Genomic and metabolomic insights into the antimicrobial compounds and plant growth-promoting potential of Bacillus velezensis Q-426.

BACKGROUND: The Q-426 strain isolated from compost samples has excellent antifungal activities against a variety of plant pathogens. However, the complete genome of Q-426 is still unclear, which limits the potential application of Q-426. RESULTS: Genome sequencing revealed that Q-426 contains a single circular chromosome 4,086,827 bp in length, with 4691 coding sequences and an average GC content of 46.3%. The Q-426 strain has a high degree of collinearity with B. velezensis FZB42, B. velezensis SQR9, and B. amyloliquefaciens DSM7, and the strain was reidentified as B. velezensis Q-426 based on the homology analysis results. Many genes in the Q-426 genome have plant growth-promoting activity, including the secondary metabolites of lipopeptides. Genome mining revealed 14 clusters and 732 genes encoding secondary metabolites with predicted functions, including the surfactin, iturin, and fengycin families. In addition, twelve lipopeptides (surfactin, iturin and fengycin) were successfully detected from the fermentation broth of B. velezensis Q-426 by ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS/MS), which is consistent with the genome analysis results. We found that Q-426 produced indole-3-acetic acid (IAA) at 1.56 mg/l on the third day of incubation, which might promote the growth of plants. Moreover, we identified eighteen volatile compounds (VOCs, including 2-heptanone, 6-methylheptan-2-one, 5-methylheptan-2-one, 2-nonanone, 2-decanone, 2-undecanone, 2-dodecanone, 2-tridecanone, 2-tetradecanone, 2-nonadecanone, pentadecanoic acid, oleic acid, dethyl phthalate, dibutyl phthalate, methyl (9E,12E)-octadeca-9,12-dienoate), pentadecane, (6E,10E)-1,2,3,4,4a,5,8,9,12,12a-decahydro-1,4-methanobenzo[10]annulene, and nonanal) based on gas chromatograph-mass spectrometer (GC/MS) results. CONCLUSIONS: We mined secondary metabolite-related genes from the genome based on whole-genome sequence results. Our study laid the theoretical foundation for the development of secondary metabolites and the application of B. velezensis Q-426. Our findings provide insights into the genetic characteristics responsible for the bioactivities and potential application of B. velezensis Q-426 as a plant growth-promoting strain in ecological agriculture.

Combinational application of the natural products 1-deoxynojirimycin and morin ameliorates insulin resistance and lipid accumulation in prediabetic mice.

BACKGROUND: Prediabetes, a stage characterized by chronic inflammation, obesity and insulin resistance. Morin and 1-deoxynojirimycin (DNJ) are natural flavonoids and alkaloids extracted from Morus nigra L., exhibiting anti-hyperglycemic efficacy. However, the benefits of DNJ are shadowed by the adverse events, and the mechanism of morin in anti-diabetes remains under investigation. PURPOSE: In this study, the combinational efficacy and mechanisms of DNJ and morin in ameliorating insulin resistance and pre-diabetes were investigated. METHODS: The mice model with prediabetes and Alpha mouse liver-12 (AML-12) cell model with insulin resistance were established. The anti-prediabetic efficacy of the drug combination was determined via analyzing the blood glucose, lipid profiles and inflammatory factors. The application of network pharmacology provided guidance for the research mechanism. RESULTS: In our study, the intervention of morin ameliorated the insulin resistance via activating the Peroxisome proliferator-activated receptor γ (PPARγ). However, PPARγ activation leaded to the lipid accumulation in prediabetic mice. The combination of 5 mg/kg dose of DNJ and 25 mg/kg morin effectively hindered the progression of T2DM by 87.56%, which was achieved via inhibition of Suppressors of cytokine signaling 3 (SOCS3) and promotion of PPARγ as well as SOCS2 expression. Furthermore, this treatment exhibited notable capabilities in combating dyslipidemia and adipogenesis, achieved by suppressing the Cluster of differentiation 36/ Sterol-regulatory element binding proteins-1/ Fatty acid synthetase (CD36/Serbp1/Fas) signaling. CONCLUSION: This research confirmed that the drug combination of DNJ and morin in ameliorating insulin resistance and lipid accumulation, and revealed the potential mechanisms. In summary, the combination of DNJ and morin is an underlying alternative pharmaceutical composition in T2DM prevention.

Does regional species diversity resist biotic invasions?

The role of regional species diversity in large-scale species invasions has been largely controversial. On the one hand, it has been proposed that diversity may facilitate invasion ("diversity begets diversity") because regions with higher diversity may indicate favorable conditions for many more species. On the other hand, high diversity may indicate high levels of niche occupation, thus making it more difficult for new species to invade. In the past, invasion biologists have evaluated how regional native and exotic richness are related. Here, we test whether the range size of exotic species may be constrained by regional native richness using plant data from three continental regions in the Northern Hemisphere, i.e., Europe, Eastern Asia, and North America. We found that regional native plant diversity is inversely related to the range size of exotic species. This result may be due to stronger species interactions such as competition in species-rich habitats that limit the establishment and spread of exotic species.

Masting is uncommon in trees that depend on mutualist dispersers in the context of global climate and fertility gradients.

The benefits of masting (volatile, quasi-synchronous seed production at lagged intervals) include satiation of seed predators, but these benefits come with a cost to mutualist pollen and seed dispersers. If the evolution of masting represents a balance between these benefits and costs, we expect mast avoidance in species that are heavily reliant on mutualist dispersers. These effects play out in the context of variable climate and site fertility among species that vary widely in nutrient demand. Meta-analyses of published data have focused on variation at the population scale, thus omitting periodicity within trees and synchronicity between trees. From raw data on 12 million tree-years worldwide, we quantified three components of masting that have not previously been analysed together: (i) volatility, defined as the frequency-weighted year-to-year variation; (ii) periodicity, representing the lag between high-seed years; and (iii) synchronicity, indicating the tree-to-tree correlation. Results show that mast avoidance (low volatility and low synchronicity) by species dependent on mutualist dispersers explains more variation than any other effect. Nutrient-demanding species have low volatility, and species that are most common on nutrient-rich and warm/wet sites exhibit short periods. The prevalence of masting in cold/dry sites coincides with climatic conditions where dependence on vertebrate dispersers is less common than in the wet tropics. Mutualist dispersers neutralize the benefits of masting for predator satiation, further balancing the effects of climate, site fertility and nutrient demands.

Integrating gradient with scale in ecological and evolutionary studies.

Gradient and scale are two key concepts in ecology and evolution that are closely related but inherently distinct. While scale commonly refers to the dimensional space of a specific ecological/evolutionary (eco-evo) issue, gradient measures the range of a given variable. Gradient and scale can jointly and interactively influence eco-evo patterns. Extensive previous research investigated how changing scales may affect the observation and interpretation of eco-evo patterns; however, relatively little attention has been paid to the role of changing gradients. Here, synthesizing recent research progress, we suggest that the role of scale in the emergence of ecological patterns should be evaluated in conjunction with considering the underlying environmental gradients. This is important because, in most studies, the range of the gradient is often part of its full potential range. The difference between sampled (partial) versus potential (full) environmental gradients may profoundly impact observed eco-evo patterns and alter scale-gradient relationships. Based on observations from both field and experimental studies, we illustrate the underlying features of gradients and how they may affect observed patterns, along with the linkages of these features to scales. Since sampled gradients often do not cover their full potential ranges, we discuss how the breadth and the starting and ending positions of key gradients may affect research design and data interpretation. We then outline potential approaches and related perspectives to better integrate gradient with scale in future studies.

Biosynthetic Profile in the Co-culture of Aspergillus sydowii and Bacillus subtilis to Produce Novel Benzoic Derivatives.

Microbial co-culture simulates the natural ecosystem through the combination of artificial microbes. This approach has been widely applied in the study of activating silent genes to reveal novel secondary metabolites. However, there are still challenges in determining the biosynthetic pathways. In this study, the effects of microbial co-culture on the morphology of the microbes were verified by the morphological observation. Subsequently, through the strategy combining substrate feeding, stable isotope labeling, and gene expression analysis, the biosynthetic pathways of five benzoic acid derivatives N1-N4 and N7 were demonstrated: the secondary metabolite 10-deoxygerfelin of A. sydowii acted as an inducer to induce B. subtilis to produce benzoic acid, which was further converted into 3-OH-benzoic acid by A. sydowii. Subsequently, A. sydowii used 3-OH-benzoic acid as the substrate to synthesize the new compound N2, and then N1, N3, N4, and N7 were biosynthesized upon the upregulation of hydrolase, hydroxylase, and acyltransferase during co-culture. The plate zone analysis suggested that the biosynthesis of the newly induced compounds N1-N4 was mainly attributed to A. sydowii, and both A. sydowii and B. subtilis were indispensable for the biosynthesis of N7. This study provides an important basis for a better understanding of the interactions among microorganisms, providing new ideas for studying the biosynthetic pathways of the newly induced secondary metabolites in co-culture.

Ameliorating Effect of the Total Flavonoids of Morus nigra L. on Prediabetic Mice Based on Regulation of Inflammation and Insulin Sensitization.

Prediabetes is a critical stage characterized by insulin resistance. Morus nigra L., an edible plant, is widely used in food and nutritive supplements and exhibits various pharmacological activities; however, its therapeutic effects and mechanisms on prediabetes have rarely been reported. In this research, the major components of total flavonoids of M. nigra L. (TFM) were identified, and TFM treatment was found to reduce prediabetes progressing to type 2 diabetes mellitus (T2DM) from 93.75 to 18.75%. The microbiota and next-generation sequencing combined with western blotting in vivo and in vitro demonstrated that TFM and its components ameliorated insulin resistance mediated by the suppressor of cytokine signaling and protein tyrosine phosphatase 1B, which benefited by maintaining intestinal homeostasis and restraining plasma levels of inflammatory factors. This study confirmed the T2DM prevention effect of TFM and revealed the underlying mechanism, setting the stage for the design of functional foods for diabetes prevention.

Limits to reproduction and seed size-number trade-offs that shape forest dominance and future recovery.

The relationships that control seed production in trees are fundamental to understanding the evolution of forest species and their capacity to recover from increasing losses to drought, fire, and harvest. A synthesis of fecundity data from 714 species worldwide allowed us to examine hypotheses that are central to quantifying reproduction, a foundation for assessing fitness in forest trees. Four major findings emerged. First, seed production is not constrained by a strict trade-off between seed size and numbers. Instead, seed numbers vary over ten orders of magnitude, with species that invest in large seeds producing more seeds than expected from the 1:1 trade-off. Second, gymnosperms have lower seed production than angiosperms, potentially due to their extra investments in protective woody cones. Third, nutrient-demanding species, indicated by high foliar phosphorus concentrations, have low seed production. Finally, sensitivity of individual species to soil fertility varies widely, limiting the response of community seed production to fertility gradients. In combination, these findings can inform models of forest response that need to incorporate reproductive potential.

Globally, tree fecundity exceeds productivity gradients.

Lack of tree fecundity data across climatic gradients precludes the analysis of how seed supply contributes to global variation in forest regeneration and biotic interactions responsible for biodiversity. A global synthesis of raw seedproduction data shows a 250-fold increase in seed abundance from cold-dry to warm-wet climates, driven primarily by a 100-fold increase in seed production for a given tree size. The modest (threefold) increase in forest productivity across the same climate gradient cannot explain the magnitudes of these trends. The increase in seeds per tree can arise from adaptive evolution driven by intense species interactions or from the direct effects of a warm, moist climate on tree fecundity. Either way, the massive differences in seed supply ramify through food webs potentially explaining a disproportionate role for species interactions in the wet tropics.

Scale dependency in native-exotic richness relationships revisited.

In their seminal paper, Shea and Chesson (Trends in Ecology & Evolution, 2002, 17, 170) developed a highly cited model (S&C model) showing scale dependency in the native-exotic richness relationships. Two decades later, extensive additional data have been accumulated, leading to new findings and insights. Accordingly, two updates were made here to the original S&C model: (1) changing the "negative" richness relationship between natives and exotics to "non-consistent" or "non-significant"; and (2) modifying the original diagram to correctly represent native and exotic species richness and their correlations across both small and large scales.

North American tree migration paced by climate in the West, lagging in the East.

Tree fecundity and recruitment have not yet been quantified at scales needed to anticipate biogeographic shifts in response to climate change. By separating their responses, this study shows coherence across species and communities, offering the strongest support to date that migration is in progress with regional limitations on rates. The southeastern continent emerges as a fecundity hotspot, but it is situated south of population centers where high seed production could contribute to poleward population spread. By contrast, seedling success is highest in the West and North, serving to partially offset limited seed production near poleward frontiers. The evidence of fecundity and recruitment control on tree migration can inform conservation planning for the expected long-term disequilibrium between climate and forest distribution.

The ecology of COVID-19 and related environmental and sustainability issues.

Around the globe, human behavior and ecosystem health have been extensively and sometimes severely affected by the unprecedented COVID-19 pandemic. Most efforts to study these complex and heterogenous effects to date have focused on public health and economics. Some studies have evaluated the pandemic's influences on the environment, but often on a single aspect such as air or water pollution. The related research opportunities are relatively rare, and the approaches are unique in multiple aspects and mostly retrospective. Here, we focus on the diverse research opportunities in disease ecology and ecosystem sustainability related to the (intermittent) lockdowns that drastically reduced human activities. We discuss several key knowledge gaps and questions to address amid the ongoing pandemic. In principle, the common knowledge accumulated from invasion biology could also be effectively applied to COVID-19, and the findings could offer much-needed information for future pandemic prevention and management.

Is there tree senescence? The fecundity evidence.

Despite its importance for forest regeneration, food webs, and human economies, changes in tree fecundity with tree size and age remain largely unknown. The allometric increase with tree diameter assumed in ecological models would substantially overestimate seed contributions from large trees if fecundity eventually declines with size. Current estimates are dominated by overrepresentation of small trees in regression models. We combined global fecundity data, including a substantial representation of large trees. We compared size-fecundity relationships against traditional allometric scaling with diameter and two models based on crown architecture. All allometric models fail to describe the declining rate of increase in fecundity with diameter found for 80% of 597 species in our analysis. The strong evidence of declining fecundity, beyond what can be explained by crown architectural change, is consistent with physiological decline. A downward revision of projected fecundity of large trees can improve the next generation of forest dynamic models.

Drivers of seedling establishment success in dryland restoration efforts.

Restoration of degraded drylands is urgently needed to mitigate climate change, reverse desertification and secure livelihoods for the two billion people who live in these areas. Bold global targets have been set for dryland restoration to restore millions of hectares of degraded land. These targets have been questioned as overly ambitious, but without a global evaluation of successes and failures it is impossible to gauge feasibility. Here we examine restoration seeding outcomes across 174 sites on six continents, encompassing 594,065 observations of 671 plant species. Our findings suggest reasons for optimism. Seeding had a positive impact on species presence: in almost a third of all treatments, 100% of species seeded were growing at first monitoring. However, dryland restoration is risky: 17% of projects failed, with no establishment of any seeded species, and consistent declines were found in seeded species as projects matured. Across projects, higher seeding rates and larger seed sizes resulted in a greater probability of recruitment, with further influences on species success including site aridity, taxonomic identity and species life form. Our findings suggest that investigations examining these predictive factors will yield more effective and informed restoration decision-making.

Continent-wide tree fecundity driven by indirect climate effects.

Indirect climate effects on tree fecundity that come through variation in size and growth (climate-condition interactions) are not currently part of models used to predict future forests. Trends in species abundances predicted from meta-analyses and species distribution models will be misleading if they depend on the conditions of individuals. Here we find from a synthesis of tree species in North America that climate-condition interactions dominate responses through two pathways, i) effects of growth that depend on climate, and ii) effects of climate that depend on tree size. Because tree fecundity first increases and then declines with size, climate change that stimulates growth promotes a shift of small trees to more fecund sizes, but the opposite can be true for large sizes. Change the depresses growth also affects fecundity. We find a biogeographic divide, with these interactions reducing fecundity in the West and increasing it in the East. Continental-scale responses of these forests are thus driven largely by indirect effects, recommending management for climate change that considers multiple demographic rates.

Worldwide effects of non-native species on species-area relationships.

Non-native species have invaded most parts of the world, and the invasion process is expected to continue and accelerate. Because many invading non-native species are likely to become permanent inhabitants, future consideration of species-area relationships (SARs) should account for non-native species, either separately or jointly with native species. If non-native species occupy unused niches and space in invaded areas and extinction rate of native species remains low (especially for plants), the resultant SARs (with both native and non-native species) will likely be stronger. We used published and newly compiled data (35 data sets worldwide) to examine how species invasions affect SARs across selected taxonomic groups and diverse ecosystems around the world. We first examined the SARs for native, non-native, and all species. We then investigated with linear regression analyses and paired or unpaired t tests how degree of invasion (proportion of non-native species) affected postinvasion SARs. Postinvasion SARs for all species (native plus non-native) became significantly stronger as degree of invasion increased (r2 = 0.31, p = 0.0006), thus, reshaping SARs worldwide. Overall, native species still showed stronger and less variable SARs. Also, slopes for native species were steeper than for non-native species (0.298 vs. 0.153). There were some differences among non-native taxonomic groups in filling new niches (especially for birds) and between islands and mainland ecosystems. We also found evidence that invasions may increase equilibrial diversity. Study of such changing species-area curves may help determine the probability of future invasions and have practical implications for conservation.

Efectos Globales de las Especies No Nativas sobre las Relaciones Especie-Área Resumen Las especies no nativas han invadido la mayor parte del mundo y se espera que el proceso de invasión continúe y se acelere. Ya que muchas especies invasoras no nativas probablemente se conviertan en habitantes permanentes, la consideración a futuro de las relaciones especie-área (REA) debería considerar a las especies no nativas, ya sea por separado o en conjunto con las especies nativas. Si las especies no nativas ocupan nichos sin usar y el espacio en las áreas invadidas y la tasa de extinción de las especies nativas permanecen bajas (especialmente para las plantas), las REA resultantes (tanto con las especies nativas como las no nativas) probablemente sean más fuertes. Usamos datos publicados y recientemente compilados (35 conjuntos de datos mundiales) para examinar cómo las invasiones de especies afectan a las REA en grupos taxonómicos selectos y en diversos ecosistemas en todo el mundo. Primero examinamos las REA para todas las especies, así como para las nativas y las no nativas. Después investigamos con análisis de regresión lineal y pruebas t emparejadas o no emparejadas cómo afectó el grado de invasión (proporción de la especie no nativa) a las REA post-invasión. Las REA post-invasión para todas las especies (nativas más no nativas) se volvieron significativamente más fuertes conforme incrementó el grado de invasión (r2 = 0.31, p = 0.0006), remodelando así las REA en todo el mundo. En general, las especies nativas todavía mostraron REA más fuertes y menos variables. De igual manera, las pendientes de las especies nativas fueron más pronunciadas para las especies no nativas (0.298 vs. 0.153). Hubo algunas diferencias entre los grupos taxonómicos no nativos al llenar nichos nuevos (especialmente para las aves) y entre las islas y los ecosistemas de tierra firme. También encontramos evidencias de que las invasiones pueden incrementar la diversidad equilibrada. El estudio de dichas curvas cambiantes de relación especie-área podría ayudar a determinar la probabilidad de las futuras invasiones y tener implicaciones prácticas para la conservación.

Predicting invasiveness of exotic woody species using a traits-based framework.

Identifying potentially invasive species and preventing their introduction and establishment are of critical importance in invasion ecology and land management. Although an extensive body of research has been dedicated to identifying traits that confer invasiveness, our current knowledge is still often inconclusive due to limitations in geographic extent and/or scope of traits analyzed. Here, using a comprehensive set of 45 traits, we performed a case study of invasive traits displayed by exotic woody plants in the United States (U.S.) by comparing 63 invasive and 794 non-invasive exotic woody plant species naturalized across the country. We found that invasive woody species often bear the following two key traits: vegetative reproduction and long-distance seed dispersal (via water, birds or mammals). Boosted classification tree models based on these traits accurately predicted species invasiveness (86% accuracy on average). Presented findings provide a generalized understanding of the relative importance of functional traits in identifying potentially invasive woody species in the U.S. The knowledge generated in this study can be used to improve current classification systems of non-native woody plants used by various U.S. governmental agencies and land managers.

Tree diversity regulates forest pest invasion.

Nonnative pests often cause cascading ecological impacts, leading to detrimental socioeconomic consequences; however, how plant diversity may influence insect and disease invasions remains unclear. High species diversity in host communities may promote pest invasions by providing more niches (i.e., facilitation), but it can also diminish invasion success because low host dominance may make it more difficult for pests to establish (i.e., dilution). Most studies to date have focused on small-scale, experimental, or individual pest/disease species, while large-scale empirical studies, especially in natural ecosystems, are extremely rare. Using subcontinental-level data, we examined the role of tree diversity on pest invasion across the conterminous United States and found that the tree-pest diversity relationships are hump-shaped. Pest diversity increases with tree diversity at low tree diversity (because of facilitation or amplification) and is reduced at higher tree diversity (as a result of dilution). Thus, tree diversity likely regulates forest pest invasion through both facilitation and dilution that operate simultaneously, but their relative strengths vary with overall diversity. Our findings suggest the role of native species diversity in regulating nonnative pest invasions.