Production of plant growth modulating volatiles is widespread among rhizosphere bacteria and strongly depends on culture conditions

Recent studies have suggested that bacterial volatiles play an important role in bacterial-plant interactions. However, few reports of bacterial species that produce plant growth modulating volatiles have been published, raising the question whether this is just an anecdotal phenomenon. To address this question, we performed a large screen of strains originating from the soil for volatile-mediated effects on Arabidopsis thaliana. All of the 42 strains tested showed significant volatile-mediated plant growth modulation, with effects ranging from plant death to a sixfold increase in plant biomass. The effects of bacterial volatiles were highly dependent on the cultivation medium and the inoculum quantity. GC-MS analysis of the tested strains revealed over 130 bacterial volatile compounds. Indole, 1-hexanol and pentadecane were selected for further studies because they appeared to promote plant growth. None of these compounds triggered a typical defence response, using production of ethylene and of reactive oxygen species (ROS) as read-outs. However, when plants were challenged with the flg-22 epitope of bacterial flagellin, a prototypical elicitor of defence responses, additional exposure to the volatiles reduced the flg-22-induced production of ethylene and ROS in a dose-dependent manner, suggesting that bacterial volatiles may act as effectors to inhibit the plant's defence response.     

Fermentative production of self-toxic fungal secondary metabolites

Fungi are well known for their vast diversity of secondary metabolites that include many life-saving drugs and highly toxic mycotoxins. In general, fungal cultures producing such metabolites are immune to their toxic effects. However, some are known to produce self-toxic compounds that can pose production optimization challenges if the metabolites are needed in large amounts for chemical modification. One such culture, LV-2841, was identified as the lead for one of our exploratory projects. This culture was found to be a slow grower that produced trace amounts of a known metabolite, cercosporamide, under the standard flask fermentation conditions, and extensive medium optimization studies failed to yield higher titers. Poor growth of the culture in liquid media was attributed to the self-toxicity of cercosporamide to the producing organism, and the minimum inhibitory concentration (MIC) of cercosporamide was estimated to be in the range of 8–16 μg/ml. Fermentations carried out in media containing Diaion^® HP20 resin afforded significantly higher titers of the desired compound. While several examples of resin-based fermentations of soil streptomyces have been published, this approach has rarely been used for fungal fermentations. Over a 100-fold increase in the production titer of cercosporamide, a self-toxic secondary metabolite, was achieved by supplementing the production medium with a commercially available neutral adsorbent resin.     

Verticillium dahliae VdBre1 is required for cotton infection by modulating lipid metabolism and secondary metabolites

The soil-borne ascomycete Verticillium dahliae causes wilt disease in more than two hundred dicotyledonous plants including the economically important crop cotton, and results in a severe reduction in cotton fiber yield and quality. During infection, V. dahliae secretes numerous secondary metabolites, which act as toxic factors to promote the infection process. However, the mechanism underlying how V. dahliae secondary metabolites regulate cotton infection remains largely unexplored. In this study, we report that VdBre1, an ubiquitin ligase (E3) enzyme to modify H2B, regulates radial growth and conidia production of V. dahliae. The VdBre1 deletion strains show nonpathogenic symptoms on cotton, and microscopic inspection and penetration assay indicated that penetration ability of the ∆VdBre1 strain was dramatically reduced. RNA-seq revealed that a total of 1643 differentially expressed genes between the ∆VdBre1 strain and the wild type strain V592, among which genes related to lipid metabolism were significantly overrepresented. Remarkably, the volume of lipid droplets in the ∆VdBre1 conidia was shown to be smaller than that of wild-type strains. Further metabolomics analysis revealed that the pathways of lipid metabolism and secondary metabolites, such as steroid biosynthesis and metabolism of terpenoids and polyketides, have dramatically changed in the ∆VdBre1 metabolome. Taken together, these results indicate that VdBre1 plays crucial roles in cotton infection and pathogenecity, by globally regulating lipid metabolism and secondary metabolism of V. dahliae.     

Vertical transmission of fungal endophytes is widespread in forbs

To date, it has been thought that endophytic fungi in forbs infect the leaves of their hosts most commonly by air‐borne spores (termed “horizontal transmission”). Here, we show that vertical transmission from mother plant to offspring, via seeds, occurs in six forb species (Centaurea cyanus, C. nigra, Papaver rhoeas, Plantago lanceolata, Rumex acetosa, and Senecio vulgaris), suggesting that this may be a widespread phenomenon. Mature seeds were collected from field‐grown plants and endophytes isolated from these, and from subsequent cotyledons and true leaves of seedlings, grown in sterile conditions. Most seeds contain one species of fungus, although the identity of the endophyte differs between plant species. Strong evidence for vertical transmission was found for two endophyte species, Alternaria alternata and Cladosporium sphaerospermum. These fungi were recovered from within seeds, cotyledons, and true leaves, although the plant species they were associated with differed. Vertical transmission appears to be an imperfect process, and germination seems to present a bottleneck for fungal growth. We also found that A. alternata and C. sphaerospermum occur on, and within pollen grains, showing that endophyte transmission can be both within and between plant generations. Fungal growth with the pollen tube is likely to be the way in which endophytes enter the developing seed. The fact that true vertical transmission seems common suggests a more mutualistic association between these fungi and their hosts than has previously been thought, and possession of endophytes by seedling plants could have far‐reaching ecological consequences. Seedlings may have different growth rates and be better protected against herbivores and pathogens, dependent on the fungi that were present in the mother plant. This would represent a novel case of trans‐generational resistance in plants.     

真菌次生代谢产物多样性及其潜在应用价值

从生物间的协同进化和微生物次生代谢产物的功能意义原理出发,本文侧重介绍了与植物和昆虫密切相关的一些真菌及其次生代谢产物在医药和农用新药物开发应用中的潜在价值。     

Evolution of bacterial and fungal growth media

Microbial media has undergone several changes since its inception but some key challenges remain. In recent years, there has beenexploration of several alternative nutrient sources, both to cater to the specificity in requirement of growth of “fussymicroorganisms” and also to reduce costs for large-scale fermentation that is required for biotechnology. Our mini-review exploresthese developments and also points at lacunas in the present areas of exploration, such as a lack of concerted effort in pH andosmolarity regulation. We hope that our commentary provides direction for future research in microbial media.     

Preservation of secondary fungal metabolites in herbarium lichen specimens

Fresh picked and herbarium thalli of Cladonia stellaris, C. rangiferina, Allocetraria nivalis, A. cucullata, Cetraria islandica, Peltigera canina, and Nephroma articum epigene lichens were studied using the immune-enzyme analysis. No big difference was observed in the contents of mycotoxin secondary metabolites, i.e., deoxynivalenol, diacetoxyscirpenol, zearalenone, alternariol, citrinin, sterigmatocystin, cyclopiazonic acid, mycophenolic acid, emodin, and PR-toxin. The discovery of these substances in the specimens preserved for several decades shows that lichens have an effective system of conservation of metabolic exchange products.     

Regulation of secondary metabolism in streptomycetes

While the biological functions of most of the secondary metabolites made by streptomycetes are not known, it is inconceivable that they do not play an adaptive ecological role. The biosynthesis of secondary metabolites under laboratory conditions usually occurs in a growth phase or developmentally controlled manner, but is also influenced by a wide variety of environmental and physiological signals, presumably reflecting the range of conditions that trigger their production in nature. The expression of secondary metabolic gene clusters is controlled by many different families of regulatory proteins, some of which are found only in actinomycetes, and is elicited by both extracellular and intracellular signalling molecules. The application of a variety of genetic and molecular approaches is now beginning to reveal fascinating insights into the complex regulatory cascades that govern this process.     

Vanadate inhibits the production and/or release of secondary metabolites without impairing growth in several fungal species

Vanadate (NaVO₃) in concentrations between 0.1–3.0 mmol/L inhibited the production of secondary metabolites (SMs) of strains of the following species:Trichoderma viride, Penicillium purpurogenum, Penicillium citrinum, Talaromyces avellaneus, andVerticillium psalliotœ. Growth was either not affected by NaVO₃, or the inhibition of the SM production occurred at lower NaVO₃, concentrations than that of the growth. Thus, at some NaVO₃ concentration the SM production was inhibited but the growth remained unaffected. The results suggest that NaVO₃ exerts a specific action either on the SM biosynthetic pathway(s) or on the export of SMs from cells.     

Manipulation of fungal development as source of novel secondary metabolites for biotechnology

Fungal genomics revealed a large potential of yet-unexplored secondary metabolites, which are not produced during vegetative growth. The discovery of novel bioactive compounds is increasingly gaining importance. The high number of resistances against established antibiotics requires novel drugs to counteract increasing human and animal mortality rates. In addition, growth of plant pathogens has to be controlled to minimize harvest losses. An additional critical issue is the post-harvest production of deleterious mycotoxins. Fungal development and secondary metabolite production are linked processes. Therefore, molecular regulators of development might be suitable to discover new bioactive fungal molecules or to serve as targets to control fungal growth, development, or secondary metabolite production. The fungal impact is relevant as well for our healthcare systems as for agriculture. We propose here to use the knowledge about mutant strains discovered in fungal model systems for a broader application to detect and explore new fungal drugs or toxins. As examples, mutant strains impaired in two conserved eukaryotic regulatory complexes are discussed. The COP9 signalosome (CSN) and the velvet complex act at the interface between development and secondary metabolism. The CSN is a multi-protein complex of up to eight subunits and controls the activation of CULLIN-RING E3 ubiquitin ligases, which mark substrates with ubiquitin chains for protein degradation by the proteasome. The nuclear velvet complex consists of the velvet-domain proteins VeA and VelB and the putative methyltransferase LaeA acting as a global regulator for secondary metabolism. Defects in both complexes disturb fungal development, light perception, and the control of secondary metabolism. The potential biotechnological relevance of these developmental fungal mutant strains for drug discovery, agriculture, food safety, and human healthcare is discussed.     

细菌肥料Agr、PfPt和Mic对曼地亚红豆杉幼苗生长和次生代谢物含量的影响

运用单因素随机区组设计,在田间栽培条件下,对曼地亚红豆杉(Taxus media Rehder)1年生幼苗施用3种细菌肥料﹝放射性土壤杆菌肥料(Agr)、荧光假单胞菌肥料(PfPt)和微球菌肥料(Mic),浓度为2×107 CFU·mL-1,施肥2次﹞,对翌年生长期幼苗株高和冠幅的增长量变化以及枝叶中4种次生代谢物﹝紫杉醇、三尖杉宁碱、10-去乙酰紫杉醇和10-去乙酰基巴卡亭Ⅲ(10-DAB Ⅲ)﹞含量进行比较分析。结果表明：施用Agr、Mic和PfPt后的翌年11月份,曼地亚红豆杉幼苗株高和冠幅的增长量均大于CK(不施肥,对照)组,其中,施用PfPt后幼苗株高增长量最大,且显著高于CK组(P<0.05);施用Mic后幼苗的冠幅增长量最大,但与CK组间无显著差异(P>0.05)。施用Agr、Mic和PfPt后枝叶中紫杉醇、三尖杉宁碱和10-DABⅢ含量均显著高于CK组,其中,施用Mic后紫杉醇含量最高,施用PfPt后三尖杉宁碱和10-DAB Ⅲ含量最高,且总体上显著高于其他处理组;施用Mic后10-去乙酰紫杉醇含量最高,且显著高于CK组及其他处理组,而施用Agr和PfPt后10-去乙酰紫杉醇含量与CK组无显著差异。研究结果显示：施用Agr、Mic和PfPt均对曼地亚红豆杉幼苗生长以及枝叶中次生代谢物积累有一定的促进作用,但不同细菌肥料的促进效应存在差异,因此,在曼地亚红豆杉的栽培过程中应根据不同需求选择适宜的细菌肥料。     

Production of plant secondary metabolites without plants: a perspective

Efforts to commercially exploit native plant secondary metabolite production patterns in cell culture systems have been largely thwarted by the repression of secondary metabolism under growth-oriented culture conditions. Where expression can be obtained by selection or elicitation, the difficulties of large scale cultivation/processing still make the cost effectiveness of cell culture systems dubious except where a very high value market niche can be identified.

The long range prospect for efficiently utilizing the catalytic genius of higher plants resides in the transfer of appropriate genetic information to microbial systems for whom the fermentation expertise and industrial facilities already exist.     

Occurrence of indole alkaloids among secondary metabolites of soil Aspergillus

The occurrence of indole alkaloids among secondary fungal metabolites was studied in species of the genus Aspergillus, isolated from soils that were sampled in various regions of Russia (a total of 102 isolates of the species A. niger, A. phoenicis, A. fumigatus, A. flavus, A. versicolor, A. ustus, A. clavatus, and A. ochraceus). Clavine alkaloids were represented by fumigaclavine, which was formed by A. fumigatus. alpha-Cyclopiazonic acid was formed by isolates of A. fumigatus, A. flavus, A. versicolor, A. phoenicis, and A. clavatus. The occurrence of indole-containing diketopiperazine alkaloids was documented for isolates of A. flavus, A. fumigatus, A. clavatus, and A. ochraceus. No indole-containing metabolites were found among the metabolites of A. ustus or A. niger.     

Production of acyl-homoserine lactone quorum-sensing signals is widespread in gram-negative Methylobacterium

Members of Methylobacterium, referred as pink-pigmented facultative methylotrophic bacteria, are frequently associated with terrestrial and aquatic plants, tending to form aggregates on the phyllosphere. We report here that the production of autoinducer molecules involved in the cell-to-cell signaling process, which is known as quorum sensing, is common among Methylobacterium species. Several strains of Methylobacterium were tested for their ability to produce N-acyl-homoserine lactone (AHL) signal molecules using different indicators. Most strains of Methylobacterium tested could elicit a positive response in Agrobacterium tumefaciens harboring lacZ fused to a gene that is regulated by autoinduction. The synthesis of these compounds was cell-density dependent, and the maximal activity was reached during the late exponential to stationary phases. The bacterial extracts were separated by thin-layer chromatography and bioassayed with A. tumefaciens NT1 (traR, tra::lacZ749). They revealed the production of various patterns of the signal molecules, which are strain dependent. At least two signal molecules could be detected in most of the strains tested, and comparison of their relative mobilities suggested that they are homologs of N-octanoyl-DL-homoserine lactone (C8-HSL) and N-decanoyl-DL-homoserine lactone (C10-HSL).     

Production of SacI and SacII isoschizomers by soil streptomycetes

Five fresh soil Streptomyces spp. strains were isolated, phylogenetically characterized on the basis of 16S rDNA sequences and analyzed for the presence of restriction modification systems. Three type II site-specific endonucleases were detected and partially purified. Two isolated enzymes were isoschizomers of SacI restriction endonuclease recognizing 5′-GAGCTC-3′ sequence; the third one recognised 5′-CCGCGG-3′ sequence and it was an isoschizomer of SacII. SacII like modification was observed in other two isolates having no detectable restriction activity. The lack of correlation between restriction and modification phenotypes and phylogenetic classification of the isolates indicates efficient gene transfer mechanism in the Streptomyces genus.     

Production of useful secondary metabolites in plants: Functional genomics approaches

The paradigm of biological research has been changed by recent developments in genomics, high-throughput biology, and bioinformatics. Conventional biology often was based on empirical, labor-intensive, and time-consuming methods. In the new paradigm, biological research e is driven by a holistic approach on the basis of rational, automatic, and high-throughput methods. New functional compounds can be discovered by using high-throughput screening systems. Secondary metabolite pathways and the genes involved in those pathways are then determined by studying functional genomics in conjunction with the data-mining tools of bioinformatics. In addition, these advances in metabolic engineering enable researchers to confer new secondary metabolic pathways to crops by transferring three to five, or more, heterologous genes taken from various other species. In the future, engineering for the production of useful compounds will be designed by a set of software tools that allows the user to specify a cell’s genes, proteins, and other molecules, as well as their individual interactions.     

Mechanisms of soil bacterial and fungal community assembly differ among and within islands

The study of islands has made substantial contributions to the development of evolutionary and ecological theory. However, we know little about microbial community assembly on islands. Using soil microbial data collected from 29 lake islands and nearby mainland, we examined the assembly mechanisms of soil bacterial and fungal communities among and within islands. We found that deterministic processes, especially homogeneous selection, tended to be more important in shaping the assembly of soil bacterial communities among islands, while stochastic processes tended to be more important within islands. Moreover, increasing island area increased the importance of homogeneous selection, but reduced the importance of variable selection, for soil bacterial community assembly within islands. By contrast, stochastic processes tended to dominate soil fungal community assembly both among and within islands, with dispersal limitation playing a more important role within than among islands. Our results highlight the scale- and taxon-dependence of insular soil microbial community assembly, suggesting that spatial scale should be explicitly considered when evaluating the influences of habitat fragmentation on soil microbial communities.