Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles

Frontiers in Microbiology, Год журнала: 2023, Номер 14

Опубликована: Июнь 2, 2023

More than 20,000 species of prokaryotes (less 1% the estimated number Earth's microbial species) have been described thus far. However, vast majority microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little known regarding ecological functions biotechnological potential these underexplored extremophiles, representing a untapped uncharacterized biological resource. Advances in cultivation approaches are key for detailed comprehensive characterization roles shaping environment and, ultimately, their exploitation, such as extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, pigments, among others), astrobiology, space exploration. Additional efforts to enhance culturable diversity required due challenges imposed by culturing plating conditions. In review, we summarize methods technologies used recover environments, while discussing advantages disadvantages associated with each approaches. Additionally, review describes alternative strategies retrieve novel taxa unknown genes, metabolisms, roles, ultimate goal increasing yields more efficient bio-based products. This summarizes unveil hidden microbiome discusses directions future studies matter its applications biotechnology astrobiology.

Язык: Английский

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Microbe-driven elemental cycling enables microbial adaptation to deep-sea ferromanganese nodule sediment fields

Microbiome, Год журнала: 2023, Номер 11(1)

Опубликована: Июль 25, 2023

Abstract Background Ferromanganese nodule-bearing deep-sea sediments cover vast areas of the ocean floor, representing a distinctive habitat in abyss. These harbor unique conditions characterized by high iron concentration and low degradable nutrient levels, which pose challenges to survival growth most microorganisms. While microbial diversity ferromanganese nodule-associated has been surveyed several times, little is known about functional capacities communities adapted these habitats. Results Seven sediment samples collected adjacent nodules from Clarion–Clipperton Fracture Zone (CCFZ) eastern Pacific Ocean were subjected metagenomic analysis. As result, 179 high-quality metagenome-assembled genomes (MAGs) reconstructed assigned 21 bacterial phyla 1 archaeal phylum, with 88.8% MAGs remaining unclassified at species level. The main mechanisms resistance heavy metals for microorganisms included oxidation (Mn), reduction (Cr Hg), efflux (Pb), synergy (As), (Cu). Iron, had highest content among all metallic elements, may occur mainly as Fe(III) that potentially functioned an electron acceptor. We found diverse array CAZymes did not exhibit higher community abundance. Instead, obtained energy metal (e.g., Mn(II)) sulfur compounds using oxygen or nitrate Chemolithoautotrophic organisms ( Thaumarchaeota Nitrospirota phyla) be potential manganese oxidizers. profile analysis dominant further indicated utilization inorganic nutrients redox reactions (rather than organic metabolism) major adaptive strategy used support their nodule sediments. Conclusions This study provides comprehensive microbes inhabiting metal-rich Our results reveal extensive redundancy across taxa pathways transformation, highly obtain nutrition, participation various element cycles environments.

Язык: Английский

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Microbial reductive mobilization of As(V) in solid phase coupled with the oxidation of sulfur compounds: An overlooked biogeochemical reaction affecting the formation of arsenic-polluted groundwater

Journal of Hazardous Materials, Год журнала: 2025, Номер unknown, С. 138234 - 138234

Опубликована: Апрель 1, 2025

Язык: Английский

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Blue light promotes zero‐valent sulfur production in a deep‐sea bacterium

The EMBO Journal, Год журнала: 2023, Номер 42(12)

Опубликована: Март 22, 2023

Abstract Increasing evidence has shown that light exists in a diverse range of deep‐sea environments. We unexpectedly found blue is necessary to produce excess zero‐valent sulfur (ZVS) Erythrobacter flavus 21‐3, bacterium been recently isolated from cold seep. E. 21‐3 able convert thiosulfate ZVS using novel oxidation pathway comprising dehydrogenase (TsdA) and thiosulfohydrolase (SoxB). Using proteomic, bacterial two‐hybrid heterologous expression assays, we the light–oxygen–voltage histidine kinase LOV‐1477 responds activates diguanylate cyclase DGC‐2902 c‐di‐GMP. Subsequently, PilZ domain‐containing protein mPilZ‐1753 binds c‐di‐GMP TsdA through direct interaction. Finally, Raman spectroscopy gene knockout results verified two SoxB homologs cooperate regulate production. As an energy source for propose provides with selective advantage seep, suggesting previously unappreciated relationship between light‐sensing pathways metabolism microorganism.

Язык: Английский

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Microorganisms uptake zero-valent sulfur via membrane lipid dissolution of octasulfur and intracellular solubilization as persulfide

The Science of The Total Environment, Год журнала: 2024, Номер 922, С. 170504 - 170504

Опубликована: Фев. 1, 2024

Язык: Английский

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Transcriptome Analysis of Cyclooctasulfur Oxidation and Reduction by the Neutrophilic Chemolithoautotrophic Sulfurovum indicum from Deep-Sea Hydrothermal Ecosystems

Antioxidants, Год журнала: 2023, Номер 12(3), С. 627 - 627

Опубликована: Март 3, 2023

Chemolithoautotrophic Campylobacterota are widespread and predominant in worldwide hydrothermal vents, they key players the turnover of zero-valence sulfur. However, at present, mechanism cyclooctasulfur activation catabolism bacteria is not clearly understood. Here, we investigated these processes a vent isolate named Sulfurovum indicum ST-419. A transcriptome analysis revealed that multiple genes related to biofilm formation were highly expressed during both sulfur oxidation reduction. Additionally, biofilms containing cells EPS coated on particles observed by SEM, suggesting may be involved S0 species. Meanwhile, several encoding outer membrane proteins OprD family also expressed, among them, gene IMZ28_RS00565 exhibited significantly high expressions 2.53- 7.63-fold changes under conditions, respectively, which play role uptake. other mechanisms could uptake, as experiments with dialysis bags showed direct contact between was mandatory for reduction activity, whereas cell growth via did require contact. This indirect reaction ascribed H2S and/or thiol-containing compounds, such cysteine GSH, produced culture medium In periplasm, sulfur-oxidation-multienzyme complexes soxABXY1Z1 soxCDY2Z2 likely responsible thiosulfate oxidation, respectively. addition, four psr clusters polysulfide reductases, only psrA3B3C3 upregulated condition, implying its essential These results expand our understanding interactions their adaptability deep-sea environments.

Язык: Английский

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Two modes of gypsum replacement by carbonate and native sulfur in the Lorca Basin, SE Spain

Frontiers in Earth Science, Год журнала: 2023, Номер 11

Опубликована: Май 12, 2023

Organoclastic sulfate reduction and bacterial sulfide oxidation have been suggested to explain the formation of authigenic carbonate native sulfur replacing gypsum in Lorca Basin, Spain. To gain more insight into nature this replacement, two types sulfur-bearing (laminated brecciated) from late Miocene Basin were studied. Petrographic observations revealed that a laminated consists clay-rich dolomite-rich laminae with pseudomorphs after gypsum. Positive δ 18 O values (δ = 2.6‰) lipid biomarkers halophilic archaea (e.g., extended archaeol) suggest under hypersaline conditions. Bacterial reduction, evidenced by such as iso -C 15 , 16 17 fatty acids, produced hydrogen inducing abiotic organic compounds. Gypsum likely dissolved due undersaturation low content carbonate-associated (3,668 ppm) 34 S-enriched S 22.4‰), reflecting limitation. Such S-enrichment implies limited fluid flow, which probably restricted supply molecular oxygen required for through sulfide. Alternatively, sulfate-reducing bacteria may mediated directly stress response environmental The calcite brecciated carbonates is post-depositional alteration. Negative −1.5‰) tenfold decrease (752 dissolution subsequent precipitation meteoric water. Relatively S-depleted 13.1‰) leaves it ambiguous whether water influx could supplied sufficient In case carbonate, methanogenesis, anaerobic methane, apparently secondary minerals indicated 13 C-depleted representative respective metabolisms. This study reveals conditions timing replacement are variable–taking place 1) during or shortly deposition 2) significantly sedimentation–and suggests methanogens addition methanotrophic be involved mineral-forming processes sedimentary subsurface.

Язык: Английский

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Study of Microbial Sulfur Metabolism in a Near Real-Time Pathway through Confocal Raman Quantitative 3D Imaging

Microbiology Spectrum, Год журнала: 2023, Номер 11(2)

Опубликована: Фев. 21, 2023

Microorganisms contribute significantly to the formation of deep-sea elemental sulfur, so studies on their growth and dynamic sulfur metabolism are important understand cycle. However, near real-time in situ nondestructive metabolic microorganisms remain a great challenge due limitations existing methods.

Язык: Английский

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Host-specific bacterial communities associated with six cold-seep sponge species in the South China Sea

Frontiers in Marine Science, Год журнала: 2023, Номер 10

Опубликована: Авг. 21, 2023

The cold-seep sponge holobionts are attracting growing attention in recent years. In this study, we utilized 16S rRNA amplicons to characterize the bacterial communities of six deep-sea species found grounds at Formosa Ridge cold seep South China Sea. Bacterial these geographically proximal dominated by Proteobacteria (mainly Gammaproteobacteria and Alphaproteobacteria) but exhibit distinct diversity compositions among communities. Further analysis revealed that SUP05 clade (Thioglobaceae) most samples. Meanwhile, phylogenetic showed harbored diverse OTU phylotypes, indicating significant divergence within clade. Additionally, operational taxonomic units (OTUs) family Methylomonadaceae, another abundant group sponges, displayed a genetic distance both from each other known species. Our findings support hypothesis host-species specificity sponge-associated communities, widely accepted concept shallow-water sponges. presence dominant functional microbes, such as sulfur- methanol-oxidizing bacteria, suggests their crucial role chemosynthetic symbionts facilitating niche adaption hosts ecosystem. conclusion, our study reveals novel sponges environments, contributing new knowledge highlighting potential significance microbes ecosystems with dynamic energy supplies.

Язык: Английский

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Seeing the light brings more food in the deep sea

The EMBO Journal, Год журнала: 2023, Номер 42(12)

Опубликована: Апрель 13, 2023

Cyclic di-GMP signaling regulates sessile-to-motile lifestyle transition and associated physiological metabolic features in bacteria. The presence of potential cyclic turnover proteins deepest branching bacteria indicates that is an ancient molecule. In this issue EMBO Journal, Cai et al (2023) describe light-induced activation a thiosulfate oxidation pathway the deep-sea cold-seep bacterium Qipengyuania flava, thus coupling with regulation global abiotic sulfur cycle.

Язык: Английский

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