Sphingomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench

Genomic-based taxonomic classification of the order Sphingomonadales

The order Sphingomonadales strains are globally distributed in various biomes and are renowned for their biodegradable and biosynthesis capabilities. At present, it consists of 4 families and 49 genera making it the third largest order within the class Alphaproteobacteria. However, their taxonomy remains complex, especially due to polyphyly in the family Sphingomonadaceae. In this study, we collected 429 Sphingomonadales type strain genomes, reconstructed robust phylogenomic relationships, and proposed delineation thresholds at the genus and family levels based on average amino acid identities (AAI) and evolutionary distances (ED). Based on the maximum-likelihood and Bayesian phylogenomic trees reconstructed by two molecular sets determined by orthologous sequence identity and the Genome Taxonomy Database, the consensus degree values were all higher than 90%, revealing that those phylogenomic trees had similar topological structures. By confirming monophyletic taxa and determining stable nodes, we reclassified the order Sphingomonadales into thirteen families including nine novel ones. AAI calculations indicated that the average intra-family AAI values ranged from 0.62 to 0.84, while inter-family ones were 0.51 to 0.60. ED summaries demonstrated that the average and median intra-family ED values were 0.16 to 0.57, and inter-family ones ranged from 0.50 to 1.22. Comparisons of AAI and ED values calculated by using genomic and phylogenetic analyses supported that those 13 families were significantly separated with p values < 2.2×10-16. Thus, it was speculated that the AAI and ED thresholds for distinguishing different families were <0.6 and >0.5, respectively. Additionally, we reclassified 163 species into new genera with their phylogenetic topologies, according to the previous genus AAI and ED boundaries of 0.7 and 0.4. Our study is the first genomic-based study of the order Sphingomonadales and will promote further insights into the evolution of this order.

Albibacterium profundi sp. nov., isolated from sediment of the Challenger Deep of Mariana Trench, and reclassification of Pedobacter indicus as Albibacterium indicum comb. nov

A rod-shaped, white-pigmented, non-motile, Gram-stain-negative bacterium, designated RHL897T, was isolated from sediments collected at the Mariana Trench Challenger Deep (10,816 m). Strain RHL897T was strictly aerobic and grew at 4-37 °C, pH 6.0-10.0 and in the presence of 0-11.0 % (w/v) NaCl. Its genomic DNA G+C content was 41.2%. Metabolic analysis revealed mechanisms for salt tolerance, abundant metal ion transport proteins and stronger resistance to heavy metals such as arsenic and mercury compared to the closest reference strains, likely linked to adaptation to the hadal sediment environment. The predominant menaquinone was MK-7, and the major polar lipids were phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified glycolipid. The main fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and iso-C17 : 0 3OH. Strain RHL897T exhibited the highest 16S rRNA gene sequence similarity to the type strain of Pedobacter indicus (97.9%) and Albibacterium bauzanense (96.1%). Phylogenetic trees constructed based on 16S rRNA gene sequences and a 549 core gene set indicated that strain RHL897T was closely related to P. indicus and A. bauzanense, with all three species clustering within a distinct clade. Combined with the analyses of average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization, strain RHL897T represented a novel species of the genus Albibacterium, for which the name Albibacterium profundi sp. nov. is proposed. The type strain is RHL897T (=MCCC 1K09221T=KCTC 102276T). Furthermore, the revised phylogeny with the inclusion of RHL897T suggested that P. indicus should be reclassified under the genus Albibacterium and renamed Albibacterium indicum.

Widespread and active piezotolerant microorganisms mediate phenolic compound degradation under high hydrostatic pressure in hadal trenches

Phenolic compounds, as well as other aromatic compounds, have been reported to be abundant in hadal trenches. Although high-throughput sequencing studies have hinted at the potential of hadal microbes to degrade these compounds, direct microbiological, genetic and biochemical evidence under in situ pressures remain absent. Here, a microbial consortium and a pure culture of Pseudomonas, newly isolated from Mariana Trench sediments, efficiently degraded phenol under pressures up to 70 and 60 MPa, respectively, with concomitant increase in biomass. By analyzing a high-pressure (70 MPa) culture metatranscriptome, not only was the entire range of metabolic processes under high pressure generated, but also genes encoding complete phenol degradation via ortho- and meta-cleavage pathways were revealed. The isolate of Pseudomonas also contained genes encoding the complete degradation pathway. Six transcribed genes (dmpKLMNOPsed) were functionally identified to encode a multicomponent hydroxylase catalyzing the hydroxylation of phenol and its methylated derivatives by heterogeneous expression. In addition, key catabolic genes identified in the metatranscriptome of the high-pressure cultures and genomes of bacterial isolates were found to be all widely distributed in 22 published hadal microbial metagenomes. At microbiological, genetic, bioinformatics, and biochemical levels, this study found that microorganisms widely found in hadal trenches were able to effectively drive phenolic compound degradation under high hydrostatic pressures. This information will bridge a knowledge gap concerning the microbial aromatics degradation within hadal trenches.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00224-2.

Diversity links to functionality: Unraveling the impact of pressure disruption and culture medium on crude oil-enriched microbial communities from the deep Eastern Mediterranean Sea

Mesopelagic water from the deep Eastern Mediterranean Sea (EMS) was collected under disrupted (REPRESS) or undisturbed (HP) pressure conditions and was acclimated to oil (OIL) or dispersed-oil (DISPOIL) under in situ pressure and temperature (10 MPa, 14 °C). Decompression resulted in oil-acclimatised microbial communities of lower diversity despite the restoration of in situ pressure conditions during the 1-week incubation. Further biodiversity loss was observed when oil-acclimatised communities were transferred to ONR7 medium to facilitate the isolation of oil-degrading bacteria. Microbial diversity loss impacted the degradation of recalcitrant oil compounds, especially PAHs, as low-abundance taxa, linked with PAH degradation, were outcompeted in the enrichment process. Thalassomonas, Pseudoalteromonas, Halomonas and Alcanivorax were enriched in ONR7 under all experimental conditions. No effect of dispersant application on the microbial community structure was identified. A. venustensis was isolated under all tested conditions suggesting a potential key role of this species in hydrocarbons removal in the deep EMS.

Adaptive characteristics of indigenous microflora in an organically contaminated high salinity groundwater

Salinity, a critical factor, could directly or indirectly affect the microbial community structure and diversity. Changes in salinity levels act as environmental filters that influence the transformation of key microbial species. This study investigates the adaptive characteristics of indigenous microflora in groundwater in relation to external organic pollutants under high salinity stress. A highly mineralized shallow groundwater in Northwest China was conducted as the study area, and six representative sampling points were chosen to explore the response of groundwater hydrochemical parameters and microflora, as well as to identify the tolerance mechanisms of indigenous microflora to combined pollution. The results revealed that the dominant genera found in high salinity groundwater contaminated with organic pollutants possess the remarkable ability to degrade such pollutants even under challenging high salinity conditions, including Halomonas, Pseudomonas, Halothiobacillus, Sphingomonas, Lutibacter, Aquabacterium, Thiomicrospira, Aequorivita, etc. The hydrochemical factors, including total dissolved solids (TDS), sulfide, nitrite, nitrate, oxidation reduction potential (ORP), NH3-N, Na, Fe, benzene series, phenols, and halogenated hydrocarbons, demonstrated a significant influence on microflora. High levels of sulphate and sulfide in groundwater can exhibit dual effects on microflora. On one hand, these compounds can inhibit the growth and metabolism of microorganisms. On the other hand, they can also serve as effective electron donors/receptors during the microbial degradation of organic pollutants. Microorganisms exhibit resilience to the inhibitory effects of high salinity and organic pollutants via a series of tolerance mechanisms, such as strengthening the extracellular membrane barrier, enhancing the synthesis of relevant enzymes, initiating novel biochemical reactions, improving cellular self-healing capabilities, responding to unfavorable environmental conditions by migration, and enhancing the S cycle for the microbial metabolism of organic pollutants.

Isolation of a Novel Thermophilic Methanogen and the Evolutionary History of the Class Methanobacteria

Methanogens can produce methane in anaerobic environments via the methanogenesis pathway, and are regarded as one of the most ancient life forms on Earth. They are ubiquitously distributed across distinct ecosystems and are considered to have a thermophilic origin. In this study, we isolated, pure cultured, and completely sequenced a single methanogen strain DL9LZB001, from a hot spring at Tengchong in Southwest China. DL9LZB001 is a thermophilic and hydrogenotrophic methanogen with an optimum growth temperature of 65 °C. It is a putative novel species, which has been named Methanothermobacter tengchongensis-a Class I methanogen belonging to the class Methanobacteria. Comparative genomic and ancestral analyses indicate that the class Methanobacteria originated in a hyperthermal environment and then evolved to adapt to ambient temperatures. This study extends the understanding of methanogens living in geothermal niches, as well as the origin and evolutionary history of these organisms in ecosystems with different temperatures.

Novel primers for 16S rRNA gene-based archaeal and bacterial community analysis in oceanic trench sediments

High-throughput sequencing of the 16S ribosomal RNA (16S rRNA) gene has been successfully applied to explore the microbial structure and dynamics in various environments. The distinctive microbial communities in oceanic trench sediments are expected because of the extremely high pressure and V-shape topology that caused the isolation from the other marine sediments. However, they have only been primarily targeted using 'universal' primers that provide variable performances for different environments. It is necessary to design specific primers to improve the detection resolution of unique microbial groups in oceanic trenches. Here, we designed one pair of bacterial and two pairs of archaeal specific primers based on 16S rRNA gene full-length sequences that truly come from trench sediment and tested their performances in 30 oceanic trench sediment samples. An in silico analysis showed that the V3-V4 hypervariable region was the most informative and representative for oceanic trench microbial groups. Compared with the 'universal' primers, 46 bacterial families were only detected by newly designed primer B344F/B749R, and eight archaeal families were only detected by the newly designed primer A306F/A713R which covered the one or two orders of magnitude more ASVs (amplicon sequence variants) (1,470,216) in the tested total 30 samples. Moreover, A306F/A713R had the largest number of observed ASVs suggesting its better performance in discovering more archaeal species which were easily ignored in universal primer-based experiments for oceanic trench sediments. The novel primers designed in this research could be a better option to access the unique microbial communities in extreme oceanic trench sediments.Key points• Defining V3-V4 as the most adequate hypervariable region for archaea and bacteria from oceanic trench sediments.• Three sets of bacterial and archaeal primers appear validity and advantage in revealing the real trench microbial communities.• The novel primers provide a better option to specifically detect the unique microbial communities in extreme oceanic trench sediments.

Genomic Characterization of Potential Plant Growth-Promoting Features of Sphingomonas Strains Isolated from the International Space Station

In an ongoing microbial tracking investigation of the International Space Station (ISS), several Sphingomonas strains were isolated. Based on the 16S rRNA gene sequence, phylogenetic analysis identified the ISS strains as Sphingomonas sanguinis (n = 2) and one strain isolated from the Kennedy Space Center cleanroom (used to assemble various Mars mission spacecraft components) as Sphingomonas paucimobilis. Metagenomic sequence analyses of different ISS locations identified 23 Sphingomonas species. An abundance of shotgun metagenomic reads were detected for S. sanguinis in the location from where the ISS strains were isolated. A complete metagenome-assembled genome was generated from the shotgun reads metagenome, and its comparison with the whole-genome sequences (WGS) of the ISS S. sanguinis isolates revealed that they were highly similar. In addition to the phylogeny, the WGS of these Sphingomonas strains were compared with the WGS of the type strains to elucidate genes that can potentially aid in plant growth promotion. Furthermore, the WGS comparison of these strains with the well-characterized Sphingomonas sp. LK11, an arid desert strain, identified several genes responsible for the production of phytohormones and for stress tolerance. Production of one of the phytohormones, indole-3-acetic acid, was further confirmed in the ISS strains using liquid chromatography-mass spectrometry. Pathways associated with phosphate uptake, metabolism, and solubilization in soil were conserved across all the S. sanguinis and S. paucimobilis strains tested. Furthermore, genes thought to promote plant resistance to abiotic stress, including heat/cold shock response, heavy metal resistance, and oxidative and osmotic stress resistance, appear to be present in these space-related S. sanguinis and S. paucimobilis strains. Characterizing these biotechnologically important microorganisms found on the ISS and harnessing their key features will aid in the development of self-sustainable long-term space missions in the future. IMPORTANCESphingomonas is ubiquitous in nature, including the anthropogenically contaminated extreme environments. Members of the Sphingomonas genus have been identified as potential candidates for space biomining beyond earth. This study describes the isolation and identification of Sphingomonas members from the ISS, which are capable of producing the phytohormone indole-3-acetic acid. Microbial production of phytohormones will help future in situ studies, grow plants beyond low earth orbit, and establish self-sustainable life support systems. Beyond phytohormone production, stable genomic elements of abiotic stress resistance, heavy metal resistance, and oxidative and osmotic stress resistance were identified, rendering the ISS Sphingomonas isolate a strong candidate for biotechnology-related applications.

Pelagovum pacificum gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from surface seawater of the Mariana Trench

A Gram-stain-negative, aerobic, ovoid-rod-shaped bacterium, designated strain SM1903^T, was isolated from surface seawater of the Mariana Trench. The strain grew at 15-37 °C (optimum, 35 °C) and with 1-15 % (optimum, 4 %) NaCl. It hydrolysed aesculin but did not reduce nitrate to nitrite and hydrolyse Tween 80. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SM1903^T formed a separate lineage within the family Rhodobacteraceae, sharing the highest 16S rRNA gene sequence similarity with type strains of Pseudooceanicola antarcticus (95.7 %) and Roseisalinus antarcticus (95.7 %). In phylogenetic trees based on single-copy OCs and whole proteins sequences, strain SM1903^T fell within a sub-cluster encompassed by Oceanicola granulosus, Roseisalinus antarcticus and Histidinibacterium lentulum and formed a branch adjacent to Oceanicola granulosus. The major cellular fatty acids were summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c), C_16 : 0 and 11-methyl-C_18 : 1  ω7c. The polar lipids mainly comprised phosphatidylglycerol, phosphatidylcholine, one unidentified lipid, one unidentified aminolipid, and one unidentified glycolipid. The solo respiratory quinone was ubiquinone-10. The genomic DNA G+C content of strain SM1903^T was 66.0 mol%. Based on the results of phenotypic, chemotaxonomic, and phylogenetic characterization for strain SM1903^T, it is considered to represent a novel species of a novel genus in the family Rhodobacteraceae, for which the name Pelagovum pacificum gen. nov., sp. nov. is proposed. The type strain is SM1903^T (=MCCC 1K03608^T=KCTC 72046^T).