Novel Alkaloids from Marine Actinobacteria: Discovery and Characterization

The marine environment is an excellent resource for natural products with therapeutic potential. Its microbial inhabitants, often associated with other marine organisms, are specialized in the synthesis of bioactive secondary metabolites. Similar to their terrestrial counterparts, marine Actinobacteria are a prevalent source of these natural products. Here, we discuss 77 newly discovered alkaloids produced by such marine Actinobacteria between 2017 and mid-2021, as well as the strategies employed in their elucidation. While 12 different classes of alkaloids were unraveled, indoles, diketopiperazines, glutarimides, indolizidines, and pyrroles were most dominant. Discoveries were mainly based on experimental approaches where microbial extracts were analyzed in relation to novel compounds. Although such experimental procedures have proven useful in the past, the methodologies need adaptations to limit the chance of compound rediscovery. On the other hand, genome mining provides a different angle for natural product discovery. While the technology is still relatively young compared to experimental screening, significant improvement has been made in recent years. Together with synthetic biology tools, both genome mining and extract screening provide excellent opportunities for continued drug discovery from marine Actinobacteria.     

克隆文库分析红树林土壤中放线菌的多样性

直接提取8个红树林土壤的总DNA,用放线菌门的特异性PCR引物进行扩增,通过构建16S rRNA文库,测序及系统发育分析,获取新颖放线菌菌株.结果发现,有酸微菌亚纲(Acidimicrobidae) (30.2％)、放线菌亚纲(Actinobacteridae) (68.0％)、红蝽菌亚纲(Coriobacteridae)(1.1％)和去腈基菌亚纲(Nitriliruptoridae)( 0.7％)成员,没有红色杆菌亚纲( Rubrobacteridae)成员.仙农指数和Chao1物种多样性指数(Schao1)表明,红树林土壤样品中含有丰富的放线菌多样性.以16S rDNA基因的相似率≥97％作为临界点,45.1％可能代表新候选种(candidate species)(未培养、分离).本研究为进一步获取新颖的红树林放线菌资源提供了基础.     

Taxa-specific changes in soil microbial community composition induced by pyrogenic carbon amendments

The effects of pyrogenic carbon on the microbial diversity of forest soils were examined by comparing two soil types, fire-impacted and non-impacted, that were incubated with laboratory-generated biochars. Molecular and culture-dependent analyses of the biochar-treated forest soils revealed shifts in the relative abundance and diversity of key taxa upon the addition of biochars, which were dependent on biochar and soil type. Specifically, there was an overall loss of microbial diversity in all soils treated with oak and grass-derived biochar as detected by automated ribosomal intergenic spacer analysis. Although the overall diversity decreased upon biochar amendments, there were increases in specific taxa during biochar-amended incubation. DNA sequencing of these taxa revealed an increase in the relative abundance of bacteria within the phyla Actinobacteria and Gemmatimonadetes in biochar-treated soils. Together, these results reveal a pronounced impact of pyrogenic carbon on soil microbial community composition and an enrichment of key taxa within the parent soil microbial community.     

铁矿尾矿放线菌分离株的系统发育分析

[目的]通过确定12株典型分离株的系统发育地位,初步探讨铁矿尾矿中放线菌生物多样性。[方法]采用酚-氯仿法提取基因组DNA,PCR扩增16S rDNA并测序后进行系统发育分析。[结果]12株铁矿尾矿放线菌均属于链霉菌属,与进化关系最近的已知菌株同源性为98.7%～100%。[结论]铁矿尾矿中可培养放线菌类群以链霉菌为主,其中存在大量潜在的新种。     

Quinone profiling of bacterial populations developed in the surface layer of volcanic mudflow deposits from Mt. Pinatubo (the Philippines)

The diversity of bacterial populations developed in the surface layer (0-0.25 m depth) of volcanic mudflow deposits from the Mt. Pinatubo volcano (the Philippines) was investigated using quinone profiling. Samples were collected from sites (named N and S1) that had been hit repeatedly by mudflows during successive rainy seasons after the violent eruption of 1991 and also from sites (F1 and F3) covered by mudflow in 1991 but with no deposition in following years. The total microscopic count ranged from 10⁸ g⁻¹ (N and S1 sites) to 3.9×10⁹ g⁻¹(site F3). In the N sample only three quinone species were detected, while the quinone profiles of samples from sites S3 and F3 showed higher diversity. Tetrahydrogenated menaquinone with eight isoprenoid units [MK-8 (H₄)] was the predominant quinone species in the sample from site N, while MK-8, MK-8 (H₂), MK-8 (H₄), MK-9 (H₄) and MK-9 (H₈) were found as major quinones in the sample from site F3. Because these MK species are known to be the major respiratory quinones of the Actinobacteria, this bacterial group is expected to predominate in the land with primary vegetation recovery following the impact of the volcanic mudflow.     

Phylogenetic Diversity and Biological Activity of Actinobacteria Isolated from the Chukchi Shelf Marine Sediments in the Arctic Ocean

Marine environments are a rich source of Actinobacteria and have the potential to produce a wide variety of biologically active secondary metabolites. In this study, we used four selective isolation media to culture Actinobacteria from the sediments collected from the Chukchi Shelf in the Arctic Ocean. A total of 73 actinobacterial strains were isolated. Based on repetitive DNA fingerprinting analysis, we selected 30 representatives for partial characterization according to their phylogenetic diversity, antimicrobial activities and secondary-metabolite biosynthesis genes. Results from the 16S rRNA gene sequence analysis indicated that the 30 strains could be sorted into 18 phylotypes belonging to 14 different genera: Agrococcus, Arsenicicoccus, Arthrobacter, Brevibacterium, Citricoccus, Janibacter, Kocuria, Microbacterium, Microlunatus, Nocardioides, Nocardiopsis, Saccharopolyspora, Salinibacterium and Streptomyces. To our knowledge, this paper is the first report on the isolation of Microlunatus genus members from marine habitats. Of the 30 isolates, 11 strains exhibited antibacterial and/or antifungal activity, seven of which have activities against Bacillus subtilis and Candida albicans. All 30 strains have at least two biosynthetic genes, one-third of which possess more than four biosynthetic genes. This study demonstrates the significant diversity of Actinobacteria in the Chukchi Shelf sediment and their potential for producing biologically active compounds and novel material for genetic manipulation or combinatorial biosynthesis.     

广西沿海地区红树林根系土壤中放线菌的分离与鉴定

本研究通过分离纯培养,从广西北海及防城港红树林根系土壤中分离出放线菌并提取其总DNA,用放线菌通用引物对获得菌株的16SrDNA进行PCR扩增,对获得的扩增产物进行DNA序列测定及菌株鉴定。研究结果表明,从红树林根系土壤样品中分离出15株典型放线菌菌株。16SrDNA测序比对鉴定结果显示,15株典型放线菌菌株中有12株属于链霉菌属（Streptomyces）,是常见菌属;3株属于拟诺卡氏菌属（Nocardiopsis）,为稀有放线菌。本研究分离纯化获得15株典型放线菌,初步揭示了广西沿海地区红树林土壤中放线菌的多样性。     

Comparative Metabologenomics Analysis of Polar Actinomycetes

Biosynthetic and chemical datasets are the two major pillars for microbial drug discovery in the omics era. Despite the advancement of analysis tools and platforms for multi-strain metabolomics and genomics, linking these information sources remains a considerable bottleneck in strain prioritisation and natural product discovery. In this study, molecular networking of the 100 metabolite extracts derived from applying the OSMAC approach to 25 Polar bacterial strains, showed growth media specificity and potential chemical novelty was suggested. Moreover, the metabolite extracts were screened for antibacterial activity and promising selective bioactivity against drug-persistent pathogens such as Klebsiella pneumoniae and Acinetobacter baumannii was observed. Genome sequencing data were combined with metabolomics experiments in the recently developed computational approach, NPLinker, which was used to link BGC and molecular features to prioritise strains for further investigation based on biosynthetic and chemical information. Herein, we putatively identified the known metabolites ectoine and chrloramphenicol which, through NPLinker, were linked to their associated BGCs. The metabologenomics approach followed in this study can potentially be applied to any large microbial datasets for accelerating the discovery of new (bioactive) specialised metabolites.     

蓝藻水华发生过程中细菌群落结构的动态变化

为探究养殖水体蓝藻水华从暴发到降解的整个过程中水体细菌群落的变化特征,于2015年5—7月在珠江水产研究所养殖基地进行为期8周的室内模拟试验,模拟养殖水体蓝藻水华从暴发到降解的整个过程,并采用高通量测序技术分析蓝藻水华发生过程中水体细菌群落的组成。结果表明,养殖水体细菌群落组成在蓝藻水华从暴发到降解的整个过程中发生了显著变化。拟杆菌门(Bacteroidetes)在水体中的比例随蓝藻水华的暴发而上升,随蓝藻水华的降解而下降;放线菌门(Actinobacteria)在水体中的比例随蓝藻水华的暴发及降解呈现一直下降的趋势;蓝藻水华衰败末期水体中的溶解氧几乎耗尽,隶属于厚壁菌门(Firmicutes)的厌氧菌嗜阳菌属(Heliophilum)在水体中的比例升高;试验期间养殖水体的细菌多样性,随蓝藻水华的暴发而降低,又随蓝藻水华的降解而升高。