Biodiversity of Actinomycetes Associated with Caribbean Sponges and Their Potential for Natural Product Discovery

Marine actinomycetes provide a rich source of structurally unique and bioactive secondary metabolites. Numerous genera of marine actinomycetes have been isolated from marine sediments as well as several sponge species. In this study, 16 different species of Caribbean sponges were collected from four different locations in the coastal waters off Puerto Rico in order to examine diversity and bioactive metabolite production of marine actinomycetes in Caribbean sponges. Sediments were also collected from each location, in order to compare actinomycete communities between these two types of samples. A total of 180 actinomycetes were isolated and identified based on 16S rRNA gene analysis. Phylogenetic analysis revealed the presence of at least 14 new phylotypes belonging to the genera Micromonospora, Verruscosispora, Streptomyces, Salinospora, Solwaraspora, Microbacterium and Cellulosimicrobium. Seventy-eight of the isolates (19 from sediments and 59 from sponges) shared 100 % sequence identity with Micromonospora sp. R1. Despite having identical 16S rRNA sequences, the bioactivity of extracts and subsequent fractions generated from the fermentation of both sponge- and sediment-derived isolates identical to Micromonospora sp. R1 varied greatly, with a marked increase in antibiotic metabolite production in those isolates derived from sponges. These results indicate that the chemical profiles of isolates with high 16S rRNA sequence homology to known strains can be diverse and dependent on the source of isolation. In addition, seven previously reported dihydroquinones produced by five different Streptomyces strains have been purified and characterized from one Streptomyces sp. strain isolated in this study from the Caribbean sponge Agelas sceptrum.     

Antimicrobial potential of deep surface sediment associated bacteria from the Sea of Japan

The aim of this study was to survey microorganisms from the deep surface sediment samples collected from the Sea of Japan and to screen them for antimicrobial and antagonistic effects. Phylogenetic analysis revealed most isolates sharing 98–100 % sequence similarity to recognized species, including those recovered previously from marine or saline environments. Alteromonas, Halomonas, Marinobacter, Pseudoalteromonas, Salinicola, within the class Gammaproteobacteria, Sulfitobacter (Alphaproteobacteria), Bacillus, Paenibacillus and Paenisporosarcina (Firmicutes), Nocardiopsis and Streptomyces (Actinobacteria) occurred abundantly in all sediment samples. Antimicrobial screening revealed twenty three strains (13 %) capable to inhibit growth of one to eight test cultures and deep sediment isolates. Based on phylogenetic analysis mostly active strains belonged to the genera Bacillus, Brevibacillus, Nocardiopsis, Paenibacillus and Streptomyces. Antimicrobial substances (1–3) were isolated from strain Paenibacillus sp. Sl 79w showing a high inhibitory activity. On the basis of combined spectral analyses (IR, UV, ¹H and ¹³C NMR) the compounds 1, 2 and 3 with [M + H]⁺ at 409.1 and 409.2 m/z, and with [M + Na]⁺ at 822.5 m/z were found to have a carbon skeleton of isocoumarin and peptide antibiotics, respectively. Our findings demonstrated that the deep surface sediments of the Sea of Japan represent an untapped source of diverse microorganisms capable of antimicrobial metabolite production.     

Ruminant feces harbor diverse uncultured symbiotic actinobacteria

To isolate actinobacteria from ruminant feces and elucidate their correlations with ruminants, the actinobacterial community in sheep (Ovis aries) and cattle (Bos taurus) feces was determined by cultivation and clone library methods. Most of actinobacteria isolated belonged to Streptomyces, Amycolatopsis, Micromonospora, and Cellulosimicrobium genera. The strains showed above 99 % similarity with the type strains, respectively. All the strains isolated could grow on media containing pectin, cellulose, or xylan as the sole carbon sources. However, most antibacterial and antifungal activities were found in Streptomyces species. Clone library analysis revealed that the genera Mycobacterium, Aeromicrobium, Rhodococcus, Cellulomonas were present in cattle and sheep feces. In contrast, the 16S rRNA genes showed less than 98 % similarity with the type strains. The analysis of actinobacterial community in ruminant feces by clone library and cultivation yielded a total of 10 actinobacterial genera and three uncultured actinobacterial taxa. The ruminant feces harbored diverse actinobacterial community. Ruminants may represent an underexplored reservoir of novel actinomycetes of potential interest for probiotics and drug discovery.     

Streptomyces polyrhachii sp. nov., a novel actinomycete isolated from an edible Chinese black ant (Polyrhachis vicina Roger)

A novel actinomycete, designated strain NEAU-ycm1^T, was isolated from an edible Chinese black ant (Polyrhachis vicina Roger) and characterized with a polyphasic approach. The organism was found to have morphological and chemotaxonomic characteristics typical of streptomycetes. Phylogenetic analysis based on the almost complete 16S rRNA gene sequence show that the novel isolate belongs to the genus Streptomyces and forms a separate subclade. The closest phylogenetic relatives were identified as the type strains of Streptomyces intermedius NBRC 13049^T (97.74 %), Streptomyces aureoverticillatus NRRL B-3326^T (97.69 %), Streptomyces rutgersensis NBRC 12819^T (97.68 %), Streptomyces gougerotii NBRC 3198^T (97.68 %) and Streptomyces diastaticus subsp. diastaticus NBRC 3714^T (97.68 %). Similarities to other type strains of the genus Streptomyces were lower than 97.55 %. A comparison between strain NEAU-ycm1^T and the closest related Streptomyces type strains revealed that it is different from them in morphological, physiological and biochemical characteristics. Therefore, it is proposed that NEAU-ycm1^T (=CGMCC 4.7094^T = DSM 42102^T) represents a novel species of the genus of Streptomyces, for which the name Streptomyces polyrhachii sp. nov. is proposed.     

Genomics of Sponge-Associated Streptomyces spp. Closely Related to Streptomyces albus J1074: Insights into Marine Adaptation and Secondary Metabolite Biosynthesis Potential

A total of 74 actinomycete isolates were cultivated from two marine sponges, Geodia barretti and Phakellia ventilabrum collected at the same spot at the bottom of the Trondheim fjord (Norway). Phylogenetic analyses of sponge-associated actinomycetes based on the 16S rRNA gene sequences demonstrated the presence of species belonging to the genera Streptomyces, Nocardiopsis, Rhodococcus, Pseudonocardia and Micromonospora. Most isolates required sea water for growth, suggesting them being adapted to the marine environment. Phylogenetic analysis of Streptomyces spp. revealed two isolates that originated from different sponges and had 99.7% identity in their 16S rRNA gene sequences, indicating that they represent very closely related strains. Sequencing, annotation, and analyses of the genomes of these Streptomyces isolates demonstrated that they are sister organisms closely related to terrestrial Streptomyces albus J1074. Unlike S. albus J1074, the two sponge streptomycetes grew and differentiated faster on the medium containing sea water. Comparative genomics revealed several genes presumably responsible for partial marine adaptation of these isolates. Genome mining targeted to secondary metabolite biosynthesis gene clusters identified several of those, which were not present in S. albus J1074, and likely to have been retained from a common ancestor, or acquired from other actinomycetes. Certain genes and gene clusters were shown to be differentially acquired or lost, supporting the hypothesis of divergent evolution of the two Streptomyces species in different sponge hosts.     

大连海域沉积物中可培养海洋链霉菌活性及其多样性

以大肠杆菌、金黄色葡萄球菌和尖孢镰刀枯萎病菌作为测试靶目标,采用9种分离培养基从大连海域13个不同采样点的海洋沉积物样品中分离到165株海洋链霉菌。从165株海洋放线菌中筛选到对金黄色葡萄球菌具有抑制活性的菌株85株,占总菌株数的51.5%;对大肠杆菌具有抑制活性的菌株27株,占总菌株数的16.4%;对尖孢镰刀枯萎病菌具有抑制活性的菌株仅有6株,占总菌株数的3.6%。因此,海洋链霉菌的活性更多地表现为对细菌的抗性,尤其对革兰氏阳性细菌具有更高的抑制活性。对其中具有抑制活性或形态独特的菌株进行了16S r DNA序列分析,并构建系统发育树,显示活性海洋链霉菌具有丰富的种类多样性和广谱抗菌活性。同种海洋链霉菌与土壤链霉菌活性比较结果也表明,海洋链霉菌多表现抗革兰氏阳性细菌活性。     

Psychrotolerant antifungal Streptomyces isolated from Tawang, India and the shift in chitinase gene family

A total of 210 Streptomyces were isolated from the soil samples of Tawang, India where temperature varied from 5 °C during daytime to ?2 °C during the night. Based on antifungal activity, a total of 33 strains, putatively Streptomyces spp., were selected. Optimal growth temperature for the 33 strains was 16 °C, with growth occurring down to 6 °C but not above 30 °C. Phylogenetic analysis based on 16S rDNA sequences revealed the taxonomic affiliation of the 33 strains as species of Streptomyces. To examine the relatedness of the chitinase genes from six strong antifungal Streptomyces strains, a phylogenetic tree was constructed using the catalytic domain nucleotide sequences and resulted in seven distinct monophyletic groups. A quantitative PCR study for chitinase expressing ability revealed that of the six antifungal strains tested, the strain Streptomyces roseochromogenus TSR12 was the most active producer of family 18 chitinase genes. Streptomyces strains with enhanced inhibitory potential usually encode a family 19 chitinase gene; however, our present study did not show expression of this family in the six strains tested.     

Streptomyces poriferorum sp. nov., a novel marine sponge-derived Actinobacteria species expressing anti-MRSA activity

Marine sponges represent a rich source of uncharacterized microbial diversity, and many are host to microorganisms that produce biologically active specialized metabolites. Here, a polyphasic approach was used to characterize two Actinobacteria strains, P01-B04^T and P01-F02, that were isolated from the marine sponges Geodia barretti (Bowerbank, 1858) and Antho dichotoma (Esper, 1794), respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains P01-B04^T and P01-F02 are closely related to Streptomyces beijiangensis DSM 41794^T, Streptomyces laculatispora NRRL B-24909^T, and Streptomyces brevispora NRRL B-24910^T. The two strains showed nearly identical 16S rRNA gene sequences (99.93%), and the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) relatedness values were 99.96% and 99.6%, respectively, suggesting that these strains are affiliated with the same species. Chemotaxonomic and culture characteristics of both strains were also consistent with the genus Streptomyces, while phenotypic properties, genome-based comparisons, and phylogenomic analyses distinguished strains P01-B04^T and P01-F02 from their closest phylogenetic relatives. In silico analysis predicted that the 8.9 Mb genome of P01-B04^T contains at least 41 biosynthetic gene clusters (BGCs) encoding secondary metabolites, indicating that this strain could express diverse bioactive metabolites; in support of this prediction, this strain expressed antibacterial activity against Gram-positive bacteria including a clinical isolate of methicillin-resistant Staphylococcus aureus (MRSA) EAMC30. Based on these results, the marine sponge-associated isolates represent a novel species of the genus Streptomyces, for which the name Streptomyces poriferorum sp. nov. is proposed, with P01-B04^T (=DSM 111306^T = CCM 9048^T) as the type strain.     

Bioactive potential of Streptomyces associated with marine sponges

The present work deals with isolation of Streptomyces associated with marine sponges and its bioactive potential. Streptomyces sp. were isolated from the marine sponges Callyspongia diffusa, Mycale mytilorum, Tedania anhelans and Dysidea fragilis. From the initial screening, 94 cultures of Streptomyces were obtained and from these 58 cultures exhibited antagonism against bacteria, 36 strains against fungi and 27 strains exhibited broad spectrum activity against both. The submerged culture extracts of the 58 anti-bacterial isolates were analysed and of these 58 strains, 37 strains showed positive inhibition against Bacillus subtilis, 43 against Staphylococcus aureus, 10 against Vibrio cholerae and 10 against Escherichia coli. The antifungal activities of the 36 strains were also evaluated and 27 strains showed positive inhibition against Aspergillus niger, 23 against Saccharomyces cerevisiae and 16 against Candida albicans. The production of polyene substances from the active extracts was confirmed by UV spectral analysis by the absorbance peaks that ranged from 225 to 262 nm and the TLC (R _f values) ranging from 0.40 to 0.78. The results indicate that Streptomyces strains isolated from marine sponges produce potential antibacterial, antifungal and broad spectrum antibiotic compounds.     

Overproduction and biological activity of prodigiosin-like pigments from recombinant fusant of endophytic marine Streptomyces species

Thirty-four endophytic marine Actinomycetes isolates were recovered from the Egyptian marine sponge Latrunculia corticata, out of them 5 isolates (14.7 %) showed red single colonies on yeast-CzAPEK plates. Isolates under the isolation code NRC50 and NRC51 were observed with the strongest red biomass. After application of protoplast fusion between NRC50 and NRC51 isolates, 26 fusants were selected and produced widely different amounts of prodigiosin-like pigments (PLPs) on different fermentation media. Among them fusant NRCF69 produced 79 and 160.4 % PLPs more than parental strains NRC50 and NRC51, respectively. According to the analysis of 16S rDNA sequence (amplified, sequenced, and submitted to GenBank under Accession no. JN232405 and JN232406, respectively), together with their morphological and biochemical characteristics, parental strains NRC50 (P1) and NRC51 (P2) were identified as Streptomyces sp. and designated as Streptomyces sp. NRC50 and Streptomyces sp. NRC51. This study describes a low cost, effective production media by using peanut seed broth, sunflower oil broth or dairy processing wastewater broth alone, or supplemented with 0.5 % mannitol that supports the production of PLPs by the Streptomyces fusant NRCF69 under study (42.03, 40.11, 36.7 and 47 g L^?1, respectively). PLPs compounds exhibited significant cytotoxic activities against three human cancer cell lines: colon cancer cell line (HCT-116), liver cancer cell line (HEPG-2) and breast cancer cell line (MCF-7) and antimycotic activity against clinical dermatophyte isolates of Trichophyton, Microsporum and Epidermophyton.     

Streptomyces jiujiangensis sp. nov., isolated from soil in South China

An actinomycete capable of lysing cyanobacteria, strain JXJ 0074^T, was isolated from a soil sample collected from Jiangxi province, south China, and characterized by using polyphasic taxonomy. The new isolate showed morphological and chemotaxonomic properties typical of members of the genus Streptomyces. Phylogenetic analysis of the near-complete 16S rRNA gene sequence indicated that strain JXJ 0074^T should be affiliated to the genus Streptomyces and exhibited highest similarities to Streptomyces shenzhenensis DSM 42034^T (98.99 %) and Streptomyces lucensis NBRC 13056^T (98.60 %), while the similarities to other members of the genus are lower than 98.22 % similarity. However, the DNA–DNA hybridization values between strain JXJ 0074^T and S. shenzhenensis DSM 42034^T or S. lucensis NBRC 13056^T were 46.2 ± 2.6 and 32.6 ± 3.1 %, respectively. Thus, on the basis of the polyphasic data, strain JXJ 0074^T represents a novel species of the genus Streptomyces, for which the name Streptomyces jiujiangensis sp. nov. is proposed. The type strain is JXJ 0074^T (= BCRC 16953^T = KCTC 29262^T).     

Mortality in the initial ontogeny of Paralabrax maculatofasciatus (Actinopterygii, Perciformes, Serranidae) caused by Chattonella spp. (Raphidophyceae)

Fish are particularly sensitive to metabolites produced by Raphidophyte species and these have caused intensive fish kills in several countries. However, the effects on embryos of marine fish are unknown but could probably provoke an important impact on new stock recruitment and hence on fisheries. We evaluated the toxic effects of Chattonella spp. strains from the Gulf of California on three development stages of spotted sand bass (Paralabrax maculatofasciatus): embryo in segmentation stage (ES), embryo (EM), and eleutheroembryo (EL). Embryos (ES) were exposed to different cell concentrations of Chattonella subsalsa, Chattonella marina, Prorocentrum micans, and f/2 medium as control. Also, one set of embryos was tested with cell-free media for C. subsalsa cultures. Incubation lasted until embryos reached apterolarva phase. The ES was the most sensitive stage reaching 98% mortality with C. subsalsa, followed by cell-free media of C. subsalsa cultures, with mortalities close to 90%, whereas EM and EL phases presented mortalities below 60%. This work demonstrates that larval stages of P. maculatofasciatus are highly sensitive to short time exposure to all Chattonella spp. strains tested, that direct physical contact with cells is not required to cause mortality, and that the toxic effect is more pronounced when embryos hatch.     

Production of xylanase by an alkaline-tolerant marine-derived Streptomyces viridochromogenes strain and improvement by ribosome engineering

Xylanase is the enzyme complex that is responsible for the degradation of xylan; however, novel xylanase producers remain to be explored in marine environment. In this study, a Streptomyces strain M11 which exhibited xylanase activity was isolated from marine sediment. The 16S rDNA sequence of M11 showed the highest identity (99 %) to that of Streptomyces viridochromogenes. The xylanase produced from M11 exhibited optimum activity at pH 6.0, and the optimum temperature was 70 °C. M11 xylanase activity was stable in the pH range of 6.0–9.0 and at 60 °C for 60 min. Xylanase activity was observed to be stable in the presence of up to 5 M NaCl. Antibiotic-resistant mutants of M11 were isolated, and among the various antibiotics tested, streptomycin showed the best effect on obtaining xylanase overproducer. Mutant M11-1(10) isolated from 10 μg/ml streptomycin-containing plate showed 14 % higher xylanase activities than that of the wild-type strain. An analysis of gene rpsL (encoding ribosomal protein S12) showed that rpsL from M11-1(10) contains a K88R mutation. This is the first report to show that marine-derived S. viridochromogenes strain can be used as a xylanase producer, and utilization of ribosome engineering for the improvement of xylanase production in Streptomyces was also first successfully demonstrated.     

智利海洋沉积物中放线菌多样性

【目的】认识智利海洋沉积物中放线菌的多样性。【方法】分别采用选择性分离培养和非培养的基于16SrRNA基因序列系统发育分析方法,对来自智利南部海域海洋沉积物中放线菌多样性进行研究。采用6种选择性分离培养基分离放线菌;利用放线菌特异性引物对样品总DNA进行16SrRNA基因序列扩增并构建了16SrRNA基因克隆文库。分别挑选不同培养特征的22株放线菌和59个基因克隆进行16SrRNA基因序列的系统进化分析;测定分离的放线菌对海水的依赖性及产生抗菌活性化合物的能力。【结果】共分离到328株放线菌;挑选的22株放线菌分别属于小单孢菌属、多形孢菌属、链霉菌属、迪茨氏菌属、气微菌属和短状杆菌属;挑取的59个克隆属于40个分类单元,其中60%分类单元属于放线菌门放线菌亚纲、酸微菌亚纲和红色杆菌亚纲,另外40%的分类单元在放线菌内形成几个独立的进化分支,有可能代表放线菌新类群。22株放线菌有19株具有抗菌活性,50%的生长依赖海水的放线菌也具有抗菌活性。【结论】智利海域沉积物存在丰富的放线菌系统发育多样性并能产生活性次级代谢产物,而且还蕴藏丰富的新类型的放线菌资源。     

Antibacterial metabolites synthesized by psychrotrophic bacteria isolated from cold-freshwater environments

The ability of three psychrotrophic Gram-negative bacilli isolated from Chilean Patagonian cold freshwater rivers to produce bioactive metabolites was evaluated. The strains were isolated from cold waters rivers and identified by their biochemical properties and 16S rRNA gene analysis. The metabolites fractions showing antibacterial activity were obtained by solvent extraction and partially characterized by gas–mass chromatography (GC-MS). Antibacterial activity of the fractions was evaluated by an agar-well diffusion test upon 14 bacterial strains, both Gram positive and Gram negative. Thermal and proteolytic resistances of the antibacterial metabolites fractions were also evaluated. Molecular analysis allows the identification of the three Patagonian strains as Pseudomonas sp. RG-6 (Pseudomonas brenneri 99.6 % identity), Pseudomonas sp. RG-8 (Pseudomonas trivialis 99.6 % identity) and Yersinia sp. RP-3 (Yersinia aldovae 99.5 % identity). These extracts were able to inhibit both Gram-positive and Gram-negative bacteria but not Listeria monocytogenes. The antibacterial activity of the filtrated supernatants was lost at temperatures ≥60 °C, and was not affected by proteinase K treatment. The chemical structure of the active molecule remains to be elucidated, although the GC-MS analysis of the filtrates suggests that compounds like sesquiterpenes derivatives from β-maaliene or δ-selinene could be responsible of this antibacterial activity. Pristine cold freshwater streams showed to be interesting sources of metabolites-producing microorganisms with antibacterial activity.     

Streptomyces amritsarensis sp. nov., exhibiting broad-spectrum antimicrobial activity

A new actinobacterium strain, designated 2A^T, was isolated from a soil sample collected from Guru Nanak Dev University, Punjab (India) and characterized using a polyphasic taxonomic approach. It showed antimicrobial activity against various Gram-positive and Gram-negative bacteria including drug resistant bacteria and fungi. The strain had chemotaxononomic and morphological properties typical of the genus Streptomyces. The 16S rRNA gene sequence of the strain showed 99.9, 99.5 and 99.5 % similarity with Streptomyces flavotricini DSM 40152^T, Streptomyces toxytricini DSM 40178^T and Streptomyces globosus DSM 40815^T, respectively. This strain formed a coherent cluster with them and shared DNA–DNA homology of 37.6 ± 0.6, 34.4 ± 0.5 and 33.1 ± 0.4 % with type strains, S. flavotricini DSM 40152^T, S. globosus DSM 40815^T and S. toxytricini DSM 40178^T, respectively. Further, the strain was readily distinguished from the phylogenetic close relatives in a variety of morphological, physiological and biochemical properties. Based on the genotypic and phenotypic characteristics, it is proposed that strain 2A^T represents a novel species in the genus Streptomyces, for which the name Streptomyces amritsarensis sp. nov. is proposed, with the type strain 2A^T (=MTCC 11845^T=JCM 19660^T).     

A NADPH-dependent (S)-imine reductase (SIR) from Streptomyces sp. GF3546 for asymmetric synthesis of optically active amines: purification, characterization, gene cloning, and expression

A NADPH-dependent (S)-imine reductase (SIR) was purified to be homogeneous from the cell-free extract of Streptomyces sp. GF3546. SIR appeared to be a homodimer protein with subunits of 30.5 kDa based on SDS-polyacrylamide gel electrophoresis and HPLC gel filtration. It also catalyzed the (S)-enantioselective reduction of not only 2-methyl-1-pyrroline (2-MPN) but also 1-methyl-3,4-dihydroisoquinoline and 6,7-dimethoxy-1-methyl-3,4-dihydroisoquinoline. Specific activities for their imines were 130, 44, and 2.6 nmol?min^?1?mg^?1, and their optical purities were 92.7 % ee, 96.4 % ee, and >99 % ee, respectively. Using a NADPH-regenerating system, 10 mM 2-MPN was converted to amine with 100 % conversion and 92 % ee after 24 h. The amino acid sequence analysis revealed that SIR showed about 60 % identity to 6-phosphogluconate dehydrogenase. However, it showed only 37 % identity with Streptomyces sp. GF3587 (R)-imine reductase. Expression of SIR in Escherichia coli was achieved, and specific activity of the cell-free extract was about two times higher than that of the cell-free extract of Streptomyces sp. GF3546.     

Optimization and production of pyrrolidone antimicrobial agent from marine sponge-associated Streptomyces sp. MAPS15

Twenty-nine actinobacterial strains were isolated from marine sponge Spongia officinalis and screened for antagonistic activity against various bacterial and fungal pathogens. The active antibiotic producer MAPS15 was identified as Streptomyces sp. using 16S rRNA phylogenetic analysis. The critical control factors were selected from Plackett–Burman (PB) factorial design and the bioprocess medium was optimized by central composite design (CCD) for the production of bioactive metabolite from Streptomyces sp. MAPS15. The maximum biomass and active compound production obtained with optimized medium was 6.13 g/L and 62.41 mg/L, respectively. The economical carbon source, paddy straw was applied for the enhanced production of bioactive compound. The purified active fraction was characterized and predicted as pyrrolidone derivative which showed broad spectrum of bioactivity towards indicator organisms. The predicted antimicrobial spectra suggested that the Streptomyces sp. MAPS15 can produce a suite of novel antimicrobial drugs.     

Photobacterium malacitanum sp. nov., and Photobacterium andalusiense sp. nov., two new bacteria isolated from diseased farmed fish in Southern Spain

Three strains, H01100409B^T, H01100413B, and H27100402H^T, were isolated from several internal organs of diseased redbanded seabream (Pagrus auriga) reared in Andalusia (Southern Spain). All strains were studied by phenotypic, including chemotaxonomy, and genomic characteristics. Phylogenetic analysis based on concatenated sequences of six housekeeping genes (gyrB, ftsZ, topA, mreB, gapA, and 16S rRNA) supported the inclusion of the strains within the clade Phosphoreum of the genus Photobacterium, and two of the strains (H27100402H^T and H01100409B^T) formed a tight group separated from the closest species P. aquimaris. Genomic analyses, including average nucleotide identity (ANIb and ANIm) and DNA–DNA hybridization (DDH), clearly separated strains H27100402H^T and H01100409B^T from the other species within the clade Phosphoreum with values below the thresholds for species delineation. The chemotaxonomic features (including FAME analysis and MALDI-TOF-MS) of H27100402H^T and H01100409B^T strains confirmed their differentiation from the related taxa. The results demonstrated that strain H01100413B was classified as P. aquimaris and the strains H27100402H^T and H01100409B^T represented a new species each in the genus Photobacterium, for which we propose the names Photobacterium malacitanum sp. nov., type strain H27100402H^T (=CECT 9190^T = LMG 29992^T), and Photobacterium andalusiense sp. nov., type strain H01100409B^T (=CECT 9192^T = LMG 29994^T).     

Actinobacterial diversity from marine sediments collected in Mexico

Seventeen different media known to support the growth and isolation of members of the class Actinobacteria were evaluated as selective isolation media for the recovery of this microbial group from marine sediments samples collected in the Gulf of California and the Gulf of Mexico. A general selective isolation procedure was employed for six sediments and nearly 300 actinomycetes were recovered from the selective isolation plates. Full 16S rRNA gene sequencing revealed that the isolates belonged to several actinobacterial taxa, notably to the genera Actinomadura, Dietzia, Gordonia, Micromonospora, Nonomuraea, Rhodococcus, Saccharomonospora, Saccharopolyspora, Salinispora, Streptomyces, “Solwaraspora” and Verrucosispora. Previous works on marine sediments have been restricted to the isolation of members of the genera Micromonospora, Rhodococcus and Streptomyces. This study provides further evidence that Actinobacteria present in marine habitats are not restricted to the Micromonospora-Rhodococcus-Streptomyces grouping. Indeed, this first systematic study shows the extent of actinobacterial diversity that can be found in marine sediments collected in Mexico and probably, worldwide. The 16S rRNA gene sequences of marine isolates A1, AA2, AA6, AB1, AB2, AG1, AI2, AK1, AL2, AO1, AO3, AR1, AW1, B1, BB1, BC1, C5, R1, R2, R3, AV1, AE1, AI1, AN1 and AP1 determined in this study have been deposited under GenBank accession numbers EU714241–EU714258 and FJ462359–FJ462365, respectively.