Network Complexity and Stability of Microbes Enhanced by Microplastic Diversity.

Microplastic mixtures are ubiquitously distributed in global ecosystems and include varying types. However, it remains unknown how microplastic diversity affects the biotic interactions of microbes. Here, we developed novel experiments of 600 microcosms with microplastic diversity ranging from 1 to 6 types and examined ecological networks for microbial communities in lake sediments after 2 months of incubation at 15 and 20 °C. We found that microplastic diversity generally enhanced the complexity of microbial networks at both temperatures, such as increasing network connectance and reducing average path length. This phenomenon was further confirmed by strengthened species interactions toward high microplastic diversity except for the negative interactions at 15 °C. Interestingly, increasing temperatures further exaggerated the effects of microplastic diversity on network structures, resulting in higher network connectivity and species interactions. Consistently, using species extinction simulations, we found that higher microplastic diversity and temperature led to more robust networks, and their effects were additionally and positively mediated by the presence of biodegradable microplastics. Our findings provide the first evidence that increasing microplastic diversity could unexpectedly promote the complexity and stability of microbial networks and that future warming could amplify this effect.

Thermal responses of dissolved organic matter under global change.

The diversity of intrinsic traits of different organic matter molecules makes it challenging to predict how they, and therefore the global carbon cycle, will respond to climate change. Here we develop an indicator of compositional-level environmental response for dissolved organic matter to quantify the aggregated response of individual molecules that positively and negatively associate with warming. We apply the indicator to assess the thermal response of sediment dissolved organic matter in 480 aquatic microcosms along nutrient gradients on three Eurasian mountainsides. Organic molecules consistently respond to temperature change within and across contrasting climate zones. At a compositional level, dissolved organic matter in warmer sites has a stronger thermal response and shows functional reorganization towards molecules with lower thermodynamic favorability for microbial decomposition. The thermal response is more sensitive to warming at higher nutrients, with increased sensitivity of up to 22% for each additional 1 mg L-1 of nitrogen loading. The utility of the thermal response indicator is further confirmed by laboratory experiments and reveals its positive links to greenhouse gas emissions.

Chemodiversity of riverine dissolved organic matter: Effects of local environments and watershed characteristics.

Riverine dissolved organic matter (DOM) is crucial to global carbon cycling and aquatic ecosystems. However, the geographical patterns and environmental drivers of DOM chemodiversity remain elusive especially in the waters and sediments of continental rivers. Here, we systematically analyzed DOM molecular diversity and composition in surface waters and sediments across 97 broadly distributed rivers using data from the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) consortium. We further examined the associations of molecular richness and composition with geographical, climatic, physicochemical variables, as well as the watershed characteristics. We found that molecular richness significantly decreased toward higher latitudes, but only in sediments (r = -0.24, p < 0.001). The environmental variables like precipitation and non-purgeable organic carbon showed strong associations with DOM molecular richness and composition. Interestingly, we identified that less-documented factors like watershed characteristics were also related to DOM molecular richness and composition. For instance, DOM molecular richness was positively correlated with the soil sand fraction for waters, while with the percentage of forest for sediments. Importantly, the effects of watershed characteristics on DOM molecular richness and composition were generally stronger in waters than sediments. This phenomenon was further supported by the fact that 11 out of 13 watershed characteristics (e.g., the percentages of impervious area and cropland) showed more positive than negative correlations with molecular abundance especially in waters. As the percentage of forest increased, there was a continuous accumulation of the compounds with higher molecular weight, aromaticity, and degree of unsaturation. In contrast, human activities accumulated the compounds with lower molecular weight and oxygenation, and higher bioavailability. Our findings imply that it may be possible to use a small set of broadly available data types to predict DOM molecular richness and composition across diverse river systems. Elucidation of mechanisms underlying these relationships will provide further enhancements to such predictions, especially when extrapolating to unsampled systems.

Increasing diversity and biotic homogenization of lake plankton during recovery from acidification.

Determining biodiversity responses to environmental change, such as acidification, is critical for ecosystem projections under future global change scenarios. Here, we analyzed three plankton communities of phytoplankton, crustaceans and rotifers in 28 lakes in the Adirondack Park, USA, during 1994-2012, and examined the spatiotemporal trends in their alpha and beta diversity during recovery from acidification. For all plankton assemblages, Shannon diversity increased towards recent years and high lake pH, and there was an increasing community dissimilarity with pH changes. The spatial mean Bray-Curtis dissimilarities across all lakes decreased over time for phytoplankton and rotifers leading to an increase in spatial homogenization. Such a homogenization cooccurred however with the overall increasing diversity in this region, which contrasts with the previous classic view that homogenization is mainly driven by loss of species and results in biodiversity loss. We further observed lower temporal mean beta diversity in low-pH lakes for crustaceans and rotifers, but not for phytoplankton. Generally, spatial and temporal mean beta diversity of the three taxonomic groups were primarily driven by lake-water ion variables, and rotifers were also constrained by nutrients and climate. Collectively, our results show how and why plankton community compositions vary over space along with acidification recovery, and further highlight the importance of spatiotemporal studies combined with long-term monitoring programs in assessing biodiversity change during the recovery of disturbed ecosystems.

Dark Matter Enhances Interactions within Both Microbes and Dissolved Organic Matter under Global Change.

There are vast but uncharacterized microbial taxa and chemical metabolites (that is, dark matter) across the Earth's ecosystems. A lack of knowledge about dark matter hinders a complete understanding of microbial ecology and biogeochemical cycles. Here, we examine sediment bacteria and dissolved organic matter (DOM) in 300 microcosms along experimental global change gradients in subtropical and subarctic climate zones of China and Norway, respectively. We develop an indicator to quantify the importance of dark matter by comparing co-occurrence network patterns with and without dark matter in bacterial or DOM assemblages. In both climate zones, dark matter constitutes approximately 30-56% of bacterial taxa and DOM metabolites and changes connectivity within bacterial and DOM assemblages by between -15.5 and +61.8%. Dark matter is generally more important for changing network connectivity within DOM assemblages than those of microbes, especially in the subtropical zone. However, the importance of dark matter along global change gradients is strongly correlated between bacteria and DOM and consistently increased toward higher primary productivity because of increasing temperatures and nutrient enrichment. Our findings highlight the importance of microbial and chemical dark matter for changing biogeochemical interactions under global change.

CARD9 in host immunity to fungal, bacterial, viral, and parasitic infections: An update.

Microbial infection, caused by fungi, bacteria, viruses, and parasites, significantly contributes to the global death burden and health costs. The innate and adaptive immune systems orchestrate a multifaceted signaling response to invading pathogens as the human antimicrobial system. In this process, caspase recruitment domain-containing protein 9 (CARD9) emerges as a critical intermediary adaptor molecule to participate in regulating a series of antimicrobial immune reactions. Previous publications have confirmed that CARD9 plays a crucial role in fungal, bacterial, viral, and parasitic infections. In this study, we aim to provide an update on the recent clinical and basic studies where the mechanism and function of CARD9 have been further studied and understood. In addition, we summarize the latest treatment and prevention strategies based on CARD9 and discuss the current perspectives and future direction of CARD9.

SAS-SEINet: A SNR-Aware Adaptive Scalable SEI Neural Network Accelerator Using Algorithm-Hardware Co-Design for High-Accuracy and Power-Efficient UAV Surveillance.

As a potential air control measure, RF-based surveillance is one of the most commonly used unmanned aerial vehicles (UAV) surveillance methods that exploits specific emitter identification (SEI) technology to identify captured RF signal from ground controllers to UAVs. Recently many SEI algorithms based on deep convolution neural network (DCNN) have emerged. However, there is a lack of the implementation of specific hardware. This paper proposes a high-accuracy and power-efficient hardware accelerator using an algorithm-hardware co-design for UAV surveillance. For the algorithm, we propose a scalable SEI neural network with SNR-aware adaptive precision computation. With SNR awareness and precision reconfiguration, it can adaptively switch between DCNN and binary DCNN to cope with low SNR and high SNR tasks, respectively. In addition, a short-time Fourier transform (STFT) reusing DCNN method is proposed to pre-extract feature of UAV signal. For hardware, we designed a SNR sensing engine, denoising engine, and specialized DCNN engine with hybrid-precision convolution and memory access, aiming at SEI acceleration. Finally, we validate the effectiveness of our design on a FPGA, using a public UAV dataset. Compared with a state-of-the-art algorithm, our method can achieve the highest accuracy of 99.3% and an F1 score of 99.3%. Compared with other hardware designs, our accelerator can achieve the highest power efficiency of 40.12 Gops/W and 96.52 Gops/W with INT16 precision and binary precision.

Soil moisture-atmosphere feedback dominates land N2 O nitrification emissions and denitrification reduction.

Soil moisture (SM) is essential to microbial nitrogen (N)-cycling networks in terrestrial ecosystems. Studies have found that SM-atmosphere feedbacks dominate the changes in land carbon fluxes. However, the influence of SM-atmosphere feedbacks on the N fluxes changes, and the underlying mechanisms remain highly unsure, leading to uncertainties in climate projections. To fill this gap, we used in situ observation coupled with gridded and remote sensing data to analyze N2 O fluxes emissions globally. Here, we investigated the synergistic effects of temperature, hydroclimate on global N2 O fluxes, as the result of SM-atmosphere feedback impact on N fluxes. We found that SM-temperature feedback dominates land N2 O emissions by controlling the balance between nitrifier and denitrifier genes. The mechanism is that atmospheric water demand increases with temperature and thereby reduces SM, which increases the dominant N2 O production nitrifier (containing amoA AOB gene) and decreases the N2 O consumption denitrifier (containing the nosZ gene), consequently will potential increasing N2 O emissions. However, we find that the spatial variations of soil-water availability as a result of the nonlinear response of SM to vapor pressure deficit caused by temperature are some of the greatest challenges in predicting future N2 O emissions. Our data-driven assessment deepens the understanding of the impact of SM-atmosphere interactions on the soil N cycle, which remains uncertain in earth system models. We suggest that the model needs to account for feedback between SM and atmospheric temperature when estimating the response of the N2 O emissions to climatic change globally, as well as when conducting field-scale investigations of the response of the ecosystem to warming.

Posttranslational modifications in diabetes: Mechanisms and functions.

As one of the most widespread chronic diseases, diabetes and its accompanying complications affect approximately one tenth of individuals worldwide and represent a growing cause of morbidity and mortality. Accumulating evidence has proven that the process of diabetes is complex and interactive, involving various cellular responses and signaling cascades by posttranslational modifications (PTMs). Therefore, understanding the mechanisms and functions of PTMs in regulatory networks has fundamental importance for understanding the prediction, onset, diagnosis, progression, and treatment of diabetes. In this review, we offer a holistic summary and illustration of the crosstalk between PTMs and diabetes, including both types 1 and 2. Meanwhile, we discuss the potential use of PTMs in diabetes treatment and provide a prospective direction for deeply understanding the metabolic diseases.

Microbial and Environmental Processes Shape the Link between Organic Matter Functional Traits and Composition.

Dissolved organic matter (DOM) is a large and complex mixture of molecules that fuels microbial metabolism and regulates biogeochemical cycles. Individual DOM molecules have unique functional traits, but how their assemblages vary deterministically under global change remains poorly understood. Here, we examine DOM and associated bacteria in 300 aquatic microcosms deployed on mountainsides that span contrasting temperatures and nutrient gradients. Based on molecular trait dimensions of reactivity and activity, we partition the DOM composition into labile-active, recalcitrant-active, recalcitrant-inactive, and labile-inactive fractions and quantify the relative influences of deterministic and stochastic processes governing the assembly of each. At both subtropical and subarctic study sites, the assembly of labile or recalcitrant molecules in active fractions is primarily governed by deterministic processes, while stochastic processes are more important for the assembly of molecules within inactive fractions. Surprisingly, the importance of deterministic selection increases with global change gradients for recalcitrant molecules in both active and inactive fractions, and this trend is paralleled by changes in the deterministic assembly of microbial communities and environmental filtering, respectively. Together, our results highlight the shift in focus from potential reactivity to realized activity and indicate that active and inactive fractions of DOM assemblages are structured by contrasting processes, and their recalcitrant components are consistently sensitive to global change. Our study partitions the DOM molecular composition across functional traits and links DOM with microbes via a shared ecological framework of assembly processes. This integrated approach opens new avenues to understand the assembly and turnover of organic carbon in a changing world.

Ecological networks of dissolved organic matter and microorganisms under global change.

Microbes regulate the composition and turnover of organic matter. Here we developed a framework called Energy-Diversity-Trait integrative Analysis to quantify how dissolved organic matter and microbes interact along global change drivers of temperature and nutrient enrichment. Negative and positive interactions suggest decomposition and production processes of organic matter, respectively. We applied this framework to manipulative field experiments on mountainsides in subarctic and subtropical climates. In both climates, negative interactions of bipartite networks were more specialized than positive interactions, showing fewer interactions between chemical molecules and bacterial taxa. Nutrient enrichment promoted specialization of positive interactions, but decreased specialization of negative interactions, indicating that organic matter was more vulnerable to decomposition by a greater range of bacteria, particularly at warmer temperatures in the subtropical climate. These two global change drivers influenced specialization of negative interactions most strongly via molecular traits, while molecular traits and bacterial diversity similarly affected specialization of positive interactions.

Embracing mountain microbiome and ecosystem functions under global change.

Mountains are pivotal to maintaining habitat heterogeneity, global biodiversity, ecosystem functions and services to humans. They have provided classic model natural systems for plant and animal diversity gradient studies for over 250 years. In the recent decade, the exploration of microorganisms on mountainsides has also achieved substantial progress. Here, we review the literature on microbial diversity across taxonomic groups and ecosystem types on global mountains. Microbial community shows climatic zonation with orderly successions along elevational gradients, which are largely consistent with traditional climatic hypotheses. However, elevational patterns are complicated for species richness without general rules in terrestrial and aquatic environments and are driven mainly by deterministic processes caused by abiotic and biotic factors. We see a major shift from documenting patterns of biodiversity towards identifying the mechanisms that shape microbial biogeographical patterns and how these patterns vary under global change by the inclusion of novel ecological theories, frameworks and approaches. We thus propose key questions and cutting-edge perspectives to advance future research in mountain microbial biogeography by focusing on biodiversity hypotheses, incorporating meta-ecosystem framework and novel key drivers, adapting recently developed approaches in trait-based ecology and manipulative field experiments, disentangling biodiversity-ecosystem functioning relationships and finally modelling and predicting their global change responses.

Metformin exerts anti-tumor effects via Sonic hedgehog signaling pathway by targeting AMPK in HepG2 cells.

Metformin, a traditional first-line pharmacological treatment for type 2 diabetes, has recently been shown to have anti-cancer effects on hepatocellular carcinoma (HCC). However, the molecular mechanism underlying the anti-tumor activity of metformin remains unclear. The Sonic hedgehog (Shh) signaling pathway is closely associated with the initiation and progression of HCC. Therefore, the aim of the current study was to investigate the effects of metformin on the biological behavior of HCC and the underlying functional mechanism of metformin in the Shh pathway. HCC was induced in HepG2 cells using recombinant human Shh (rhShh). The effects of metformin on proliferation and metastasis were evaluated using in vitro proliferation, wound healing, and invasion assays. The mRNA and protein expression levels of proteins related to the Shh pathway were measured using western blotting, quantitative PCR, and immunofluorescence staining. Metformin inhibited rhShh-induced proliferation and metastasis. Furthermore, metformin decreased the mRNA and protein expression of Shh pathway components, including Shh, Ptch, Smo, and Gli-1. Silencing of AMPK in the presence of metformin revealed that metformin exerted its inhibitory effects via AMPK. Our findings demonstrate that metformin suppresses the migration and invasion of HepG2 cells via AMPK-mediated inhibition of the Shh pathway.

Impact of urbanization on the food-water-land-ecosystem nexus: A study of Shenzhen, China.

The food-water-land-ecosystem (FWLE) nexus is fundamental for achieving sustainable development. This study examines the influence of urbanization on the FWLE nexus. Toward this end, land was deemed as an entry point. Therefore, the impact of urbanization on the nexus was explored based on changes in land use. We selected Shenzhen, a city in China, as the study area. First, a land change modeler was employed to analyze historical land-use changes from 2000 to 2010, to build transition potential submodels, and to project future land-use patterns for 2030 under a business-as-usual scenario. Second, based on land-use maps, we assessed habitat quality, water yield, and water supply from 2000 to 2030 using Integrated Valuation of Ecosystem Services and Tradeoffs. Moreover, crop production was estimated according to statistical materials. Finally, the study presents the analyses and discussion of the impacts of urbanization on ecosystem services related to the FWLE nexus. The results of land-use changes indicated that a significant expansion of artificial surfaces occurred in Shenzhen with varying degrees of decrease in cultivated land, forest, and grassland. Furthermore, habitat quality, water supply, and crop production decreased evidently due to rapid urbanization. In contrast, the total water yield indicated an upward trend owing to the increased water yield from increasing artificial surfaces, whereas water yield from other land-use areas declined, such as the forest and grassland. The results demonstrated a significant positive correlation between artificial surfaces and total water yield. However, negative correlations were observed in the interaction among habitat quality, water supply, and crop production. The study presented temporal and spatial assessments to provide an effective and convenient means of exploring the interactions and tradeoffs within the FWLE nexus, which, thus, contributed to the sustainable transformation of urbanization.

Intercropping enhances microbial community diversity and ecosystem functioning in maize fields.

Background and aims: Intercropping, a widely used planting pattern, could affect soil physicochemical properties, microbial community diversity, and further crop yields. However, its impacts on soil microbial diversity and ecosystem functioning and further soil sustainability are poorly understood. Methods: We conducted field experiments by intercropping maize with four important crops (i.e., sesame, peanut, soybean, and sweet potato), and examined soil microbial community diversity and ecosystem functioning such as microbial biomass and enzyme activities under monocropping and intercropping. We quantified their intercropping effects on microbial diversity and ecosystem functions with effect size metric Cohen d by comparing to the monocropping of maize. Results: We found that the four intercropping systems significantly increased soil aggregates in respective of the 2-0.25 mm grain size. Intercropping consistently elevated ecosystem functioning, such as soil enzyme activities of urease, phosphatase, and catalase, soil microbial biomass carbon and soil microbial biomass nitrogen. The Cohen d of bacterial richness also increased from 0.39 to 2.36, the latter of which was significant for maize/peanut intercropping. Notably, these ecosystem functions were strongly associated with the diversity of bacteria and fungi and the relative abundance of their ecological clusters identified with network analysis. Conclusion: Together, our findings indicate that intercropping generally affected soil physicochemical properties, ecosystem functions, and promoted microbial community diversity. More importantly, our findings highlight the important roles of microbial diversity of ecological clusters (that is, network modules) in maintaining ecosystem functioning after intercropping. These results will help to better understand the microbial diversity and ecosystem function in intercropping systems and guide agricultural practice.

DNA methylation plays important roles in retinal development and diseases.

DNA methylation is important in developing and post-mitotic cells in various tissues. Recent studies have shown that DNA methylation is highly dynamic, and plays important roles during retinal development and aging. In addition, the dynamic regulation of DNA methylation is involved in the occurrence and development of age-related macular degeneration and diabetic retinopathy and shows potential in disease diagnoses and prognoses. This review introduces the epigenetic concepts of DNA methylation and demethylation with an emphasis on their regulatory roles in retinal development and related diseases. Moreover, we propose exciting ideas such as its crosstalk with other epigenetic modifications and retinal regeneration, to provide a potential direction for understanding retinal diseases from the epigenetic perspective.

Quantitative stable isotope probing technique and its applications in microbial ecology.

Quantitative stable isotope probing (qSIP) is a powerful tool, which links microbial taxon with functional metabolism in ecosystems and quantitatively determines the metabolic activity or growth rate of individual microbial taxa exposed to isotope tracers in the environment. qSIP technique employs quantitative PCR, high-throughput sequencing and stable isotope probing (SIP) techniques. The procedure involves adding labeled substrates to environmental samples for cultivation, separating labeled heavy fraction from unlabeled light fraction via isopycnic ultracentrifugation, making absolute quantification and sequencing analysis for microbial populations in all fractions, and then quantifying the isotope abundance of DNA involved in uptake and transformation based on the DNA density curve of unlabeled treatment and GC content. Here, we reviewed the rationale, data analysis and application of qSIP in microbial ecology, and discussed the existing problems and prospects of qSIP.

Microbial species performance responses to environmental changes: genomic traits and nutrient availability.

How microbial species performance indicators, such as growth rate and carbon assimilation rate, respond to environmental changes is a challenging question, especially for complex communities. This limits our ability to understand how species performance responses to environmental changes (that is, species environmental responses) of microbes could be linked to genomic traits and nutrient availability. Based on stable isotope labeling of DNA, we propose a new approach with effect-size metrics to quantify the species environmental responses of microbes by comparing the species performance between defined control and treatment groups. The species performance within microbial communities of the natural or altered environments could be quantitatively determined with quantitative stable isotope probing (qSIP). We further apply this approach, namely effect-size qSIP, to measure species environmental responses upon carbon and nitrogen additions for soil bacteria on mountainsides and to understand their responses from the perspective of genomic traits. Towards high elevations, there is a stronger nitrogen limitation that is indicated by the higher aggregated responses, measured as community-weighted means, of bacterial growth rate upon nitrogen additions. The aggregated responses are further explained by genomic traits, which show higher percentages of significant Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologues (KOs) and more diverse KEGG pathways under nutrient additions including nitrogen, and further improve the explanatory power of microbial environmental responses. Nitrogen-induced responses at the species level show the strongest associations with essential KOs for rare species, whereas carbon-induced responses show the strongest associations for dominant species. We conclude that, in addition to environmental determinants such as nitrogen limitation, genomic traits are extremely important for predicting microbial environmental responses at both the community and species levels. Taking advantage of this new approach at the species level, we reveal that rare and dominant species differentially respond to nutrient enrichment via their metabolic traits. The approach and findings can lead to a more holistic understanding of microbial environmental responses in natural habitats, which will be essential for predicting microbial community responses to global environmental changes.