The marine environmental microbiome mediates physiological outcomes in host nematodes.

BACKGROUND: Nematodes are the most abundant metazoans in marine sediments, many of which are bacterivores; however, how habitat bacteria affect physiological outcomes in marine nematodes remains largely unknown.  RESULTS: Here, we used a Litoditis marina inbred line to assess how native bacteria modulate host nematode physiology. We characterized seasonal dynamic bacterial compositions in L. marina habitats and examined the impacts of 448 habitat bacteria isolates on L. marina development, then focused on HQbiome with 73 native bacteria, of which we generated 72 whole genomes sequences. Unexpectedly, we found that the effects of marine native bacteria on the development of L. marina and its terrestrial relative Caenorhabditis elegans were significantly positively correlated. Next, we reconstructed bacterial metabolic networks and identified several bacterial metabolic pathways positively correlated with L. marina development (e.g., ubiquinol and heme b biosynthesis), while pyridoxal 5'-phosphate biosynthesis pathway was negatively associated. Through single metabolite supplementation, we verified CoQ10, heme b, acetyl-CoA, and acetaldehyde promoted L. marina development, while vitamin B6 attenuated growth. Notably, we found that only four development correlated metabolic pathways were shared between L. marina and C. elegans. Furthermore, we identified two bacterial metabolic pathways correlated with L. marina lifespan, while a distinct one in C. elegans. Strikingly, we found that glycerol supplementation significantly extended L. marina but not C. elegans longevity. Moreover, we comparatively demonstrated the distinct gut microbiota characteristics and their effects on L. marina and C. elegans physiology. CONCLUSIONS: Given that both bacteria and marine nematodes are dominant taxa in sedimentary ecosystems, the resource presented here will provide novel insights to identify mechanisms underpinning how habitat bacteria affect nematode biology in a more natural context. Our integrative approach will provide a microbe-nematodes framework for microbiome mediated effects on host animal fitness.

Purines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress.

The root-associated microbiota plays an important role in the response to environmental stress. However, the underlying mechanisms controlling the interaction between salt-stressed plants and microbiota are poorly understood. Here, by focusing on a salt-tolerant plant wild soybean (Glycine soja), we demonstrate that highly conserved microbes dominated by Pseudomonas are enriched in the root and rhizosphere microbiota of salt-stressed plant. Two corresponding Pseudomonas isolates are confirmed to enhance the salt tolerance of wild soybean. Shotgun metagenomic and metatranscriptomic sequencing reveal that motility-associated genes, mainly chemotaxis and flagellar assembly, are significantly enriched and expressed in salt-treated samples. We further find that roots of salt stressed plants secreted purines, especially xanthine, which induce motility of the Pseudomonas isolates. Moreover, exogenous application for xanthine to non-stressed plants results in Pseudomonas enrichment, reproducing the microbiota shift in salt-stressed root. Finally, Pseudomonas mutant analysis shows that the motility related gene cheW is required for chemotaxis toward xanthine and for enhancing plant salt tolerance. Our study proposes that wild soybean recruits beneficial Pseudomonas species by exudating key metabolites (i.e., purine) against salt stress.

Giants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores.

Siphonophores (Cnidaria: Hydrozoa) are abundant predators found throughout the ocean and are important constituents of the global zooplankton community. They range in length from a few centimeters to tens of meters. They are gelatinous, fragile, and difficult to collect, so many aspects of the biology of these roughly 200 species remain poorly understood. To survey siphonophore genome diversity, we performed Illumina sequencing of 32 species sampled broadly across the phylogeny. Sequencing depth was sufficient to estimate nuclear genome size from k-mer spectra in six specimens, ranging from 0.7 to 2.3 Gb, with heterozygosity estimates between 0.69% and 2.32%. Incremental k-mer counting indicates k-mer peaks can be absent with nearly 20× read coverage, suggesting minimum genome sizes range from 1.4 to 5.6 Gb in the 25 samples without peaks in the k-mer spectra. This work confirms most siphonophore nuclear genomes are large relative to the genomes of other cnidarians, but also identifies several with reduced size that are tractable targets for future siphonophore nuclear genome assembly projects. We also assembled complete mitochondrial genomes for 33 specimens from these new data, indicating a conserved gene order shared among nonsiphonophore hydrozoans, Cystonectae, and some Physonectae, revealing the ancestral mitochondrial gene order of siphonophores. Our results also suggest extensive rearrangement of mitochondrial genomes within other Physonectae and in Calycophorae. Though siphonophores comprise a small fraction of cnidarian species, this survey greatly expands our understanding of cnidarian genome diversity. This study further illustrates both the importance of deep phylogenetic sampling and the utility of k-mer-based genome skimming in understanding the genomic diversity of a clade.

Decoupling of the Confused Complex in Oxidation of 3,3',5,5'-Tetramethylbenzidine for the Reliable Chromogenic Bioassay.

Regulation of the reaction pathways is a perennial theme in the field of chemistry. As a typical chromogenic substrate, 3,3',5,5'-tetramethylbenzidine (TMB) generally undertakes one-electron oxidation, but the product (TMBox1) is essentially a confused complex and is unstable, which significantly hampers the clinic chromogenic bioassays for more than 50 years. Herein, we report that sodium dodecyl sulfate (SDS)-based micelles could drive the direct two-electron oxidation of TMB to the final stable TMBox2. Rather than activation of H2O2 oxidant in the one-electron TMB oxidation by common natural peroxidase, activation of the TMB substrate by SDS micelles decoupled the thermodynamically favorable complex between TMBox2 with unreacted TMB, leading to an unusual direct two-electron oxidation pathway. Mechanism studies demonstrated that the complementary spatial and electrostatic isolation effects, caused by the confined hydrophobic cavities and negatively charged outer surfaces of SDS micelles, were crucial. Further cascading with glucose oxidase, as a proof-of-concept application, allowed glucose to be more reliably measured, even in a broader range of concentrations without any conventional strong acid termination.

EAT-2 attenuates C. elegans development via metabolic remodeling in a chemically defined food environment.

Dietary intake and nutrient composition regulate animal growth and development; however, the underlying mechanisms remain elusive. Our previous study has shown that either the mammalian deafness homolog gene tmc-1 or its downstream acetylcholine receptor gene eat-2 attenuates Caenorhabditis elegans development in a chemically defined food CeMM (C. elegans maintenance medium) environment, but the underpinning mechanisms are not well-understood. Here, we found that, in CeMM food environment, for both eat-2 and tmc-1 fast-growing mutants, several fatty acid synthesis and elongation genes were highly expressed, while many fatty acid ß-oxidation genes were repressed. Accordingly, dietary supplementation of individual fatty acids, such as monomethyl branch chain fatty acid C17ISO, palmitic acid and stearic acid significantly promoted wild-type animal development on CeMM, and mutations in either C17ISO synthesis gene elo-5 or elo-6 slowed the rapid growth of eat-2 mutant. Tissue-specific rescue experiments showed that elo-6 promoted animal development mainly in the intestine. Furthermore, transcriptome and metabolome analyses revealed that elo-6/C17ISO regulation of C. elegans development may be correlated with up-regulating expression of cuticle synthetic and hedgehog signaling genes, as well as promoting biosynthesis of amino acids, amino acid derivatives and vitamins. Correspondingly, we found that amino acid derivative S-adenosylmethionine and its upstream metabolite methionine sulfoxide significantly promoted C. elegans development on CeMM. This study demonstrated that C17ISO, palmitic acid, stearic acid, S-adenosylmethionine and methionine sulfoxide inhibited or bypassed the TMC-1 and EAT-2-mediated attenuation of development via metabolic remodeling, and allowed the animals to adapt to the new nutritional niche.

Effect of planting salt-tolerant legumes on coastal saline soil nutrient availability and microbial communities.

Soil salinization is a serious global environmental problem affecting sustainable development of agriculture. Legumes are excellent candidates for the phytoremediation of saline soils; however, how soil microbes mediate the amelioration of coastal saline ecosystems is unknown. In this study, two salt-tolerant legumes, Glycine soja and Sesbania cannabina were planted in coastal saline soil for three years. Soil nutrient availability and microbiota structure (including bacteria, fungi, and diazotrophs) were compared between the phytoremediated soils and control soil (barren land). Planting legumes reduced soil salinity, and increased total carbon, total nitrogen, and NO3--N contents. Among the soil microbiota, some nitrogen-fixing bacteria (e.g., Azotobacter) were enriched in legumes, which were probably responsible for soil nitrogen accumulation. The complexity of the bacterial, fungal, and diazotrophic networks increased significantly from the control to the phytoremediated soils, suggesting that the soil microbial community formed closer ecological interactions during remediation. Furthermore, the dominant microbial functions were chemoheterotrophy (24.75%) and aerobic chemoheterotrophy (21.97%) involved in the carbon cycle, followed by nitrification (13.68%) and aerobic ammonia oxidation (13.34%) involved in the nitrogen cycle. Overall, our findings suggested that G. soja and S. cannabina legumes were suitable for ameliorating saline soils as they decreased soil salinity and increased soil nutrient content, with microorganisms especially nitrogen-fixing bacteria, playing an important role in this remediation process.

Cascade nanozymatic network mimicking cells with selective and linear perception of H2O2.

A single stimulus leading to multiple responses is an essential function of many biological networks, which enable complex life activities. However, it is challenging to duplicate a similar chemical reaction network (CRN) using non-living chemicals, aiming at the disclosure of the origin of life. Herein, we report a nanozyme-based CRN with feedback and feedforward functions for the first time. It demonstrates multiple responses at different modes and intensities upon a single H2O2 stimulus. In the two-electron cascade oxidation of 3,3',5,5'-tetramethylbenzidine (TMB), the endogenous product H2O2 competitively inhibited substrates in the first one-electron oxidation reaction on a single-atom nanozyme (Co-N-CNTs) and strikingly accelerated the second one-electron oxidation reaction under a micellar nanozyme. As a proof-of-concept, we further confined the nanozymatic network to a microfluidic chip as a simplified artificial cell. It exhibited remarkable selectivity and linearity in the perception of H2O2 stimulus against more than 20 interferences in a wide range of concentrations (0.01-100 mM) and offered an instructive platform for studying primordial life-like processes.

Adaptable graphitic C6N6-based copper single-atom catalyst for intelligent biosensing.

Self-adaptability is highly envisioned for artificial devices such as robots with chemical noses. For this goal, seeking catalysts with multiple and modulable reaction pathways is promising but generally hampered by inconsistent reaction conditions and negative internal interferences. Herein, we report an adaptable graphitic C6N6-based copper single-atom catalyst. It drives the basic oxidation of peroxidase substrates by a bound copper-oxo pathway, and undertakes a second gain reaction triggered by light via a free hydroxyl radical pathway. Such multiformity of reactive oxygen-related intermediates for the same oxidation reaction makes the reaction conditions capable to be the same. Moreover, the unique topological structure of CuSAC6N6 along with the specialized donor-π-acceptor linker promotes intramolecular charge separation and migration, thus inhibiting negative interferences of the above two reaction pathways. As a result, a sound basic activity and a superb gain of up to 3.6 times under household lights are observed, superior to that of the controls, including peroxidase-like catalysts, photocatalysts, or their mixtures. CuSAC6N6 is further applied to a glucose biosensor, which can intelligently switch sensitivity and linear detection range in vitro.

Insight into Iron Leaching from an Ascorbate-Oxidase-like Fe-N-C Nanozyme and Oxygen Reduction Selectivity.

Ascorbate (H2 A) is a well-known antioxidant to protect cellular components from free radical damage and has also emerged as a pro-oxidant in cancer therapies. However, such "contradictory" mechanisms underlying H2 A oxidation are not well understood. Herein, we report Fe leaching during catalytic H2 A oxidation using an Fe-N-C nanozyme as a ferritin mimic and its influence on the selectivity of the oxygen reduction reaction (ORR). Owing to the heterogeneity, the Fe-Nx sites in Fe-N-C primarily catalyzed H2 A oxidation and 4 e- ORR via an iron-oxo intermediate. Nonetheless, trace O2 ⋅- produced by marginal N-C sites through 2 e- ORR accumulated and attacked Fe-Nx sites, leading to the linear leakage of unstable Fe ions up to 420 ppb when the H2 A concentration increased to 2 mM. As a result, a substantial fraction (ca. 40 %) of the N-C sites on Fe-N-C were activated, and a new 2+2 e- ORR path was finally enabled, along with Fenton-type H2 A oxidation. Consequently, after Fe ions diffused into the bulk solution, the ORR at the N-C sites stopped at H2 O2 production, which was the origin of the pro-oxidant effect of H2 A.

Highly Efficient Wavelength-Resolved Electrochemiluminescence of Carbon Nitride Films for Ultrasensitive Multiplex MicroRNA Detection.

The development of electrochemiluminescence (ECL) emitters of different colors with high ECL efficiency (ΦECL) is appealing yet challenging for ultrasensitive multiplexed bioassays. Herein, we report the synthesis of highly efficient polymeric carbon nitride (CN) films with fine-tuned ECL emission from blue to green (410, 450, 470, and 525 nm) using the precursor crystallization method. More importantly, naked eye-observable and significantly enhanced ECL emission was achieved, and the cathodic ΦECL values were ca. 112, 394, 353, and 251 times those of the aqueous Ru(bpy)3Cl2/K2S2O8 reference. Mechanism studies showed that the density of surface-trapped electrons, the associated nonradiative decay pathways, and electron-hole recombination kinetics were crucial factors for the high ΦECL of CN. Based on high ΦECL and different colors of ECL emission, the wavelength-resolved multiplexing ECL biosensor was constructed to simultaneously detect miRNA-21 and miRNA-141 with superior low detection limits of 0.13 fM and 25.17 aM, respectively. This work provides a facile method to synthesize wavelength-resolved ECL emitters based on metal-free CN polymers with high ΦECL for multiplexed bioassays.

An Empirical Study on the Relationship between New Energy Vehicle' Export Sophistication and Industrial Structure Upgrading in China.

Following decades of reducing greenhouse gas emissions in the transportation industry, most car companies will stop producing petrol cars and promote the development of new energy vehicles in the near future, even in China. This study is based on energy vehicle exports using China's 31 provinces' panel data from 2010 to 2020. Considering that China mainly engages in processing trade, this study analyzes the domestic energy vehicle's export sophistication after deleting intermediate goods, measuring the relationship between export sophistication and industrial upgrading with static and dynamic panel models. Then, heterogeneity tests were deployed to examine the domestic export sophistication of three major economic belts partition. The results revealed that improving export sophistication is conducive to realizing China's industrial upgrading. China's new energy vehicles industry is positively affected by export sophistication, R&D, foreign direct investment, average GDP growth rate, market factors, and human resources over the long run. Regarding regional stratification, domestic export sophistication in the eastern and western regions has more significant effects on promoting industrial upgrading than in the central region. In particular, in western regions, every increase in export sophistication by one unit will bring a significant industrial upgrading effect. Given this, China's new energy vehicles should increase export sophistication to help the country's industrial upgrading.

Transcriptome Analysis of the Nematode Caenorhabditis elegans in Acidic Stress Environments.

Ocean acidification and acid rain, caused by modern industries' fossil fuel burning, lead to a decrease in the living environmental pH, which results in a series of negative effects on many organisms. However, the underlying mechanisms of animals' response to acidic pH stress are largely unknown. In this study, we used the nematode Caenorhabditis elegans as an animal model to explore the regulatory mechanisms of organisms' response to pH decline. Two major stress-responsive pathways were found through transcriptome analysis in acidic stress environments. First, when the pH dropped from 6.33 to 4.33, the worms responded to the pH stress by upregulation of the col, nas, and dpy genes, which are required for cuticle synthesis and structure integrity. Second, when the pH continued to decrease from 4.33, the metabolism of xenobiotics by cytochrome P450 pathway genes (cyp, gst, ugt, and ABC transporters) played a major role in protecting the nematodes from the toxic substances probably produced by the more acidic environment. At the same time, the slowing down of cuticle synthesis might be due to its insufficient protective ability. Moreover, the systematic regulation pattern we found in nematodes might also be applied to other invertebrate and vertebrate animals to survive in the changing pH environments. Thus, our data might lay the foundation to identify the master gene(s) responding and adapting to acidic pH stress in further studies, and might also provide new solutions to improve assessment and monitoring of ecological restoration outcomes, or generate novel genotypes via genome editing for restoring in challenging environments especially in the context of acidic stress through global climate change.

Identification of Ly2 members as antimicrobial peptides from zebrafish Danio rerio.

The emergence of multidrug-resistant (MDR) microbes caused by overuse of antibiotics leads to urgent demands for novel antibiotics exploration. Our recent data showed that Ly2.1-3 (a novel lymphocyte antigen 6 (Ly6) gene cluster) were proteins with cationic nature and rich in cysteine content, that are characteristic of antimicrobial peptides (AMPs) and their expression were all significantly up-regulated after challenge with lipopolysaccharide (LPS). These strongly suggested that Ly2.1-3 are potential AMPs, but firm evidence are lacking. Here, we clearly showed that the recombinant proteins of Ly2.1-3 were capable of killing Gram-negative bacteria Aeromonas hydrophila and Escherichia coli, while they had little bactericidal activity against the Gram-positive bacteria Staphylococcus aureus and Bacillus subtilis We also showed that recombinant proteins Ly2.1-3 (rLy2.1-3) were able to bind to the Gram-negative bacteria A. hydrophila, E. coli and the microbial signature molecule LPS, but not to the Gram-positive bacteria S. aureus and B. subtilis as well as the microbial signature molecule LTA. Moreover, the Scatchard analysis revealed that rLy2.1-3 could specifically bind to LPS. Finally, we found that Ly2.1-3 were not cytotoxic to mammalian cells. All these together indicate that Ly2.1-3 can function as AMPs.