Testacosides A-D, glycoglycerolipids produced by Microbacterium testaceum isolated from Tedania brasiliensis

Marine bacteria living in association with marine sponges have proven to be a reliable source of biologically active secondary metabolites. However, no studies have yet reported natural products from Microbacterium testaceum spp. We herein report the isolation of a M. testaceum strain from the sponge Tedania brasiliensis. Molecular networking analysis of bioactive pre-fractionated extracts from culture media of M. testaceum enabled the discovery of testacosides A-D. Analysis of spectroscopic data and chemical derivatizations allowed the identification of testacosides A-D as glycoglycerolipids bearing a 1-[α-glucopyranosyl-(1 → 3)-(α-mannopyranosyl)]-glycerol moiety connected to 12-methyltetradecanoic acid for testacoside A (1), 14-methylpentadecanoic acid for testacoside B (2), and 14-methylhexadecanoic acid for testacosides C (3) and D (4). The absolute configuration of the monosaccharide residues was determined by 1H-NMR analysis of the respective diastereomeric thiazolidine derivatives. This is the first report of natural products isolated from cultures of M. testaceum. KEY POINTS: • The first report of metabolites produced by Microbacterium testaceum. • 1-[α-Glucopyranosyl-(1 → 3)-(α-mannopyranosyl)]-glycerol lipids isolated and identified. • Microbacterium testaceum strain isolated from the sponge Tedania brasiliensis.

Discovery of sesquiterpenoids from an actinomycete Crossiella cryophila through genome mining and heterologous expression

Genome mining of the Actinomycete Crossiella cryophila facilitated the discovery of a minimal terpenoid biosynthetic gene cluster of cry consisting of a class I terpene cyclase CryA and a CYP450 monooxygenase CryB. Heterologous expression of cry allowed the isolation and characterization of two new sesquiterpenoids, ent-viridiflorol (1) and cryophilain (2). Notably, cryophilain (2) possesses a 5/7/3-fused tricyclic skeleton bearing a distinctive bridgehead hydroxy group. The combined in vivo and in vitro experiments revealed that CryA, the first ent-viridiflorol terpene cyclase, catalyzes farnesyl diphosphate to form the 5/7/3 sesquiterpene core scaffold and P450 CryB serves as a tailoring enzyme responsible for installing a hydroxy group at the bridgehead carbon.

Resuscitation of baijiu pit mud bacteria based on Rpf protein of Umezawaea beigongshangensis

The pit mud in the Baijiu fermentation cellar is an abundant microbial resource that is closely related to the quality of baijiu. However, many naturally existing species might be in a viable but nonculturable (VBNC) state, posing challenges to the isolation and application of functional species. Herein, a previously isolated strain from baijiu mash, Umezawaea beigongshangensis, was found to contain the rpf gene that encodes resuscitation promotion factor (Rpf). Therefore, the gene was cloned and heterologously expressed, and the recombinant protein (Ub-Rpf 2) was purified. Ub-Rpf 2 was found to significantly promote the growth of resuscitated VBNC state Corynebacterium beijingensis and Sphingomonas beigongshangensis. To determine the resuscitation effect of Ub-Rpf 2 on real ecological samples, the protein was supplemented in pit mud for enrichment culture. Results revealed that specific families and genera were enriched in abundance upon Ub-Rpf 2 incubation, including a new family of Symbiobacteraceae and culturable Symbiobacterium genus. Furthermore, 14 species belonging to 12 genera were obtained in Ub-Rpf 2 treated samples, including a suspected novel species. This study lays a foundation for applying Rpf from U. beigongshangensis to exploit microbial resources in baijiu pit mud.

Simultaneous decarbonization and phosphorus removal by Tetrasphaera elongata with glucose as carbon source under aerobic conditions

Previous researches have recognized the vital role of Tetrasphaera elongata in enhanced biological phosphorus removal systems, but the underlying mechanisms remain under-investigated. To address this issue, this study investigated the metabolic characteristics of Tetrasphaera elongata when utilizing glucose as the sole carbon source. Results showed under aerobic conditions, Tetrasphaera elongata exhibited a glucose uptake rate of 136.6 mg/(L·h) and a corresponding phosphorus removal rate of 8.6 mg P/(L·h). Upregulations of genes associated with the glycolytic pathway and oxidative phosphorylation were observed. Noteworthily, the genes encoding the two-component sensor histidine kinase and response regulator transcription factor exhibited a remarkable 28.3 and 27.4-fold increase compared with the group without glucose. Since these genes play a pivotal role in phosphate-specific transport systems, collectively, these findings shed light on a potential mechanism for simultaneous decarbonization and phosphorus removal by Tetrasphaera elongata under aerobic conditions, providing fresh insights into phosphorus removal from wastewaters.

Oleic-acid functionalized mesoporous silica nanoparticles with a hydroxyapatite core enhanced growth of the hydrocarbon degrader Dietzia maris at oil-water interfaces

Rapid biodegradation of poorly water-soluble hydrocarbons as nonaqueous (oil) phases in contaminated aquatic environments is enabled by attachment of hydrocarbon-degrading bacteria to the oil-water interface. Herein, we report the synthesis of nanoparticles comprising a hydroxyapatite (Ca5(PO4)3(OH)) core encapsulated in a mesoporous silica shell and surface-modified with oleic acid (OA-nHAP@MSN) for targeted binding at the oil-water interface and to supply P to bacteria at the interface. P is an essential and often limiting nutrient for bacteria in hydrocarbon-contaminated environments. In microcosm experiments, where the hydrocarbon-degrading bacteria, Dietzia maris strain NWWC4, and OA-nHAP@MSN were inoculated in mineral media in contact with pure liquid hexadecane (sole C source), there was 419.6-fold growth at the hexadecane-water interface, compared to 31.2-fold in identical, but NP-free microcosms. The continuous release of P from the hydroxyapatite core in OA-nHAP@MSN to water was demonstrated in separate experiments in well mixed batch systems and was found to be pH-sensitive. Environmental Scanning Electron Microscopy showed significantly larger cell aggregates and dense biofilms in the OA-nHAP@MSN-amended systems, compared to NP-free systems. Our results demonstrate a strategy for enhancing oil-spill bioremediation using NPs targeting nutrient supply to hydrocarbon-degrading bacteria at oil-water interfaces.

Biodegradation of 1,4-dioxane in a continuous-flow bioelectrochemical reactor by biofilm of Pseudonocardia dioxanivorans CB1190 and microbial community on conductive carriers

Bioelectrochemical degradation is an environmentally friendly, cost-effective and controllable way of providing electron acceptor to the microorganisms. A two-chamber continuous-flow bioelectrochemical reactor (BER) was developed in this study. The objective was to investigate the potential for enhancing the bioelectrochemical degradation of 1,4-dioxane (DX) by Pseudonocardia dioxanivorans CB1190 (CB1190) and microbial community biofilm on conductive and non-conductive carriers in low potentials (1.0-1.2 V) and currents (<2 mA). In the case of CB1190, biodegradation experiments at 1.0 V did not result in any observable change in DX removal efficiency (32.63 ± 2.48%) compared to the 0.0 V (31.69 ± 2.33%). However, the removal efficiency was much higher at 1.2 V (59.08 ± 0.86%). The higher removal at 1.2 V was attributed to an increase in dissolved oxygen (DO) concentration from 3.77 ± 0.33 mg/L at 0.0 V to 5.40 ± 0.11 mg/L at 1.2 V, which resulted from water electrolysis. In the case of microbial community, on the other hand, DX removal efficiency increased at 1.0 V (30.98 ± 1.10%) compared to 0.0 V (23.40 ± 1.02%) that can be attributed to a simultaneous increase in microbial activity from 2389 ± 118.5 ngATP/mgVSS at 0.0 V to 2942 ± 109 ngATP/mgVSS at 1.0 V. Analysis of the changes in microbial composition indicated enrichment of Alistipes and Lutispora at 1.0 V due to the ability of these genera to directly transfer electrons with conductive surface. On the other hand, no change was observed in the microbial community in the case of non-conductive carriers. Results of this study showed that electro-assisted biodegradation of DX at low potentials is possible through two different mechanisms (oxygen production and direct electron transfer with electrode) which makes this technique flexible and cost-effective. The novelty of this work lies in exploring the use of electrical assistance to enhance the biodegradation of DX in the presence of CB1190 and the microbial community. This study more specifically investigated lower potential than required water electrolysis potential, allowing microorganisms to be stimulated through mechanisms unrelated to oxygen generation.

Development of a CRISPR/Cas9D10A Nickase (nCas9)-Mediated Genome Editing Tool in Streptomyces

Streptomycetes have a strong ability to produce a vast array of bioactive natural products (NPs) widely used in agriculture and veterinary/human medicine. The recently developed CRISPR/Cas9-based genome editing tools have greatly facilitated strain improvement for target NP overproduction as well as novel NP discovery in Streptomyces. However, CRISPR/Cas9 shows high toxicity to the host, limiting its application in many Streptomyces strains with a low DNA transformation efficiency. In this study, we developed a low-toxicity CRISPR/Cas9D10A nickase (nCas9)-based genome editing tool in the model strain Streptomyces coelicolor M145. We showed that in the presence of both targeting sgRNA and Cas proteins, utilization of nCas9 instead of Cas9 significantly reduced the toxicity to the host and greatly enhanced cell survival. Using this tool, we achieved deletion of single genes and gene clusters with efficiencies of 87-100 and 63-87%, and simultaneous deletion of two genes or gene clusters with efficiencies of 47 and 43%, respectively. The editing efficiency of nCas9 is comparable to that of the Cas9-mediated editing tool. Finally, the nCas9-based editing tool was successfully applied for genome editing in the industrial rapamycin-producing strain Streptomyces rapamycinicus, in which CRISPR/Cas9 cannot work well. We achieved the deletion of three tested genes with an efficiency of 27.2-30%. Collectively, the CRISPR/nCas9-based editing tool offers a convenient and efficient genetic modification system for the engineering of streptomycetes, particularly those with low DNA transformation efficiency.

Insights into molecular mechanism of plasticizer biodegradation in Dietzia kunjamensis IITR165 and Brucella intermedia IITR166 isolated from a solid waste dumpsite

AIMS

Isolation of phthalate esters (PAEs) degrading bacteria from a solid waste dumpsite could degrade many plasticizers efficiently and to investigate their degrading kinetics, pathways, and genes.

METHODS AND RESULTS

Based on their 16S rRNA gene sequence the strains were identified as Dietzia kunjamensis IITR165 and Brucella intermedia IITR166, which showed a first-order degradation kinetic model under lab conditions. The quantification of phthalates and their intermediate metabolites identification were done by using ultra-high-performance liquid chromatography (UHPLC) and gas chromatography-tandem mass-spectrometry (GC-MS/MS), respectively. Both the bacteria utilized >99% dibutyl phthalate at a high concentration of 100-400 mg L-1 within 192 h as monitored by UHPLC. GC-MS/MS revealed the presence of metabolites dimethyl phthalate (DMP), phthalic acid (PA), and benzoic acid (BA) during DBP degradation by IITR165 while monobutyl phthalate (MBP) and PA were identified in IITR166. Phthalate esters degrading gene cluster in IITR165 comprised two novel genes coding for carboxylesterase (dkca1) and mono-alkyl phthalate hydrolase (maph), having only 37.47% and 47.74% homology, respectively, with reported phthalate degradation genes, along with the terephthalate dioxygenase system (tphA1, A2, A3, and B). However, IITR166 harbored different gene clusters comprising di-alkyl phthalate hydrolase (dph_bi), and phthalate dioxygenase (ophA, B, and C) genes.

CONCLUSIONS

Two novel bacterial strains, Dietzia kunjamensis IITR165 and Brucella intermedia IITR166, were isolated and found to efficiently degrade DBP at high concentrations. The degradation followed first-order kinetics, and both strains exhibited a removal efficiency of over 99%. Metabolite analysis revealed that both bacteria utilized de-methylation, de-esterification, and decarboxylation steps during degradation.

Microbiome assembly mechanism and functional potential in enhanced biological phosphorus removal system enriched with Tetrasphaera-related polyphosphate accumulating organisms

Tetrasphaera-related polyphosphate accumulating organisms (PAOs) are the key functional guilds for enhanced biological phosphorus removal (EBPR) systems. Their biomass enrichment can be enhanced by the nitrification inhibitor allylthiourea (ATU). However, the underlying assembly mechanism and the functional potential of the EBPR microbiome regulated by ATU are unclear. This study investigates the effect of ATU on microbiome assembly and functional potential by closely following the microbiota dynamics in an EBPR system enriched with Tetrasphaera-related PAOs for 288-days before, during and after ATU addition. The results showed that ATU addition increased microbiota structural similarity and compositional convergence, and enhanced determinism in the assembly of EBPR microbiome. During exposure to ATU, Tetrasphaera-related PAOs were governed by homogeneous selection and the dominant species revealed by 16S rRNA gene-based phylogenetic analysis shifted from clade III to clade I. Meanwhile, ATU supply promoted significant enrichment of functional genes involved in phosphate transport (pit) and polyphosphate synthesis and degradation (ppk1 and ppk2), whereas both Nitrosomonas and ammonia monooxygenase-encoding genes (amoA/B/C) assignable to this group of nitrifying bacteria decreased. Moreover, ATU addition relieved the significant abundance correlation between filamentous bacteria Ca. Promineofilum and denitrifying Brevundimonas (FDR-adjusted P < 0.01), damaging their potential synergic or cooperative interactions, thus weakening their competitiveness against Tetrasphaera-related PAOs. Notably, ATU withdrawn created opportunistic conditions for the unexpected explosive growth and predominance of Thiothrix filaments, leading to a serious bulking event. Our study provides new insights into the microbial ecology of Tetrasphaera-related PAOs in EBPR system, which could guide the establishment of an efficient microbiota for EBPR.

Metabolic engineering of the shikimate pathway in Amycolatopsis strains for optimized glycopeptide antibiotic production

Glycopeptide antibiotics (GPA) consist of a glycosylated heptapeptide backbone enriched in aromatic residues originating from the shikimate pathway. Since the enzymatic reactions within the shikimate pathway are highly feedback-regulated, this raises the question as to how GPA producers control the delivery of precursors for GPA assembly. We chose Amycolatopsis balhimycina, the producer of balhimycin, as a model strain for analyzing the key enzymes of the shikimate pathway. A. balhimycina contains two copies each of the key enzymes of the shikimate pathway, deoxy-d-arabino-heptulosonate-7-phosphate synthase (Dahp) and prephenate dehydrogenase (Pdh), with one pair (Dahpsec and Pdhsec) encoded within the balhimycin biosynthetic gene cluster and one pair (Dahpprim and Pdhprim) in the core genome. While overexpression of the dahpsec gene resulted in a significant (>4-fold) increase in balhimycin yield, no positive effects were observed after overexpression of the pdhprim or pdhsec genes. Investigation of allosteric enzyme inhibition revealed that cross-regulation between the tyrosine and phenylalanine pathways plays an important role. Tyrosine, a key precursor of GPAs, was found to be a putative activator of prephenate dehydratase (Pdt), which catalyzes the first step reaction from prephenate to phenylalanine in the shikimate pathway. Surprisingly, overexpression of pdt in A. balhimycina led to an increase in antibiotic production in this modified strain. In order to demonstrate that this metabolic engineering approach is generally applicable to GPA producers, we subsequently applied this strategy to Amycolatopsis japonicum and improved the production of ristomycin A, which is used in diagnosis of genetic disorders. Comparison of "cluster-specific" enzymes with the isoenzymes from the primary metabolism's pathway provided insights into the adaptive mechanisms used by producers to ensure adequate precursor supply and GPA yields. These insights further demonstrate the importance of a holistic approach in bioengineering efforts that takes into account not only peptide assembly but also adequate precursor supply.

A novel thermostable and salt-tolerant carboxylesterase involved in the initial aerobic degradation pathway for pyrethroids in Glycomyces salinus

The long-term and excessive use of pyrethroid pesticides poses substantial health risks and ecosystem concerns. Several bacteria and fungi have been reported that could degrade pyrethroids. The ester-bond hydrolysis using hydrolases is the initial regulatory metabolic reaction of pyrethroids. However, the thoroughly biochemical characterization of hydrolases involved in this process is limited. Here, a novel carboxylesterase, designated as EstGS1 that could hydrolyze pyrethroid pesticides was characterized. EstGS1 showed low sequence identity (<27.03%) compared to other reported pyrethroid hydrolases and belonged to the hydroxynitrile lyase family that preferred short short-chain acyl esters (C2 to C8). EstGS1 displayed the maximal activity of 213.38 U/mg at 60 °C and pH 8.5 using pNPC2 as substrate, with K_m and V_max were 2.21 ± 0.72 mM and 212.90 ± 41.78 µM/min, respectively. EstGS1 is a halotolerant esterase and remains stable in 5.1 M NaCl. Based on molecular docking and mutational analysis, the catalytic triad of S⁷⁴-D¹⁸¹-H²¹² and three other substrate-binding residues I¹⁰⁸, S¹⁵⁹, and G⁷⁵ are critical for the enzymatic activity of EstGS1. Additionally, 61 and 40 mg/L of deltamethrin and λ-cyhalothrin were hydrolyzed by 20 U of EstGS1 in 4 h. This work presents the first report on a pyrethroid pesticide hydrolase characterized from a halophilic actinobacteria.

Bioaugmentation with Tetrasphaera to improve biological phosphorus removal from anaerobic digestate of swine wastewater

Tetrasphaera-enhanced biological phosphorus removal (T-EBPR) was developed by augmenting conventional EBPR (C-EBPR) with Tetrasphaera to improve phosphorus removal from anaerobic digestate of swine wastewater. At influent total phosphorus (TP) concentrations of 45-55 mg/L, T-EBPR achieved effluent TP concentration of 4.17 ± 1.02 mg/L, 54 % lower than that in C-EBPR (8.98 ± 0.76 mg/L). The enhanced phosphorous removal was presumably due to the synergistic effect of Candidatus Accumulibacter and Tetrasphaera occupying different ecological niches. Bioaugmentation with Tetrasphaera promoted the polyphosphate accumulation metabolism depending more on the glycolysis pathway, as evidenced by an increase in intracellular storage compounds of glycogen and polyhydroxyalkanoates by 0.87 and 0.34 mmol C/L, respectively. The enhanced intracellular storage capacity was coincidentally linked to the increase in phosphorus release and uptake rates by 1.23 and 1.01 times, respectively. These results suggest bioaugmentation with Tetrasphaera could be an efficient way for improved phosphorus removal from high-strength wastewater.

Cloning and Expression of Metagenomic DNA in Streptomyces lividans and Its Subsequent Fermentation for Optimized Production

The choice of an expression system for the metagenomic DNA of interest is of vital importance for the detection of any particular gene or gene cluster. Most of the screens to date have used the Gram-negative bacterium Escherichia coli as a host for metagenomic gene libraries. However, the use of E. coli introduces a potential host bias since only 40% of the enzymatic activities may be readily recovered by random cloning in E. coli. To recover some of the remaining 60%, alternative cloning hosts such as Streptomyces spp. have been used. Streptomycetes are high-GC Gram-positive bacteria belonging to the Actinomycetales and they have been studied extensively for more than 25 years as an alternative expression system. They are extremely well suited for the expression of DNA from other actinomycetes and genomes of high GC content. Furthermore, due to its high innate, extracellular secretion capacity, Streptomyces can be a better system than E. coli for the production of many extracellular proteins. In this article, an overview is given about the materials and methods for growth and successful expression and secretion of heterologous proteins from diverse origin using Streptomyces lividans as a host. More in detail, an overview is given about the protocols of transformation, type of plasmids used and of vectors useful for integration of DNA into the host chromosome, and accompanying cloning strategies. In addition, various control elements for gene expression including synthetic promoters are discussed, and methods to compare their strength are described. Stable and efficient marker-less integration of the gene of interest under the control of the promoter of choice into S. lividans chromosome via homologous recombination using pAMR23A-based system will be explained. Finally, a basic protocol for bench-top bioreactor experiments which can form the start in the production process optimization and up-scaling will be provided.

Research advances of the phosphorus-accumulating organisms of Candidatus Accumulibacter, Dechloromonas and Tetrasphaera: Metabolic mechanisms, applications and influencing factors

Phosphorus-accumulating organisms (PAOs), which harbor metabolic mechanisms for phosphorus removal, are widely applied in wastewater treatment. Recently, novel PAOs and phosphorus removal metabolic pathways have been identified and studied. Specifically, Dechloromonas and Tetrasphaera can remove phosphorus via the denitrifying phosphorus removal and fermentation phosphorus removal pathways, respectively. As the main PAOs in biological phosphorus removal systems, the conventional PAO Candidatus Accumulibacter and the novel PAOs Dechloromonas and Tetrasphaera are thoroughly discussed in this paper, with a specific focus on their phosphorus removal metabolic mechanisms, process applications, community abundance and influencing factors. Dechloromonas can achieve simultaneous nitrogen and phosphorus removal in an anoxic environment through the denitrifying phosphorus removal metabolic pathway, which can further reduce carbon source requirements and aeration energy consumption. The metabolic pathways of Tetrasphaera are diverse, with phosphorus removal occurring in conjunction with macromolecular organics degradation through anaerobic fermentation. A collaborative oxic phosphorus removal pathway between Tetrasphaera and Ca. Accumulibacter, or a collaborative anoxic denitrifying phosphorus removal pathway between Tetrasphaera and Dechloromonas are future development directions for biological phosphorus removal technologies, which can further reduce carbon source and energy consumption while achieving enhanced phosphorus removal.

Phosphorus removal performance, intracellular metabolites and clade-level community structure of Tetrasphaera-dominated polyphosphate accumulating organisms at different temperatures

Tetrasphaera are polyphosphate accumulating organisms (PAOs) that play an important role in enhanced biological phosphorus removal (EBPR) from wastewater. The effect of a wide range of temperature changes (1-30 °C) on phosphorus removal, metabolism and clade-level community structure of Tetrasphaera-dominated PAOs was investigated. At 10 °C, the bioactivities of Tetrasphaera-dominated communities were obviously inhibited and the EBPR efficiency was only 73 %. Yet at 20-30 °C, EBPR efficiency reached 99 % and the relative abundance of Tetrasphaera was up to 90 %. The temperature variation changed the community distribution of Tetrasphaera clades, which was possibly a main reason for EBPR performance. Amino acids and PHA with different contents were intracellular metabolite of Tetrasphaera-dominated communities during phosphorus release and uptake at different temperatures. Moreover, Tetrasphaera fermented protein and amino acids and released VFAs. The outcomes suggested the great potential of Tetrasphaera-PAOs in the treatment of wastewater with varying temperatures and limited carbon sources.

Biochemical characterization of a novel glucose-tolerant GH3 β-glucosidase (Bgl1973) from Leifsonia sp. ZF2019

Beta-glucosidase (Bgl) is an enzyme with considerable food, beverage, and biofuel processing potential. However, as many Bgls are inhibited by their reaction end product glucose, their industrial applications are greatly limited. In this study, a novel Bgl gene (Bgl1973) was cloned from Leifsonia sp. ZF2019 and heterologously expressed in E. coli. Sequence analysis and structure modeling revealed that Bgl1973 was 748 aa, giving it a molecular weight of 78 kDa, and it showed high similarity with the glycoside hydrolase 3 (GH3) family Bgls with which its active site residues were conserved. By using pNPGlc (p-nitrophenyl-β-D-glucopyranoside) as substrate, the optimum temperature and pH of Bgl1973 were shown to be 50 °C and 7.0, respectively. Bgl1973 was insensitive to most metal ions (12.5 mM), 1% urea, and even 0.1% Tween-80. This enzyme maintained 60% of its original activity in the presence of 20% NaCl, demonstrating its excellent salt tolerance. Furthermore, it still had 83% residual activity in 1 M of glucose, displaying its outstanding glucose tolerance. The K_m, V_max, and k_cat of Bgl1973 were 0.22 mM, 44.44 μmol/min mg, and 57.78 s^-1, respectively. Bgl1973 had a high specific activity for pNPGlc (19.10 ± 0.59 U/mg) and salicin (20.43 ± 0.92 U/mg). Furthermore, molecular docking indicated that the glucose binding location and the narrow and deep active channel geometry might contribute to the glucose tolerance of Bgl1973. Our results lay a foundation for the studying of this glucose-tolerant β-glucosidase and its applications in many industrial settings. KEY POINTS: • A novel β-glucosidase from GH3 was obtained from Leifsonia sp. ZF2019. • Bgl1973 demonstrated excellent glucose tolerance. • The glucose tolerance of Bgl1973 was explained using molecular docking analysis.

Carbon uptake bioenergetics of PAOs and GAOs in full-scale enhanced biological phosphorus removal systems

This work analyzed, for the first time, the bioenergetics of PAOs and GAOs in full-scale wastewater treatment plants (WWTPs) for the uptake of different carbon sources. Fifteen samples were collected from five full-scale WWTPs. Predominance of different PAOs, i.e., Ca. Accumulibacter (0.00-0.49%), Tetrasphaera (0.37-3.94%), Microlunatus phosphovorus (0.01-0.18%), etc., and GAOs, i.e., Ca. Competibacter (0.08-5.39%), Defluviicoccus (0.05-5.34%), Micropruina (0.17-1.87%), etc., were shown by 16S rRNA gene amplicon sequencing. Despite the distinct PAO/GAO community compositions in different samples, proton motive force (PMF) was found as the key driving force (up to 90.1%) for the uptake of volatile fatty acids (VFAs, acetate and propionate) and amino acids (glutamate and aspartate) by both GAOs and PAOs at the community level, contrasting the previous understanding that Defluviicoccus have a low demand of PMF for acetate uptake. For the uptake of acetate or propionate, PAOs rarely activated F1, F0- ATPase (< 11.7%) or fumarate reductase (< 5.3%) for PMF generation; whereas, intensive involvements of these two pathways (up to 49.2% and 61.0%, respectively) were observed for GAOs, highlighting a major and community-level difference in their VFA uptake biogenetics in full-scale systems. However, different from VFAs, the uptake of glutamate and aspartate by both PAOs and GAOs commonly involved fumarate reductase and F1, F0-ATPase activities. Apart from these major and community-level differences, high level fine-scale micro-diversity in carbon uptake bioenergetics was observed within PAO and GAO lineages, probably resulting from their versatilities in employing different pathways for reducing power generation. Ca. Accumulibacter and Halomonas seemed to show higher dependency on the reverse operation of F1, F0-ATPase than other PAOs, likely due to the low involvement of glyoxylate shunt pathway. Unlike Tetrasphaera, but similar to Ca. Accumulibacter, Microlunatus phosphovorus took up glutamate and aspartate via the proton/glutamate-aspartate symporter driven by PMF. This feature was testified using a pure culture of Microlunatus phosphovorus stain NM-1. The major difference between PAOs and GAOs highlights the potential to selectively suppress GAOs for community regulation in EBPR systems. The finer-scale carbon uptake bioenergetics of PAOs or GAOs from different lineages benefits in understanding their interactions in community assembly in complex environment.

Microbiological Study in Petrol-Spiked Soil

The pollution of arable lands and water with petroleum-derived products is still a valid problem, mainly due the extensive works aimed to improve their production technology to reduce fuel consumption and protect engines. An example of the upgraded fuels is the BP 98 unleaded petrol with Active technology. A pot experiment was carried out in which Eutric Cambisol soil was polluted with petrol to determine its effect on the microbiological and biochemical properties of this soil. Analyses were carried out to determine soil microbiome composition-with the incubation and metagenomic methods, the activity of seven enzymes, and cocksfoot effect on hydrocarbon degradation. The following indices were determined: colony development index (CD); ecophysiological diversity index (EP); index of cocksfoot effect on soil microorganisms and enzymes (IFG); index of petrol effect on soil microorganisms and enzymes (IFP); index of the resistance of microorganisms, enzymes, and cocksfoot to soil pollution with petrol (RS); Shannon-Weaver's index of bacterial taxa diversity (H); and Shannon-Weaver's index of hydrocarbon degradation (IDH). The soil pollution with petrol was found to increase population numbers of bacteria and fungi, and Protebacteria phylum abundance as well as to decrease the abundance of Actinobacteria and Acidobacteria phyla. The cultivation of cocksfoot on the petrol-polluted soil had an especially beneficial effect mainly on the bacteria belonging to the Ramlibacter, Pseudoxanthomonas, Mycoplana, and Sphingobium genera. The least susceptible to the soil pollution with petrol and cocksfoot cultivation were the bacteria of the following genera: Kaistobacter, Rhodoplanes, Bacillus, Streptomyces, Paenibacillus, Phenylobacterium, and Terracoccus. Cocksfoot proved effective in the phytoremediation of petrol-polluted soil, as it accelerated hydrocarbon degradation and increased the genetic diversity of bacteria. It additionally enhanced the activities of soil enzymes.

Sessile bacterium unlocks ability of surface motility through mutualistic interspecies interaction

In addition to their common planktonic lifestyle, bacteria frequently live in surface-associated habitats. Surface motility is essential for exploring these habitats for food sources. However, many bacteria are found on surfaces, even though they lack features required for migrating along surfaces. How these canonical non-motile bacteria adapt to the environmental fluctuations on surfaces remains unknown. Here, we report a previously unknown surface motility mode of the canonical non-motile bacterium, Dietzia sp. DQ12-45-1b, which is triggered by interaction with a dimorphic prosthecate bacterium, Glycocaulis alkaliphilus 6B-8T. Dietzia cells exhibits 'sliding'-like motility in an area where the strain Glycocaulis cells was pre-colonized with a sufficient density. Our analysis also demonstrates that Dietzia degrade n-alkanes and provide Glycocaulis with the resulting metabolites for survival, which in turn induced directional migration of Dietzia towards nutrient-rich environments. Such interaction-triggered migration was also found between Dietzia and Glycocaulis strains isolated from other habitats, suggesting that this mutualistic relationship ubiquitously occurs in natural environments. In conclusion, we propose a novel model for such a 'win-win' strategy, whereby non-motile bacteria pay metabolites to dimorphic prosthecate bacteria in return for migrating to seek for nutrients, which may represent a common strategy for canonically non-motile bacteria living on a surface.

Actinobacteria from Antarctica as a source for anticancer discovery

Although many advances have been achieved to treat aggressive tumours, cancer remains a leading cause of death and a public health problem worldwide. Among the main approaches for the discovery of new bioactive agents, the prospect of microbial secondary metabolites represents an effective source for the development of drug leads. In this study, we investigated the actinobacterial diversity associated with an endemic Antarctic species, Deschampsia antarctica, by integrated culture-dependent and culture-independent methods and acknowledged this niche as a reservoir of bioactive strains for the production of antitumour compounds. The 16S rRNA-based analysis showed the predominance of the Actinomycetales order, a well-known group of bioactive metabolite producers belonging to the Actinobacteria phylum. Cultivation techniques were applied, and 72 psychrotolerant Actinobacteria strains belonging to the genera Actinoplanes, Arthrobacter, Kribbella, Mycobacterium, Nocardia, Pilimelia, Pseudarthrobacter, Rhodococcus, Streptacidiphilus, Streptomyces and Tsukamurella were identified. The secondary metabolites were screened, and 17 isolates were identified as promising antitumour compound producers. However, the bio-guided assay showed a pronounced antiproliferative activity for the crude extracts of Streptomyces sp. CMAA 1527 and Streptomyces sp. CMAA 1653. The TGI and LC50 values revealed the potential of these natural products to control the proliferation of breast (MCF-7), glioblastoma (U251), lung/non-small (NCI-H460) and kidney (786-0) human cancer cell lines. Cinerubin B and actinomycin V were the predominant compounds identified in Streptomyces sp. CMAA 1527 and Streptomyces sp. CMAA 1653, respectively. Our results suggest that the rhizosphere of D. antarctica represents a prominent reservoir of bioactive actinobacteria strains and reveals it as an important environment for potential antitumour agents.

Metabolic Exchange with Non-Alkane-Consuming Pseudomonas stutzeri SLG510A3-8 Improves n-Alkane Biodegradation by the Alkane Degrader Dietzia sp. Strain DQ12-45-1b

Biodegradation of alkanes by microbial communities is ubiquitous in nature. Interestingly, the microbial communities with high hydrocarbon-degrading performances are sometimes composed of not only hydrocarbon degraders but also nonconsumers, but the synergistic mechanisms remain unknown. Here, we found that two bacterial strains isolated from Chinese oil fields, Dietzia sp. strain DQ12-45-1b and Pseudomonas stutzeri SLG510A3-8, had a synergistic effect on hexadecane (C₁₆ compound) biodegradation, even though P. stutzeri could not utilize C₁₆ individually. To gain a better understanding of the roles of the alkane nonconsumer P. stutzeri in the C₁₆-degrading consortium, we reconstructed a two-species stoichiometric metabolic model, iBH1908, and integrated in silico prediction with the following in vitro validation, a comparative proteomics analysis, and extracellular metabolomic detection. Metabolic interactions between P. stutzeri and Dietzia sp. were successfully revealed to have importance in efficient C₁₆ degradation. In the process, P. stutzeri survived on C₁₆ metabolic intermediates from Dietzia sp., including hexadecanoate, 3-hydroxybutanoate, and α-ketoglutarate. In return, P. stutzeri reorganized its metabolic flux distribution to fed back acetate and glutamate to Dietzia sp. to enhance its C₁₆ degradation efficiency by improving Dietzia cell accumulation and by regulating the expression of Dietzia succinate dehydrogenase. By using the synergistic microbial consortium of Dietzia sp. and P. stutzeri with the addition of the in silico-predicted key exchanged metabolites, diesel oil was effectively disposed of in 15 days with a removal fraction of 85.54% ± 6.42%, leaving small amounts of C₁₅ to C₂₀ isomers. Our finding provides a novel microbial assembling mode for efficient bioremediation or chemical production in the future.IMPORTANCE Many natural and synthetic microbial communities are composed of not only species whose biological properties are consistent with their corresponding communities but also ones whose chemophysical characteristics do not directly contribute to the performance of their communities. Even though the latter species are often essential to the microbial communities, their roles are unclear. Here, by investigation of an artificial two-member microbial consortium in n-alkane biodegradation, we showed that the microbial member without the n-alkane-degrading capability had a cross-feeding interaction with and metabolic regulation to the leading member for the synergistic n-alkane biodegradation. Our study improves the current understanding of microbial interactions. Because "assistant" microbes showed importance in communities in addition to the functional microbes, our findings also suggest a useful "assistant-microbe" principle in the design of microbial communities for either bioremediation or chemical production.

Madurastatin D1 and D2, Oxazoline Containing Siderophores Isolated from an Actinomadura sp

Two new siderophores, madurastatin D1 and D2, together with (-)-madurastatin C1, the enantiomer of a known compound, were isolated from marine-derived Actinomadura sp. The presence of an unusual 4-imidazolidinone ring in madurastatins D1 and D2 inspired us to sequence the Actinomadura sp. genome and to identify the mad biosynthetic gene cluster, knowledge of which enables us to now propose a biosynthetic pathway. Madurastatin D1 and D2 are moderately active in antimicrobial assays with M. luteus.

Identification of proteins induced by polycyclic aromatic hydrocarbon and proposal of the phenanthrene catabolic pathway in Amycolatopsis tucumanensis DSM 45259

In the present study the polycyclic aromatic hydrocarbon removal and metabolic adaptation of Amycolatopsis tucumanensis DSM 45259 were investigated. Analysis of one-dimensional gel electrophoresis of crude cell extracts revealed differential synthesis of proteins which were identified by MALDI-TOF. To elucidate the phenanthrene metabolic pathway in A. tucumanensis DSM45259, two-dimensional electrophoresis and detection of phenanthrene degradation intermediates by GS-MS were performed. The presence of aromatic substrates resulted in changes in the abundance of proteins involved in the metabolism of aromatic compounds, oxidative stress response, energy production and protein synthesis. The obtained results allowed us to clarify the phenanthrene catabolic pathway, by confirming the roles of several proteins involved in the degradation process and comprehensive adaptation. This may clear the way for more efficient engineering of bacteria in the direction of more effective bioremediation applications.

Characterization of Stackebrandtia nassauensis GH 20 Beta-Hexosaminidase, a Versatile Biocatalyst for Chitobiose Degradation

An unstudied β-N-acetylhexosaminidase (SnHex) from the soil bacterium Stackebrandtia nassauensis was successfully cloned and subsequently expressed as a soluble protein in Escherichia coli. Activity tests and the biochemical characterization of the purified protein revealed an optimum pH of 6.0 and a robust thermal stability at 50 °C within 24 h. The addition of urea (1 M) or sodium dodecyl sulfate (1% w/v) reduced the activity of the enzyme by 44% and 58%, respectively, whereas the addition of divalent metal ions had no effect on the enzymatic activity. PUGNAc (O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino-N-phenylcarbamate) strongly inhibited the enzyme in sub-micromolar concentrations. The β-N-acetylhexosaminidase was able to hydrolyze β1,2-linked, β1,3-linked, β1,4-linked, and β1,6-linked GlcNAc residues from the non-reducing end of various tested glycan standards, including bisecting GlcNAc from one of the tested hybrid-type N-glycan substrates. A mutational study revealed that the amino acids D306 and E307 bear the catalytically relevant side acid/base side chains. When coupled with a chitinase, the β-N-acetylhexosaminidase was able to generate GlcNAc directly from colloidal chitin, which showed the potential of this enzyme for biotechnological applications.

A rapid methods development workflow for high-throughput quantitative proteomic applications

Recent improvements in the speed and sensitivity of liquid chromatography-mass spectrometry systems have driven significant progress toward system-wide characterization of the proteome of many species. These efforts create large proteomic datasets that provide insight into biological processes and identify diagnostic proteins whose abundance changes significantly under different experimental conditions. Yet, these system-wide experiments are typically the starting point for hypothesis-driven, follow-up experiments to elucidate the extent of the phenomenon or the utility of the diagnostic marker, wherein many samples must be analyzed. Transitioning from a few discovery experiments to quantitative analyses on hundreds of samples requires significant resources both to develop sensitive and specific methods as well as analyze them in a high-throughput manner. To aid these efforts, we developed a workflow using data acquired from discovery proteomic experiments, retention time prediction, and standard-flow chromatography to rapidly develop targeted proteomic assays. We demonstrated this workflow by developing MRM assays to quantify proteins of multiple metabolic pathways from multiple microbes under different experimental conditions. With this workflow, one can also target peptides in scheduled/dynamic acquisition methods from a shotgun proteomic dataset downloaded from online repositories, validate with appropriate control samples or standard peptides, and begin analyzing hundreds of samples in only a few minutes.

Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora

BACKGROUND

There is little published regarding metabolism of Salinispora species. In continuation with efforts performed towards this goal, this study is focused on new insights into the metabolism of the three-identified species of Salinispora using constraints-based modeling. At present, only one manually curated genome-scale metabolic model (GSM) for Salinispora tropica strain CNB-440T has been built despite the role of Salinispora strains in drug discovery.

RESULTS

Here, we updated, and expanded the scope of the model of Salinispora tropica CNB-440T, and GSMs were constructed for two sequenced type strains covering the three-identified species. We also constructed a Salinispora core model that contains the genes shared by 93 sequenced strains and a few non-conserved genes associated with essential reactions. The models predicted no auxotrophies for essential amino acids, which was corroborated experimentally using a defined minimal medium (DMM). Experimental observations suggest possible sulfur accumulation. The Core metabolic content shows that the biosynthesis of specialised metabolites is the less conserved subsystem. Sets of reactions were analyzed to explore the differences between the reconstructions. Unique reactions associated to each GSM were mainly due to genome sequence data except for the ST-CNB440 reconstruction. In this case, additional reactions were added from experimental evidence. This reveals that by reaction content the ST-CNB440 model is different from the other species models. The differences identified in reaction content between models gave rise to different functional predictions of essential nutrient usage by each species in DMM. Furthermore, models were used to evaluate in silico single gene knockouts under DMM and complex medium. Cluster analysis of these results shows that ST-CNB440, and SP-CNR114 models are more similar when considering predicted essential genes.

CONCLUSIONS

Models were built for each of the three currently identified Salinispora species, and a core model representing the conserved metabolic capabilities of Salinispora was constructed. Models will allow in silico metabolism studies of Salinispora strains, and help researchers to guide and increase the production of specialised metabolites. Also, models can be used as templates to build GSMs models of closely related organisms with high biotechnology potential.

Phosphate Lock Residues of Acidothermus cellulolyticus Cas9 Are Critical to Its Substrate Specificity

Despite being utilized widely in genome sciences, CRISPR-Cas9 remains limited in achieving high fidelity in cleaving DNA. A better understanding of the molecular basis of Cas9 holds the key to improve Cas9-based tools. We employed direct evolution and in vitro characterizations to explore structural parameters that impact the specificity of the thermophilic Cas9 from Acidothermus cellulolyticus (AceCas9). By identifying variants that are able to cleave mismatched protospacers within the seed region, we found a critical role of the phosphate lock residues in substrate specificity in a manner that depends on their sizes and charges. Removal of the negative charge from the phosphate lock residues significantly decreases sensitivity to the guide-DNA mismatches. An increase in size of the substituted residues further reduces the sensitivity to mismatches at the first position of the protospacer. Our findings identify the phosphate lock residues as an important site for tuning the specificity and catalytic efficiency of Cas9.

Chromate Resistance Mechanisms in Leucobacter chromiiresistens

Chromate is one of the major anthropogenic contaminants on Earth. Leucobacter chromiiresistens is a highly chromate-resistant strain, tolerating chromate concentrations in LB medium of up to 400 mM. In response to chromate stress, L. chromiiresistens forms biofilms, which are held together via extracellular DNA. Inhibition of biofilm formation leads to drastically decreased chromate tolerance. Moreover, chromate is reduced intracellularly to the less-toxic Cr(III). The oxidation status and localization of chromium in cell aggregates were analyzed by energy-dispersive X-ray spectroscopy coupled to scanning transmission electron microscopy and X-ray absorption spectroscopy measurements. Most of the heavy metal is localized as Cr(III) at the cytoplasmic membrane. As a new cellular response to chromate stress, we observed an increased production of the carotenoid lutein. Carotenoid production could increase membrane stability and reduce the concentration of reactive oxygen species. Bioinformatic analysis of the L. chromiiresistens genome revealed several gene clusters that could enable heavy-metal resistance. The extreme chromate tolerance and the unique set of resistance factors suggest the use of L. chromiiresistens as a new model organism to study microbial chromate resistance.IMPORTANCE Chromate is a highly toxic oxyanion. Extensive industrial use and inadequate waste management has caused the toxic pollution of several field sites. Understanding the chromate resistance mechanisms that enable organisms to thrive under these conditions is fundamental to develop (micro)biological strategies and applications aiming at bioremediation of contaminated soils or waters. Potential detoxifying microorganisms are often not sufficient in their resistance characteristics to effectively perform, e.g., chromate reduction or biosorption. In this study, we describe the manifold strategies of L. chromiiresistens to establish an extremely high level of chromate resistance. The multitude of mechanisms conferring it make this organism suitable for consideration as a new model organism to study chromate resistance.

Identification and characterization of a highly S-enantioselective halohydrin dehalogenase from Tsukamurella sp. 1534 for kinetic resolution of halohydrins

Halohydrin dehalogenases are remarkable enzymes which possess promiscuous catalytic activity and serve as potential biocatalysts for the synthesis of chiral halohydrins, epoxides and β-substituted alcohols. The enzyme HheC exhibits a highly R enantioselectivity in the processes of dehalogenation of vicinal halohydrins and ring-opening of epoxides, which attracts more attentions in organic synthesis. Recently dozens of novel potential halohydrin dehalogenases have been identified by gene mining, however, most of the characterized enzymes showed low stereoselectivity. In this study, a novel halohydrin dehalogenase of HheA10 from Tsukamurella sp. 1534 has been heterologously expressed, purified and characterized. Substrate spectrum and kinetic resolution studies indicated the HheA10 was a highly S enantioselective enzyme toward several halohydrins, which produced the corresponding epoxides with the ee (enantiomeric excess) and E values up to >99% and >200 respectively. Our results revealed the HheA10 was a promising biocatalyst for the synthesis of enantiopure aromatic halohydrins and epoxides via enzymatic kinetic resolution of racemic halohydrins. What's more important, the HheA10 as the first individual halohydrin dehalogenase with the highly S enantioselectivity provides a complementary enantioselectivity to the HheC.

Ornithinimicrobium cavernae sp. nov., an actinobacterium isolated from a karst cave

A novel actinobacterium, designated strain CFH 30183^T, was isolated from a soil sample collected from a karst cave in Luoyang, Henan Province. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of strain CFH 30183^T were observed to be Gram-stain positive, motile, asporogenous and coccoid to rod shaped. The strain was found to be aerobic and oxidase positive. On the basis of 16S rRNA gene sequence analysis, strain CFH 30183^T was found to be closely related to Ornithinimicrobium murale 01-Gi-040^T (97.8% sequence identity). The ANIb/ANIm values between strain CFH 30183^T and O. murale DSM 22056^T were found to be 80.3%/85.9%. Strain CFH 30183^T was found to grow optimally at 28-32 °C, at pH 8.0-9.0 and in the presence of up to 7% NaCl (w/v). Whole cell hydrolysates of strain CFH 30183^T contained L-ornithine as the diagnostic diamino acid, and arabinose, glucose, mannose and rhamnose as whole cell sugars. The respiratory quinone was determined to be MK-8(H₄), while the major fatty acids were found to consist of iso-C_15:0 and iso-C_16:0. The polar lipids profile was found to include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid, an unidentified phosphoglycolipid and four unidentified lipids. The DNA G + C content of strain CFH 30183^T was calculated to be 70.9%. Based on the phenotypic, genotypic and phylogenetic data obtained, strain CFH 30183^T is considered to represent a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium cavernae sp. nov. is proposed. The type strain is CFH 30183^T (= KCTC 49018^T = CGMCC 1.16393^T).

GlnR positive transcriptional regulation of the phosphate-specific transport system pstSCAB in Amycolatopsis mediterranei U32

Amycolatopsis mediterranei U32 is an important industrial strain for the production of rifamycin SV. Rifampicin, a derivative of rifamycin SV, is commonly used to treat mycobacterial infections. Although phosphate has long been known to affect rifamycin biosynthesis, phosphate transport, metabolism, and regulation are poorly understood in A. mediterranei. In this study, the functional phosphate transport system pstSCAB was isolated by RNA sequencing and inactivated by insertion mutation in A. mediterranei U32. The mycelium morphology changed from a filamentous shape in the wild-type and pstS1+ strains to irregular swollen shape at the end of filamentous in the ΔpstS1 strain. RT-PCR assay revealed that pstSCAB genes are co-transcribed as a polycistronic messenger. The pstSCAB transcription was significantly activated by nitrate supplementation and positively regulated by GlnR which is a global regulator of nitrogen metabolism in actinomycetes. At the same time, the yield of rifamycin SV decreased after mutation (ΔpstS1) compared with wild-type U32, which indicated a strong connection among phosphate metabolism, nitrogen metabolism, and rifamycin production in actinomycetes.

Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species

BACKGROUND

Genome mining tools have enabled us to predict biosynthetic gene clusters that might encode compounds with valuable functions for industrial and medical applications. With the continuously increasing number of genomes sequenced, we are confronted with an overwhelming number of predicted clusters. In order to guide the effective prioritization of biosynthetic gene clusters towards finding the most promising compounds, knowledge about diversity, phylogenetic relationships and distribution patterns of biosynthetic gene clusters is necessary.

RESULTS

Here, we provide a comprehensive analysis of the model actinobacterial genus Amycolatopsis and its potential for the production of secondary metabolites. A phylogenetic characterization, together with a pan-genome analysis showed that within this highly diverse genus, four major lineages could be distinguished which differed in their potential to produce secondary metabolites. Furthermore, we were able to distinguish gene cluster families whose distribution correlated with phylogeny, indicating that vertical gene transfer plays a major role in the evolution of secondary metabolite gene clusters. Still, the vast majority of the diverse biosynthetic gene clusters were derived from clusters unique to the genus, and also unique in comparison to a database of known compounds. Our study on the locations of biosynthetic gene clusters in the genomes of Amycolatopsis' strains showed that clusters acquired by horizontal gene transfer tend to be incorporated into non-conserved regions of the genome thereby allowing us to distinguish core and hypervariable regions in Amycolatopsis genomes.

CONCLUSIONS

Using a comparative genomics approach, it was possible to determine the potential of the genus Amycolatopsis to produce a huge diversity of secondary metabolites. Furthermore, the analysis demonstrates that horizontal and vertical gene transfer play an important role in the acquisition and maintenance of valuable secondary metabolites. Our results cast light on the interconnections between secondary metabolite gene clusters and provide a way to prioritize biosynthetic pathways in the search and discovery of novel compounds.

Rathayibacter toxicus, Other Rathayibacter Species Inducing Bacterial Head Blight of Grasses, and the Potential for Livestock Poisonings

Rathayibacter toxicus, a Select Agent in the United States, is one of six recognized species in the genus Rathayibacter and the best known due to its association with annual ryegrass toxicity, which occurs only in parts of Australia. The Rathayibacter species are unusual among phytopathogenic bacteria in that they are transmitted by anguinid seed gall nematodes and produce extracellular polysaccharides in infected plants resulting in bacteriosis diseases with common names such as yellow slime and bacterial head blight. R. toxicus is distinguished from the other species by producing corynetoxins in infected plants; toxin production is associated with infection by a bacteriophage. These toxins cause grazing animals feeding on infected plants to develop convulsions and abnormal gate, which is referred to as "staggers," and often results in death of affected animals. R. toxicus is the only recognized Rathayibacter species to produce toxin, although reports of livestock deaths in the United States suggest a closely related toxigenic species may be present. A closely related but undescribed species, Rathayibacter sp. EV, originally isolated from Ehrharta villosa var. villosa in South Africa, is suspected of producing toxin. Many of the diseases caused by Rathayibacter species occur in arid areas and the extracellular polysaccharide they produce is believed to aid in their survival between crops. For example, R. "agropyri" was isolated from infected plant material after being stored for 50 years in a herbarium. Similarly, the anguinid vectors associated with these bacteria form seed galls in infected plants and are capable of surviving for very long periods of time under dry conditions. The addition of R. toxicus to the list of Select Agents has raised concern over its potential introduction and a realization that current diagnostic methods are inadequate to distinguish among Rathayibacter species. In addition, little is known about the Rathayibacter species and their seed gall nematode vectors present in the United States.

Hindrance of 1,4-dioxane biodegradation in microcosms biostimulated with inducing or non-inducing auxiliary substrates

A microcosm study was conducted to assess two biostimulation strategies (relative to natural attenuation) to bioremediate 1,4-dioxane contamination at a site in west Texas. Dioxane concentrations were relatively low (<300 μg/L), which represents a potential challenge to sustain and induce specific degraders. Thus, biostimulation was attempted with an auxiliary substrate known to induce dioxane-degrading monooxygenases (i.e., tetrahydrohyran [THF]) or with a non-inducing growth substrate (1-butanol [1-BuOH]). Amendment of 1-BuOH (100 mg/L) to microcosms that were not oxygen-limited temporarily enhanced dioxane biodegradation by the indigenous microorganisms. However, this stimulatory effect was not sustained by repeated amendments, which might be attributed to i) the inability of 1-BuOH to induce dioxane-degrading enzymes, ii) curing of catabolic plasmids, iii) metabolic flux dilution and catabolite repression, and iv) increased competition by commensal bacteria that do not degrade dioxane. Experiments with the archetype dioxane degrader Pseudonocardia dioxanivorans CB1190 repeatedly amended with 1-BuOH (500 mg/L added weekly for 4 weeks) corroborated the partial curing of catabolic plasmids (9.5 ± 7.4% was the plasmid retention ratio) and proliferation of derivative segregants that lost their ability to degrade dioxane. Addition of THF (300 μg/L) also had limited benefit due to competitive inhibition; significant dioxane degradation occurred only when the THF concentration decreased below approximately 160 μg/L. Overall, these results illustrate the importance of considering the possibility of unintentional hindrance of catabolism associated with the addition of auxiliary carbon sources to bioremediate aquifers impacted with trace concentrations of dioxane.

Comparative genomics of Clavibacter michiganensis subspecies, pathogens of important agricultural crops

Subspecies of Clavibacter michiganensis are important phytobacterial pathogens causing devastating diseases in several agricultural crops. The genome organizations of these pathogens are poorly understood. Here, the complete genomes of 5 subspecies (C. michiganensis subsp. michiganensis, Cmi; C. michiganensis subsp. sepedonicus, Cms; C. michiganensis subsp. nebraskensis, Cmn; C. michiganensis subsp. insidiosus, Cmi and C. michiganensis subsp. capsici, Cmc) were analyzed. This study assessed the taxonomic position of the subspecies based on 16S rRNA and genome-based DNA homology and concludes that there is ample evidence to elevate some of the subspecies to species-level. Comparative genomics analysis indicated distinct genomic features evident on the DNA structural atlases and annotation features. Based on orthologous gene analysis, about 2300 CDSs are shared across all the subspecies; and Cms showed the highest number of subspecies-specific CDS, most of which are mobile elements suggesting that Cms could be more prone to translocation of foreign genes. Cms and Cmi had the highest number of pseudogenes, an indication of potential degenerating genomes. The stress response factors that may be involved in cold/heat shock, detoxification, oxidative stress, osmoregulation, and carbon utilization are outlined. For example, the wco-cluster encoding for extracellular polysaccharide II is highly conserved while the sucrose-6-phosphate hydrolase that catalyzes the hydrolysis of sucrose-6-phosphate yielding glucose-6-phosphate and fructose is highly divergent. A unique second form of the enzyme is only present in Cmn NCPPB 2581. Also, twenty-eight plasmid-borne CDSs in the other subspecies were found to have homologues in the chromosomal genome of Cmn which is known not to carry plasmids. These CDSs include pathogenesis-related factors such as Endocellulases E1 and Beta-glucosidase. The results presented here provide an insight of the functional organization of the genomes of five core C. michiganensis subspecies, enabling a better understanding of these phytobacteria.

Rhizoremediation of cadmium-contaminated soil associated with hydroxamate siderophores isolated from Cd-resistant plant growth-promoting Dietzia maris and Lysinibacillus strains

In search of multitrait plant growth-promoting (PGP) inoculants, we introduced two cadmium-resistant bacterial strains, C4 (PG), C5 (WB), and their consortium C6 (PG × WB) isolated from metal-contaminated industrial waste-fed canal near West Bengal. The test isolates were biochemically characterized and screened in vitro for siderophore production. The infrared spectra revealed the hydroxamate nature of the siderophore produced. Further in green house, siderophore-based seed inoculation with selected PGP isolates exhibited stimulatory effects on seed germination (up to 85.4%), chlorophyll index (22.9 spad unit), shoot and root length (70% and 62.7%), tiller numbers (38.82%), spikelet numbers (52.2%), straw yield (62.2%), grain yield (76.1%), total dry matter of root and shoot (55.56% and 64.4%, respectively), and grain yields (76.1%) of tested wheat cultivars. The 16S rRNA sequencing identified strain PG and WB as Dietzia maris and Lysinibacillus sp. strains. Furthermore, inoculation of C6 (consortium) in both cultivar UP-2565 and KS-227 showed maximum Cd sorption capacity in roots (38.3% and 67.1%) and shoots (68.4% and 67.5%), respectively. Both the strains and their consortium showed a great potential to increase the growth and yield of wheat cultivars, which can also be utilized for rhizoremediation process.

Pilot-scale whole-cell biocatalysis for the hydroxylation of cyclosporine derivative, FR901459, at higher concentrations by Lentzea sp. 7887 using soybean flour as a novel substrate dispersant

Pilot-scale hydroxylation of FR901459, an immunosuppressive cyclosporine derivative, was performed using resting cells of a Gram-positive bacteria Lentzea sp. 7887 (as whole-cell biocatalysts) and soybean flour as a substrate dispersant. Through biocatalysis, FR901459 was hydroxylated at position 9, producing AS1837812, an important intermediate in the production of drug candidates against hepatitis C. Since FR901459 is insoluble in water, the conversion ratio ([moles of AS1837812 produced/moles of FR901459 added]×100) of the biocatalysis decreased under conditions with substrate concentrations higher than 0.615 mM. To increase the concentration of FR901459 for biocatalysis, we screened various materials to effectively disperse FR901459 in the biocatalysis mixture and found that soybean flour was the best substrate dispersant. The addition of soybean flour to the biocatalysis mixture increased the FR901459 concentration in a 3-L reactor up to 3-fold (1.85 mM). Thus, we successfully established a pilot-scale (1-m3) biocatalysis with a 2-fold higher concentration (1.23 mM) of FR901459 using soybean flour as the substrate dispersant and obtained 419 g of AS1837812 at a conversion ratio of 34.5% in a 28-h batch reaction. Soybean flour can be used as a substrate dispersant for various industrial biocatalysis processes because of its low cost, high availability, and low environmental impact.

Proteomic insight into the primycin fermentation process of Saccharomonospora azurea

Saccharomonospora azurea SZMC 14600 is a member of the family Pseudonocardiaceae exclusively used for industrial scale production of primycin a large 36-membered non-polyene macrolide lactone antibiotic belonging to the polyketide class of natural products. Even though maximum antibiotic yield has been achieved by empirically optimized two-step fermentation process, little is known about the molecular components and mechanisms underlying the efficient antibiotic production. In order to identify differentially expressed proteins (DEPs) between the pre- and main-fermentation stages of primycin, comparative 2D-PAGE experiments were performed. In total, 98 DEP spots were reproducibly detected, out of which four spots were excised from gels, and identified through MALDI-TOF/TOF mass spectrometry. Peptide mass fingerprint analysis revealed peptide matches to HicB antitoxin for the HicAB toxin-antitoxin system (EHK86651), to a nucleoside diphosphate kinase regulator ((Ndk; EHK81899) and two other proteins with unknown function (EHK88946 and EHK86777).

Characterization of Roseomonas and Nocardioides spp. for arsenic transformation

The metalloid arsenic predominantly exists in the arsenite [As(III)] and arsenate [As(V)]. These two forms are respectively oxidized and reduced by microbial redox processes. This study was designed to bioprospect arsenic tolerating bacteria from Lonar lake and to characterize their arsenic redoxing ability. Screening of sixty-nine bacterial species isolated from Lonar lake led to identification of three arsenic-oxidizing and seven arsenic-reducing species. Arsenite oxidizing isolate Roseomonas sp. L-159a being closely related to Roseomonas cervicalis ATCC 49957 oxidized 2mM As(III) in 60h. Gene expression of large and small subunits of arsenite oxidase respectively showed 15- and 17-fold higher expression. Another isolate Nocardioides sp. L-37a formed a clade with Nocardioides ghangwensis JC2055, exhibited normal growth with different carbon sources and pH ranges. It reduced 2mM As(V) in 36h and showed constitutive expression of arsenate reductase which increased over 4-fold upon As(V) exposure. Genetic markers related to arsenic transformation were identified and characterized from the two isolates. Moderate resistance against the arsenicals was exhibited by the two isolates in the range of 1-5mM for As(III) and 1-200mM for As(V). Altogether we provide multiple evidences to indicate that Roseomonas sp. and Nocardioides sp. exhibited arsenic transformation ability.

Nocardioides, Sediminibacterium, Aquabacterium, Variovorax, and Pseudomonas linked to carbon uptake during aerobic vinyl chloride biodegradation

Vinyl chloride (VC) is a frequent groundwater contaminant and a known human carcinogen. Bioremediation is a potential cleanup strategy for contaminated sites; however, little is known about the bacteria responsible for aerobic VC degradation in mixed microbial communities. In attempts to address this knowledge gap, the microorganisms able to assimilate labeled carbon ((13)C) from VC within a mixed culture capable of rapid VC degradation (120 μmol in 7 days) were identified using stable isotope probing (SIP). For this, at two time points during VC degradation (days 3 and 7), DNA was extracted from replicate cultures initially supplied with labeled or unlabeled VC. The extracted DNA was ultracentrifuged, fractioned, and the fractions of greater buoyant density (heavy fractions, 1.758 to 1.780 g mL(-1)) were subject to high-throughput sequencing. Following this, specific primers were designed for the most abundant phylotypes in the heavy fractions. Then, quantitative PCR (qPCR) was used across the buoyant density gradient to confirm label uptake by these phylotypes. From qPCR and/or sequencing data, five phylotypes were found to be dominant in the heavy fractions, including Nocardioides (∼40 %), Sediminibacterium (∼25 %), Aquabacterium (∼17 %), Variovorax (∼6 %), and Pseudomonas (∼1 %). The abundance of two functional genes (etnC and etnE) associated with VC degradation was also investigated in the SIP fractions. Peak shifts of etnC and etnE gene abundance toward heavier fractions were observed, indicating uptake of (13)C into the microorganisms harboring these genes. Analysis of the total microbial community indicated a significant dominance of Nocardioides over the other label-enriched phylotypes. Overall, the data indicate Nocardioides is primarily responsible for VC degradation in this mixed culture, with the other putative VC degraders generating a small growth benefit from VC degradation. The specific primers designed toward the putative VC degraders may be of use for investigating VC degradation potential at contaminated sites.

Effects of DO levels on surface force, cell membrane properties and microbial community dynamics of activated sludge

In this paper, we employ atomic force microscopy (AFM), fluorescence recovery after photobleaching (FRAP) technique, phospholipid fatty acids (PLFA) and MiSeq analysis to study the effects of traditional dissolved oxygen (DO) levels (0.71-1.32mg/L, 2.13-3.02mg/L and 4.31-5.16mg/L) on surface force, cell membrane properties and microbial community dynamics of activated sludge. Results showed that low DO level enhanced the surface force and roughness of activated sludge; the medium DO level decreased cell membrane fluidity by reducing the synthesis of branched fatty acids in the cell membrane; high DO level resulted in the highest protein content in the effluent by EEM scanning. Abundance of Micropruina, Zoogloea and Nakamurella increased and Paracoccus and Rudaea decreased with the increase of DO levels. RDA analysis suggested that saturated fatty acids (SFA), anteiso-fatty acids (AFA) and iso-fatty acids (IFA) were closely related to effluent quality as well as some genera.

Bacterial biodegradation of melamine-contaminated aged soil: influence of different pre-culture media or addition of activation material

This study aimed to investigate the biodegrading potential of Arthrobacter sp. MCO, Arthrobacter sp. CSP, and Nocardioides sp. ATD6 in melamine-contaminated upland soil (melamine: approx. 10.5 mg/kg dry weight) after 30 days of incubation. The soil sample used in this study had undergone annual treatment of lime nitrogen, which included melamine; it was aged for more than 10 years in field. When R2A broth was used as the pre-culture medium, Arthrobacter sp. MCO could degrade 55 % of melamine after 30 days of incubation, but the other strains could hardly degrade melamine (approximately 25 %). The addition of trimethylglycine (betaine) in soil as an activation material enhanced the degradation rate of melamine by each strain; more than 50 % of melamine was degraded by all strains after 30 days of incubation. In particular, strain MCO could degrade 72 % of melamine. When the strains were pre-cultured in R2A broth containing melamine, the degradation rate of melamine in soil increased remarkably. The highest (72 %) melamine degradation rate was noted when strain MCO was used with betaine addition.

The VanRS Homologous Two-Component System VnlRSAb of the Glycopeptide Producer Amycolatopsis balhimycina Activates Transcription of the vanHAXSc Genes in Streptomyces coelicolor, but not in A. balhimycina

In enterococci and in Streptomyces coelicolor, a glycopeptide nonproducer, the glycopeptide resistance genes vanHAX are colocalized with vanRS. The two-component system (TCS) VanRS activates vanHAX transcription upon sensing the presence of glycopeptides. Amycolatopsis balhimycina, the producer of the vancomycin-like glycopeptide balhimycin, also possesses vanHAXAb genes. The genes for the VanRS-like TCS VnlRSAb, together with the carboxypeptidase gene vanYAb, are part of the balhimycin biosynthetic gene cluster, which is located 2 Mb separate from the vanHAXAb. The deletion of vnlRSAb did not affect glycopeptide resistance or balhimycin production. In the A. balhimycina vnlRAb deletion mutant, the vanHAXAb genes were expressed at the same level as in the wild type, and peptidoglycan (PG) analyses proved the synthesis of resistant PG precursors. Whereas vanHAXAb expression in A. balhimycina does not depend on VnlRAb, a VnlRAb-depending regulation of vanYAb was demonstrated by reverse transcriptase polymerase chain reaction (RT-PCR) and RNA-seq analyses. Although VnlRAb does not regulate the vanHAXAb genes in A. balhimycina, its heterologous expression in the glycopeptide-sensitive S. coelicolor ΔvanRSSc deletion mutant restored glycopeptide resistance. VnlRAb activates the vanHAXSc genes even in the absence of VanS. In addition, expression of vnlRAb increases actinorhodin production and influences morphological differentiation in S. coelicolor.

Long-term ferrocyanide application via deicing salts promotes the establishment of Actinomycetales assimilating ferrocyanide-derived carbon in soil

Cyanides are highly toxic and produced by various microorganisms as defence strategy or to increase their competitiveness. As degradation is the most efficient way of detoxification, some microbes developed the capability to use cyanides as carbon and nitrogen source. However, it is not clear if this potential also helps to lower cyanide concentrations in roadside soils where deicing salt application leads to significant inputs of ferrocyanide. The question remains if biodegradation in soils can occur without previous photolysis. By conducting a microcosm experiment using soils with/without pre-exposition to road salts spiked with (13) C-labelled ferrocyanide, we were able to confirm biodegradation and in parallel to identify bacteria using ferrocyanide as C source via DNA stable isotope probing (DNA-SIP), TRFLP fingerprinting and pyrosequencing. Bacteria assimilating (13) C were highly similar in the pre-exposed soils, belonging mostly to Actinomycetales (Kineosporia, Mycobacterium, Micromonosporaceae). In the soil without pre-exposition, bacteria belonging to Acidobacteria (Gp3, Gp4, Gp6), Gemmatimonadetes (Gemmatimonas) and Gammaproteobacteria (Thermomonas, Xanthomonadaceae) used ferrocyanide as C source but not the present Actinomycetales. This indicated that (i) various bacteria are able to assimilate ferrocyanide-derived C and (ii) long-term exposition to ferrocyanide applied with deicing salts leads to Actinomycetales outcompeting other microorganisms for the use of ferrocyanide as C source.

Production of the Ramoplanin Activity Analogue by Double Gene Inactivation

Glycopeptides such as vancomycin and telavancin are essential for treating infections caused by Gram-positive bacteria. But the dwindling availability of new antibiotics and the emergence of resistant bacteria are making effective antibiotic treatment increasingly difficult. Ramoplanin, an inhibitor of bacterial cell wall biosynthesis, is a highly effective antibiotic against a wide range of Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus, vancomycin-intermediate resistant Clostridium difficile and vancomycin-resistant Enterococcus sp. Here, two tailoring enzyme genes in the biosynthesis of ramoplanin were deleted by double in-frame gene knockouts to produce new ramoplanin derivatives. The deschlororamoplanin A2 aglycone was purified and its structure was identified with LC-MS/MS. Deschlororamoplanin A2 aglycone and ramoplanin aglycone showed similar activity to ramoplanin A2. The results showed that α-1,2-dimannosyl disaccharide at Hpg¹¹ and chlorination at Chp¹⁷ in the ramoplanin structure are not essential for its antimicrobial activity. This work provides new precursor compounds for the semisynthetic modification of ramoplanin.

Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis

Soils contaminated with crude oil are rich sources of enzymes suitable for both degradation of hydrocarbons through bioremediation processes and improvement of crude oil during its refining steps. Due to the long term selection, crude oil fields are unique environments for the identification of microorganisms with the ability to produce these enzymes. In this metagenomic study, based on Hiseq Illumina sequencing of samples obtained from a crude oil field and analysis of data on MG-RAST, Actinomycetales (9.8%) were found to be the dominant microorganisms, followed by Rhizobiales (3.3%). Furthermore, several functional genes were found in this study, mostly belong to Actinobacteria (12.35%), which have a role in the metabolism of aliphatic and aromatic hydrocarbons (2.51%), desulfurization (0.03%), element shortage (5.6%), and resistance to heavy metals (1.1%). This information will be useful for assisting in the application of microorganisms in the removal of hydrocarbon contamination and/or for improving the quality of crude oil. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:638-648, 2016.

Classification of thermophilic actinobacteria isolated from arid desert soils, including the description of Amycolatopsis deserti sp. nov

The taxonomic position of 26 filamentous actinobacteria isolated from a hyper-arid Atacama Desert soil and 2 from an arid Australian composite soil was established using a polyphasic approach. All of the isolates gave the diagnostic amplification product using 16S rRNA oligonucleotide primers specific for the genus Amycolatopsis. Representative isolates had chemotaxonomic and morphological properties typical of members of the genus Amycolatopsis. 16S rRNA gene analyses showed that all of the isolates belong to the Amycolatopsis methanolica 16S rRNA gene clade. The Atacama Desert isolates were assigned to one or other of two recognised species, namely Amycolatopsis ruanii and Amycolatopsis thermalba, based on 16S rRNA gene sequence, DNA:DNA relatedness and phenotypic data; emended descriptions are given for these species. In contrast, the two strains from the arid Australian composite soil, isolates GY024(T) and GY142, formed a distinct branch at the periphery of the A. methanolica 16S rRNA phyletic line, a taxon that was supported by all of the tree-making algorithms and by a 100 % bootstrap value. These strains shared a high degree of DNA:DNA relatedness and have many phenotypic properties in common, some of which distinguished them from all of the constituent species classified in the A. methanolica 16S rRNA clade. Isolates GY024(T) and GY142 merit recognition as a new species within the A. methanolica group of thermophilic strains. The name proposed for the new species is Amycolatopsis deserti sp. nov.; the type strain is GY024(T) (=NCIMB 14972(T) = NRRL B-65266(T)).

High-yield production of lipoglycopeptide antibiotic A40926 using a mutant strain Nonomuraea sp. DP-13 in optimized medium

The lipoglycopeptide antibiotic A40926 produced by Nonomuraea sp. is a complex of structurally related components differing in the fatty acid moiety. Besides showing an intrinsic antibacterial activity, A40926 is the precursor of the semisynthetic antibiotic Dalvance. In this work, A40926 production by a mutant strain Nonomuraea sp. DP-13 was investigated. It was found that A40926 production was markedly promoted by using poorly assimilated carbon source maltodextrin and nitrogen source soybean meal. Addition of Cu(2+) resulted in a stimulation of A40926 production, but Co(2+) had an inhibitory effect. L-Leucine addition greatly improved total A40926 production and modified the complex composition toward factor B0. An optimized production medium IM-3 was developed and a maximum A40926 production of 1096 mg/L was obtained in the 10-L fermenter. This was the highest A40926 productivity so far reported.

Killing of Mycolic Acid-Containing Bacteria Aborted Induction of Antibiotic Production by Streptomyces in Combined-Culture

Co-culture of Streptomyces with mycolic acid-containing bacteria (MACB), which we termed “combined-culture,” alters the secondary metabolism pattern in Streptomyces and has been a useful method for the discovery of bioactive natural products. In the course of our investigation to identify the inducing factor(s) of MACB, we previously observed that production of pigments in Streptomyces lividans was not induced by factors such as culture extracts or mycolic acids. Although dynamic changes occurred in culture conditions because of MACB, the activation of pigment production by S. lividans was observed in a limited area where both colonies were in direct contact. This suggested that direct attachment of cells is a requirement and that components on the MACB cell membrane may play an important role in the response by S. lividans. Here we examined whether this response was influenced by dead MACB that possess intact mycolic acids assembled on the outer cell membrane. Formaldehyde fixation and γ-irradiation were used to prepare dead cells that retain their shape and mycolic acids of three MACB species: Tsukamurella pulmonis, Rhodococcus erythropolis, and Rhodococcus opacus. Culturing tests verified that S. lividans does not respond to the intact dead cells of three MACB. Observation of combined-culture by scanning electron microscopy (SEM) indicated that adhesion of live MACB to S. lividans mycelia were a significant interaction that resulted in formation of co-aggregation. In contrast, in the SEM analysis, dead cells were not observed to adhere. Therefore, direct attachment by live MACB cells is proposed as one of the possible factors that causes Streptomyces to alter its specialized metabolism in combined-culture.

Actinomadura algeriensis sp. nov., an actinobacterium isolated from Saharan soil

During the course of a screening programme for new taxa of actinobacteria, a strain designated ACD1(T), was isolated from a Saharan soil in the Hoggar region (Algeria). The taxonomic position of this strain was determined using a polyphasic taxonomic approach. The strain was observed to form extensively branched, non-fragmenting substrate mycelium, and aerial mycelium with straight to flexuous, hooked and irregular spirals (1-2 turns) forming short chains of spores. The diamino acid present in the cell wall is meso-diaminopimelic acid. Galactose, glucose, madurose, mannose and ribose occur in whole-cell hydrolysates. The diagnostic phospholipids detected were diphosphatidylglycerol and phosphatidylinositol. The major menaquinones were identified as MK-9 (H4) and MK-9 (H2). The major fatty acids were found to be C16:0, C18:1 cis9, iso-C16:0 and 10-methyl C18:0. Phylogenetic analysis based on the 16S rRNA gene showed that the strain belongs to the genus Actinomadura, and is closely related to Actinomadura sediminis DSM 45500(T) (98.5 % similarity) and Actinomadura cremea subsp. cremea DSM 43676(T) (98.3 % similarity). However, DNA-DNA hybridization revealed only 48.0 % relatedness with A. sediminis DSM 45500(T) and 33.2 % relatedness with A. cremea subsp. cremea DSM 43676(T). The combined phenotypic and genotypic data showed that the strain represents a novel species of the genus Actinomadura, for which the name Actinomadura algeriensis sp. nov. is proposed, with the type strain ACD1(T) (= DSM 46744(T) = CECT 8841(T)).