Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential

Microorganisms that inhabit unchartered unique soil such as in the highly saline and hot Red Sea lagoons on the Saudi Arabian coastline, represent untapped sources of potentially new bioactive compounds. In this study, a culture-dependent approach was applied to three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS), collected from Rabigh harbor lagoon (RHL) and Al-Kharrar lagoon (AKL). The isolated bacteria were evaluated for their potential to produce bioactive compounds. The phylogenetic characterization of 251 bacterial isolates based on the 16S rRNA gene sequencing, supported their assignment to five different phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Planctomycetes. Fifteen putative novel species were identified based on a 16S rRNA gene sequence similarity to other strain sequences in the NCBI database, being ≤98%. We demonstrate that 49 of the 251 isolates exhibit the potential to produce antimicrobial compounds. Additionally, at least one type of biosynthetic gene sequence, responsible for the synthesis of secondary metabolites, was recovered from 25 of the 49 isolates. Moreover, 10 of the isolates had a growth inhibition effect towards Staphylococcus aureus, Salmonella typhimurium and Pseudomonas syringae. We report the previously unknown antimicrobial activity of B. borstelensis, P. dendritiformis and M. salipaludis against all three indicator pathogens. Our study demonstrates the evidence of diverse cultured microbes associated with the Red Sea harbor/lagoon environments and their potential to produce antimicrobial compounds.     

Sponge-Derived Kocuria and Micrococcus spp. as Sources of the New Thiazolyl Peptide Antibiotic Kocurin

Forty four marine actinomycetes of the family Microccocaceae isolated from sponges collected primarily in Florida Keys (USA) were selected from our strain collection to be studied as new sources for the production of bioactive natural products. A 16S rRNA gene based phylogenetic analysis showed that the strains are members of the genera Kocuria and Micrococcus. To assess their biosynthetic potential, the strains were PCR screened for the presence of secondary metabolite genes encoding nonribosomal synthetase (NRPS) and polyketide synthases (PKS). A small extract collection of 528 crude extracts generated from nutritional microfermentation arrays was tested for the production of bioactive secondary metabolites against clinically relevant strains (Bacillus subtilis, methicillin-resistant Staphylococcus aureus (MRSA), Acinetobacter baumannii and Candida albicans). Three independent isolates were shown to produce a new anti-MRSA bioactive compound that was identified as kocurin, a new member of the thiazolyl peptide family of antibiotics emphasizing the role of this family as a prolific resource for novel drugs.     

小水榕茎部内生菌的分离及鉴定

采用稀释涂板法,对小水榕茎部的内生菌进行分离、纯化及16S rDNA鉴定,通过同源性比对构建系统发育树。结果表明：分离到的24株内生菌分别属于5个类群(Alphaproteobacteria、Gammaproteobacteria、Firmicutes、Bacteroidetes、Filimonas)的11个属(Phenylobacterium、Rhizobium、Caulobacter、Sphingobium、Paenibacillus、Staphylococcus、Bacillus、Pseudomona、Chitinophaga sancti、Filimonas、Agrobacterium),其中Alphaproteobacteria、Firmicutes为优势种群,占总数的45.8%;所有菌株与其同源菌株的相似性均在98% 以上。本研究有助于揭示小水榕茎部内生菌的多样性,为发掘其应用潜力提供参考资料。     

Bacterial diversity and bioprospecting for cold-active hydrolytic enzymes from culturable bacteria associated with sediment from Nella Fjord, Eastern Antarctica

The diversity and cold-active hydrolytic enzymes of culturable bacteria associated with sandy sediment from Nella Fjord, Eastern Antarctica (69°22'6″ S, 76°21'45″ E) was investigated. A total of 33 aerobic heterotrophic bacterial strains were isolated at 4 °C. These bacterial isolates could be sorted into 18 phylotypes based on the 16S rRNA gene sequence belonging to four phyla, namely Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Actinobacteria. Only seven isolates were psychrophilic, 15 isolates were moderately psychrophilic, and 11 isolates were psychrotolerant. More than 72% of the isolates required sodium chloride to grow. Esterase, β-glucosidase and proteases activities at 4 °C were detected in more than 45% of the strains while approximately 21%, 15% and 12% of the strains possessed lipase, amylase and chitinase, respectively. These results indicate that a relatively high culturable bacterial diversity is present within marine sediment of Nella Fjord and it could serve as an ideal candidate region for bioprospecting.     

利用ITS1和ITS4通用引物扩增香蕉枯萎病菌核酸片段鉴定其生理小种

利用真菌核糖体rDNA区通用引物ITS1和ITS4,扩增采集自香蕉的13株镰刀菌包括18S rDNA部分序列、ITS1-5.8S-ITS2全部序列和28S rDNA部分序列的片段,通过BLAST序列比对分析,确定13株菌为尖孢镰刀菌[Fusarium oxysporum]。采用最大简约法,以层出镰刀菌[F.proliferatum(EU151490)]和茄病镰刀菌[F.solani(GQ376116)]为外群,将13株菌的序列与BLAST检索获得的尖镰孢古巴专化型(F.oxysporum f.sp.Cubense)相应序列构建了系统发育树。系统发育分析结果显示,13株菌与NCBI登录的4个尖镰孢古巴专化型菌株一起被分成3个亚群,亚群聚类结果与回接鉴定结果及文献报道的生理小种结果完全一致。     

红树共附生微生物分离与抗白色念珠菌活性评价

对湛江市廉江高桥、东简北港2个红树林区红树的根、叶、花、果不同部位27份样品进行共附生微生物的分离及抗白色念珠菌活性的评价。采用改良M1培养基、改良马丁培养基和改良高氏一号培养基进行细菌、真菌和放线菌的分离,用美蓝酶标仪法对所筛菌株进行抗白色念珠菌活性评价。利用SPSS13.0软件对数据进行单因素方差分析和多重比较。从27份样品中共分离出384株红树林共附生微生物,其中细菌170株,真菌160株,放线菌54株,细菌和真菌为优势菌群,两者占分离总菌株数的86.0%;从384株分离菌中检测出64株具有抗白色念珠菌活性,占分离菌的16.7%;统计分析显示,除2个地区的抗白色念珠菌活性数无显著差异外,2个地区的红树共附生微生物的组成、不同类型共附生微生物的数量、不同类型共附生微生物的抗白色念珠菌活性、红树不同部位的共附生微生物数量与活性菌株数量均存在一定的差异。     

山东花生茎腐病病原菌研究

从山东省多地采集的花生茎腐病株上分离到15个茎腐病菌株,选取6个典型菌株,对病原菌进行形态特征、致病性、生物学特性研究。核糖体DNA-ITS序列分析表明,6个菌株的核糖体DNA-ITS序列同源性高达99%。根据病原菌的形态特征、核糖体DNA-ITS序列同源性比较,确认供试6个菌株为同一种病原菌,与GenBank中可可毛色二孢属（Ｌasiodiplodia）（Diplodia的同物异名）的同源性高达99%以上。根据6个菌株的形态特征、致病性测定结果及生物学特性,并结合核糖体DNA-ITS序列分析,将山东花生茎腐病的病原鉴定为棉色二孢菌（Diplodia gossypina )。     

人参内生真菌多样性的初步研究

对人参两个栽培品种园参和移山参的内生真菌多样性进行初步研究。新鲜园参和移山参根经酒精和次氯酸钠消毒后,接种于PDA平板培养基上进行内生真菌的分离、纯化;根据菌落形态和孢子等形态特征,结合真菌的5.8S和ITS序列进行菌株鉴定。从人参中共计分离到内生真菌48株,园参中分离得到27株,移山参中分离到21株。通过形态鉴定及分子生物学方法鉴定了15株,分为14个分类单元,归属到8科9属12种。不同栽培品种的人参内生真菌形态各异,表现出了较丰富的多样性。     

花生条纹病毒株系生物学特性及壳蛋白基因序列分析

根据在花生上的症状,将５个ＰＳｔＶ中国分离物划分为轻斑驳,斑块和坏死三个株系类型。在其它鉴别寄主上,５个ＰＳｔＶ上分离物有相似所症状。轻斑驳株系对花生主茎高度影响不明显,荚果减产２１．０％－３５．６％,种子带毒率高。而斑块型株系分别降低花生高度和荚果产量９．２％－１６．３％,和３０．３％－５４．４％,种子带毒率低。     

Insights into the Variation in Bioactivities of Closely Related Streptomyces Strains from Marine Sediments of the Visayan Sea against ESKAPE and Ovarian Cancer

Marine sediments host diverse actinomycetes that serve as a source of new natural products to combat infectious diseases and cancer. Here, we report the biodiversity, bioactivities against ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) and ovarian cancer, and metabolites variation among culturable actinomycetes isolated from the marine sediments of Visayan Sea, Philippines. We identified 15 Streptomyces species based on a 16S rRNA gene sequence analysis. The crude extracts of 10 Streptomyces species have inhibited the growth of ESKAPE pathogens with minimum inhibitory concentration (MIC) values ranging from 0.312 mg/mL to 20 mg/mL depending on the strain and pathogens targeted. Additionally, ten crude extracts have antiproliferative activity against A2780 human ovarian carcinoma at 2 mg/mL. To highlight, we observed that four phylogenetically identical Streptomyces albogriseolus strains demonstrated variation in antibiotic and anticancer activities. These strains harbored type I and II polyketide synthase (PKS) and non-ribosomal synthetase (NRPS) genes in their genomes, implying that their bioactivity is independent of the polymerase chain reaction (PCR)-detected bio-synthetic gene clusters (BGCs) in this study. Metabolite profiling revealed that the taxonomically identical strains produced core and strain-specific metabolites. Thus, the chemical diversity among these strains influences the variation observed in their biological activities. This study expanded our knowledge on the potential of marine-derived Streptomyces residing from the unexplored regions of the Visayan Sea as a source of small molecules against ESKAPE pathogens and cancer. It also highlights that Streptomyces species strains produce unique strain-specific secondary metabolites; thus, offering new chemical space for natural product discovery.     

Enhancement of Growth and Grain Yield of Rice in Nutrient Deficient Soils by Rice Probiotic Bacteria

Plant associated bacteria are promising alternatives to chemical fertilizers for plant growth and yield improvement in an eco-friendly manner.In this study,rice associated bacteria were isolated and assessed for mineral phosphate solubilization and indole-3-acetic acid(IAA) production activity in vitro.Six promising strains,which were tentatively identified as phylotaxon Pseudochrobactrum sp.(BRRh-1),Burkholderia sp.(BRRh-2),Burkholderia sp.(BRRh-3),Burkholderia sp.(BRRh-4),Pseudomonas aeruginosa(BRRh-5 and BRRh-6) based on their 16 S rRNA gene phylogeny,exhibited significant phosphate solubilizing activity in National Botanical Research Institute phosphate growth medium,and BRRh-4 displayed the highest phosphate solubilizing activity,followed by BRRh-5.The p H of the culture broth declined,resulting in increase of growth rate of bacteria at p H 7,which might be due to organic acid secretion by the strains.In presence of L-tryptophan,five isolates synthesized IAA and the maximum IAA was produced by BRRh-2,followed by BRRh-1.Application of two most efficient phosphate solubilizing isolates BRRh-4 and BRRh-5 by root dipping(colonization) of seedling and spraying at the flowering stage significantly enhanced the growth and grain yield of rice variety BRRI dhan-29.Interestingly,application of both strains with 50% of recommended nitrogen,phosphorus and potassium fertilizers produced equivalent or higher grain yield of rice compared to the control grown with full recommended fertilizer doses,which suggests that these strains may have the potential to be used as bioinoculants for sustainable rice production.     

Antibacterial and Antibiofilm Activities of Tryptoquivalines and Meroditerpenes Isolated from the Marine-Derived Fungi Neosartorya paulistensis,N. laciniosa,N. tsunodae,and the Soil Fungi N. fischeri and N. siamensis

A new meroditerpene, sartorypyrone C (5), was isolated, together with the known tryptoquivalines l (1a), H (1b), F (1c), 3′-(4-oxoquinazolin-3-yl) spiro[1H-indole-3,5′]-2,2′-dione (2) and 4(3H)-quinazolinone (3), from the culture of the marine sponge-associated fungus Neosartorya paulistensis (KUFC 7897), while reexamination of the fractions remaining from a previous study of the culture of the diseased coral-derived fungus N. laciniosa (KUFC 7896) led to isolation of a new tryptoquivaline derivative tryptoquivaline T (1d). Compounds 1a–d, 2, 3, and 5, together with aszonapyrones A (4a) and B (4b), chevalones B (6) and C (7a), sartorypyrones B (7b) and A (8), were tested for their antibacterial activity against four reference strains (Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Pseudomonas aeruginosa), as well as the environmental multidrug-resistant isolates. Only aszonapyrone A (4a) and sartorypyrone A (8) exhibited significant antibacterial activity as well as synergism with antibiotics against the Gram-positive multidrug-resistant strains. Antibiofilm assays of aszonapyrone A (4a) and sartorypyrone A (8) showed that practically no biofilm was formed in the presence of their 2× MIC and MIC. However, the presence of a sub-inhibitory concentration of ½ MIC of 4a and 8 was found to increase the biofilm production in both reference strain and the multidrug-resistant isolates of S. aureus.     

Geographic variability and anti-staphylococcal activity of the chrysophaentins and their synthetic fragments

Drug-resistant Staphylococcus aureus is a continuing public health concern, both in the hospital and community settings. Antibacterial compounds that possess novel structural scaffolds and are effective against multiple S. aureus strains, including current drug-resistant ones, are needed. Previously, we have described the chrysophaentins, a family of bisdiarylbutene macrocycles from the chrysophyte alga Chrysophaeum taylori that inhibit the growth of S. aureus and methicillin-resistant S. aureus (MRSA). In this study we have analyzed the geographic variability of chrysophaentin production in C. taylori located at different sites on the island of St. John, U.S. Virgin Islands, and identified two new linear chrysophaentin analogs, E2 and E3. In addition, we have expanded the structure activity relationship through synthesis of fragments comprising conserved portions of the chrysophaentins, and determined the antimicrobial activity of natural chrysophaentins and their synthetic analogs against five diverse S. aureus strains. We find that the chrysophaentins show similar activity against all S. aureus strains, regardless of their drug sensitivity profiles. The synthetic chrysophaentin fragments indeed mimic the natural compounds in their spectrum of antibacterial activity, and therefore represent logical starting points for future medicinal chemistry studies of the natural products and their analogs.     

尖孢镰刀菌胡麻专化型(Fusarium oxysporum f . sp. lini) ISSR标记聚类分析

结合形态学特征和分子生物学方法对我国尖孢镰刀菌胡麻专化型菌株进行鉴定、聚类分析和遗传变异分析。结合传统分类方法和ITS序列分析,确定6省区96株菌株为尖孢镰刀菌。采用ISSR（简单重复序列区间）分子标记技术对这96株菌株进行分析,12条引物共扩增出800个条带,多态性条带数为797条,多态性为99.62%;在相似性系数为0.88处,96株供试菌株被分为5个类群。聚类结果表明,胡麻枯萎病菌种内存在明显的多态性,且ISSR类群与地理来源存在相关性。     

Growth enhancement of effective microorganisms for bioremediation of crude oil contaminated waters

The bioremediation of polluted groundwater, wastewater aeration pond and biopond sites was investigated using bacteria isolated from these sites located at the oil refinery Terengganu Malaysia. Out of 62 isolates, only 16 isolates from groundwater (8) and wastewater aeration pond (3) and biopond (5) were chosen based on growth medium containing 1% (v/v) Tapis crude oil. Only four isolates; Acinetobacter faecalis, Staphylococcus sp., Pseudomonas putida and Neisseria elongata showed percentage biodegradation of crude oil more than 50% after 5 days using Mineral Salts Medium (MSM). The effect of physical parameters (temperature, pH and agitation) on growth by all four strains showed a maximum growth in MSM medium with 1% Tapis crude oil at 37 degrees C with pH 7 and agitation of 130 rpm.     

河北省藁城花生病毒病的RT-PCR检测及外壳蛋白基因序列分析

采用RT-PCR技术对采自河北省农林科学研究院粮油作物研究所藁城堤上试验基地的12份花生叶片样品进行花生病毒病的检测,结果表明:从表现花叶和矮化症状的10份样品中检测到花生条纹病毒(peanut stripe virus,PStV),检出率高达90%,未检测到花生矮化病毒和黄瓜花叶病毒;对其中2个PStV分离物cp基因序列分析的结果表明,该cp全长864 bp。这两个分离物与已报道的PStV其他株系的cp核苷酸序列相似性分别为94.4%~99.2%和94.7%~99.7%,氨基酸相似性分别为95.5%~99.7%和95.8%~100.0%。PStV cp核苷酸序列构建的系统进化树中,这两个分离物与中国大陆其它分离物及美国分离物亲缘关系较近,而与中国台湾、泰国和越南分离物亲缘关系较远。     

不同产区青稞根部可培养内生固氮菌的多样性研究

为认识青稞内生固氮菌群落组成,丰富内生固氮菌资源,明确产地对青稞内生固氮菌多样性的影响,本研究利用纯培养技术分别对在拉萨、林芝、日喀则栽培的藏青2000根部内生固氮菌进行分离、纯化,并测定各菌株的固氮酶活性及高固氮酶活性菌株的溶磷、溶钾及产IAA特性,最后,通过16SrDNA基因测序和构建系统发育树研究了高固氮酶活性菌株的分类学地位。结果显示,通过Ashby培养基分离、纯化得到内生固氮菌37株,其中,具有高固氮酶活性的11株,占总分离菌株27%,有6株菌株具有分泌IAA的能力,2株具有溶钾能力,1株具有溶磷能力。16S rDNA测序结果表明,11株高固氮酶活性的菌中,有5株菌属于Bacillus,为优势菌属,其余菌株分别属于Gemmatimonas、Sphingomonas、Devosia、Agrobacterium、Mesorhizobium和Burkholderia。     

Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential

The deep-sea constitutes a true unexplored frontier and a potential source of innovative drug scaffolds. Here, we present the genome sequence of two novel marine actinobacterial strains, MA3_2.13 and S07_1.15, isolated from deep-sea samples (sediments and sponge) and collected at Madeira archipelago (NE Atlantic Ocean; Portugal). The de novo assembly of both genomes was achieved using a hybrid strategy that combines short-reads (Illumina) and long-reads (PacBio) sequencing data. Phylogenetic analyses showed that strain MA3_2.13 is a new species of the Streptomyces genus, whereas strain S07_1.15 is closely related to the type strain of Streptomyces xinghaiensis. In silico analysis revealed that the total length of predicted biosynthetic gene clusters (BGCs) accounted for a high percentage of the MA3_2.13 genome, with several potential new metabolites identified. Strain S07_1.15 had, with a few exceptions, a predicted metabolic profile similar to S. xinghaiensis. In this work, we implemented a straightforward approach for generating high-quality genomes of new bacterial isolates and analyse in silico their potential to produce novel NPs. The inclusion of these in silico dereplication steps allows to minimize the rediscovery rates of traditional natural products screening methodologies and expedite the drug discovery process.     

春季油樟可培养内生真菌多样性及产黄酮功能初筛

为开发油樟内生菌资源并发现潜在活性成分,本研究以春季油樟健康植株的根、茎、叶为材料,采用组织培养法分离纯化可培养内生真菌,结合ITS序列和系统发育树分析菌株多样性,筛选具有产黄酮功能菌株,设计单因素和正交试验优化产黄酮效果最佳菌株的发酵条件。结果表明：从油樟中共分离到62株可培养内生真菌,划分为3门、7纲、14目、22科、28属、54种。其中优势门为子囊菌门（Ascomycota,RF为88.71%）,优势纲为座囊菌纲（Dothideomycetes,RF为45.16%）,优势目为格孢腔菌目（Pleosporales,RF为37.10%）,优势科为格孢菌科（Pleosporineae,RF为14.52%）、亚隔孢壳科（Didymellaceae,RF为12.90%）,优势属为链格孢属（Alternaria,RF为12.90%）、附球菌属（Epicoccum,RF为11.29%）。以纲为类群单位,根组织分离的16属20种21株真菌的系统发育可分为7个类群,茎分离的13属24种30株真菌则分为2个类群,叶的8属10种11株真菌则分为3个类群。多样性指数和均匀度系数结果表明,油樟根部内生真菌种群多样性相对较丰富,群落分布相对均匀。10株内生真菌具有产黄酮功能,5株来自根部,5株来自于茎部,隶属2门3纲5目8科9属,其中YZ-29菌株产黄酮能力相对较强。YZ-29菌株最优发酵条件为初始pH 7、时间7 d、温度30℃、转速175 r/min、装液量80 mL/150 mL。综上结果显示,内生真菌在油樟不同组织数量、种群及组成上存在差异,分离得到的功能性菌株值得深入挖掘和开发利用,为开展内生真菌在油樟抗氧化成分的生物合成机制方面的研究奠定基础。