Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial-resistant Salmonella enterica

Genetic variation in a pathogen, including the causative agent of salmonellosis, Salmonella enterica, can occur as a result of eco-evolutionary forces triggered by dissimilarities of ecological niches. Here, we applied comparative genomics to study 90 antimicrobial resistant (AMR) S. enterica isolates from bovine and human hosts in New York and Washington states to understand host- and geographic-associated population structure. Results revealed distinct presence/absence profiles of functional genes and pseudogenes (e.g., virulence genes) associated with bovine and human isolates. Notably, bovine isolates contained significantly more transposase genes but fewer transposase pseudogenes than human isolates, suggesting the occurrence of large-scale transposition in genomes of bovine and human isolates at different times. The high correlation between transposase genes and AMR genes, as well as plasmid replicons, highlights the potential role of horizontally transferred transposons in promoting adaptation to antibiotics. By contrast, a number of potentially geographic-associated single-nucleotide polymorphisms (SNPs), rather than geographic-associated genes, were identified. Interestingly, 38% of these SNPs were in genes annotated as cell surface protein-encoding genes, including some essential for antibiotic resistance and host colonization. Overall, different evolutionary forces and limited recent inter-population transmission appear to shape AMR S. enterica population structure in different hosts and geographic origins.     

耐盐碱促生菌的筛选及性能

盐分是影响作物生长最重要的因素,使用能促进植物生长的耐盐碱促生菌减轻盐胁迫引起的损害是一种农业上的有效方法。文中从盐碱地筛选得到7株耐盐细菌,并考察筛选菌株的产胞外聚合物(EPS)能力、降碱能力和产吲哚-3-乙酸(IAA)能力。经综合评价选出1株优势菌株DB01,菌株DB01产EPS能力为0.21 g/g,降碱能力为8.7%,产IAA的能力为8.97 mg/L。菌株经16S rRNA鉴定为海水盐单胞菌Halomonas aquamarina,并且有抑制香蕉枯萎病、番茄早疫病、大豆疫霉病、小麦纹枯病病原菌的能力,同时能够在盐胁迫下促进小麦幼苗的发芽率和根长。海水盐单胞菌Halomonas aquamarina DB01可为土壤微生物资源开发利用和盐碱地改良提供理论依据。     

中国地衣的濒危等级评估

地衣是大型真菌的重要组成部分, 是中国大型真菌红色名录评估的主要对象之一。本次评估的地衣共2,164种, 其中子囊菌地衣2,145种, 担子菌地衣19种, 分属于2门9纲34目92科352属。评估结果显示, 地衣受威胁物种共28种, 占被评估地衣物种总数的1.29%, 其中极危3种, 濒危7种, 易危18种; 近危6种, 无危657种, 而数据不足的物种达1,473种。这类因为缺乏足够的数据资料而未能进一步评估其生存状态和红色名录等级的物种占评估地衣总数的68.07%, 凸显了我国地衣学研究的严峻形势及对地衣分类学人才的迫切需要。对受威胁物种的分析表明, 地衣由于自身生长缓慢和对环境污染敏感, 并且绝大多数分布区域狭窄, 种群数量少, 对生境退化的适应和恢复生长的能力弱, 人类活动和气候变化导致的栖息地破坏和碎片化使得这些地衣的生存受到严重威胁。值得注意的是, 评为易危的一些地衣, 因具有较大的食药用价值而被过度采挖利用, 如不采取有效保护措施, 其受威胁程度将进一步加剧。     

全球中华鲎资源保护现状及对策建议

鲎是古老的海洋节肢动物。中华鲎(Tachypleus tridentatus)是世界现存4种鲎中体型最大的一种, 是河口生态系统的标志物种, 同时其血液被用于生产医用检验试剂――鲎试剂。中华鲎的自然地理分布范围相当狭窄, 仅局限于日本濑户内海向南延伸至印度尼西亚爪哇岛北岸以北的太平洋西岸海域, 其中在中国东岸和日本南部海域的历史产量较高。自20世纪50年代以来中华鲎种群数量出现了显著减少, 2019年中华鲎在IUCN红色名录中的濒危等级正式更新为濒危(EN), 明确了中华鲎资源呈现全球性衰退的状态, 究其原因可归纳为鲎生境破坏和过度捕捞两个方面。在开展鲎资源保护的实践工作中, 作者深刻反思当前鲎资源保护在海洋保护区划定、增殖放流及科普和野生动物保护法宣传中存在的问题并提出相应建议, 包括加快完善种群基线数据, 制定标准化种群和生境基线监测指南, 构建科学放流体系等, 以期推进全球范围内的中华鲎资源保护与科学管理。     

Energy–water and seasonal variations in climate underlie the spatial distribution patterns of gymnosperm species richness in China

Studying the pattern of species richness is crucial in understanding the diversity and distribution of organisms in the earth. Climate and human influences are the major driving factors that directly influence the large‐scale distributions of plant species, including gymnosperms. Understanding how gymnosperms respond to climate, topography, and human‐induced changes is useful in predicting the impacts of global change. Here, we attempt to evaluate how climatic and human‐induced processes could affect the spatial richness patterns of gymnosperms in China. Initially, we divided a map of the country into grid cells of 50 × 50 km² spatial resolution and plotted the geographical coordinate distribution occurrence of 236 native gymnosperm taxa. The gymnosperm taxa were separated into three response variables: (a) all species, (b) endemic species, and (c) nonendemic species, based on their distribution. The species richness patterns of these response variables to four predictor sets were also evaluated: (a) energy–water, (b) climatic seasonality, (c) habitat heterogeneity, and (d) human influences. We performed generalized linear models (GLMs) and variation partitioning analyses to determine the effect of predictors on spatial richness patterns. The results showed that the distribution pattern of species richness was highest in the southwestern mountainous area and Taiwan in China. We found a significant relationship between the predictor variable set and species richness pattern. Further, our findings provide evidence that climatic seasonality is the most important factor in explaining distinct fractions of variations in the species richness patterns of all studied response variables. Moreover, it was found that energy–water was the best predictor set to determine the richness pattern of all species and endemic species, while habitat heterogeneity has a better influence on nonendemic species. Therefore, we conclude that with the current climate fluctuations as a result of climate change and increasing human activities, gymnosperms might face a high risk of extinction.     

The complete chloroplast genome of Myriophyllum spicatum reveals a 4‐kb inversion and new insights regarding plastome evolution in Haloragaceae

Myriophyllum, among the most species‐rich genera of aquatic angiosperms with ca. 68 species, is an extensively distributed hydrophyte lineage in the cosmopolitan family Haloragaceae. The chloroplast (cp) genome is useful in the study of genetic evolution, phylogenetic analysis, and molecular dating of controversial taxa. Here, we sequenced and assembled the whole chloroplast genome of Myriophyllum spicatum L. and compared it to other species in the order Saxifragales. The complete chloroplast genome sequence of M. spicatum is 158,858 bp long and displays a quadripartite structure with two inverted repeats (IR) separating the large single copy (LSC) region from the small single copy (SSC) region. Based on sequence identification and the phylogenetic analysis, a 4‐kb phylogenetically informative inversion between trnE‐trnC in Myriophyllum was determined, and we have placed this inversion on a lineage specific to Myriophyllum and its close relatives. The divergence time estimation suggested that the trnE‐trnC inversion possibly occurred between the upper Cretaceous (72.54 MYA) and middle Eocene (47.28 MYA) before the divergence of Myriophyllum from its most recent common ancestor. The unique 4‐kb inversion might be caused by an occurrence of nonrandom recombination associated with climate changes around the K‐Pg boundary, making it interesting for future evolutionary investigations.     

Proteomic Analysis of High Temperature Stress-Responsive Proteins in Chrysanthemum Leaves

Chrysanthemum is one of the most important ornamental flowers in the world, and temperature has a significant influence on its field production. In the present study, differentially expressed proteins were investigated in the leaves of Dendranthema grandiflorum ‘Jinba’ under high temperature stress using label-free quantitative proteomics techniques. The expressed proteins were comparatively identified and analyzed. A total of 1,463 heat-related, differentially expressed proteins were successfully identified by Liquid Chromatography-tandem Mass Spectrometry (LC-MS/MS), and 1,463 heat-related, differentially expressed proteins were successfully identified by mass spectrometry after a high temperature treatment. Among these, 701 proteins were upregulated and 762 proteins were downregulated. The in-depth bioinformatics analysis of these differentially expressed proteins revealed that these were involved in energy metabolism pathways, protein metabolism, and heat shock. In the present study, the investigators determined the changes in the levels of some proteins, and their expression at the protein and molecular levels in chrysanthemum to help reveal the mechanism of heat resistance in chrysanthemum. Furthermore, the present study elucidated some of the proteins correlated to heat resistance in chrysanthemum, and their expression changes at the protein and molecular levels to help reveal the mechanism of heat resistance in this flower species. These results provide a theoretical basis for the selection of new heat resistant varieties of chrysanthemum in the field.