. This significance is attributed to the sharing of water and nutrients in the vascular bundle of clonal ramets under heterogeneous water conditions. However, the physiological characteristics of physiological integration under heterogeneous water stress remain unclear. To investigate these physiological characteristics, particularly second messenger Ca2+ signaling characteristics, long-distance hormone signaling molecules, antioxidant enzyme activity, osmotic adjustment substance, and nitrogen metabolism, ramets with a connected (where integration was allowed to take place) and severed rhizome (with no integration) were compared in this study. The vascular bundle structure of the rhizome was also observed using laser confocal microscopy. Overall, the results suggest that interconnected rhizome of P. edulis can enhance its physiological function in response to drought-induced stress under heterogeneous water deficiency. These measured changes in physiological indices serve to improve the clonal ramets' drought adaptivity through the interconnected rhizome.

Bamboo vs. crops: an integrated emergy and economic evaluation of using bamboo to replace crops in south Sichuan Province, China.

Based on long-term monitoring conducted in Chang-ning county, a pilot site of the 'Grain for Green Program' (GFGP), an integrated emergy and economic method was applied to evaluate the dynamic ecological-economic performance of 3 kinds of bamboo systems planted on sloping farmland. The results confirmed the positive effects of all 3 kinds of bamboo systems on water conservation and soil erosion control. The benefits gained progressively increased during the first 8 years after conversion, going from 4639 to 16127 EMyuan/ha/yr on average. All three bamboo plantations were much more sustainable than common agricultural crops planted on sloping land (CP) on both the short and long-term scales with their Emergy Sustainability Index (ESI) and Emergy Index for Sustainable Development (EISD), respectively, being 14.07-325.71 and 80.35-265.80 times that of CP. However, all 3 bamboo plantations had a Net Economic Benefit (NEB) less than that of CP during the first 8 years after conversion. Even with the government-mandated ecological compensation applied, the annual NEBECs of the Bambusa rigida (BR) and Phyllostachys pubescense (PP) plantations were, respectively, 3922.03 and 7422.77 yuan/ha/yr lower than the NEB of CP. Emergy-based evaluation of ecosystem services provides an objective reference for applying ecological compensation in strategy-making, but it cannot wholly solve the economic viability problem faced by all bamboo plantations. Inter-planting annual herbs or edible fungus, such as Dictyophora echinovolvata, within bamboo forests, especially in young bamboo plantations, might be a direction for optimizing bamboo cultivation that would improve its economic viability.

Diversity and antimicrobial activity of culturable endophytic fungi isolated from moso bamboo seeds.

Bamboos, regarded as therapeutic agents in ethnomedicine, have been used to inhibit inflammation and enhance natural immunity for a long time in Asia, and there are many bamboo associated fungi with medical and edible value. In the present study, a total of 350 fungal strains were isolated from the uncommon moso bamboo (Phyllostachys edulis) seeds for the first time. The molecular diversity of these endophytic fungi was investigated and bioactive compound producers were screened for the first time. All the fungal endophytes were categorized into 69 morphotypes according to culturable characteristics and their internal transcriber spacer (ITS) regions were analyzed by BLAST search with the NCBI database. The fungal isolates showed high diversity and were divided in Ascomycota (98.0%) and Basidiomycota (2.0%), including at least 19 genera in nine orders. Four particular genera were considered to be newly recorded bambusicolous fungi, including Leptosphaerulina, Simplicillium, Sebacina and an unknown genus in Basidiomycetes. Furthermore, inhibitory effects against clinical pathogens and phytopathogens were screened preliminarily and strains B09 (Cladosporium sp.), B34 (Curvularia sp.), B35 (undefined genus 1), B38 (Penicillium sp.) and zzz816 (Shiraia sp.) displayed broad-spectrum activity against clinical bacteria and yeasts by the agar diffusion method. The crude extracts of isolates B09, B34, B35, B38 and zzz816 under submerged fermentation, also demonstrated various levels of bioactivities against bambusicolous pathogenic fungi. This study is the first report on the antimicrobial activity of endophytic fungi associated with moso bamboo seeds, and the results show that they could be exploited as a potential source of bioactive compounds and plant defense activators. In addition, it is the first time that strains of Shiraia sp. have been isolated and cultured from moso bamboo seeds, and one of them (zzz816) could produce hypocrellin A at high yield, which is significantly different from the other strains published.

[Soil heavy metals concentration in different type plantations in Harbin City].

In order to understand the soil heavy metals characteristics in different type plantations in Harbin City, 0-10 cm and 10-30 cm soil samples were collected from eight mono-cultured plantations (Larix gmelinii, Pinus sylvestris var. mongolica, Pinus tabulaeformis var. mukdensis, Phellodendron amurense, Juglans mandshurica, Fraxinus mandshurica, Betula platyphylla, and Quercus mongolica) and one mixed plantation (P. sylvestris var. mongolica + F. mandshurica + Pinus koraiensis + P. amurense + B. platyphylla) established in the Urban Forestry Demonstration Research Base of Northeast Forestry University in the 1950s to analyze the concentrations of Cu, Zn, Cd, Ni, Pb, and As, and the comprehensive pollution index was used to assess the soil heavy metals pollution in the plantations, based on the background values of black soil in the City. There existed significant differences in the heavy metals concentration in the same soil layers among different type plantations. In the test plantations, the concentrations of soil heavy metals except As and Ni tended to decrease with soil depth. In the same soil layers, Zn had the highest concentration (62.29-126.35 mg x kg(-1)), while Cd had the lowest one (0.06-0.47 mg x kg(-1)). The abundance and accumulation tendency of test heavy metals in the plantations was in the order of Zn>Pb>Cu(Ni)> Ni(Cu)>As>Cd, and Cd>Pb>Zn>Cu>Ni>As, respectively. There existed positive correlations among soil Cu, Zn, Pb, and Cd concentrations in the plantations except F. mandshurica, and the concentrations of these four heavy metals in the plantations except F. mandshurica and Q. mongolica were positively correlated with soil organic matter, N, P, and K. The concentrations of soil Cd, Pb, Zn, and Cu were higher than the background values, suggesting the anthropogenic inputs; while those of Ni and As were similar to or lower than the background values, suggesting the origin from soil materials. The soil comprehensive pollution index of the plantations was decreased in the order of F. mandshurica > P. amurense > mixed plantation > J. mandshurica > P. sylvestris var. mongolica > P. tabulaeformis var. mukdensis > L. gmelinii >B. platyphylla > Q. mongolica.

[Effects of different type urban forest plantations on soil fertility].

Aimed to study the effects of different urban forest plantations on soil fertility, soil samples were collected from eight mono-cultured plantations (Larix gmelinii, Pinus sylvestris var. mongolica, Pinus tabulaeformis var. mukdensis, Phellodendron amurense, Juglans mandshurica, Fraxinus mandshurica, Betula platyphylla, and Quercus mongolica) and one mixed plantation (P. sylvestris var. mongolica + F. mandshurica + Picea koraiensis + P. amurense + B. platyphylla) established in Northeast Forestry University's Urban Forestry Demonstration Research Base in the 1950s, with two sites of neighboring farmland and abandoned farmland as the control. The soils in broadleaved forest plantations except Q. mongolica were near neutral, those in mixed plantation, L. gmelinii, P. sylvestris var. mongolica, and P. tabulaeformis var. mukdensis were slightly acidic, and that in Q. mongolica was acidic. The contents of soil organic matter, total N and P, available P and K, and hydrolysable N tended to decrease with soil depth. There existed significant differences in the chemical indices of the same soil layers among different plantations. The soil fertility was decreased in the order of F. mandshurica > P. amurense > mixed plantation > J. mandshurica > B. platyphylla > abandoned farmland > farmland > P. sylvestris var. mongolica > L. gmelinii > Q. mongolica > P. tabulaeformis var. mukdensis, suggesting that the soil fertility in broadleaved forest plantations except Q. mongolica and in mixed plantation increased, while that in needle-leaved forest plantations tended to decrease.