Search Results (44)

This study investigates the biodeterioration of mosaic surfaces in a semi-confined archaeological environment along the Phlegraean coast (Baiae, Italy), focusing on the interaction between salt efflorescence and phototrophic biofilms. A multi-analytical approach was employed, integrating in situ observations with ex situ analyses, including SEM/EDS, FTIR spectroscopy, and metabarcoding (16S and 18S rRNA), to characterize both abiotic and biotic alteration patterns. Results highlight subtle traces of spatial differentiation: samples from the more exposed sector showed a more consistent colonization by halotolerant and halophilic taxa, particularly among Halobacteria and Rubrobacter, along with abundant sodium, chloride, and sulfate signals suggestive of active salt crystallization. Protected areas exhibit a comparable presence of salts with less diverse halophilic communities that vary along a vertical gradient of light exposure. The integration of chemical and biological data supports a model in which salt stress and biofilm development are co-dependent and synergistic in driving surface degradation. These findings emphasize the need for context-specific conservation strategies that account for the combined action of environmental salinity and microbial communities on historical materials. Full article

The mechanisms underlying groundwater microbial community assembly have long attracted attention in earth, environmental, and ecological studies. Nevertheless, limited knowledge is available regarding microbial community assembly within the intact groundwater flow systems in arid regions. In this study, long-term hydrochemical data and microbial community profiles were integrated to unravel the assembly processes and driving forces mediating microbial communities in the Golmud River watershed. Our results indicated that hydrochemical conditions gradually transitioned from oxidizing to reducing environments along the groundwater flow path, as evidenced by a 28.57% and 65.45% decrease in DO and ORP, respectively. Major ions, represented by TDS, displayed minimal variations in phreatic (519.72 ± 16.83 mg/L) and artesian groundwater (486.01 ± 27.71 mg/L), followed by pronounced enrichment in high-salinity groundwater (TDS: 316,112.74 ± 12,452.19 mg/L). Gammaproteobacteria and Actinobacteria declined markedly from phreatic (51.69 ± 6.83% and 9.54 ± 3.40%, respectively) to high-salinity groundwater (13.97 ± 3.70% and 4.77 ± 2.46%). Conversely, halophiles such as Halobacteria and Parcubacteria were rarely detected in low-TDS groundwater, but increased sharply in high-salinity groundwater, reaching 23.22 ± 10.42% and 8.34 ± 3.71%, respectively. Deterministic processes primarily controlled groundwater microbial communities across hydrochemical conditions (relative importance > 50%, NST index < 50%). Microbial co-occurrence networks revealed increasingly tight interactions and intensified competition among communities, driven by accumulated salinity–oxygen stress along the groundwater flow path. This study emphasizes the role of deterministic processes in shaping groundwater microbial community structure, particularly the impact of salinity–oxygen stress. Our findings advance the current understanding of the mechanisms by which hydrochemical processes shape groundwater microbial assemblages. Full article

The genus Haloarcula is one of the most extensively studied genera within the class Halobacteria. In this study, analyses of average nucleotide identity (ANI), average amino acid identity (AAI), digital DNA–DNA hybridization (dDDH) values, and phylogenomic data indicated that “Haloarcula californiae” ATCC 33799 and “Haloarcula sinaiiensis” ATCC 33800 served as reference strains for Haloarcula marismortui. Furthermore, a halophilic archaeal strain, GH36^T, isolated from the inland Gahai Salt Lake in China, was subjected to comprehensive polyphasic taxonomic characterization. The ANI, AAI, and dDDH comparisons between strain GH36^T and other Haloarcula species were below the established thresholds for species demarcation. Strain GH36^T was assigned to a novel species within the genus Haloarcula based on phylogenetic, phylogenomic, and comparative genomic analyses. Moreover, distinct phenotypic differences were observed in strain GH36^T. In strain GH36^T, the primary phospholipids detected were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), and phosphatidylglycerol sulfate (PGS), whereas the principal glycolipids were sulfated mannosyl glucosyl diether (S-DGD-1) and mannosyl glucosyl diether (DGD-1). Accordingly, the novel species Haloarcula montana sp. nov. is proposed to accommodate strain GH36^T (=CGMCC 1.62631^T = MCCC 4K00122^T). Full article

The rhizosphere microbiota of arid plants plays a crucial role in adaptation to environmental stress. However, few studies have characterized microorganisms associated with Agave species and their contribution to resilience against salinity and drought. This study aimed to isolate and characterize halotolerant bacteria from the rhizosphere of Agave potatorum Zucc from two different sites and evaluate their in vitro Na⁺ sequestration, desiccation resistance, and phytohormone production. These traits were compared with those of halotolerant bacteria isolated from a highly saline soil at a third site. Bacteria were obtained through serial dilutions and cultured on R2A plates supplemented with varying NaCl concentrations. The most efficient Na⁺-sequestering isolates underwent an 18-day desiccation assay, and their production of indole-3-acetic acid (IAA) and gibberellic acid (GA₃) was quantified. Among the 48 halotolerant isolates obtained, 7 (SM1, SM10, SPM5, SM7, SM19, VZ9, and SPM1) exhibited the highest Na⁺ sequestration efficiency. Among these isolates, SM1 exhibited the highest in vitro Na⁺ sequestration capacity (10.74 μg L⁻¹, p < 0.05). SM1 and SPM1 demonstrated the greatest desiccation resistance, at 88.39% and 83.05%, respectively. Additionally, SM7 produced the highest levels of IAA (13.69 μg mL⁻¹, p < 0.05), while SM1 exhibited the highest GA₃ production (1285.38 μg mL⁻¹, p < 0.05). Based on these characteristics, isolates SPM1 and SM1 exhibited the highest efficiency in tolerating drought and salinity stress. However, isolate SPM1 may colonize the rhizosphere of A. potatorum more effectively, likely due to its adaptation as a native isolate to the edaphic and environmental conditions in which this agave thrives. Molecular identification confirmed that the isolates belong to the genera Kosakonia, Priestia, Streptomyces, Bacillus, Stutzerimonas, Pseudomonas, and Exiguobacterium. This study highlights the diversity of halotolerant bacteria in the rhizosphere of A. potatorum and their potential as bioinoculants for enhancing soil fertility and restoring degraded soils. Full article

The Amuyo Ponds (APs) are a group of three brackish hydrothermal lagoons located at 3700 m above sea level in a pre-Andean setting in the Atacama Desert. Each pond shows a conspicuous green (GP), red (RP), or yellow (YP) coloration, and discharges water rich in arsenic and boron into the Caritaya River (Camarones Basin, northern Chile). Microorganisms are subjected to harsh environmental conditions in these ponds, and the microbial composition and diversity in the Amuyo Ponds’ sediments are unknown. The microbial life colonizing AP sediments was explored by metagenomics analyses, showing a diverse microbial life dominated by members of the bacterial domain, with nearly 800 bacterial genome sequences, and sequences associated with Archaea, Eukarya, and viruses. The genus Pseudomonas was more abundant in GP and YP sediments, while the genera Pseudomonas, Aeromonas, and Shewanella were enriched in RP sediments. Archaeal composition was similar in all sediments, and enriched with methanogens sequences from the Archaeoglobi and Halobacteria classes. Abundant fungi sequences were detected in all sediments from the phyla Blastocladiomycota and Ascomycota. We also report putative functional capabilities related to virulence and defense genes, the biosynthesis of secondary metabolites, and tolerance to arsenic. Thirteen bacterial and fourteen viral metagenome-assembled genomes were reconstructed and informed here. This work expands our knowledge on the richness of the microorganisms in the APs and open further studies on the ecology and genomics of this striking Andean geosite. Full article

Australian isolates of Haloquadratum walsbyi, a square-shaped haloarchaeon, often harbor small cryptic plasmids of the pL6-family, approximately 6 kb in size, and five examples have been previously described. These plasmids exhibit a highly conserved gene arrangement and encode replicases similar to those of betapleolipoviruses. To assess their global distribution and recover more examples for analysis, fifteen additional plasmids were reconstructed from the metagenomes of seven hypersaline sites across four countries: Argentina, Australia, Puerto Rico, and Spain. Including the five previously described plasmids, the average plasmid size is 6002 bp, with an average G+C content of 52.5%. The tetramers GGCC and CTAG are either absent or significantly under-represented, except in the two plasmids with the highest %G+C. All plasmids share a similar arrangement of genes organized as outwardly facing replication and ATPase modules, but variations were observed in some core genes, such as F2, and some plasmids had acquired accessory genes. Two plasmids, pCOLO-c1 and pISLA-c6, shared 92.7% nt identity despite originating from Argentina and Spain, respectively. Numerous metagenomic CRISPR spacers matched sequences in the fifteen reconstructed plasmids, indicating frequent invasion of haloarchaea. Spacers could be assigned to haloarchaeal genera by mapping their associated direct repeats (DR), with half of these matching Haloquadratum. Finally, strand-specific metatranscriptome (RNA-seq) data could be used to demonstrate the active transcription of two pL6-family plasmids, including antisense transcripts. Full article

Prokaryotes play a key role in particulate organic matter’s decomposition and remineralization processes in the vertical scale of seawater, and prokaryotes contribute to more than 70% of the estimated remineralization. However, little is known about the microbial community and metabolic activity of the vertical distribution in the trenches. The composition and distribution of prokaryotes in the water columns and benthic boundary layers of the Kermadec Trench and the Diamantina Trench were investigated using high-throughput sequencing and quantitative PCR, together with the Biolog Ecoplate^TM microplates culture to analyze the microbial metabolic activity. Microbial communities in both trenches were dominated by Nitrososphaera and Halobacteria in archaea, and by Alphaproteobacteria and Gammaproteobacteria in bacteria, and the microbial community structure was significantly different between the water column and the benthic boundary layer. At the surface water, amino acids and polymers were used preferentially; at the benthic boundary layers, amino acids and amines were used preferentially. Cooperative relationships among different microbial groups and their carbon utilization capabilities could help to make better use of various carbon sources along the water depths, reflected by the predominantly positive relationships based on the co-occurrence network analysis. In addition, the distinct microbial metabolic activity detected at 800 m, which was the lower boundary of the twilight zone, had the lowest salinity and might have had higher proportions of refractory carbon sources than the shallower water depths and benthic boundary layers. This study reflected the initial preference of the carbon source by the natural microbes in the vertical scale of different trenches and should be complemented with stable isotopic tracing experiments in future studies to enhance the understanding of the complex carbon utilization pathways along the vertical scale by prokaryotes among different trenches. Full article

Background and Aims: Gut microbial imbalances are linked to colorectal cancer (CRC), but archaea’s role remains underexplored. Here, using previously published metagenomic data from different populations including Austria, Germany, Italy, Japan, China, and India, we performed bioinformatic and statistical analysis to identify archaeal taxonomic and functional signatures related to CRC. Methods: We analyzed published fecal metagenomic data from 390 subjects, comparing the archaeomes of CRC and healthy individuals. We conducted a biostatistical analysis to investigate the relationship between Candidatus Mancarchaeum acidiphilum (DPANN superphylum) and other archaeal species associated with CRC. Using the Prokka tool, we annotated the data focusing on archaeal genes, subsequently linking them to CRC and mapping them against UniprotKB and GO databases for specific archaeal gene functions. Results: Our analysis identified enrichment of methanogenic archaea in healthy subjects, with an exception for Methanobrevibacter smithii, which correlated with CRC. Notably, CRC showed a strong association with archaeal species, particularly Natrinema sp. J7-2, Ferroglobus placidus, and Candidatus Mancarchaeum acidiphilum. Furthermore, the DPANN archaeon exhibited a significant correlation with other CRC-associated archaea (p < 0.001). Functionally, we found a marked association between MvhB-type polyferredoxin and colorectal cancer. We also highlighted the association of archaeal proteins involved in the biosynthesis of leucine and the galactose metabolism process with the healthy phenotype. Conclusions: The archaeomes of CRC patients show identifiable alterations, including a decline in methanogens and an increase in Halobacteria species. MvhB-type polyferredoxin, linked with CRC and species like Candidatus Mancarchaeum acidiphilum, Natrinema sp. J7-2, and Ferroglobus placidus emerge as potential archaeal biomarkers. Archaeal proteins may also offer gut protection, underscoring archaea’s role in CRC dynamics. Full article

Herein, we report on the production, characterization, and antioxidant power assessment of carotenoids from the haloarchaeon Halorhabdus utahensis. It was grown at 37 °C and 180 rpm agitation in halobacteria medium supplemented with glucose, fructose, and xylose, each at concentrations of 0.2%, 1%, and 2%, and the carotenoid yield and composition were investigated. The microorganism produced the carotenoids under all the conditions tested, and their amount followed the order glucose < xylose < fructose. The highest yield was achieved in 2% fructose growth medium with 550.60 ± 7.91 μg/g dry cell and 2428.15 ± 49.33 μg/L. Separation and identification of the carotenoids were performed by RP-HPLC and HPLC/APCI-ITMSⁿ. Bacterioruberin was the main carotenoid detected and accounted for 60.6%, 56.4%, and 58.9% in 2% glucose, 1% xylose, and 2% fructose extracts, respectively. Several geometric isomers of bacterioruberin were distinguished, and representatives of monoanhydrobacterioruberin, and bisanhydrobacterioruberin were also detected. The assignment to cis-isomers was attempted through analysis of the UV/Vis spectra, intensity of cis peaks, and spectral fine structures. The extracts exhibited superoxide scavenging activity higher than butylhydroxytoluene, ascorbic acid, and Trolox, selected as antioxidant references. The anti-hyaluronidase capacity was investigated, and the 2% fructose extract showed the highest activity reaching 90% enzyme inhibition with 1.5 μg. The overall data confirm that Hrd. utahensis can be regarded as an interesting source of antioxidants that can find applications in the food and cosmetic sectors. Full article

Colorectal cancer (CRC) is a serious public health problem known to have a multifactorial etiology. The association between gut microbiota and CRC has been widely studied; however, the link between archaea and CRC has not been sufficiently studied. To investigate the involvement of archaea in colorectal carcinogenesis, we performed a metagenomic analysis of 68 formalin-embedded paraffin fixed tissues from tumoral (n = 33) and healthy mucosa (n = 35) collected from 35 CRC Tunisian patients. We used two DNA extraction methods: Generead DNA FFPE kit (Qiagen, Germantown, MD, USA) and Chelex. We then sequenced the samples using Illumina Miseq. Interestingly, DNA extraction exclusively using Chelex generated enough DNA for sequencing of all samples. After data filtering and processing, we reported the presence of archaeal sequences, which represented 0.33% of all the reads generated. In terms of abundance, we highlighted a depletion in methanogens and an enrichment in Halobacteria in the tumor tissues, while the correlation analysis revealed a significant association between the Halobacteria and the tumor mucosa (p < 0.05). We reported a strong correlation between Natrialba magadii, Sulfolobus acidocaldarius, and tumor tissues, and a weak correlation between Methanococcus voltae and healthy adjacent mucosa. Here, we demonstrated the feasibility of archaeome analysis from formol fixed paraffin-embedded (FFPE) tissues using simple protocols ranging from sampling to data analysis, and reported a significant association between Halobacteria and tumor tissues in Tunisian patients with CRC. The importance of our study is that it represents the first metagenomic analysis of Tunisian CRC patients’ gut microbiome, which consists of sequencing DNA extracted from paired tumor-adjacent FFPE tissues collected from CRC patients. The detection of archaeal sequences in our samples confirms the feasibility of carrying out an archaeome analysis from FFPE tissues using a simple DNA extraction protocol. Our analysis revealed the enrichment of Halobacteria, especially Natrialba magadii, in tumor mucosa compared to the normal mucosa in CRC Tunisian patients. Other species were also associated with CRC, including Sulfolobus acidocaldarius and Methanococcus voltae, which is a methanogenic archaea; both species were found to be correlated with adjacent healthy tissues. Full article

Salt mines feature both autochthonous and allochthonous microbial communities introduced by industrialization. It is important to generate the information on the diversity of the microbial communities present in the salt mines and how they are shaped by the environment representing ecological diversification. Brine from Mahai potash mine (Qianghai, China), an extreme hypersaline environment, is used to produce potash salts for hundreds of millions of people. However, halophiles preserved in this niche during deposition are still unknown. In this study, using high-throughput 16S rRNA gene amplicon sequencing and estimation of physicochemical variables, we examined brine samples collected from locations with the gradient of industrial activity intensity and discrete hydrochemical compositions in the Mahai potash mine. Our findings revealed a highly diverse bacterial community, mainly composed of Pseudomonadota in the hypersaline brines from the industrial area, whereas in the natural brine collected from the upstream Mahai salt lake, most of the 16S rRNA gene reads were assigned to Bacteroidota. Halobacteria and halophilic methanogens dominated archaeal populations. Furthermore, we discovered that in the Mahai potash mining area, bacterial communities tended to respond to anthropogenic influences. In contrast, archaeal diversity and compositions were primarily shaped by the chemical properties of the hypersaline brines. Conspicuously, distinct methanogenic communities were discovered in sets of samples with varying ionic compositions, indicating their strong sensitivity to the brine hydrochemical alterations. Our findings provide the first taxonomic snapshot of microbial communities from the Mahai potash mine and reveal the different responses of bacteria and archaea to environmental variations in this high-altitude aquatic ecosystem. Full article

Salt mines are a special type of hypersaline environment. Current research mainly focuses on prokaryotes, and the understanding of viruses in salt mines remains limited. Understanding viruses in hypersaline environments is of great significance for revealing the formation and maintenance of microbial communities, energy flow and element cycling, and host ecological functions. A phage infecting Halomonas titanicae was isolated from Yipinglang Salt Mine in China, designated Halomonas titanicae phage vB_HtiS_YPHTV-1 (YPHTV-1). Transmission electron microscopy revealed that YPHTV-1 had an icosahedral head with a diameter of 49.12 ± 0.15 nm (n = 5) and a long noncontractile tail with a length of 141.7 ± 0.58 nm (n = 5), indicating that it was a siphovirus. The one-step growth curve showed that the burst size of YPHTV-1 was 69 plaque forming units (PFUs) cell⁻¹. The genome of YPHTV-1 was 37,980 bp with a GC content of 36.2%. The phylogenetic analysis of the six conserved proteins indicated that YPHTV-1 formed a cluster with Bacillus phages and was separated from phages infecting Halomonas. The average nucleotide identity (ANI), phylogenetic, and network analyses indicated that the phage YPHTV-1 represented a new genus under Caudoviricetes. In total, 57 open reading frames (ORFs) were predicted in the YPHTV-1 genome, 30 of which could be annotated in the database. Notably, several auxiliary metabolic genes were encoded by YPHTV-1, such as ImmA/IrrE family metalloendopeptidase, mannose-binding lectin (MBL) folding metallohydrolase, M15 family of metal peptidases, MazG-like family protein, O antigen ligase, and acyltransferase. These genes potentially enabled the host bacterium to resist ionizing radiation, ultraviolet light (UV), mitomycin C, β-lactam antibiotic, high osmotic pressure, and nutritional deficiencies. These findings highlight the role of haloviruses in the life cycle of halobacteria. Full article

Abiotic and biotic stresses such as salt stress and fungal infections significantly affect plant growth and productivity, leading to reduced crop yield. Traditional methods of managing stress factors, such as developing resistant varieties, chemical fertilizers, and pesticides, have shown limited success in the presence of combined biotic and abiotic stress factors. Halotolerant bacteria found in saline environments have potential as plant promoters under stressful conditions. These microorganisms produce bioactive molecules and plant growth regulators, making them a promising agent for enhancing soil fertility, improving plant resistance to adversities, and increasing crop production. This review highlights the capability of plant-growth-promoting halobacteria (PGPH) to stimulate plant growth in non-saline conditions, strengthen plant tolerance and resistance to biotic and abiotic stressors, and sustain soil fertility. The major attempted points are: (i) the various abiotic and biotic challenges that limit agriculture sustainability and food safety, (ii) the mechanisms employed by PGPH to promote plant tolerance and resistance to both biotic and abiotic stressors, (iii) the important role played by PGPH in the recovery and remediation of agricultural affected soils, and (iv) the concerns and limitations of using PGHB as an innovative approach to boost crop production and food security. Full article

The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq proteins. Sm and Lsm proteins are found in the Eukarya and Archaea domains, respectively, while Hfq proteins exist in the Bacteria domain. Even though Sm and Hfq proteins have been extensively studied, archaeal Lsm proteins still require further exploration. In this work, different bioinformatics tools are used to understand the diversity and distribution of 168 Lsm proteins in 109 archaeal species to increase the global understanding of these proteins. All 109 archaeal species analyzed encode one to three Lsm proteins in their genome. Lsm proteins can be classified into two groups based on molecular weight. Regarding the gene environment of lsm genes, many of these genes are located adjacent to transcriptional regulators of the Lrp/AsnC and MarR families, RNA-binding proteins, and ribosomal protein L37e. Notably, only proteins from species of the class Halobacteria conserved the internal and external residues of the RNA-binding site identified in Pyrococcus abyssi, despite belonging to different taxonomic orders. In most species, the Lsm genes show associations with 11 genes: rpl7ae, rpl37e, fusA, flpA, purF, rrp4, rrp41, hel308, rpoD, rpoH, and rpoN. We propose that most archaeal Lsm proteins are related to the RNA metabolism, and the larger Lsm proteins could perform different functions and/or act through other mechanisms of action. Full article

Archaeal cell factories are becoming of great interest given their ability to produce a broad range of value-added compounds. Moreover, the Archaea domain often includes extremophilic microorganisms, facilitating their cultivation at the industrial level under nonsterile conditions. Halophilic archaea are studied for their ability to grow in environments with high NaCl concentrations. In this study, nine strains of Halobacterium salinarum were isolated from three different types of salted food, sausage casings, salted codfish, and bacon, and their genomes were sequenced along with the genome of the collection strain CECT 395. A comparative genomic analysis was performed on these newly sequenced genomes and the publicly available ones for a total of 19 H. salinarum strains. We elucidated the presence of unique gene clusters of the species in relation to the different ecological niches of isolation (salted foods, animal hides, and solar saltern sediments). Moreover, genome mining at the single-strain level highlighted the metabolic potential of H. salinarum UC4242, which revealed the presence of different protechnological genes (vitamins and myo-inositol biosynthetic pathways, aroma- and texture-related features, and antimicrobial compounds). Despite the presence of genes of potential concern (e.g., those involved in biogenic amine production), all the food isolates presented archaeocin-related genes (halocin-C8 and sactipeptides). Full article