Whole Genome Sequence of Dermacoccus abyssi MT1.1 Isolated from the Challenger Deep of the Mariana Trench Reveals Phenazine Biosynthesis Locus and Environmental Adaptation Factors

Recent Advances in Phenazine Natural Products: Biosynthesis and Metabolic Engineering

Phenazine natural products are a class of nitrogen-containing heterocyclic compounds produced by microorganisms. The tricyclic ring molecules show various chemical structures and extensive pharmacological activities, such as antimicrobial, anticancer, antiparasitic, anti-inflammatory, and insecticidal activities, with low toxicity to the environment. Since phenazine-1-carboxylic acid has been developed as a registered biopesticide, the application of phenazine natural products will be promising in the field of agriculture pathogenic fungi control based on broad-spectrum antifungal activity, minimal toxicity to the environment, and improvement of crop production. Currently, there are still plenty of intriguing hidden biosynthetic pathways of phenazine natural products to be discovered, and the titer of naturally occurring phenazine natural products is insufficient for agricultural applications. In this review, we spotlight the progress regarding biosynthesis and metabolic engineering research of phenazine natural products in the past decade. The review provides useful insights concerning phenazine natural products production and more clues on new phenazine derivatives biosynthesis.

Distinct microbial nitrogen cycling processes in the deepest part of the ocean

The Mariana Trench (MT) is the deepest part of the ocean on Earth. Previous studies have described the microbial community structures and functional potential in the seawater and surface sediment of MT. Still, the metabolic features and adaptation strategies of the microorganisms involved in nitrogen cycling processes are poorly understood. In this study, comparative metagenomic approaches were used to study microbial nitrogen cycling in three MT habitats, including hadal seawater [9,600-10,500 m below sea level (mbsl)], surface sediments [0-46 cm below seafloor (cmbsf) at a water depth between 7,143 and 8,638 mbsl], and deep sediments (200-306 cmbsf at a water depth of 8,300 mbsl). We identified five new nitrite-oxidizing bacteria (NOB) lineages that had adapted to the oligotrophic MT slope sediment, via their CO2 fixation capability through the reductive tricarboxylic acid (rTCA) or Calvin-Benson-Bassham (CBB) cycle; an anammox bacterium might perform aerobic respiration and utilize sedimentary carbohydrates for energy generation because it contains genes encoding type A cytochrome c oxidase and complete glycolysis pathway. In seawater, abundant alkane-oxidizing Ketobacter species can fix inert N2 released from other denitrifying and/or anammox bacteria. This study further expands our understanding of microbial life in the largely unexplored deepest part of the ocean.

IMPORTANCE

The metabolic features and adaptation strategies of the nitrogen cycling microorganisms in the deepest part of the ocean are largely unknown. This study revealed that anammox bacteria might perform aerobic respiration in response to nutrient limitation or O2 fluctuations in the Mariana Trench sediments. Meanwhile, an abundant alkane-oxidizing Ketobacter species could fix N2 in hadal seawater. This study provides new insights into the roles of hadal microorganisms in global nitrogen biogeochemical cycles. It substantially expands our understanding of the microbial life in the largely unexplored deepest part of the ocean.

The dermacozines and light: a novel phenazine semiquinone radical based photocatalytic system from the deepest oceanic trench of the Earth

Dermacozines, the secondary metabolites of the Mariana Trench sediment bacterium Dermacoccus abyssi MT1.1T, were studied using cyclic voltammetry (CV), electron paramagnetic resonance (EPR), furthermore literature and own experimental UV-Vis spectroscopic data. With those measurements, we determined experimentally the positions of the HOMO, which shifts towards more positive potentials, and the constant LUMO on the standard hydrogen electrode scale, while the HOMO-LUMO gap gets deeper, respectively. The HOMO energies of dermacozines experimentally were proven to be water oxidising. EPR spectroscopy demonstrated the formation of semiquinone radicals in the case of dermacozines E and O upon irradiation with visible light corresponding to the absorption maxima (AM) of the chromophores. Our findings suggest that the dermacozines may assist the strain by maintaining redox homeostasis through its respiratory chain.

Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance

Democratizing genomic data science, including bioinformatics, can diversify the STEM workforce and may, in turn, bring new perspectives into the space sciences. In this respect, the development of education and research programs that bridge genome science with "place" and world-views specific to a given region are valuable for Indigenous students and educators. Through a multi-institutional collaboration, we developed an ongoing education program and model that includes Illumina and Oxford Nanopore sequencing, free bioinformatic platforms, and teacher training workshops to address our research and education goals through a place-based science education lens. High school students and researchers cultivated, sequenced, assembled, and annotated the genomes of 13 bacteria from Mars analog sites with cultural relevance, 10 of which were novel species. Students, teachers, and community members assisted with the discovery of new, potentially chemolithotrophic bacteria relevant to astrobiology. This joint education-research program also led to the discovery of species from Mars analog sites capable of producing N-acyl homoserine lactones, which are quorum-sensing molecules used in bacterial communication. Whole genome sequencing was completed in high school classrooms, and connected students to funded space research, increased research output, and provided culturally relevant, place-based science education, with participants naming three novel species described here. Students at St. Andrew's School (Honolulu, Hawai'i) proposed the name Bradyrhizobium prioritasuperba for the type strain, BL16AT, of the new species (DSM 112479T = NCTC 14602T). The nonprofit organization Kauluakalana proposed the name Brenneria ulupoensis for the type strain, K61T, of the new species (DSM 116657T = LMG = 33184T), and Hawai'i Baptist Academy students proposed the name Paraflavitalea speifideiaquila for the type strain, BL16ET, of the new species (DSM 112478T = NCTC 14603T).

The Diversity of Deep-Sea Actinobacteria and Their Natural Products: An Epitome of Curiosity and Drug Discovery

Bioprospecting of novel antibiotics has been the conventional norm of research fostered by researchers worldwide to combat drug resistance. With the exhaustion of incessant leads, the search for new chemical entities moves into uncharted territories such as the deep sea. The deep sea is a furthermost ecosystem with much untapped biodiversity thriving under extreme conditions. Accordingly, it also encompasses a vast pool of ancient natural products. Actinobacteria are frequently regarded as the bacteria of research interest due to their inherent antibiotic-producing capabilities. These interesting groups of bacteria occupy diverse ecological habitats including a multitude of different deep-sea habitats. In this review, we provide a recent update on the novel species and compounds of actinomycetes from the deep-sea environments within a period of 2016–2022. Within this period, a total of 24 new species of actinomycetes were discovered and characterized as well as 101 new compounds of various biological activities. The microbial communities of various deep-sea ecosystems are the emerging frontiers of bioprospecting.

Spatial Variability of Bacterial Community Compositions in the Mariana Trench

Hadal microorganisms play an important role in the biogeochemical processes in marine ecosystems and act as a valuable resource for industrial applications. This paper presents the bacterial community analysis of samples taken from the Challenger Deep within the Mariana Trench, which is the deepest site in the ocean. High-throughput 16S rRNA gene amplicon sequencing was used to reveal that the vertically sampled bacterial populations at eight stations varied at the surface to 10 km depth. The surface water samples harbored a distinct bacterial assemblage, while the mesopelagic and bathyal samples manifested different bacterial community composition, which was not consistent with previous studies. Gammaproteobacteria was the most abundant bacteria in the bathyal and hadal water. The hadal bacterial community consisted mostly of Alteromonadales and Oceanospirillales. The former was widely spread in the water column, which might suggest habitat partitioning at the genus and OTU levels, while the latter might represent hadal-enriched hydrocarbon degraders. The present work complements the current knowledge and understanding of the bathyal and hadal bacterial communities of the Mariana Trench.

Marine natural products

Covering: 2020This review covers the literature published in 2020 for marine natural products (MNPs), with 757 citations (747 for the period January to December 2020) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1407 in 420 papers for 2020), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. A meta analysis of bioactivity data relating to new MNPs reported over the last five years is also presented.

Plant Beneficial Deep-Sea Actinobacterium, Dermacoccus abyssi MT1.1T Promote Growth of Tomato (Solanum lycopersicum) under Salinity Stress

Simple Summary

Salt stress is an important environmental problem that negatively affects agricultural and food production in the world. Currently, the use of plant beneficial bacteria for plant growth promotion is attractive due to the demand for eco-friendly and sustainable agriculture. In this study, salt tolerant deep-sea actinobacterium, Dermacoccus abyssi MT1.1^T was investigated plant growth promotion and salt stress mitigation in tomato seedlings. In addition, D. abyssi MT1.1^T whole genome was analyzed for plant growth promoting traits and genes related to salt stress alleviation in plants. We also evaluated the biosafety of this strain on human health and organisms in the environment. Our results highlight that the inoculation of D. abyssi MT1.1^T could reduce the negative effects of salt stress in tomato seedlings by growth improvement, total soluble sugars accumulation and hydrogen peroxide reduction. Moreover, this strain could survive and colonize tomato roots. Biosafety testing and genome analysis of D. abyssi MT1.1^T showed no pathogenicity risk. In conclusion, we provide supporting evidence on the potential of D. abyssi MT1.1^T as a safe strain for use in plant growth promotion under salt stress.

Abstract

Salt stress is a serious agricultural problem threatens plant growth and development resulted in productivity loss and global food security concerns. Salt tolerant plant growth promoting actinobacteria, especially deep-sea actinobacteria are an alternative strategy to mitigate deleterious effects of salt stress. In this study, we aimed to investigate the potential of deep-sea Dermacoccus abyssi MT1.1^T to mitigate salt stress in tomato seedlings and identified genes related to plant growth promotion and salt stress mitigation. D. abyssi MT1.1^T exhibited plant growth promoting traits namely indole-3-acetic acid (IAA) and siderophore production and phosphate solubilization under 0, 150, 300, and 450 mM NaCl in vitro. Inoculation of D. abyssi MT1.1^T improved tomato seedlings growth in terms of shoot length and dry weight compared with non-inoculated seedlings under 150 mM NaCl. In addition, increased total soluble sugar and total chlorophyll content and decreased hydrogen peroxide content were observed in tomato inoculated with D. abyssi MT1.1^T. These results suggested that this strain mitigated salt stress in tomatoes via osmoregulation by accumulation of soluble sugars and H₂O₂ scavenging activity. Genome analysis data supported plant growth promoting and salt stress mitigation potential of D. abyssi MT1.1^T. Survival and colonization of D. abyssi MT1.1^T were observed in roots of inoculated tomato seedlings. Biosafety testing on D. abyssi MT1.1^T and in silico analysis of its whole genome sequence revealed no evidence of its pathogenicity. Our results demonstrate the potential of deep-sea D. abyssi MT1.1^T to mitigate salt stress in tomato seedlings and as a candidate of eco-friendly bio-inoculants for sustainable agriculture.

Bioactive Molecules from Extreme Environments II

Marine organisms are known to produce a wide variety of natural products that are unique in terms of diversity, structural, and functional properties [...].

Deep-Sea Actinobacteria Mitigate Salinity Stress in Tomato Seedlings and Their Biosafety Testing

Soil salinity is an enormous problem affecting global agricultural productivity. Deep-sea actinobacteria are interesting due to their salt tolerance mechanisms. In the present study, we aim to determine the ability of deep-sea Dermacoccus (D. barathri MT2.1^T and D. profundi MT2.2^T) to promote tomato seedlings under 150 mM NaCl compared with the terrestrial strain D. nishinomiyaensis DSM20448^T. All strains exhibit in vitro plant growth-promoting traits of indole-3-acetic acid production, phosphate solubilization, and siderophore production. Tomato seedlings inoculated with D. barathri MT2.1^T showed higher growth parameters (shoot and root length, dry weight, and chlorophyll content) than non-inoculated tomato and the terrestrial strain under 150 mM NaCl. In addition, hydrogen peroxide (H₂O₂) in leaves of tomatoes inoculated with deep-sea Dermacoccus was lower than the control seedlings. This observation suggested that deep-sea Dermacoccus mitigated salt stress by reducing oxidative stress caused by hydrogen peroxide. D. barathri MT2.1^T showed no harmful effects on Caenorhabditis elegans, Daphnia magna, Eisenia foetida, and Escherichia coli MC4100 in biosafety tests. This evidence suggests that D. barathri MT2.1^T would be safe for use in the environment. Our results highlight the potential of deep-sea Dermacoccus as a plant growth promoter for tomatoes under salinity stress.

Dermacozine N, the First Natural Linear Pentacyclic Oxazinophenazine with UV-Vis Absorption Maxima in the Near Infrared Region, along with Dermacozines O and P Isolated from the Mariana Trench Sediment Strain Dermacoccus abyssi MT 1.1T

Three dermacozines, dermacozines N-P (1-3), were isolated from the piezotolerant Actinomycete strain Dermacoccus abyssi MT 1.1T, which was isolated from a Mariana Trench sediment in 2006. Herein, we report the elucidation of their structures using a combination of 1D/2D NMR, LC-HRESI-MSn, UV-Visible, and IR spectroscopy. Further confirmation of the structures was achieved through the analysis of data from density functional theory (DFT)-UV-Visible spectral calculations and statistical analysis such as two tailed t-test, linear regression-, and multiple linear regression analysis applied to either solely experimental or to experimental and calculated 13C-NMR chemical shift data. Dermacozine N (1) bears a novel linear pentacyclic phenoxazine framework that has never been reported as a natural product. Dermacozine O (2) is a constitutional isomer of the known dermacozine F while dermacozine P (3) is 8-benzoyl-6-carbamoylphenazine-1-carboxylic acid. Dermacozine N (1) is unique among phenoxazines due to its near infrared (NIR) absorption maxima, which would make this compound an excellent candidate for research in biosensing chemistry, photodynamic therapy (PDT), opto-electronic applications, and metabolic mapping at the cellular level. Furthermore, dermacozine N (1) possesses weak cytotoxic activity against melanoma (A2058) and hepatocellular carcinoma cells (HepG2) with IC50 values of 51 and 38 μM, respectively.

The diverse functional genes of maize rhizosphere microbiota assessed using shotgun metagenomics

BACKGROUND

The geographical diversification in chemical, biological and physical properties of plant biospheres instigates heterogenicity in the proliferation of important soil microbiome. Controlling functions and structure of plant rhizosphere from a better understanding and prediction of a plant's immediate environment will help assess plant-microbe interplay, improve the productivity of plant ecosystems and improve plant response to adverse soil conditions. Here we characterized functional genes of the microbial community of maize rhizosphere using a culture-independent method.

RESULTS

Our metadata showed microbial genes involved in nitrogen fixation, phosphate solubilization, quorum sensing molecules, trehalose, siderophore production, phenazine biosynthesis protein, daunorubicin resistance, acetoin, 1-aminocyclopropane-1-carboxylate deaminase, 4-hydroxybenzoate, disease control and stress-reducing genes (superoxidase dismutase, catalase, peroxidase, etc.). β-Diversity showed that there is a highly significant difference between most of the genes mined from rhizosphere soil samples and surrounding soils.

CONCLUSIONS

The high relative abundance of stress-reducing genes mined from this study showed that the sampling sites harbor not only important plant-beneficial organisms but also a hotspot for developing bio-fertilizers. Nevertheless, since most of these organisms are unculturable, mapping cultivation strategies for their growth could make them readily available as bio-inoculants and possible biotechnological applications in the future. © 2020 Society of Chemical Industry.

Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench

A Micromonospora strain, isolate MT25^T, was recovered from a sediment collected from the Challenger Deep of the Mariana Trench using a selective isolation procedure. The isolate produced two major metabolites, n-acetylglutaminyl glutamine amide and desferrioxamine B, the chemical structures of which were determined using 1D and 2D-NMR, including ¹H-¹⁵N HSQC and ¹H-¹⁵N HMBC 2D-NMR, as well as high resolution MS. A whole genome sequence of the strain showed the presence of ten natural product-biosynthetic gene clusters, including one responsible for the biosynthesis of desferrioxamine B. Whilst 16S rRNA gene sequence analyses showed that the isolate was most closely related to the type strain of Micromonospora chalcea, a whole genome sequence analysis revealed it to be most closely related to Micromonospora tulbaghiae 45142^T. The two strains were distinguished using a combination of genomic and phenotypic features. Based on these data, it is proposed that strain MT25^T (NCIMB 15245^T, TISTR 2834^T) be classified as Micromonospora provocatoris sp. nov. Analysis of the genome sequence of strain MT25^T (genome size 6.1 Mbp) revealed genes predicted to responsible for its adaptation to extreme environmental conditions that prevail in deep-sea sediments.

Genomic analysis of Brevundimonas mediterranea D151-2-6 isolated from hadal sediment of the Pacific Ocean

Brevundimonas mediterranea D151-2-6 is a marine bacterium that has been isolated from 6582-m hadal sediment of the Pacific Ocean. Here, we present the complete genome sequence of B. mediterranea D151-2-6. The genome of strain D151-2-6 is 3,383,373 base pairs in size. It contains one circular chromosome with an average G + C content of 67.41%, 53 tRNAs, and 3270 protein-coding genes. Genomic analysis of strain D151-2-6 revealed that its genome is more highly enriched in genes that encode proteins involved in signal transduction and transcription than any of the other available completely sequenced Brevundimonas genomes. Some of these genes might improve ecological fitness in the hadal extreme environment. Genomic information on B. mediterranea D151-2-6 provides insights into the adaptation strategies and physiological features of Brevundimonas spp. in the hadal environment.