Oleaginous Microbial Lipids' Potential in the Prevention and Treatment of Neurological Disorders

The products of oleaginous microbes, primarily lipids, have gained tremendous attention for their health benefits in food-based applications as supplements. However, this emerging biotechnology also offers a neuroprotective treatment/management potential for various diseases that are seldom discussed. Essential fatty acids, such as DHA, are known to make up the majority of brain phospholipid membranes and are integral to cognitive function, which forms an important defense against Alzheimer's disease. Omega-3 polyunsaturated fatty acids have also been shown to reduce recurrent epilepsy seizures and have been used in brain cancer therapies. The ratio of omega-3 to omega-6 PUFAs is essential in maintaining physiological function. Furthermore, lipids have also been employed as an effective vehicle to deliver drugs for the treatment of diseases. Lipid nanoparticle technology, used in pharmaceuticals and cosmeceuticals, has recently emerged as a biocompatible, biodegradable, low-toxicity, and high-stability means for drug delivery to address the drawbacks associated with traditional medicine delivery methods. This review aims to highlight the dual benefit that lipids offer in maintaining good health for disease prevention and in the treatment of neurological diseases.

Development of sustainable downstream processing for nutritional oil production

Nutritional oils (mainly omega-3 fatty acids) are receiving increased attention as critical supplementary compounds for the improvement and maintenance of human health and wellbeing. However, the predominant sources of these oils have historically shown numerous limitations relating to desirability and sustainability; hence the crucial focus is now on developing smarter, greener, and more environmentally favourable alternatives. This study was undertaken to consider and assess the numerous prevailing and emerging techniques implicated across the stages of fatty acid downstream processing. A structured and critical comparison of the major classes of disruption methodology (physical, chemical, thermal, and biological) is presented, with discussion and consideration of the viability of new extraction techniques. Owing to a greater desire for sustainable industrial practices, and a desperate need to make nutritional oils more available; great emphasis has been placed on the discovery and adoption of highly sought-after 'green' alternatives, which demonstrate improved efficiency and reduced toxicity compared to conventional practices. Based on these findings, this review also advocates new forays into application of novel nanomaterials in fatty acid separation to improve the sustainability of nutritional oil downstream processing. In summary, this review provides a detailed overview of the current and developing landscape of nutritional oil; and concludes that adoption and refinement of these sustainable alternatives could promptly allow for development of a more complete 'green' process for nutritional oil extraction; allowing us to better meet worldwide needs without costing the environment.

Cytobacts: Abundant and Diverse Vertically Seed-Transmitted Cultivation-Recalcitrant Intracellular Bacteria Ubiquitous to Vascular Plants

We have recently described ‘Cytobacts’ as abundant intracellular endophytic bacteria inhabiting live plant cells based on the observations with callus and cell suspension cultures of grapevine and other plant species with the origin ascribable to field explants. In this study, we investigated the prevalence of such cytoplasmic bacterial associations in field plants across different taxa, their cultivability, and the extent of taxonomic diversity and explored the possibility of their embryo-mediated vertical transmission. Over 100 genera of field plants were surveyed for ‘Cytobacts’ through bright-field live-cell imaging as per our previous experience using fresh tissue sections from surface-sterilized shoot-tissues with parallel cultivation-based assessments. This revealed widespread cellular bacterial associations visualized as copious motile micro-particles in the cytoplasm with no or sparse colony forming units (CFU) from the tissue-homogenates indicating their general non-cultivability. Based on the ease of detection and the abundance of ‘Cytobacts’ in fresh tissue sections, the surveyed plants were empirically classified into three groups: (i) motile bacteria detected instantly in most cells; (ii) motility not so widely observed, but seen in some cells; and (iii) only occasional motile units observed, but abundant non-motile bacterial cells present. Microscopy versus 16S-rRNA V3–V4 amplicon profiling on shoot-tip tissues of four representative plants—tomato, watermelon, periwinkle, and maize—showed high bacterial abundance and taxonomic diversity (11–15 phyla) with the dominance of Proteobacteria followed by Firmicutes/Actinobacteria, and several other phyla in minor shares. The low CFU/absence of bacterial CFU from the tissue homogenates on standard bacteriological media endorsed their cultivation-recalcitrance. Intracellular bacterial colonization implied that the associated organisms are able to transmit vertically to the next generation through the seed-embryos. Microscopy and 16S-rRNA V3–V4 amplicon/metagenome profiling of mature embryos excised from fresh watermelon seeds revealed heavy embryo colonization by diverse bacteria with sparse or no CFU. Observations with grapevine fresh fruit-derived seeds and seed-embryos endorsed the vertical transmission by diverse cultivation-recalcitrant endophytic bacteria (CREB). By and large, Proteobacteria formed the major phylum in fresh seed-embryos with varying shares of diverse phyla. Thus, we document ‘Cytobacts’ comprising diverse and vertically transmissible CREBs as a ubiquitous phenomenon in vascular plants.

Factors affecting the isolation and diversity of marine sponge-associated bacteria

Abstract

Marine sponges are an ideal source for isolating as yet undiscovered microorganisms with some sponges having about 50% of their biomass composed of microbial symbionts. This study used a variety of approaches to investigate the culturable diversity of the sponge-associated bacterial community from samples collected from the South Australian marine environment. Twelve sponge samples were selected from two sites and their bacterial population cultivated using seven different agar media at two temperatures and three oxygen levels over 3 months. These isolates were identified using microscopic, macroscopic, and 16S rRNA gene analysis. A total of 1234 bacterial colonies were isolated which consisted of four phyla: Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes, containing 21 genera. The diversity of the bacterial population was demonstrated to be influenced by the type of isolation medium, length of the incubation period and temperature, sponge type, and oxygen level. The findings of this study showed that marine sponges of South Australia can yield considerable bacterial culturable diversity if a comprehensive isolation strategy is implemented. Two sponges, with the highest and the lowest diversity of culturable isolates, were examined using next-generation sequencing to better profile the bacterial population. A marked difference in terms of phyla and genera was observed using culture-based and culture-independent approaches. This observed variation displays the importance of utilizing both methods to reflect a more complete picture of the microbial population of marine sponges.

Key points

Improved bacterial diversity due to long incubations, 2 temperatures, and 3 oxygen levels.

Isolates identified by morphology, restriction digests, and 16S rRNA gene sequencing.

At least 70% of culturable genera were not revealed by NGS methods.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-11791-8.

Intracellular Bacteria in Plants: Elucidation of Abundant and Diverse Cytoplasmic Bacteria in Healthy Plant Cells Using In Vitro Cell and Callus Cultures

This study was initiated to assess whether the supposedly axenic plant cell cultures harbored any cultivation-recalcitrant endophytic bacteria (CREB). Adopting live-cell imaging with bright-field, fluorescent and confocal microscopy and bacterial 16S-rRNA gene taxonomic profiling, we report the cytoplasmic association of abundant and diverse CREBs in long-term actively maintained callus and cell suspension cultures of different plant species. Preliminary bright-field live-cell imaging on grape cell cultures showed abundant intracellular motile micro-particles resembling bacteria, which proved uncultivable on enriched media. Bacterial probing employing DNA stains, transmission electron microscopy, and Eubacterial FISH indicated abundant and diverse cytoplasmic bacteria. Observations on long-term maintained/freshly established callus stocks of different plant species-grapevine, barley, tobacco, Arabidopsis, and medicinal species-indicated intracellular bacteria as a common phenomenon apparently originating from field shoot tissues.Cultivation-independent 16S rRNA gene V3/V3-V4 amplicon profiling on 40-year-old grape cell/callus tissues revealed a high bacterial diversity (>250 genera), predominantly Proteobacteria, succeeded by Firmicutes, Actinobacteria, Bacteriodetes, Planctomycetes, and 20 other phyla, including several candidate phyla. PICRUSt analysis revealed diverse functional roles for the bacterial microbiome, majorly metabolic pathways. Thus, we unearth the widespread association of cultivation-recalcitrant intracellular bacteria "Cytobacts" inhabiting healthy plant cells, sharing a dynamic mutualistic association with cell hosts.

Antimicrobial Activities of Marine Sponge-Associated Bacteria

The misuse and overuse of antibiotics have led to the emergence of multidrug-resistant microorganisms, which decreases the chance of treating those infected with existing antibiotics. This resistance calls for the search of new antimicrobials from prolific producers of novel natural products including marine sponges. Many of the novel active compounds reported from sponges have originated from their microbial symbionts. Therefore, this study aims to screen for bioactive metabolites from bacteria isolated from sponges. Twelve sponge samples were collected from South Australian marine environments and grown on seven isolation media under four incubation conditions; a total of 1234 bacterial isolates were obtained. Of these, 169 bacteria were tested in media optimized for production of antimicrobial metabolites and screened against eleven human pathogens. Seventy bacteria were found to be active against at least one test bacterial or fungal pathogen, while 37% of the tested bacteria showed activity against Staphylococcus aureus including methicillin-resistant strains and antifungal activity was produced by 21% the isolates. A potential novel active compound was purified possessing inhibitory activity against S. aureus. Using 16S rRNA, the strain was identified as Streptomyces sp. Our study highlights that the marine sponges of South Australia are a rich source of abundant and diverse bacteria producing metabolites with antimicrobial activities against human pathogenic bacteria and fungi.

Untapped sponge microbiomes: structure specificity at host order and family levels

Sponges are complex holobionts in which the structure of the microbiome has seldom been characterized above the host species level. The hypothesis tested in this study is that the structure of the sponge microbiomes is specific to the host at the order and family levels. This was done by using 33 sponge species belonging to 19 families representing five orders. A combination of three primer sets covering the V1-V8 regions of the 16S rRNA gene provided a more comprehensive coverage of the microbiomes. Both the diversity and structure of sponge microbiomes were demonstrated to be highly specific to the host phylogeny at the order and family levels. There are always dominant operational taxonomic units (OTUs) (relative abundance >1%) shared between microbial communities of sponges within the same family or order, but these shared OTUs showed high levels of dissimilarity between different sponge families and orders. The unique OTUs for a particular sponge family or order could be regarded as their 'signature identity'. 70%-87% of these unique OTUs (class level) are unaffiliated and represent a vast resource of untapped microbiota. This study contributes to a deeper understanding on the concept of host-specificity of sponge microbiomes and highlights a hidden reservoir of sponge-associated microbial resources.

The antifungal action mode of the rice endophyte Streptomyces hygroscopicus OsiSh-2 as a potential biocontrol agent against the rice blast pathogen

Microbial antagonists and their bioactive metabolites provide one of the best alternatives to chemical pesticides to control crop disease for sustainable agriculture and global food security. The rice endophyte Streptomyces hygroscopicus OsiSh-2, with remarkable antagonistic activity towards the rice blast fungus Magnaporthe oryzae, was reported in our previous study. The present study deciphered the possible direct interaction mode of OsiSh-2 against M. oryzae. An in vitro antibiotic assay for OsiSh-2 culture filtrate revealed strong suppression of mycelial growth, conidial germination and appressorial formation of M. oryzae. Meanwhile, severe morphological and internal abnormalities in M. oryzae hyphae were observed under a scanning electron microscope and transmission electron microscope. Foliar treatment of rice seedlings by OsiSh-2 culture filtrate in the greenhouse and in the field showed 23.5% and 28.3% disease reduction, respectively. Correspondingly, OsiSh-2 culture filtrate could induce disorganized chitin deposition in the cell wall and lowered ergosterol content in the cell membrane of M. oryzae. Additionally, cell wall integrity pathway activation, large cell electrolytes release, reactive oxygen species accumulation and tricarboxylic acid cycle-related enzyme activity changes were found in M. oryzae. All these results suggested that the direct antagonistic activity of OsiSh-2 against M. oryzae may be attributed to damaging the integrity of the cell wall and membrane and disrupting mitochondrial function in the pathogen.

Uncovering the hidden marine sponge microbiome by applying a multi-primer approach

Marine sponges (phylum Porifera) are hosts to microorganisms that make up to 40–60% of the mesohyl volume. The challenge is to characterise this microbial diversity more comprehensively. To accomplish this, a new method was for the first time proposed to obtain sequence coverage of all the variable regions of the 16S rRNA gene to analyze the amplicon-based microbiomes of four representative sponge species belonging to different orders. The five primer sets targeting nine variable regions of the 16S rRNA gene revealed a significant increase in microbiome coverage of 29.5% of phylum level OTUs and 35.5% class level OTUs compared to the community revealed by the commonly used V4 region-specific primer set alone. Among the resulting OTUs, 52.6% and 61.3% were unaffiliated, including candidate OTUs, at the phylum and class levels, respectively, which demonstrated a substantially superior performance in uncovering taxonomic ‘blind spots’. Overall, a more complete sponge microbiome profile was achieved by this multi-primer approach, given the significant improvement of microbial taxonomic coverage and the enhanced capacity to uncover novel microbial taxa. This multi-primer approach represents a fundamental and practical change from the conventional single primer set amplicon-based microbiome approach, and can be broadly applicable to other microbiome studies.

Evaluation of ACC-deaminase-producing rhizobacteria to alleviate water-stress impacts in wheat (Triticum aestivum L.) plants

Application of plant-growth-promoting rhizobacteria (PGPR) is an environmentally sustainable option to reduce the effects of abiotic and biotic stresses on plant growth and productivity. Bacteria isolated from rain-fed agriculture field soils in the Central Himalaya Kumaun region, India, were evaluated for the production of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase. Those producing ACC deaminase in high amounts were evaluated for their potential to improve wheat (Triticum aestivum L.) plant growth under irrigated and water-stress conditions in two glasshouse experiments. Some of the isolates also showed other plant-growth-promoting (PGP) traits, e.g., N₂ fixation, siderophore production, and phosphate solubilization; however, strains with higher ACC deaminase activity showed the greatest effects. These were Variovorax paradoxus RAA3; Pseudomonas spp. DPC12, DPB13, DPB15, DPB16; Achromobacter spp. PSA7, PSB8; and Ochrobactrum anthropi DPC9. In both simulated irrigated and water-stress conditions, a single inoculation of RAA3 and a consortium of DPC9 + DPB13 + DPB15 + DPB16 significantly improved wheat plant growth and foliar nutrient concentrations and caused significant positive changes in antioxidant properties compared with noninoculated plants especially under water stress. These findings imply that PGPB having ACC deaminase activity together with other PGP traits could potentially be effective inoculants to improve the growth of wheat plants in water-stressed rain-fed environments.

A controlled aquarium system and approach to study the role of sponge-bacteria interactions using Aplysilla rosea and Vibrio natriegens

Sponge-bacteria interactions are very important due to their ecological and biological significance. To understand the impact of interactions between sponges and bacteria (both associated with and external to sponges) on sponge-associated microbial diversity, sponge metabolite profiles and bioactivity, we used a controlled aquarium system and designed an experimental approach that allows the study of sponge-bacteria interactions in a well-defined manner. To test the feasibility of this approach, this system was used to study the interaction between a sponge Aplysilla rosea and a marine bacterium commonly found in seawater, Vibrio natriegens. Sponge explants were exposed to V. natriegens, at 5 × 106 cfu/ml, and changes were monitored for 48 hours. Pyro-sequencing revealed significant shifts in microbial communities associated with the sponges after 24 to 48 hours. Both the control (sponge only without added bacteria) and Vibrio-exposed sponges showed a distinct shift in bacterial diversity and abundance with time. Vibrio exposure significantly increased bacterial diversity, the abundance of a number of taxa compared to control sponges. The result experimentally supports the notion of dynamic and concerted responses by the sponge when interacting with a bacterium, and demonstrates the feasibility of using this controlled aquarium system for the study of sponge-bacteria interactions.

Promicromonospora callitridis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized root of an Australian native pine tree

A new strain of the genus Promicromonospora, CAP94T, was isolated from the surface sterilized root of Callitrispreissii (Australian native pine tree). This strain was a Gram-stain-positive, aerobic actinobacterium with hyphae breaking up into fragments which were non-motile, rod-like, coccoid elements. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this isolate as a member of the family Promicromonospora ceae, and most closely to Promicromonospora sukumoe NBRC 14650T (99.4 %), Promicromonospora kroppenstedtii DSM 19349T (99.2 %) and Promicromonosporaaerolata V54AT (99.1 %). Chemotaxonomic data including cell-wall components, major menaquinone and major fatty acids confirmed the affiliation of strain CAP94T to the genus Promicromonospora. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with DNA-DNA hybridization, allowed the genotypic and phenotypic differentiation of strain CAP94T and the closest species with validly published names. The name proposed for the new species is Promicromonospora callitridis sp. nov. The type strain is CAP94T (=DSM 103339T=TBRC 6025T).

Development of a multilocus-based approach for sponge (phylum Porifera) identification: refinement and limitations

For sponges (phylum Porifera), there is no reliable molecular protocol available for species identification. To address this gap, we developed a multilocus-based Sponge Identification Protocol (SIP) validated by a sample of 37 sponge species belonging to 10 orders from South Australia. The universal barcode COI mtDNA, 28S rRNA gene (D3-D5), and the nuclear ITS1-5.8S-ITS2 region were evaluated for their suitability and capacity for sponge identification. The highest Bit Score was applied to infer the identity. The reliability of SIP was validated by phylogenetic analysis. The 28S rRNA gene and COI mtDNA performed better than the ITS region in classifying sponges at various taxonomic levels. A major limitation is that the databases are not well populated and possess low diversity, making it difficult to conduct the molecular identification protocol. The identification is also impacted by the accuracy of the morphological classification of the sponges whose sequences have been submitted to the database. Re-examination of the morphological identification further demonstrated and improved the reliability of sponge identification by SIP. Integrated with morphological identification, the multilocus-based SIP offers an improved protocol for more reliable and effective sponge identification, by coupling the accuracy of different DNA markers.

Acetylated Triterpene Glycosides and Their Biological Activity from Holothuroidea Reported in the Past Six Decades

Sea cucumbers have been valued for many centuries as a tonic and functional food, dietary delicacies and important ingredients of traditional medicine in many Asian countries. An assortment of bioactive compounds has been described in sea cucumbers. The most important and abundant secondary metabolites from sea cucumbers are triterpene glycosides (saponins). Due to the wide range of their potential biological activities, these natural compounds have gained attention and this has led to their emergence as high value compounds with extended application in nutraceutical, cosmeceutical, medicinal and pharmaceutical products. They are characterized by bearing a wide spectrum of structures, such as sulfated, non-sulfated and acetylated glycosides. Over 700 triterpene glycosides have been reported from the Holothuroidea in which more than 145 are decorated with an acetoxy group having 38 different aglycones. The majority of sea cucumber triterpene glycosides are of the holostane type containing a C18 (20) lactone group and either Δ(7(8)) or Δ(9(11)) double bond in their genins. The acetoxy group is mainly connected to the C-16, C-22, C-23 and/or C-25 of their aglycone. Apparently, the presence of an acetoxy group, particularly at C-16 of the aglycone, plays a significant role in the bioactivity; including induction of caspase, apoptosis, cytotoxicity, anticancer, antifungal and antibacterial activities of these compounds. This manuscript highlights the structure of acetylated saponins, their biological activity, and their structure-activity relationships.

Sponge-associated actinobacterial diversity: validation of the methods of actinobacterial DNA extraction and optimization of 16S rRNA gene amplification

Experiments were designed to validate the two common DNA extraction protocols (CTAB-based method and DNeasy Blood & Tissue Kit) used to effectively recover actinobacterial DNA from sponge samples in order to study the sponge-associated actinobacterial diversity. This was done by artificially spiking sponge samples with actinobacteria (spores, mycelia and a combination of the two). Our results demonstrated that both DNA extraction methods were effective in obtaining DNA from the sponge samples as well as the sponge samples spiked with different amounts of actinobacteria. However, it was noted that in the presence of the sponge, the bacterial 16S rRNA gene could not be amplified unless the combined DNA template was diluted. To test the hypothesis that the extracted sponge DNA contained inhibitors, dilutions of the DNA extracts were tested for six sponge species representing five orders. The results suggested that the inhibitors were co-extracted with the sponge DNA, and a high dilution of this DNA was required for the successful PCR amplification for most of the samples. The optimized PCR conditions, including primer selection, PCR reaction system and program optimization, further improved the PCR performance. However, no single PCR condition was found to be suitable for the diverse sponge samples using various primer sets. These results highlight for the first time that the DNA extraction methods used are effective in obtaining actinobacterial DNA and that the presence of inhibitors in the sponge DNA requires high dilution coupled with fine tuning of the PCR conditions to achieve success in the study of sponge-associated actinobacterial diversity.

Streptomyces kebangsaanensis sp. nov., an endophytic actinomycete isolated from an ethnomedicinal plant, which produces phenazine-1-carboxylic acid

A spore-forming streptomycete designated strain SUK12(T) was isolated from a Malaysian ethnomedicinal plant. Its taxonomic position, established using a polyphasic approach, indicates that it is a novel species of the genus Streptomyces. Morphological and chemical characteristics of the strain were consistent with those of members of the genus Streptomyces. Analysis of the almost complete 16S rRNA gene sequence placed strain SUK12(T) in the genus Streptomyces where it formed a distinct phyletic line with recognized species of this genus. The strain exhibited highest sequence similarity to Streptomyces corchorusii DSM 40340(T) (98.2 %) followed by Streptomyces chrestomyceticus NRRL B-3310(T) (98.1 %). The G+C content of the genomic DNA was 74 mol%. Chemotaxonomic data [MK-9(H8) as the major menaquinone; LL-diaminopimelic acid as a component of cell-wall peptidoglycan; C12 : 0, C14 : 0, C15 : 0 and C17 : 1 as the major fatty acids; phospholipid type II] supported the affiliation of strain SUK12(T) to the genus Streptomyces. The results of the phylogenetic analysis and phenotypic data derived from this and previous studies allowed the genotypic and phenotypic differentiation of strain SUK12(T) from the related species of the genus Streptomyces. The DNA-DNA relatedness value between strain SUK12(T) and S. corchorusii DSM 40340(T) is 18.85±4.55 %. Strain SUK12(T) produces phenazine-1-carboxylic acid, known as tubermycin B, an antibacterial agent. It is proposed, therefore, that strain SUK12(T) ( = DSM 42048(T) = NRRL B-24860(T)) be classified in the genus Streptomyces as the type strain of Streptomyces kebangsaanensis sp. nov.

Rational approaches to improving the isolation of endophytic actinobacteria from Australian native trees

In recent years, new actinobacterial species have been isolated as endophytes of plants and shrubs and are sought after both for their role as potential producers of new drug candidates for the pharmaceutical industry and as biocontrol inoculants for sustainable agriculture. Molecular-based approaches to the study of microbial ecology generally reveal a broader microbial diversity than can be obtained by cultivation methods. This study aimed to improve the success of isolating individual members of the actinobacterial population as pure cultures as well as improving the ability to characterise the large numbers obtained in pure culture. To achieve this objective, our study successfully employed rational and holistic approaches including the use of isolation media with low concentrations of nutrients normally available to the microorganism in the plant, plating larger quantities of plant sample, incubating isolation plates for up to 16 weeks, excising colonies when they are visible and choosing Australian endemic trees as the source of the actinobacteria. A hierarchy of polyphasic methods based on culture morphology, amplified 16S rRNA gene restriction analysis and limited sequencing was used to classify all 576 actinobacterial isolates from leaf, stem and root samples of two eucalypts: a Grey Box and Red Gum, a native apricot tree and a native pine tree. The classification revealed that, in addition to 413 Streptomyces spp., isolates belonged to 16 other actinobacterial genera: Actinomadura (two strains), Actinomycetospora (six), Actinopolymorpha (two), Amycolatopsis (six), Gordonia (one), Kribbella (25), Micromonospora (six), Nocardia (ten), Nocardioides (11), Nocardiopsis (one), Nonomuraea (one), Polymorphospora (two), Promicromonospora (51), Pseudonocardia (36), Williamsia (two) and a novel genus Flindersiella (one). In order to prove novelty, 12 strains were characterised fully to the species level based on polyphasic taxonomy. One strain represented a novel genus in the family Nocardioides, and the other 11 strains were accepted as novel species. In summary, the holistic isolation strategies were successful in obtaining significant culturable actinobacterial diversity within Australian native trees that includes rare and novel species.

Promicromonospora endophytica sp. nov., an endophytic actinobacterium isolated from the root of an Australian native Grey Box tree

A novel aerobic actinobacterium, strain EUM 273T, was isolated from the root of a Grey Box tree (Eucalyptus microcarpa Maiden). Cells were Gram-staining-positive with well-developed substrate mycelia which were non-motile and rod-like, with coccoid elements. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed the isolate as a member of the family Promicromonosporaceae that was most closely related to Promicromonospora xylanilytica YIM 61515T (98.2 %) and Promicromonospora vindobonensis V45T (98 %). Chemotaxonomic data including cell wall components, major menaquinone and major fatty acids confirmed the affiliation of strain EUM 273T to the genus Promicromonospora . The results of the phylogenetic analysis, including physiological and biochemical studies in combination with DNA–DNA hybridization, allowed the genotypic and phenotypic differentiation of strain EUM 273T from the closest related species with validly published names. The name proposed for the novel species is Promicromonospora endophytica sp. nov. The type strain is EUM 273T ( = DSM 23716T = NRRL B-24816T).

Actinopolymorpha pittospori sp. nov., an endophyte isolated from surface-sterilized leaves of an apricot tree (Pittosporum phylliraeoides)

A member of the genus Actinopolymorpha, designated PIP 143T, was isolated from the leaves of an Australian native apricot tree (Pittosporum phylliraeoides). The isolate was a Gram-reaction-positive, aerobic actinobacterium, with a well-developed substrate mycelium that fragmented into small rods. Phylogenetic evaluation based on 16S rRNA gene sequences placed the isolate in the family Nocardioidaceae. Strain PIP 143T was most closely related to Actinopolymorpha cephalotaxi I06-2230T (98.7 %) and Actinopolymorpha rutila YIM 45725T (98.1 %). Chemotaxonomic data, including cell-wall components, menaquinones and fatty acids, confirmed the affiliation of strain PIP 143T to the genus Actinopolymorpha. Phylogenetic analysis and physiological and biochemical studies, in combination with DNA–DNA hybridization studies, allowed the differentiation of strain PIP 143T from its closest phylogenetic neighbours with validly published names. Therefore, a novel species is proposed, with the name Actinopolymorpha pittospori sp. nov. The type strain is PIP 143T ( = DSM 45354T  = ACM 5288T  = NRRL B-24810T).

Pseudonocardia eucalypti sp. nov., an endophytic actinobacterium with a unique knobby spore surface, isolated from roots of a native Australian eucalyptus tree

A novel strain, designated EUM 374T, was isolated from the root of a native Australian eucalyptus tree, Eucalyptus microcarpa, and subjected to a range of morphological, phylogenetic and chemotaxonomic analyses. The strain was Gram-reaction-positive with well-developed aerial mycelia, which fragmented into rod-shaped spores that had unique knobby protrusions on the spore surface. Substrate mycelia were not present in the media used. Strain EUM 374T grew as a film on the surface of static liquid culture medium but did not grow under shaking conditions. Phylogenetic evaluation based on 16S rRNA gene sequences identified the new isolate as belonging to the family Pseudonocardiaceae with sequence similarities of 96.1 and 96.3 % to Pseudonocardia acaciae GMKU095T and Pseudonocardia spinosispora LM 141T, respectively, and 93–96 % sequence similarity to other members of the genus Pseudonocardia. The results of comprehensive phylogenetic analyses, including physiological and biochemical tests, differentiated strain EUM 374T from related members of the genus Pseudonocardia. Based on the phenotypic, phylogenetic and chemotaxonomic evidence, strain EUM 374T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia eucalypti sp. nov. is proposed. The type strain is EUM 374T ( = DSM 45351T  = ACM 5285T).

Pseudonocardia adelaidensis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of a grey box tree (Eucalyptus microcarpa)

An aerobic, actinobacterial strain with rod-shaped spores, EUM 221T, which was isolated from the surface-sterilized stem of a grey box tree (Eucalyptus microcarpa), is described. Phylogenetic evaluation based on 16S rRNA gene sequence similarity showed that this isolate belongs to the family Pseudonocardiaceae, with the closest neighbour being Pseudonocardia zijingensis 6330T (98.7 %). The level of 16S rRNA gene sequence similarity between the isolate and species of the genus Pseudonocardia with validly published names ranged from 95 to 98 %. Chemotaxonomic data (meso-diaminopimelic acid; major menaquinone MK-8(H4); major fatty acid iso-C16 : 0) confirmed the affiliation of strain EUM 221T to the genus Pseudonocardia. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with DNA–DNA hybridization, allowed the genotypic and phenotypic differentiation of strain EUM 221T from the closest described species. Therefore, this strain represented a novel species and the name proposed is Pseudonocardia adelaidensis sp. nov. The type strain is EUM 221T (=DSM 45352T =ACM 5286T).

Flindersiella endophytica gen. nov., sp. nov., an endophytic actinobacterium isolated from the root of Grey Box, an endemic eucalyptus tree

A novel endophytic actinobacterium, designated strain EUM 378(T), was isolated from the surface-sterilized root tissue of Eucalyptus microcarpa, a eucalyptus tree known as Grey Box. Phylogenetic evaluation based on 16S rRNA gene sequence analysis, including alignment with taxon-specific 16S rRNA gene signature nucleotides, placed this isolate as a member of the family Nocardioidaceae. Strain EUM 378(T) showed >5.5 % 16S rRNA gene sequence divergence from other members of this family and was related most closely to Actinopolymorpha alba YIM 48868(T) (94.2 %) and Actinopolymorpha singaporensis IM 7744(T) (94.4 %). This Gram-positive, aerobic actinobacterium has well-developed substrate mycelia that fragment into small rods. Chemotaxonomic data revealed that the cell wall contains LL-diaminopimelic acid, ribose, glucose and rhamnose. MK-10(H₆) is the predominant menaquinone. Chemotaxonomic and phylogenetic evidence confirmed that strain EUM 378(T) represents a novel species of a new genus, for which the name Flindersiella endophytica gen. nov., sp. nov. is proposed. The type strain is EUM 378(T) ( = DSM 45355(T) = ACM 5289(T)).

Nocardia callitridis sp. nov., an endophytic actinobacterium isolated from a surface-sterilized root of an Australian native pine tree

A novel actinobacterium strain, CAP 290T, was isolated from a surface-sterilized root of an Australian native pine tree, Callitris preissii. Comparative 16S rRNA gene sequence analysis showed that the strain belongs to the family Nocardiaceae. Strain CAP 290T was most closely related to Nocardia nova JCM 6044T (97.4 % 16S rRNA gene sequence similarity) and Nocardia terpenica IFM 0706T (96.7 %); similarity to other type strains of the genus Nocardia ranged from 95 to 97 %. Chemotaxonomic data [meso-diaminopimelic acid, major menaquinone MK-8(H4ωcycl.), major fatty acid C16 : 0 and mycolate in the cell wall] confirmed the affiliation of strain CAP 290T to the genus Nocardia. The results of the phylogenetic analysis, together with the physiological and biochemical tests, allowed the differentiation of strain CAP 290T from strains of other Nocardia species. Therefore, strain CAP 290T represents a novel species, the first endophytic actinobacterium to be identified as belonging to the genus Nocardia, for which the name Nocardia callitridis sp. nov. is proposed. The type strain is strain CAP 290T (=DSM 45353T =ACM 5287T).

Endophytic actinobacteria induce defense pathways in Arabidopsis thaliana

Endophytic actinobacteria, isolated from healthy wheat tissue, which are capable of suppressing a number wheat fungal pathogens both in vitro and in planta, were investigated for the ability to activate key genes in the systemic acquired resistance (SAR) or the jasmonate/ethylene (JA/ET) pathways in Arabidopsis thaliana. Inoculation of A. thaliana (Col-0) with selected endophytic strains induced a low level of SAR and JA/ET gene expression, measured using quantitative polymerase chain reaction. Upon pathogen challenge, endophyte-treated plants demonstrated a higher abundance of defense gene expression compared with the non-endophyte-treated controls. Resistance to the bacterial pathogen Erwinia carotovora subsp. carotovora required the JA/ET pathway. On the other hand, resistance to the fungal pathogen Fusarium oxysporum involved primarily the SAR pathway. The endophytic actinobacteria appear to be able to "prime" both the SAR and JA/ET pathways, upregulating genes in either pathway depending on the infecting pathogen. Culture filtrates of the endophytic actinobacteria were investigated for the ability to also activate defense pathways. The culture filtrate of Micromonospora sp. strain EN43 grown in a minimal medium resulted in the induction of the SAR pathway; however, when grown in a complex medium, the JA/ET pathway was activated. Further analysis using Streptomyces sp. strain EN27 and defense-compromised mutants of A. thaliana indicated that resistance to E. carotovora subsp. carotovora occurred via an NPR1-independent pathway and required salicylic acid whereas the JA/ET signaling molecules were not essential. In contrast, resistance to F. oxysporum mediated by Streptomyces sp. strain EN27 occurred via an NPR1-dependent pathway but also required salicylic acid and was JA/ET independent.

Effect of microbial inoculants on the indigenous actinobacterial endophyte population in the roots of wheat as determined by terminal restriction fragment length polymorphism

The effect of single actinobacterial endophyte seed inoculants and a mixed microbial soil inoculant on the indigenous endophytic actinobacterial population in wheat roots was investigated by using the molecular technique terminal restriction fragment length polymorphism (T-RFLP). Wheat was cultivated either from seeds coated with the spores of single pure actinobacterial endophytes of Microbispora sp. strain EN2, Streptomyces sp. strain EN27, and Nocardioides albus EN46 or from untreated seeds sown in soil with and without a commercial mixed microbial soil inoculant. The endophytic actinobacterial population within the roots of 6-week-old wheat plants was assessed by T-RFLP. Colonization of the wheat roots by the inoculated actinobacterial endophytes was detected by T-RFLP, as were 28 to 42 indigenous actinobacterial genera present in the inoculated and uninoculated plants. The presence of the commercial mixed inoculant in the soil reduced the endophytic actinobacterial diversity from 40 genera to 21 genera and reduced the detectable root colonization by approximately half. The results indicate that the addition of a nonadapted microbial inoculum to the soil disrupted the natural actinobacterial endophyte population, reducing diversity and colonization levels. This was in contrast to the addition of a single actinobacterial endophyte to the wheat plant, where the increase in colonization level could be confirmed even though the indigenous endophyte population was not adversely affected.

Analysis of the endophytic actinobacterial population in the roots of wheat (Triticum aestivum L.) by terminal restriction fragment length polymorphism and sequencing of 16S rRNA clones

The endophytic actinobacterial population in the roots of wheat grown in three different soils obtained from the southeast part of South Australia was investigated by terminal restriction fragment length polymorphism (T-RFLP) analysis of the amplified 16S rRNA genes. A new, validated approach was applied to the T-RFLP analysis in order to estimate, to the genus level, the actinobacterial population that was identified. Actinobacterium-biased primers were used together with three restriction enzymes to obtain terminal restriction fragments (TRFs). The TRFs were matched to bacterial genera by the T-RFLP Analysis Program, and the data were analyzed to validate and semiquantify the genera present within the plant roots. The highest diversity and level of endophytic colonization were found in the roots of wheat grown in a dark loam from Swedes Flat, and the lowest were found in water-repellent sand from Western Flat. This molecular approach detected a greater diversity of actinobacteria than did previous culture-dependent methods, with the predominant genera being Mycobacterium (21.02%) in Swedes Flat, Streptomyces (14.35%) in Red Loam, and Kitasatospora (15.02%) in Western Flat. This study indicates that the soil that supported a higher number of indigenous organisms resulted in wheat roots with higher actinobacterial diversity and levels of colonization within the plant tissue. Sequencing of 16S rRNA clones, obtained using the same actinobacterium-biased PCR primers that were used in the T-RFLP analysis, confirmed the presence of the actinobacterial diversity and identified a number of Mycobacterium and Streptomyces species.

Isolation and identification of actinobacteria from surface-sterilized wheat roots

This is the first report of filamentous actinobacteria isolated from surface-sterilized root tissues of healthy wheat plants (Triticum aestivum L.). Wheat roots from a range of sites across South Australia were used as the source material for the isolation of the endophytic actinobacteria. Roots were surface-sterilized by using ethanol and sodium hypochlorite prior to the isolation of the actinobacteria. Forty-nine of these isolates were identified by using 16S ribosomal DNA (rDNA) sequencing and found to belong to a small group of actinobacterial genera including Streptomyces, Microbispora, Micromonospora, and Nocardiodes spp. Many of the Streptomyces spp. were found to be similar, on the basis of their 16S rDNA gene sequence, to Streptomyces spp. that had been isolated from potato scabs. In particular, several isolates exhibited high 16S rDNA gene sequence homology to Streptomyces caviscabies and S. setonii. None of these isolates, nor the S. caviscabies and S. setonii type strains, were found to carry the nec1 pathogenicity-associated gene or to produce the toxin thaxtomin, indicating that they were nonpathogenic. These isolates were recovered from healthy plants over a range of geographically and temporally isolated sampling events and constitute an important plant-microbe interaction.

Visualization of an endophytic Streptomyces species in wheat seed

Endophytic filamentous actinobacteria were isolated from surface-sterilized roots of wheat plants. Endophytic colonization of germinating wheat seed was examined using one of these endophytes, Streptomyces sp. strain EN27, tagged with the egfp gene. Endophytic colonization was observed from a very early stage of plant development with colonization of the embryo, endosperm, and emerging radicle.

Complete sequencing and analysis of pEN2701, a novel 13-kb plasmid from an endophytic Streptomyces sp

A 12,855 bp cryptic plasmid was isolated from strains of an endophytic Streptomyces sp. over a wide geographical area in South Australia. This plasmid was completely sequenced and 13 putative ORFs were identified. Two of the ORFs may be involved in the regulation of host plant genes. ORF7 exhibited homology to a plant transcriptional regulatory protein and ORF1 was a homolog of a plant protein synthesis initiation factor. The plasmid appears to use a novel transfer mechanism for a Streptomyces plasmid. Pocks were detected during conjugative transfer and kor but not tra homologs could be identified. This structure and the sequence of the putative Kor protein are similar to the pFQ series of plasmids isolated from Frankia, another endophytic actinomycete.