Amycolatopsis eburnea sp. nov., an actinomycete associated with arbuscular mycorrhizal fungal spores

Peterkaempfera podocarpi sp. nov., a novel actinobacterium isolated from rhizosphere soil of Podocarpus rumphii in Sumba Island, Indonesia

A novel actinobacterial strain, designated as SMS 1(5)aT, was isolated from the rhizosphere soil of Podocarpus rumphii in Laiwangi Wanggameti National Park, Indonesia. A comprehensive polyphasic approach was used to determine its taxonomic position. Strain SMS 1(5)aT exhibited the highest 16S rRNA gene sequence similarity to Peterkaempfera griseoplana NRRL B-3064T (98.89%), followed by Peterkaempfera bronchialis DSM 106435T (98.68%). Phylogenetic and phylogenomic analyses confirmed its affiliation with the genus Peterkaempfera. The genome size of strain SMS 1(5)aT was 8.8 Mb, with a DNA G+C content of 72 mol%. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain SMS 1(5)aT and P. griseoplana NRRL B-3064T were 41.9 and 90.47%, respectively, which were below the established thresholds for species delineation. Strain SMS 1(5)aT grew between 15 and 40 °C, within a pH range of 5–8, and showed tolerance to 0–2% (w/v) NaCl. The morphological and chemotaxonomic properties of strain SMS 1(5)aT were consistent with those of Peterkaempfera. The strain formed long, flexuous-to-spiral spore chains with a warty surface. The whole-cell hydrolysates of strain SMS 1(5)aT contained ll -diaminopimelic acid ( ll -DAP) as the diagnostic diamino acid as well as whole-cell sugars, including glucose, mannose and ribose. The predominant menaquinone was MK-9(H8), and its polar lipid profile included phosphatidylethanolamine (PE), phosphatidylinositol (PI) and diphosphatidylglycerol (DPG). Additionally, the major fatty acid in strain SMS 1(5)aᵀ was iso-C15:0, differentiating it from the other two type strains. Characterization based on genotypic, genomic, phenotypic and chemotaxonomic studies suggests strain SMS 1(5)aT as a novel species of the genus Peterkaempfera, for which the name Peterkaempfera podocarpi sp. nov. (type strain SMS 1(5)aT = InaCC A1244T = NBRC 116964T) is proposed.

Amycolatopsis heterodermiae sp. nov. and Actinacidiphila polyblastidii sp. nov., two new actinobacteria isolated from foliose lichens

Two novel actinomycete strains, designated as V23-08T and V4-01T, were isolated from a foliose lichen collected in Doi Inthanon National Park, Chiang Mai Province, Thailand. Strain V23-08T showed the highest similarity (98.40%) to Amycolatopsis tolypomycina DSM 44544T. Similarly, strain V4-01T showed the highest 16S rRNA gene similarity relatedness (98.89%) to Actinacidiphila acidipaludis PLK6-54T. Chemotaxonomic analysis revealed distinct characteristics for each strain. The isomers of diaminopimelic acid were identified as meso-DAP in strain V23-08T and ll -DAP in strain V4-01T. The predominant menaquinones were MK-9(H2) for strain V23-08T and MK-9(H6) and MK-9(H8) for strain V4-01T. Strain V23-08T contained mannose, glucose, galactose and arabinose as whole-cell sugars, with iso-C16:0 as the major fatty acid. The polar lipid profile included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, unidentified aminophospholipids, unidentified phospholipids and unidentified lipids. In contrast, strain V4-01T exhibited glucose and galactose as whole-cell sugars, with iso-C16:0, anteiso-C16:0 and C16:0 as major fatty acids, and a polar lipid composition of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The taxonomic data, supported by digital DNA–DNA hybridization and average nucleotide identity analyses, confirm that strains V23-08T and V4-01T represent novel species within the genera Amycolatopsis and Actinacidiphila, respectively. Based on these findings, the names Amycolatopsis heterodermiae sp. nov. (strain V23-08T: TBRC 16208T and NBRC 115837T) and Actinacidiphila polyblastidii sp. nov. (strain V4-01T: TBRC 16209T and NBRC 115865T) are proposed.

Building blocks toward sustainable biofertilizers: variation in arbuscular mycorrhizal spore germination when immobilized with diazotrophic bacteria in biodegradable hydrogel beads

AIM

We investigated whether there was interspecies and intraspecies variation in spore germination of 12 strains of arbuscular mycorrhizal fungi when co-entrapped with the diazotrophic plant growth-promoting bacteria, Azospirillum brasilense Sp7 in alginate hydrogel beads.

METHODS AND RESULTS

Twelve Rhizophagus irregularis, Rhizophagus intraradices, and Funneliformis mosseae strains were separately combined with a live culture of Azospirillum brasilense Sp7. Each fungal-bacterial consortia was supplemented with sodium alginate to a 2% concentration (v/v) and cross-linked in calcium chloride (2% w/v) to form biodegradable hydrogel beads. One hundred beads from each combination (total of 1200) were fixed in solidified modified Strullu and Romand media. Beads were observed for successful spore germination and bacterial growth over 14 days. In all cases, successful growth of A. brasilense was observed. For arbuscular mycorrhizal fungi, interspecies variation in spore germination was observed, with R. intraradices having the highest germination rate (64.3%), followed by R. irregularis (45.5%) and F. mosseae (40.3%). However, a difference in intraspecies germination was only observed among strains of R. irregularis and F. mosseae. Despite having varying levels of germination, even the strains with the lowest potential were still able to establish with the plant host Brachypodium distachyon in a model system.

CONCLUSIONS

Arbuscular mycorrhizal spore germination varied across strains when co-entrapped with a diazotrophic plant growth-promoting bacteria. This demonstrates that hydrogel beads containing a mixed consortium hold potential as a sustainable biofertilizer and that compatibility tests remain an important building block when aiming to create a hydrogel biofertilizer that encases a diversity of bacteria and fungi. Moving forward, further studies should be conducted to test the efficacy of these hydrogel biofertilizers on different crops across varying climatic conditions in order to optimize their potential.

Comparative genomics reveals insight into the phylogeny and habitat adaptation of novel Amycolatopsis species, an endophytic actinomycete associated with scab lesions on potato tubers

A novel endophytic actinomycete, strain MEP2-6T, was isolated from scab tissues of potato tubers collected from Mae Fag Mai Sub-district, San Sai District, Chiang Mai Province, Thailand. Strain MEP2-6T is a gram-positive filamentous bacteria characterized by meso-diaminopimelic acid in cell wall peptidoglycan and arabinose, galactose, glucose, and ribose in whole-cell hydrolysates. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and hydroxy-phosphatidylethanolamine were the major phospholipids, of which MK-9(H6) was the predominant menaquinone, whereas iso-C16:0 and iso-C15:0 were the major cellular fatty acids. The genome of the strain was 10,277,369 bp in size with a G + C content of 71.7%. The 16S rRNA gene phylogenetic and core phylogenomic analyses revealed that strain MEP2-6T was closely related to Amycolatopsis lexingtonensis NRRL B-24131T (99.4%), A. pretoriensis DSM 44654T (99.3%), and A. eburnea GLM-1T (98.9%). Notably, strain MEP2-6T displayed 91.7%, 91.8%, and 87% ANIb and 49%, 48.8%, and 35.4% dDDH to A. lexingtonensis DSM 44653T (=NRRL B-24131T), A. eburnea GLM-1T, and A. pretoriensis DSM 44654T, respectively. Based on phenotypic, chemotaxonomic, and genomic data, strain MEP2-6T could be officially assigned to a novel species within the genus Amycolatopsis, for which the name Amycolatopsis solani sp. nov. has been proposed. The type of strain is MEP2-6T (=JCM 36309T = TBRC 17632T = NBRC 116395T). Amycolatopsis solani MEP2-6T was strongly proven to be a non-phytopathogen of potato scab disease because stunting of seedlings and necrotic lesions on potato tuber slices were not observed, and there were no core biosynthetic genes associated with the BGCs of phytotoxin-inducing scab lesions. Furthermore, comparative genomics can provide a better understanding of the genetic mechanisms that enable A. solani MEP2-6T to adapt to the plant endosphere. Importantly, the strain smBGCs accommodated 33 smBGCs encoded for several bioactive compounds, which could be beneficially applied in the fields of agriculture and medicine. Consequently, strain MEP2-6T is a promising candidate as a novel biocontrol agent and antibiotic producer.

Winogradskyella luteola sp.nov., Erythrobacter ani sp. nov., and Erythrobacter crassostrea sp.nov., isolated from the hemolymph of the Pacific Oyster Crassostrea gigas

Three new bacterial strains, WHY3^T, WH131^T, and WH158^T, were isolated and described from the hemolymph of the Pacific oyster Crassostrea gigas utilizing polyphasic taxonomic techniques. The 16S rRNA gene sequence analysis revealed that strain WHY3^T was a member of the genus Winogradskyella, whereas strains WHI31^T and WH158^T were members of the genus Erythrobacter. According to the polygenomic study the three strains formed individual lineages with strong bootstrap support. The comparison of dDDH-and ANI values, percentage of conserved proteins (POCP), and average amino acid identity (AAl) between the three strains and their relatives established that the three strains represented two separate genera. Menaquinone-6 was reported as the major respiratory quinone in strain WHY3^T and Ubiquinone-10 for strains WH131^T and WH158^T, respectively. The major cellular fatty acids for strain WHY3^T were C_15:0, anteiso-C_15:1 ω7c, iso-C_15:0, C_16:1ω7c. The major cellular fatty acids for strains WH131^T and WH158^T were C_14:02-OH and t_18:1ω12 for WH131^T and C_17:0, and C_18:1ω7c for strain WH158^T. Positive Sudan Black B staining Indicated the presence of polyhydroxyalkanoic acid granules for strains WH131^T and WH158^T but not for strain WHY3^T. The DNA G + C contents of strains WHY3^T, WH131^T and WH158^T were 34.4, 59.7 and 56.6%, respectively. Gene clusters predicted some important genes involved in the bioremediation process. Due to the accomplishment of polyphasic taxonomy, we propose three novel species Winogradskyella luteola sp.nov. (type strain WHY3^T = DSM 111804^T = NCCB 100833^T), Erythrobacter ani sp.nov. (WH131^T = DSM 112099^T = NCCB 100824^T) and Erythrobacter crassostrea sp.nov. (WH158^T = DSM 112102^T = NCCB 100877^T).

Photobacterium arenosum WH24, Isolated from the Gill of Pacific Oyster Crassostrea gigas from the North Sea of Germany: Co-cultivation and Prediction of Virulence

Cream colored bacteria from marine agar, strain WH24, WH77, and WH80 were isolated from the gill of the Crassostrea gigas a Pacific oyster with a filter-feeding habit that compels accompanying bacteria to demonstrate a high metabolic capacity, has proven able to colonize locations with changing circumstances. Based on the 16S rRNA gene sequence, all strains had high similarity to Photobacterium arenosum CAU 1568^T (99.72%). This study involved phenotypic traits, phylogenetic analysis, antimicrobial activity evaluation, genome mining, Co-cultivation experiments, and chemical studies of crude extracts using HPLC and LC-HRESIMS. Photobacterium arenosum WH24 and Zooshikella harenae WH53^Twere co-cultivated for 3 days in a rotary shaker at 160 rpm at 30 °C, and LC-MS monitored the chemical profiles of the co-cultures on the third day. The UV chromatograms of the extracts of the co-cultivation experiments show that Zooshikella harenae WH53^T could be inhibited by strain WH24. The high virulence of Photobacterium arenosum WH24 was confirmed by genome analysis. Gene groups with high virulence potential were detected: tssA (ImpA), tssB (ImpB/vipA), tssC (ImpC/vipB), tssE, tssF (ImpG/vasA), tssG (ImpH/vasB), tssM (IcmF/vasK), tssJ (vasD), tssK (ImpJ/vasE), tssL (ImpK/vasF), clpV (tssH), vasH, hcp, lapP, plpD, and tpsB family.

Amycolatopsis camponoti sp. nov., new tetracenomycin-producing actinomycete isolated from carpenter ant Camponotus vagus

An actinobacterial strain A23T, isolated from adult ant Camponotus vagus collected in Ryazan region (Russia) and established as tetracenomycin X producer, was subjected to a polyphasic taxonomic study. Morphological characteristics of this strain included well-branched substrate mycelium and aerial hyphae fragmented into rod-shaped elements. Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that strain A23T was most closely related to Amycolatopsis pretoriensis DSM 44654T. Average nucleotide identity and digital DNA-DNA hybridization values between the genome sequences of isolate A23T and its closest relative, Amycolatopsis pretoriensis DSM 44654T, were 39.5% and 88.6%, which were below the 70% and 95-96% cut-off point recommended for bacterial species demarcation, respectively. The genome size of the isolate A23T was 10,560,374 bp with a DNA G + C content of 71.2%. The whole-cell hydrolysate contained meso-diaminopimelic acid and arabinose and galactose as main diagnostic sugars as well as ribose and rhamnose. It contained MK-9(H4) as the predominant menaquinone and iso-C16:0, iso-C15:0, anteiso-C17:0 and C16:0 as the major cellular fatty acids. Diphosphatidylglycerol and phosphatidylethanolamine prevailed among phospholipids. Mycolic acids were not detected. Based on the phenotypic, genomic and phylogenetic data, isolate A23T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis camponoti sp. nov. is proposed, and the type strain is A23T (= DSM 111725T = VKM 2882T).

Isolation, Characterization, and Efficacy of Actinobacteria Associated with Arbuscular Mycorrhizal Spores in Promoting Plant Growth of Chili (Capsicum flutescens L.)

Nowadays, microorganisms that display plant growth promoting properties are significantly interesting for their potential role in reducing the use of chemical fertilizers. This research study proposed the isolation of the actinobacteria associated with arbuscular mycorrhizal fungi (AMF) spores and the investigation of their plant growth promoting properties in the in vitro assay. Three actinobacterial strains were obtained and identified to the genus Streptomyces (GETU-1 and GIG-1) and Amycolatopsis (GLM-2). The results indicated that all actinobacterial strains produced indole-3-acetic acid (IAA) and were positive in terms of siderophore, endoglucanase, and ammonia productions. In the in vitro assay, all strains were grown in the presence of water activity within a range of 0.897 to 0.998, pH values within a range of 5–11, and in the presence of 2.5% NaCl for the investigation of drought, pH, and salt tolerances, respectively. Additionally, all strains were able to tolerate commercial insecticides (propargite and methomyl) and fungicides (captan) at the recommended dosages for field applications. Only, Amycolatopsis sp. GLM-2 showed tolerance to benomyl at the recommended dose. All the obtained actinobacteria were characterized as plant growth promoting strains by improving the growth of chili plants (Capsicum flutescens L.). Moreover, the co-inoculation treatment of the obtained actinobacteria and AMF (Claroideoglomus etunicatum) spores could significantly increase plant growth, contribute to the chlorophyll index, and enhance fruit production in chili plants. Additionally, the highest value of AMF spore production and the greatest percentage of root colonization were observed in the treatment that had been co-inoculated with Streptomyces sp. GETU-1.