Actinophytocola gilvus sp. nov., isolated from desert soil crusts, and emended description of the genus Actinophytocola Indananda et al. 2010

Actinophytocola gossypii sp. nov. and Streptomyces gossypii sp. nov., two novel actinomycetes isolated from rhizosphere soil of cotton

Two Gram-positive, aerobic and non-motile actinomycetes, designated S1-96^T and N2-109^T, were isolated from soils collected from a cotton field. They are described as representing two novel species of genera Actinophytocola and Streptomyces through a polyphasic approach. Analysis of 16S rRNA gene sequences revealed that strains S1-96^T and N2-109^T showed highest similarity to Actinophytocola xinjiangensis CGMCC 4.4663^T (99.10 %) and Streptomyces iconiensis BNT558^T (98.21 %), respectively. Phylogenetic analyses based on 16S rRNA and core genes confirmed the close relationships of these strains. Genomic analyses further supported the novel taxonomic delimitation of these two species based on digital DNA-DNA hybridization and average nucleotide identity. Strains S1-96^T and N2-109^T contained MK-9(H₄) and MK-9(H₆) as the most abundant menaquinone, respectively. High abundances of iso-fatty acids were detected in both strains, which was similar to their close relatives. Physiological and polar lipid analyses also revealed differences between these strains and their phylogenetic neighbours, supporting their taxonomic delimitation as novel species. The names Actinophytocola gossypii sp. nov. (type strain S1-96^T=JCM 34412^T=CGMCC 4.7707^T) and Streptomyces gossypii sp. nov. (type strain N2-109^T=JCM 34628^T=CGMCC 4.7717^T) are proposed.

Actinobacteria From Desert: Diversity and Biotechnological Applications

Deserts, as an unexplored extreme ecosystem, are known to harbor diverse actinobacteria with biotechnological potential. Both multidrug-resistant (MDR) pathogens and environmental issues have sharply raised the emerging demand for functional actinobacteria. From 2000 to 2021, 129 new species have been continuously reported from 35 deserts worldwide. The two largest numbers are of the members of the genera Streptomyces and Geodermatophilus, followed by other functional extremophilic strains such as alkaliphiles, halotolerant species, thermophiles, and psychrotolerant species. Improved isolation strategies for the recovery of culturable and unculturable desert actinobacteria are crucial for the exploration of their diversity and offer a better understanding of their survival mechanisms under extreme environmental stresses. The main bioprospecting processes involve isolation of target actinobacteria on selective media and incubation and selection of representatives from isolation plates for further investigations. Bioactive compounds obtained from desert actinobacteria are being continuously explored for their biotechnological potential, especially in medicine. To date, there are more than 50 novel compounds discovered from these gifted actinobacteria with potential antimicrobial activities, including anti-MDR pathogens and anti-inflammatory, antivirus, antifungal, antiallergic, antibacterial, antitumor, and cytotoxic activities. A range of plant growth-promoting abilities of the desert actinobacteria inspired great interest in their agricultural potential. In addition, several degradative, oxidative, and other functional enzymes from desert strains can be applied in the industry and the environment. This review aims to provide a comprehensive overview of desert environments as a remarkable source of diverse actinobacteria while such rich diversity offers an underexplored resource for biotechnological exploitations.

Coupling the endophytic microbiome with the host transcriptome in olive roots

The connection between olive genetic responses to environmental and agro-climatic conditions and the composition, structure and functioning of host-associated, belowground microbiota has never been studied under the holobiont conceptual framework. Two groups of cultivars growing under the same environmental, pedological and agronomic conditions, and showing highest (AH) and lowest (AL) Actinophytocola relative abundances, were earlier identified. We aimed now to: i) compare the root transcriptome profiles of these two groups harboring significantly different relative abundances in the above-mentioned bacterial genus; ii) examine their rhizosphere and root-endosphere microbiota co-occurrence networks; and iii) connect the root host transcriptome pattern to the composition of the root microbial communities by correlation and co-occurrence network analyses. Significant differences in olive gene expression were found between the two groups. Co-occurrence networks of the root endosphere microbiota were clearly different as well. Pearson's correlation analysis enabled a first portray of the interaction occurring between the root host transcriptome and the endophytic community. To further identify keystone operational taxonomic units (OTUs) and genes, subsequent co-occurrence network analysis showed significant interactions between 32 differentially expressed genes (DEGs) and 19 OTUs. Overall, negative correlation was detected between all upregulated genes in the AH group and all OTUs except of Actinophytocola. While two groups of olive cultivars grown under the same conditions showed significantly different microbial profiles, the most remarkable finding was to unveil a strong correlation between these profiles and the differential gene expression pattern of each group. In conclusion, this study shows a holistic view of the plant-microbiome communication.

Defining the root endosphere and rhizosphere microbiomes from the World Olive Germplasm Collection

The bacterial and fungal communities from the olive (Olea europaea L.) root systems have not yet been simultaneously studied. We show in this work that microbial communities from the olive root endosphere are less diverse than those from the rhizosphere. But more relevant was to unveil that olive belowground communities are mainly shaped by the genotype of the cultivar when growing under the same environmental, pedological and agronomic conditions. Furthermore, Actinophytocola, Streptomyces and Pseudonocardia are the most abundant bacterial genera in the olive root endosphere, Actinophytocola being the most prevalent genus by far. In contrast, Gp6, Gp4, Rhizobium and Sphingomonas are the main genera in the olive rhizosphere. Canalisporium, Aspergillus, Minimelanolocus and Macrophomina are the main fungal genera present in the olive root system. Interestingly enough, a large number of as yet unclassified fungal sequences (class level) were detected in the rhizosphere. From the belowground microbial profiles here reported, it can be concluded that the genus Actinophytocola may play an important role in olive adaptation to environmental stresses. Moreover, the huge unknown fungal diversity here uncovered suggests that fungi with important ecological function and biotechnological potential are yet to be identified.

Actinophytocola glycyrrhizae sp. nov. isolated from the rhizosphere of Glycyrrhiza inflata

A Gram-stain-positive, aerobic actinomycete, designated strain BMP B8152^T, was isolated from the rhizosphere of Glycyrrhiza inflata collected ashore, in Kashi, Xinjiang province, northwest PR China. A polyphasic approach was used to establish the taxonomic position of this strain. BMP B8152^T was observed to form non-fragmented substrate mycelium, and relatively scanty aerial mycelium with rod-shaped spores. Cell-wall hydrolysates contained meso-diaminopimelic acid, galactose, arabinose, glucose and rhamnose (trace). Mycolic acids were not detected. The diagnostic phospholipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, ninhydrin-positive phosphoglycolipid and phosphatidylinositol. The predominant menaquinone and fatty acid were MK-9(H4) and iso-branched hexadecanoate (iso-C16 : 0), respectively. The phylogenetic analyses based on the 16S rRNA gene sequences indicated that BMP B8152^T formed a distinct monophyletic clade clustered with Actinophytocola timorensisID05-A0653^T (98.8 % 16S rRNA gene sequence similarity), Actinophytocola oryzaeGMKU 367^T (98.6 %), Actinophytocola corallinaID06-A0464^T (98.2 %) and Actinophytocola burenkhanensisMN08-A0203^T (97.5 %). In addition, DNA-DNA hybridization values between BMP B8152^T and A. timorensisID05-A0653^T(44.2±3.6 %) and A. oryzaeGMKU 367^T(36.7±2.3 %) were well below the 70 % limit for species identification. The combined phenotypic and genotypic data indicate that the isolate represents a novel species of the genus Actinophytocola, for which the name Actinophytocola glycyrrhizae sp. nov., is proposed, with the type strain BMP B8152^T (=KCTC 49002^T=CGMCC 4.7433^T).

Actinophytocola xanthii sp. nov., an actinomycete isolated from rhizosphere soil of the plant Xanthium sibiricum

A novel actinomycete strain, 11-183T, was isolated from the rhizosphere soil of Xanthium sibiricum, which was collected in Tangshan, Hebei, China. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain 11-183T formed a clade within the genus Actinophytocola, with a maximum similarity of 98.44 % to Actinophytocola xinjiangensis QAIII60T, followed by 97.76 % similarity to Actinophytocola sediminis YIM M13705T. The average nucleotide identity and digital DNA-DNA hybridization values differed by 79.24 and 23.4 %, respectively, between strain 11-183T and Actinophytocolaxinjiangensis QAIII60T. Strain 11-183T grew well on N-Z-amine agar, and it produced a scant, white aerial mycelium. The isolate formed pale yellow to brown-black colonies and a dense, non-fragmented, branched substrate mycelium, and produced aerial hyphae on which nodular spore chains formed. Growth was observed at salinities ranging from 0 to 2 %, at pH values ranging from pH 6.5 to 8.0 and at temperatures ranging from 15 to 37 °C. The cell-wall amino acids included meso-diaminopimelic acid. Whole cell hydrolysates contained galactose and glucose. The principal fatty acids were iso-C16 : 0, iso-C16 : 1 H and C17 : 1ω6c. Diphosphatidylglycerol, phosphatidylmonomethylethanolamine and phosphatidylethanolamine were the diagnostic phospholipids. The isoprenoid quinones included MK-9(H4) and MK-10(H4). The G+C content of the genomic DNA was 71.7 mol%. Based on the genotypic and phenotypic data, we conclude that strain 11-183T belongs to a novel species of the genus Actinophytocola. The name proposed for the novel species is Actinophytocola xanthii sp. nov., with the type strain 11-183T (=KCTC 39690T= MCCC 1K02062T).

Description of Deinococcus oregonensis sp. nov., from biological soil crusts in the Southwestern arid lands of the United States of America

Biological soil crusts are distinct habitats, harbor unique prokaryotic diversity and gave an impetus to isolate novel species. In the present study, a pink-pigmented bacterium, (OR316-6^T), was isolated from biological soil crusts using oligotrophic BG11-PGY medium. Strain OR316-6^T was Gram-positive, short rods, non-motile and non-spore forming. Cells were positive for catalase, oxidase and β-galactosidase and negative for most of the enzymatic activities. The major fatty acids present were C_16:0, C_17:0, and C_16:1ω7c and contained MK-8 and MK-10 as the predominant menaquinones. The cell wall peptidoglycan was of A3β variant with L-ornithine as the diamino acid. Based on the above characteristics, strain OR316-6^T was assigned to the genus Deinococcus. The phylogenetic analysis indicated that strain OR316-6^T was closely related to D. aquatilis DSM 23025^T with a 16S rRNA gene similarity of 99.3 % and clustered with a bootstrap value of 100 %. DNA-DNA similarity between strain OR316-6^T and D. aquatilis DSM 23025^T was 37.0 % indicating that strain OR316-6^T was a novel species. Further, DNA fingerprinting of stains OR316-6^T and D. aquatilis DSM 23035^T demonstrated that both strains were related to each other with a similarity coefficient of only 0.32 and supported the species status to strain OR316-6^T. In addition, phenotypic characteristics distinguished strain OR316-6^T from D. aquatilis DSM 23025^T. Based on the cumulative differences, strain OR316-16^T exhibited with its closely related species, it was identified as a novel species and proposed the name Deinococcus oregonensis sp. nov. The type strain is D. oregonensis sp. nov. (OR316-6^T = JCM 13503^T = DSM 17762^T).

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

During our investigations of new actinobacterial taxa, a novel actinobacterial strain, designated MB20^T, was isolated from a Saharan soil sample, collected in the Mzab region (Ghardaïa province, southern Algeria). In order to reveal its taxonomic position, the novel strain was characterized following a polyphasic taxonomic approach. It was noticed that strain MB20^T produced white, branched and fragmented substrate mycelium with no aerial mycelium on most of the media tested. Chemotaxonomic and phylogenetic studies clearly demonstrated that strain MB20^T belonged to the family Pseudonocardiaceae and was closely related to the genus Actinophytocola. Cell-wall hydrolysates contained meso-diaminopimelic acid but not glycine, and whole-cell hydrolysates contained galactose, glucose and ribose. The diagnostic phospholipid was phosphatidylethanolamine. Mycolic acids were not detected while the predominant fatty acid was found to be iso-branched hexadecanoate (iso-C16 : 0). The major menaquinone was MK-9(H4). Results of the 16S rRNA gene sequence comparison revealed that strain MB20^T shared the highest degree of similarity with Actinophytocola gilvus DSM 45828^T (98.5 %), Actinophytocola corallina DSM 45659^T (98.0 %) and Actinophytocola timorensis DSM 45660^T (97.5 %). However, DNA-DNA hybridization studies showed only 32.9 % similarity with A. timorensis, 23.7 % similarity with A. gilvus and 17.9 % similarity with A. corallina. On the basis of phenotypic characteristics, 16S rRNA gene sequence comparisons and DNA-DNA hybridization, strain MB20^T was revealed to be a representative of a novel species of the genus Actinophytocola, for which the name Actinophytocola algeriensis sp. nov. (type strain MB20^T =DSM 46746^T =CECT 8960^T) is proposed.