Complete ammonia oxidization in agricultural soils: High ammonia fertilizer loss but low N2O production

The contribution of agriculture to the sustainable development goals requires climate-smart and profitable farm innovations. Increasing the ammonia fertilizer applications to meet the global food demands results in high agricultural costs, environmental quality deterioration, and global warming, without a significant increase in crop yield. Here, we reported that a third microbial ammonia oxidation process, complete ammonia oxidation (comammox), is contributing to a significant ammonia fertilizer loss (41.9 ± 4.8%) at the rate of 3.53 ± 0.55 mg N kg⁻¹ day⁻¹ in agricultural soils around the world. The contribution of comammox to ammonia fertilizer loss, occurring mainly in surface agricultural soil profiles (0–0.2 m), was equivalent to that of bacterial ammonia oxidation (48.6 ± 4.5%); both processes were significantly more important than archaeal ammonia oxidation (9.5 ± 3.6%). In contrast, comammox produced less N₂O (0.98 ± 0.44 μg N kg⁻¹ day⁻¹, 11.7 ± 3.1%), comparable to that produced by archaeal ammonia oxidation (16.4 ± 4.4%) but significantly lower than that of bacterial ammonia oxidation (72.0 ± 5.1%). The efficiency of ammonia conversion to N₂O by comammox (0.02 ± 0.01%) was evidently lower than that of bacterial (0.24 ± 0.06%) and archaeal (0.16 ± 0.04%) ammonia oxidation. The comammox rate increased with increasing soil pH values, which is the only physicochemical characteristic that significantly influenced both comammox bacterial abundance and rates. Ammonia fertilizer loss, dominated by comammox and bacterial ammonia oxidation, was more intense in soils with pH >6.5 than in soils with pH <6.5. Our results revealed that comammox plays a vital role in ammonia fertilizer loss and sustainable development in agroecosystems that have been previously overlooked for a long term.     

中国喀斯特地区微生物群落结构和功能的研究进展

频繁的人类生产活动使植被遭到破坏,造成基岩裸露的石漠化现象,严重制约了喀斯特地区自然和社会经济的发展,随着生态修复工程的大力开展,微生物群落的结构和功能在生态修复中逐渐受到重视,因为微生物作为喀斯特生态系统的重要组成部分,不仅在物质循环过程中起着重要作用,也在喀斯特生态系统修复中占有十分重要的地位。所以微生物群落结构和功能的研究可以作为衡量生态系统稳定性的重要指标。就中国喀斯特地区的典型植被恢复的不同阶段、成土过程、不同的土地利用方式、矿山修复过程以及不同水域中的微生物群落结构及功能等方面的研究状况进行系统梳理,结合实例综合论述喀斯特地区生态修复过程中微生物作用的研究进展,以期为喀斯特地区生态修复提供参考。     

UreB immunodominant epitope-specific CD8+ T-cell responses were beneficial in reducing gastric symptoms in Helicobacter pylori-infected individuals

Background and aims

Although Helicobacter pylori is recognized as an extracellular infection bacterium, it can lead to an increase in the number of CD8⁺ T cells after infection. At present, the characteristics of H. pylori antigen-specific CD8⁺ T cells and the epitope response have not been elucidated. This study was focused on putative protective antigen UreB to detect specific CD8⁺ T-cell responses in vitro and screen for predominant response epitopes.

Methods

The PBMCs collected from H. pylori-infected individuals were stimulated by UreB peptide pools in vitro to identify the immunodominant CD8⁺ T-cell epitopes. Furthermore, their HLA restriction characteristics were detected accordingly by NGS. Finally, the relationship between immunodominant responses and appearance of gastric symptoms after H. pylori infection was conducted.

Results

UreB-specific CD8⁺ T-cell responses were detected in H. pylori-infected individuals. Three of UreB dominant epitopes (A-2 (UreB_443–451: GVKPNMIIK), B-4 (UreB_420–428: SEYVGSVEV), and C-1 (UreB_5–13: SRKEYVSMY)) were firstly identified and mainly presented by HLA-A*1101, HLA-B*4001 and HLA-C*0702 alleles, respectively. C-1 responses were mostly occurred in H. pylori-infected subjects without gastric symptoms and may alleviate the degree of gastric inflammation.

Conclusions

The UreB dominant epitope-specific CD8⁺ T-cell response was closely related to the gastric symptoms after H. pylori infection, and the C-1 (UreB_5-13) dominant peptides may be protective epitopes.     

Circular RNA SLTM as a miR-421-competing endogenous RNA to mediate HMGB2 expression stimulates apoptosis and inflammation in arthritic chondrocytes

Osteoarthritis (OA) is the most common age-related joint disease characterized by chronic inflammation, progressive articular cartilage destruction, and subchondral sclerosis. Accumulating evidence suggests that circular RNAs (circRNAs) play key roles in OA, but the function of circSLTM in OA remains greatly unknown. Therefore, this study focused on interleukin-1β (IL-1β)-treated primary human chondrocytes as well as a rat model to investigate the expression pattern and functional role of circSLTM in OA in vitro and in vivo. CircSLTM and high mobility group protein B2 (HMGB2) were upregulated in IL-1β-induced chondrocytes, whereas miR-421 was downregulated. Knockdown of circSLTM or overexpression of miR-421 ameliorated IL-1β-induced chondrocyte apoptosis and inflammation. The regulatory relationship between circSLTM and miR-421, as well as that between miR-421 and HMGB2, was predicted by bioinformatics and then verified by the RNA immunoprecipitation experiment and dual-luciferase reporter gene assay. Furthermore, silencing of circSLTM increased cartilage destruction and decreased cartilage tissue apoptosis rate and inflammation in a rat model of OA. Taken together, our findings demonstrate the fundamental role of circSLTM in OA progression and provide a potential molecular target for OA therapy.     

土壤理化性质驱动烤烟根际细菌群落的组配及其共现性网络互作

【目的】解析土壤微生物在植物根际的组配机制对于认识和维护农田生态系统的稳定性至关重要。【方法】通过Illumina高通量测序和生物信息学分析方法明确了我国主要种植烟草生态区烤烟根际土壤细菌群落与土壤理化性质的互作关系。【结果】烤烟根际细菌类群主要为放线菌纲(Actinobacteria)、α-变形菌纲(Alphaproteobacteria)、γ-变形菌纲(Gammaproteobacteria)和嗜热油菌纲(Thermoleophilia)。细菌群落组成按生态区聚类,且样本空间距离和细菌群落相似度显著负相关。共现性网络分析表明,烤烟根际细菌群落间协同作用大于拮抗作用,武陵秦巴生态区、黄淮平原生态区、南岭丘陵生态区和沂蒙丘陵生态区细菌群落高度模块化,小单胞菌属(Micromonospora)为南岭丘陵生态区和黄淮生态区细菌共现性网络的网络中心,Bryobacter和气单胞菌属(Arenimonas)为南岭丘陵生态区细菌网络的模块核心,其菌群特性而非相对丰度决定了其在稳定细菌网络中的重要作用。冗余分析结果证实pH、有效铁、交换性镁和有效锰能显著影响烤烟根际细菌群落结构。【结论】烤烟根际细...     

撕裂蜡孔菌HG2011对光叶紫花苕结瘤固氮的影响及其潜在机制

【目的】 在我国南方尤其是西南地区,光叶紫花苕(Vicia villosa Roth.)作为重要的青饲和绿肥两用豆科作物被广泛种植,有助于提高土壤氮素和后茬作物的产量品质。接种有益微生物是促进豆科作物生物固氮和生长的重要措施之一。为此,本文研究了一株自主分离获得的白腐真菌¾¾撕裂蜡孔菌(Careporia lacerata HG2011)对光叶紫花苕结瘤固氮和生长的影响,并揭示其潜在机制。【方法】 采用微生物培养、植物培养和田间试验,研究C. lacerata磷铁活化能力、代谢产物构成、与根瘤菌Rhizobium sophorae S3的相互作用,及其对光叶紫花苕结瘤、生长、产量、品质和土壤有效磷铁的影响。【结果】 C. lacerata和根瘤菌之间无拮抗作用。液相色谱-质谱(liquid chromatography-mass spectrometry, LC-MS)分析发现,C. lacerata发酵液含有氨基酸、有机酸和类黄酮等化感物质,能增强根瘤菌的趋化性并促进生物膜形成。此外,C. lacerata还能释放生长素、赤霉素、水杨酸和铁载体,活化难溶性有机和无机磷。在植物培养试验中,单独接种C. lacerata或根瘤菌均能促进光叶紫花苕生长,但以共接种处理效果最佳。C. lacerata定殖于光叶紫花苕根际,导致根长、根系表面积和结瘤数显著增加。田间试验发现,接种C. lacerata显著提高了光叶紫花苕单株根瘤数、根瘤质量和固氮酶活性,以及土壤有效磷铁含量和磷酸酶活性,产量比常规施肥处理增加12.15%且品质无显著变化。【结论】 C. lacerata能够在光叶紫花苕根际定殖,通过分泌化感物质、生长素和活化土壤磷铁等机制促进结瘤固氮和生长发育。C. lacerata易于培养,菌剂制备成本低廉,施用简便,对提高豆科作物产量品质具有一定应用价值。     

基于Golden Gate技术的齐整小核菌转录单元高效组装系统

【目的】为齐整小核菌代谢工程研究建立高效的转录单元组装系统。【方法】通过应用Golden Gate技术,以mobius assembly为基础,分别设计并构建DNA元件标准化接口改造、单转录单元组装、应用质粒(多转录单元)组装等功能的载体,从而形成一套完整的多转录单元组装系统。【结果】构建了2个用于DNA元件标准化接口改造的Level 0载体,4个用于单转录单元组装的Level 1载体,4个用于应用质粒组装的Level 2载体和13个应用质粒组装的辅助质粒。然后应用此系统为齐整小核菌组装了若干经过标准化接口改造的DNA元件质粒、单转录单元质粒和硬葡聚糖相关基因的功能分析质粒。所构建的最终应用质粒可以同时适用于齐整小核菌的根癌农杆菌介导转化法、电穿孔转化法和原生质体转化法。【结论】此质粒系统具有强大的DNA设计、组装和容纳能力,为未来齐整小核菌代谢工程和功能基因组学研究提供了高效的质粒构建技术平台。     

Deciphering RNA m6A regulation in aging: Perspectives on current advances and future directions

N⁶-methyladenosine (m⁶A) is a dynamic and reversible RNA modification that has emerged as a crucial player in the life cycle of RNA, thus playing a pivotal role in various biological processes. In recent years, the potential involvement of RNA m⁶A modification in aging and age-related diseases has gained increasing attention, making it a promising target for understanding the molecular mechanisms underlying aging and developing new therapeutic strategies. This Perspective article will summarize the current advances in aging-related m⁶A regulation, highlighting the most significant findings and their implications for our understanding of cellular senescence and aging, and the potential for targeting RNA m⁶A regulation as a therapeutic strategy. We will also discuss the limitations and challenges in this field and provide insights into future research directions. By providing a comprehensive overview of the current state of the field, this Perspective article aims to facilitate further advances in our understanding of the molecular mechanisms underlying aging and to identify new therapeutic targets for aging-related diseases.