Haloarchaea in halite crystals
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ABSTRACT:
PROVIDER: PRJEB34255 | ENA |
REPOSITORIES: ENA
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Project description:Halophilic microorganisms have long been known to survive within the brine inclusions of salt crystals, as evidenced by their pigmentation. However, the molecular mechanisms allowing this survival has remained an open question for decades. While protocols for the surface sterilization of halite (NaCl) have enabled isolation of cells and DNA from within halite brine inclusions, “-omics” based approaches have faced two main technical challenges: (1) removal of all contaminating organic biomolecules (including proteins) from halite surfaces, and (2) performing selective biomolecule extractions directly from cells contained within halite brine inclusions with sufficient speed to avoid modifications in gene expression during extraction. In this study, we present methods to resolve these two technical challenges. In addition, we apply these methods to perform the first examination of the early acclimation of a model haloarchaeon (Halobacterium salinarum NRC-1) to halite brine inclusions. Examinations of the proteome of Halobacterium cells two months post-evaporation revealed a high degree of similarity with stationary phase liquid cultures, but with a sharp down-regulation of ribosomal proteins. Low quantities of RNA from halite brine inclusions corroborate the hypothesis of low transcriptional and translational activities. While proteins for central metabolism were part of the shared proteome between liquid cultures and halite brine inclusions, proteins involved in cell mobility (archaellum, gas vesicles) were either absent or less abundant in halite samples. Proteins unique to cells within brine inclusions included transporters, suggesting modified interactions between cells and the surrounding brine inclusions microenvironment. The methods and hypotheses presented here enable future studies of the survival of halophiles in both culture model and natural halite systems.
2023-03-10 | PXD037167 | Pride
Project description:In hypersaline brines, biodegradation of recalcitrant plant polymers can be inhibited by salt-induced microbial stress and/or caused by inadequate metabolic capabilities of extremely halophilic microbes. Therefore, woody materials can be well-preserved even in NaCl brines that are less biologically hostile than most other brines. Here, we considered whether the nanohaloarchaea, that live alongside (the related) haloarchaea, ever partake in the degradation of xylan, a major hemicellulose component of wood. Samples were taken from natural evaporitic brines and anthropogenic solar salterns located in various parts of Europe and Asia. We recently demonstrated that nanohaloarchaeon Ca. Nanohalobium constans lives as an ectosymbiont associated with the chitinolytic haloarchaeon Halomicrobium. Here, we describe an extremely halophilic xylan-degrading consortium with three members, where nanohaloarchaea act as ectosymbionts of Haloferax lucertensis, which in turn acts as a scavenger of xylan-degradation products, produced by a primary xylan hydrolytic Halorhabdus species. The two corresponding binary associations of nanohaloarchaea, Candidatus Nanohalococcus occultus SVXNc and Candidatus Nanohalovita haloferacivicina BNXNv and their hosts were obtained, stably cultivated and characterized. In contrast to the previously described association of chitinolytic haloarchaeon Halomicrobium and its amylolytic symbiont Ca. Nanohalobium, the host haloarchaea within the xylan-degrading consortium could metabolize α-glucans (glycogen and starch), and, thus, obtained no obvious trophic benefit from ectosymbionts. The current study has broadened the range of culturable ectosymbiontic nanohaloarchaea and demonstrates that they are an important ecophysiological component of polysaccharide-degrading halophilic microbial communities and can be readily isolated in binary co-cultures by using the appropriate enrichment strategy.
2023-10-24 | PXD036877 | Pride
Project description:SG1-2017 halite metagenome and metatranscriptome
| PRJNA510804 | ENA
Project description:Halite metagenomic and metatranscriptomic profiling sequence reads
| PRJNA560058 | ENA
Project description:Functional analysis of the archaea, bacteria, and viruses from a halite endolithic microbial community
| PRJEB11415 | ENA
Project description:Responce of halite microbiomes to rain in Atacama Desert, Chile
| PRJNA484015 | ENA
Project description:Chemical communication is crucial in ecosystems with complex microbial assemblages. However, due to archaeal cultivation challenges, our understanding of the structure diversity and function of secondary metabolites (SMs) within archaeal communities is limited compared to the extensively studied and well-documented bacterial counterparts. Our comprehensive investigation into the biosynthetic potential of archaea, combined with metabolic analyses and the first report of heterologous expression in archaea, has unveiled the previously unexplored biosynthetic capabilities and chemical diversity of archaeal ribosomally synthesized and post-translationally modified peptide (RiPP). We have identified twenty-four new lanthipeptides of RiPPs exhibiting unique chemical characteristics, including a novel subfamily featuring an unexplored type with diamino-dicarboxylic (DADC) termini, largely expanding the chemical landscape of archaeal SMs. This sheds light on the chemical novelty of archaeal metabolites and emphasizes their potential as an untapped resource for natural product discovery. Additionally, archaeal lanthipeptides demonstrate specific antagonistic activity against haloarchaea, mediating the unique biotic interaction in the halophilic niche. Furthermore, they showcased a unique ecological role in enhancing the host's motility by inducing the rod-shaped cell morphology and upregulating the archaellum gene flgA1, facilitating the archaeal interaction with abiotic environments. These discoveries broaden our understanding of archaeal chemical language and provide promising prospects for future exploration of SM-mediated interaction.
2024-11-09 | GSE281021 | GEO