South China Botanical Garden

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is thatthere is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the completeprocess including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increasedautophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in manycases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as forreviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multipleassays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagyrelated protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.

fertilization effect. Six Earth system models have consistently projected continuous increases of VPD throughout the current century. Our results highlight that the impacts of VPD on vegetation growth should be adequately considered to assess ecosystem responses to future climate conditions.

Artificial intelligence (AI) coupled with promising machine learning (ML) techniques well known from computer science is broadly affecting many aspects of various fields including science and technology, industry, and even our day-to-day life. The ML techniques have been developed to analyze high-throughput data with a view to obtaining useful insights, categorizing, predicting, and making evidence-based decisions in novel ways, which will promote the growth of novel applications and fuel the sustainable booming of AI. This paper undertakes a comprehensive survey on the development and application of AI in different aspects of fundamental sciences, including information science, mathematics, medical science, materials science, geoscience, life science, physics, and chemistry. The challenges that each discipline of science meets, and the potentials of AI techniques to handle these challenges, are discussed in detail. Moreover, we shed light on new research trends entailing the integration of AI into each scientific discipline. The aim of this paper is to provide a broad research guideline on fundamental sciences with potential infusion of AI, to help motivate researchers to deeply understand the state-of-the-art applications of AI-based fundamental sciences, and thereby to help promote the continuous development of these fundamental sciences.

from the atmosphere. Herein, we review innovative technologies that offer solutions achieving carbon (C) neutrality and sustainable development, including those for renewable energy production, food system transformation, waste valorization, C sink conservation, and C-negative manufacturing. The wealth of knowledge disseminated in this review could inspire the global community and drive the further development of innovative technologies to mitigate climate change and sustainably support human activities.

We aim to construct a comprehensive global database of litter decomposition rate (k value) estimated by surface floor litterbags, and investigate the direct and indirect effects of impact factors such as geographic factors (latitude and altitude), climatic factors (mean annual tempePlrature, MAT; mean annual precipitation, MAP) and litter quality factors (the contents of N, P, K, Ca, Mg and C:N ratio, lignin:N ratio) on litter decomposition. We compiled a large data set of litter decomposition rates (k values) from 110 research sites and conducted simple, multiple regression and path analyses to explore the relationship between the k values and impact factors at the global scale. The k values tended to decrease with latitude (LAT) and lignin content (LIGN) of litter but increased with temperature, precipitation and nutrient concentrations at the large spatial scale. Single factor such as climate, litter quality and geographic variable could not explain litter decomposition rates well. However, the combination of total nutrient (TN) elements and C:N accounted for 70.2% of the variation in the litter decomposition rates. The combination of LAT, MAT, C:N and TN accounted for 87.54% of the variation in the litter decomposition rates. These results indicate that litter quality is the most important direct regulator of litter decomposition at the global scale. This data synthesis revealed significant relationships between litter decomposition rates and the combination of climatic factor (MAT) and litter quality (C:N, TN). The global-scale empirical relationships developed here are useful for a better understanding and modeling of the effects of litter quality and climatic factors on litter decomposition rates.

The capability of terrestrial ecosystems to sequester carbon (C) plays a critical role in regulating future climatic change yet depends on nitrogen (N) availability. To predict long-term ecosystem C storage, it is essential to examine whether soil N becomes progressively limiting as C and N are sequestered in long-lived plant biomass and soil organic matter. A critical parameter to indicate the long-term progressive N limitation (PNL) is net change in ecosystem N content in association with C accumulation in plant and soil pools under elevated CO2. We compiled data from 104 published papers that study C and N dynamics at ambient and elevated CO2. The compiled database contains C contents, N contents, and C:N ratio in various plant and soil pools, and root:shoot ratio. Averaged C and N pool sizes in plant and soil all significantly increase at elevated CO2 in comparison to those at ambient CO2, ranging from a 5% increase in shoot N content to a 32% increase in root C content. The C and N contents in litter pools are consistently higher in elevated than ambient CO2 among all the surveyed studies whereas C and N contents in the other pools increase in some studies and decrease in other studies. The high variability in CO2-induced changes in C and N pool sizes results from diverse responses of various C and N processes to elevated CO2. Averaged C:N ratios are higher by 3% in litter and soil pools and 11% in root and shoot pools at elevated relative to ambient CO2. Elevated CO2 slightly increases root:shoot ratio. The net N accumulation in plant and soil pools at least helps prevent complete down-regulation of, and likely supports, long-term CO2 stimulation of C sequestration. The concomitant C and N accumulations in response to rising atmospheric CO2 may reflect intrinsic nature of ecosystem development as revealed before by studies of succession over hundreds to millions of years.

China's terrestrial ecosystems have functioned as important carbon sinks. However, previous estimates of carbon budgets have included large uncertainties owing to the limitations of sample size, multiple data sources, and inconsistent methodologies. In this study, we conducted an intensive field campaign involving 14,371 field plots to investigate all sectors of carbon stocks in China's forests, shrublands, grasslands, and croplands to better estimate the regional and national carbon pools and to explore the biogeographical patterns and potential drivers of these pools. The total carbon pool in these four ecosystems was 79.24 ± 2.42 Pg C, of which 82.9% was stored in soil (to a depth of 1 m), 16.5% in biomass, and 0.60% in litter. Forests, shrublands, grasslands, and croplands contained 30.83 ± 1.57 Pg C, 6.69 ± 0.32 Pg C, 25.40 ± 1.49 Pg C, and 16.32 ± 0.41 Pg C, respectively. When all terrestrial ecosystems are taken into account, the country's total carbon pool is 89.27 ± 1.05 Pg C. The carbon density of the forests, shrublands, and grasslands exhibited a strong correlation with climate: it decreased with increasing temperature but increased with increasing precipitation. Our analysis also suggests a significant sequestration potential of 1.9-3.4 Pg C in forest biomass in the next 10-20 years assuming no removals, mainly because of forest growth. Our results update the estimates of carbon pools in China's terrestrial ecosystems based on direct field measurements, and these estimates are essential to the validation and parameterization of carbon models in China and globally.

Significance China has launched six key ecological restoration projects since the late 1970s, but the contribution of these projects to terrestrial C sequestration remains unknown. In this study we examined the ecosystem C sink in the project area (∼16% of the country’s land area) and evaluated the project-induced C sequestration. The total annual C sink in the project area between 2001 and 2010 was estimated to be 132 Tg C per y, over half of which (74 Tg C per y, 56%) was caused by the implementation of the six projects. This finding indicates that the implementation of the ecological restoration projects in China has significantly increased ecosystem C sequestration across the country.

Phosphorus (P) limitation of aboveground plant production is usually assumed to occur in tropical regions but rarely elsewhere. Here we report that such P limitation is more widespread and much stronger than previously estimated. In our global meta-analysis, almost half (46.2%) of 652 P-addition field experiments reveal a significant P limitation on aboveground plant production. Globally, P additions increase aboveground plant production by 34.9% in natural terrestrial ecosystems, which is 7.0-15.9% higher than previously suggested. In croplands, by contrast, P additions increase aboveground plant production by only 13.9%, probably because of historical fertilizations. The magnitude of P limitation also differs among climate zones and regions, and is driven by climate, ecosystem properties, and fertilization regimes. In addition to confirming that P limitation is widespread in tropical regions, our study demonstrates that P limitation often occurs in other regions. This suggests that previous studies have underestimated the importance of altered P supply on aboveground plant production in natural terrestrial ecosystems.

Despite evidence from experimental grasslands that plant diversity increases biomass production and soil organic carbon (SOC) storage, it remains unclear whether this is true in natural ecosystems, especially under climatic variations and human disturbances. Based on field observations from 6,098 forest, shrubland, and grassland sites across China and predictions from an integrative model combining multiple theories, we systematically examined the direct effects of climate, soils, and human impacts on SOC storage versus the indirect effects mediated by species richness (SR), aboveground net primary productivity (ANPP), and belowground biomass (BB). We found that favorable climates (high temperature and precipitation) had a consistent negative effect on SOC storage in forests and shrublands, but not in grasslands. Climate favorability, particularly high precipitation, was associated with both higher SR and higher BB, which had consistent positive effects on SOC storage, thus offsetting the direct negative effect of favorable climate on SOC. The indirect effects of climate on SOC storage depended on the relationships of SR with ANPP and BB, which were consistently positive in all biome types. In addition, human disturbance and soil pH had both direct and indirect effects on SOC storage, with the indirect effects mediated by changes in SR, ANPP, and BB. High soil pH had a consistently negative effect on SOC storage. Our findings have important implications for improving global carbon cycling models and ecosystem management: Maintaining high levels of diversity can enhance soil carbon sequestration and help sustain the benefits of plant diversity and productivity.

Fruits and vegetables are colorful pigment-containing food sources. Owing to their nutritional benefits and phytochemicals, they are considered as 'functional food ingredients'. Carotenoids are some of the most vital colored phytochemicals, occurring as all-trans and cis-isomers, and accounting for the brilliant colors of a variety of fruits and vegetables. Carotenoids extensively studied in this regard include β-carotene, lycopene, lutein and zeaxanthin. Coloration of fruits and vegetables depends on their growth maturity, concentration of carotenoid isomers, and food processing methods. This article focuses more on several carotenoids and their isomers present in different fruits and vegetables along with their concentrations. Carotenoids and their geometric isomers also play an important role in protecting cells from oxidation and cellular damages.

Elevated anthropogenic nitrogen (N) deposition has greatly altered terrestrial ecosystem functioning, threatening ecosystem health via acidification and eutrophication in temperate and boreal forests across the northern hemisphere. However, response of forest soil acidification to N deposition has been less studied in humid tropics compared to other forest types. This study was designed to explore impacts of long-term N deposition on soil acidification processes in tropical forests. We have established a long-term N-deposition experiment in an N-rich lowland tropical forest of Southern China since 2002 with N addition as NH4 NO3 of 0, 50, 100 and 150 kg N ha(-1) yr(-1) . We measured soil acidification status and element leaching in soil drainage solution after 6-year N addition. Results showed that our study site has been experiencing serious soil acidification and was quite acid-sensitive showing high acidification (pH(H2O) <4.0), negative water-extracted acid neutralizing capacity (ANC) and low base saturation (BS,< 8%) throughout soil profiles. Long-term N addition significantly accelerated soil acidification, leading to depleted base cations and decreased BS, and further lowered ANC. However, N addition did not alter exchangeable Al(3+) , but increased cation exchange capacity (CEC). Nitrogen addition-induced increase in SOC is suggested to contribute to both higher CEC and lower pH. We further found that increased N addition greatly decreased soil solution pH at 20 cm depth, but not at 40 cm. Furthermore, there was no evidence that Al(3+) was leaching out from the deeper soils. These unique responses in tropical climate likely resulted from: exchangeable H(+) dominating changes of soil cation pool, an exhausted base cation pool, N-addition stimulating SOC production, and N saturation. Our results suggest that long-term N addition can contribute measurably to soil acidification, and that shortage of Ca and Mg should receive more attention than soil exchangeable Al in tropical forests with elevated N deposition in the future.

Old-growth forests have traditionally been considered negligible as carbon sinks because carbon uptake has been thought to be balanced by respiration. We show that the top 20-centimeter soil layer in preserved old-growth forests in southern China accumulated atmospheric carbon at an unexpectedly high average rate of 0.61 megagrams of carbon hectare-1 year-1 from 1979 to 2003. This study suggests that the carbon cycle processes in the belowground system of these forests are changing in response to the changing environment. The result directly challenges the prevailing belief in ecosystem ecology regarding carbon budget in old-growth forests and supports the establishment of a new, nonequilibrium conceptual framework to study soil carbon dynamics.

BACKGROUND: Various expansions or contractions of inverted repeats (IRs) in chloroplast genomes led to fluxes in the IR-LSC (large single copy) junctions. Previous studies revealed that some monocot IRs contain a trnH-rps19 gene cluster, and it has been speculated that this may be an evidence of a duplication event prior to the divergence of monocot lineages. Therefore, we compared the organizations of genes flanking two IR-LSC junctions in 123 angiosperm representatives to uncover the evolutionary dynamics of IR-LSC junctions in basal angiosperms and monocots. RESULTS: The organizations of genes flanking IR-LSC junctions in angiosperms can be classified into three types. Generally each IR of monocots contains a trnH-rps19 gene cluster near the IR-LSC junctions, which differs from those in non-monocot angiosperms. Moreover, IRs expanded more progressively in monocots than in non-monocot angiosperms. IR-LSC junctions commonly occurred at polyA tract or A-rich regions in angiosperms. Our RT-PCR assays indicate that in monocot IRA the trnH-rps19 gene cluster is regulated by two opposing promoters, S10A and psbA. CONCLUSION: Two hypotheses are proposed to account for the evolution of IR expansions in monocots. Based on our observations, the inclusion of a trnH-rps19 cluster in majority of monocot IRs could be reasonably explained by the hypothesis that a DSB event first occurred at IRB and led to the expansion of IRs to trnH, followed by a successive DSB event within IRA and lead to the expansion of IRs to rps19 or to rpl22 so far. This implies that the duplication of trnH-rps19 gene cluster was prior to the diversification of extant monocot lineages. The duplicated trnH genes in the IRB of most monocots and non-monocot angiosperms have distinct fates, which are likely regulated by different expression levels of S10A and S10B promoters. Further study is needed to unravel the evolutionary significance of IR expansion in more recently diverged monocots.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated (Cas) systems have been successfully used as efficient tools for genome editing in a variety of species. We used the CRISPR/Cas9 system to mutate the Gn1a (Os01g0197700), DEP1 (Os09g0441900), GS3 (Os03g0407400), and IPA1 (Os08g0509600) genes of rice cultivar Zhonghua 11, genes which have been reported to function as regulators of grain number, panicle architecture, grain size and plant architecture, respectively. Analysis of the phenotypes and frequencies of edited genes in the first generation of transformed plants (T0) showed that the CRISPR/Cas9 system was highly efficient in inducing targeted gene editing, with the desired genes being edited in 42.5% (Gn1a), 67.5% (DEP1), 57.5% (GS3), and 27.5% (IPA1) of the transformed plants. The T2 generation of the gn1a, dep1, and gs3 mutants featured enhanced grain number, dense erect panicles, and larger grain size, respectively. Furthermore, semi-dwarf, and grain with long awn, phenotypes were observed in dep1 and gs3 mutants, respectively. The ipa1 mutants showed two contrasting phenotypes, having either fewer tillers or more tillers, depending on the changes induced in the OsmiR156 target region. In addition, we found that mutants with deletions occurred more frequently than previous reports had indicated and that off-targeting had taken place in highly similar target sequences. These results proved that multiple regulators of important traits can be modified in a single cultivar by CRISPR/Cas9, and thus facilitate the dissection of complex gene regulatory networks in the same genomic background and the stacking of important traits in cultivated varieties.

Anthropogenic nitrogen (N) deposition is expected to increase substantially and continuously in the future. Soil N availability regulates microbial communities and the decomposition and formation of soil organic matter, which have great impacts on global carbon (C) cycling. We conducted a meta-analysis based on 454 N-addition experiments in order to synthesize the patterns and mechanisms of responses by soil microbial communities to N addition in various biomes (i.e., boreal forest, temperate forest, tropical/subtropical forest, grassland, and desert). Results showed that the effects of N addition on the total microbial biomass varied depending on biome types, methodologies (fumigation–extraction technique vs. total phospholipid fatty acid), and N-addition rates. Nitrogen addition consistently decreased the microbial C:N and fungi to bacteria ratio (F:B), but increased Gram positive bacteria to Gram negative bacteria ratio (GP:GN) among biome types and N-addition rates. Nitrogen addition increased soil N availability and thereby resulted in soil acidification. Regression technique and principal component analyses showed that the shifts in the F:B and GP:GN mainly resulted from enhanced N availability due to N addition rather than soil acidification. When the N addition rate is lower than 100 kg N ha−1 year−1, about ten times higher than of global normal rate, the positive response of microbial growth was found. Overall, these findings revised the previous notion that N addition inhibited the microbial growth. Microbial species shifts might accentuate or mitigate the effects of alterations in microbial biomass at the ecosystem level, highlighting the critical role of microbial community composition in soil ecosystem functions under N deposition scenarios.

Abstract Response of soil respiration (CO 2 emission) to simulated nitrogen (N) deposition in a mature tropical forest in southern China was studied from October 2005 to September 2006. The objective was to test the hypothesis that N addition would reduce soil respiration in N saturated tropical forests. Static chamber and gas chromatography techniques were used to quantify the soil respiration, following four‐levels of N treatments (Control, no N addition; Low‐N, 5 g N m −2 yr −1 ; Medium‐N, 10 g N m −2 yr −1 ; and High‐N, 15 g N m −2 yr −1 experimental inputs), which had been applied for 26 months before and continued throughout the respiration measurement period. Results showed that soil respiration exhibited a strong seasonal pattern, with the highest rates found in the warm and wet growing season (April–September) and the lowest rates in the dry dormant season (December–February). Soil respiration rates showed a significant positive exponential relationship with soil temperature, whereas soil moisture only affect soil respiration at dry conditions in the dormant season. Annual accumulative soil respiration was 601±30 g CO 2 ‐C m −2 yr −1 in the Controls. Annual mean soil respiration rate in the Control, Low‐N and Medium‐N treatments (69±3, 72±3 and 63±1 mg CO 2 ‐C m −2 h −1 , respectively) did not differ significantly, whereas it was 14% lower in the High‐N treatment (58±3 mg CO 2 ‐C m −2 h −1 ) compared with the Control treatment, also the temperature sensitivity of respiration, Q 10 was reduced from 2.6 in the Control with 2.2 in the High‐N treatment. The decrease in soil respiration occurred in the warm and wet growing season and were correlated with a decrease in soil microbial activities and in fine root biomass in the N‐treated plots. Our results suggest that response of soil respiration to atmospheric N deposition in tropical forests is a decline, but it may vary depending on the rate of N deposition.

Demand for bean products is growing because of the presence of several health-promoting components in edible bean products such as saponins. Saponins are naturally occurring compounds that are widely distributed in all cells of legume plants. Saponins, which derive their name from their ability to form stable, soaplike foams in aqueous solutions, constitute a complex and chemically diverse group of compounds. In chemical terms, saponins contain a carbohydrate moiety attached to a triterpenoid or steroids. Saponins are attracting considerable interest as a result of their diverse properties, both deleterious and beneficial. Clinical studies have suggested that these health-promoting components, saponins, affect the immune system in ways that help to protect the human body against cancers, and also lower cholesterol levels. Saponins decrease blood lipids, lower cancer risks, and lower blood glucose response. A high saponin diet can be used in the inhibition of dental caries and platelet aggregation, in the treatment of hypercalciuria in humans, and as an antidote against acute lead poisoning. In epidemiological studies, saponins have been shown to have an inverse relationship with the incidence of renal stones. Thermal processing such as canning is the typical method to process beans. This study reviews the effect of thermal processing on the characteristics and stability of saponins in canned bean products. Saponins are thermal sensitive. During soaking and blanching, portions of saponins are dissolved in water and lost in the soaking, washing, and blanching liquors. An optimum thermal process can increase the stability and maintain the saponins in canned bean products, which is useful for assisting the food industry to improve thermal processing technology and enhance bean product quality.