Sulfur Respiration in a Group of Facultatively Anaerobic Natronoarchaea Ubiquitous in Hypersaline Soda Lakes

The ubiquity of strictly anaerobic sulfur-respiring haloarchaea in hypersaline systems with circumneutral pH has shaken a traditional concept of this group as predominantly aerobic heterotrophs. Here, we demonstrated that this functional group of haloarchaea also has its representatives in hypersaline alkaline lakes. Sediments from various hypersaline soda lakes showed high activity of sulfur reduction only partially inhibited by antibiotics. Eight pure cultures of sulfur-reducing natronoarchaea were isolated from such sediments using formate and butyrate as electron donors and sulfur as an electron acceptor. Unlike strict anaerobic haloarchaea, these novel sulfur-reducing natronoarchaea are facultative anaerobes, whose metabolic capabilities were inferred from cultivation experiments and genomic/proteomic reconstruction. While sharing many physiological traits with strict anaerobic haloarchaea, following metabolic distinctions make these new organisms be successful in both anoxic and aerobic habitats: the recruiting of heme-copper quinol oxidases as terminal electron sink in aerobic respiratory chain and the utilization of formate, hydrogen or short-chain fatty acids as electron donors during anaerobic growth with elemental sulfur. Obtained results significantly advance the emerging concept of halo(natrono)archaea as important players in the anaerobic sulfur and carbon cycling in various salt-saturated habitats.BT/Environmental Biotechnolog

Ferrous iron- and ammonium-rich diffuse vents support habitat-specific communities in a shallow hydrothermal field off the Basiluzzo Islet (Aeolian Volcanic Archipelago)

Ammonium- and Fe(II)-rich fluid flows, known from deep-sea hydrothermal systems, have been extensively studied in the last decades and are considered as sites with high microbial diversity and activity. Their shallow-submarine counterparts, despite their easier accessibility, have so far been under-investigated, and as a consequence, much less is known about microbial communities inhabiting these ecosystems. A field of shallow expulsion of hydrothermal fluids has been discovered at depths of 170-400 meters off the base of the Basiluzzo Islet (Aeolian Volcanic Archipelago, Southern Tyrrhenian Sea). This area consists predominantly of both actively diffusing and inactive 1-3 meters-high structures in the form of vertical pinnacles, steeples and mounds covered by a thick orange to brown crust deposits hosting rich benthic fauna. Integrated morphological, mineralogical, and geochemical analyses revealed that, above all, these crusts are formed by ferrihydrite-type Fe3+ oxyhydroxides. Two cruises in 2013 allowed us to monitor and sampled this novel ecosystem, certainly interesting in terms of shallow-water iron-rich site. The main objective of this work was to characterize the composition of extant communities of iron microbial mats in relation to the environmental setting and the observed patterns of macrofaunal colonization. We demonstrated that iron-rich deposits contain complex and stratified microbial communities with a high proportion of prokaryotes akin to ammonium- and iron-oxidizing chemoautotrophs, belonging to Thaumarchaeota, Nitrospira, and Zetaproteobacteria. Colonizers of iron-rich mounds, while composed of the common macrobenthic grazers, predators, filter-feeders, and tube-dwellers with no representatives of vent endemic fauna, differed from the surrounding populations. Thus, it is very likely that reduced electron donors (Fe2+ and NH4+) are important energy sources in supporting primary production in microbial mats, which form a habitat-specific trophic base of the whole Basiluzzo hydrothermal ecosystem, including macrobenthic fauna

Nanohaloarchaea as beneficiaries of xylan degradation by haloarchaea

Climate change, desertification, salinisation of soils and the changing hydrology of the Earth are creating or modifying microbial habitats at all scales including the oceans, saline groundwaters and brine lakes. In environments that are saline or hypersaline, the biodegradation of recalcitrant plant and animal polysaccharides can be inhibited by salt-induced microbial stress and/or by limitation of the metabolic capabilities of halophilic microbes. We recently demonstrated that the chitinolytic haloarchaeon Halomicrobium can serve as the host for an ectosymbiont, nanohaloarchaeon ‘Candidatus Nanohalobium constans’. Here, we consider whether nanohaloarchaea can benefit from the haloarchaea-mediated degradation of xylan, a major hemicellulose component of wood. Using samples of natural evaporitic brines and anthropogenic solar salterns, we describe genome-inferred trophic relations in two extremely halophilic xylan-degrading three-member consortia. We succeeded in genome assembly and closure for all members of both xylan-degrading cultures and elucidated the respective food chains within these consortia. We provide evidence that ectosymbiontic nanohaloarchaea is an active ecophysiological component of extremely halophilic xylan-degrading communities (although by proxy) in hypersaline environments. In each consortium, nanohaloarchaea occur as ectosymbionts of Haloferax, which in turn act as scavenger of oligosaccharides produced by xylan-hydrolysing Halorhabdus. We further obtained and characterised the nanohaloarchaea–host associations using microscopy, multi-omics and cultivation approaches. The current study also doubled culturable nanohaloarchaeal symbionts and demonstrated that these enigmatic nano-sized archaea can be readily isolated in binary co-cultures using an appropriate enrichment strategy. We discuss the implications of xylan degradation by halophiles in biotechnology and for the United Nation's Sustainable Development Goals

Tecnología en maquinaria y equipos para la producción familiar en el Cono Sur

Este estudio reúne por un lado, información ya generada por distintas instituciones, como son los casos de Argentina, Brasil, Chile y parte del trabajo de Bolivia. Por otro lado, en los países en donde no existían estos trabajos, la PTR_AF contribuyó a generar la información correspondiente, como son los casos de Paraguay, Uruguay y parte de la información presentada por Bolivia.Contiene: 1 Producción familiar en Argentina. 2 Producción familiar en Bolivia. 3 Producción familiar en Brasil. 4 Producción familiar en Chile. 5 Producción familiar en Paraguay. 6 Producción familiar en Uruguay

“ARMAN” archaea depend on association with euryarchaeal host in culture and in situ

AbstractIntriguing, yet uncultured ‘ARMAN’-like archaea are metabolically dependent on other members of the microbial community. It remains uncertain though which hosts they rely upon, and, because of the lack of complete genomes, to what extent. Here, we report the co-culturing of ARMAN-2-related organism, Mia14, with Cuniculiplasma divulgatum PM4 during the isolation of this strain from acidic streamer in Parys Mountain (Isle of Anglesey, UK). Mia14 is highly enriched in the binary culture (ca. 10% genomic reads) and its ungapped 0.95 Mbp genome points at severe voids in central metabolic pathways, indicating dependence on the host, C. divulgatum PM4. Analysis of C. divulgatum isolates from different sites and shotgun sequence data of Parys Mountain samples suggests an extensive genetic exchange between Mia14 and hosts in situ. Within the subset of organisms with high-quality genomic assemblies representing the ‘DPANN’ superphylum, the Mia14 lineage has had the largest gene flux, with dozens of genes gained that are implicated in the host interaction.</jats:p

Microbial community of the deep-sea brine Lake <em>Kryos </em>seawater-brine interface is active below the chaotropicity limit of life as revealed by recovery of mRNA

Within the complex of deep, hypersaline anoxic lakes (DHALs) of the Mediterranean Ridge we identified a new, unexplored DHAL and named it "Lake Kryos" after a nearby depression. This lake is filled with MgCl2-rich, athalassohaline brine (salinity >470 practical salinity units), presumably formed by the dissolution of Messinian bischofite. Compared to the DHAL Discovery, it contains elevated concentrations of kosmotropic sodium and sulfate ions, which are capable of reducing the net chaotropicily of MgCl2-rich solutions. The brine of Lake Kryos may therefore be biologically permissive at MgCl2 concentrations previously considered incompatible with life. We characterized the microbiology of the seawater-Kryos brine interface and managed to recover mRNA from the 2.27-3.03 M MgCl2 layer (equivalent to 0.747-0.631 water-activity) thereby expanding the established chaotropicity window-for-life. The primary bacterial taxa present there were KB1 candidate division and DHAL-specific group of organisms, distantly related to Desulfohalobium. Two euryarchaeal candidate divisions MSBL1 and HC1, detected in minority in the overlaying layers, accounted for more than 85% of the rRNA-containing archaeal clones analyzed in 2.27-3.03 M MgCl2 layer. These findings shed light on the plausibility of life in highly chaotropic environments, geochemical windows for microbial extremophiles, and have implications for habitability elsewhere in the Solar System

Functional diversity of nanohaloarchaea within xylan-degrading consortia

DATA AVAILABILITY STATEMENT : The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.Extremely halophilic representatives of the phylum Candidatus Nanohaloarchaeota (members of the DPANN superphyla) are obligately associated with extremely halophilic archaea of the phylum Halobacteriota (according to the GTDB taxonomy). Using culture-independent molecular techniques, their presence in various hypersaline ecosystems around the world has been confirmed over the past decade. However, the vast majority of nanohaloarchaea remain uncultivated, and thus their metabolic capabilities and ecophysiology are currently poorly understood. Using the (meta)genomic, transcriptomic, and DNA methylome platforms, the metabolism and functional prediction of the ecophysiology of two novel extremely halophilic symbiotic nanohaloarchaea (Ca. Nanohalococcus occultus and Ca. Nanohalovita haloferacivicina) stably cultivated in the laboratory as members of a xylose-degrading binary culture with a haloarchaeal host, Haloferax lucentense, was determined. Like all known DPANN superphylum nanoorganisms, these new sugar-fermenting nanohaloarchaea lack many fundamental biosynthetic repertoires, making them exclusively dependent on their respective host for survival. In addition, given the cultivability of the new nanohaloarchaea, we managed to discover many unique features in these new organisms that have never been observed in nano-sized archaea both within the phylum Ca. Nanohaloarchaeota and the entire superphylum DPANN. This includes the analysis of the expression of organism-specific non-coding regulatory (nc)RNAs (with an elucidation of their 2D-secondary structures) as well as profiling of DNA methylation. While some ncRNA molecules have been predicted with high confidence as RNAs of an archaeal signal recognition particle involved in delaying protein translation, others resemble the structure of ribosome-associated ncRNAs, although none belong to any known family. Moreover, the new nanohaloarchaea have very complex cellular defense mechanisms. In addition to the defense mechanism provided by the type II restriction-modification system, consisting of Dcm-like DNA methyltransferase and Mrr restriction endonuclease, Ca. Nanohalococcus encodes an active type I-D CRISPR/Cas system, containing 77 spacers divided into two loci. Despite their diminutive genomes and as part of their host interaction mechanism, the genomes of new nanohaloarchaea do encode giant surface proteins, and one of them (9,409 amino acids long) is the largest protein of any sequenced nanohaloarchaea and the largest protein ever discovered in cultivated archaea.The FUTURENZYMES Project funded by the European Union's Horizon 2020 Research Program; Agence Nationale de la Recherche grant; the project “Emergence of virulence and antibiotic-resistance vectors in coastal and deep sea marine environments and analysis of the mechanisms and conditions underlying their spread and evolution” funded by the MIUR Progetti di Ricerca di Rilevante Interesse Nazionale (PRIN) Bando 2017; nd by the project “Innovazione tecnologica per la tutela e valorizzazione degli ecosistemi marini (ITEM)” funded by MIUR CTN02_00059_9948371.frontiersin.orghttp://www.frontiersin.org/Microbiologyam2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-15:Life on lan

Interplay of intracellular and trans-cellular DNA methylation in natural archaeal consortia

DATA AVAILABILITY STATEMENT : In-house software tool SeqWord MotifMapper 3.1 developed for this study for visualization and analysis of methylation profiles supplemented with all input files: GBK genomes and GFF files generated by the program ipdSummary for H. lucertense and its symbiont, containing genome methylation data at different growth conditions: https://zenodo.org/doi/10.5281/zenodo.10700787. Accession numbers in the NCBI repository: Whole genome sequences: Halorhabdus sp. SVX81 – CP104322; H. lucertense SVX82 – CP104741-44; and Ca. Na. occultus SVXNc – CP104395; PacBio raw read data: Archaeal consortium I, PacBio Exp 1.1 – SRX22141242; Archaeal consortium I, PacBio Exp 1.2 – SRX22141245; Archaeal consortium II, PacBio Exp 2.1 – SRX22141234; Archaeal consortium II, PacBio Exp 2.2 – SRX22141235; Archaeal consortium III, PacBio Exp 3.1 – SRX22141243; Archaeal consortium III, PacBio Exp 3.2 – SRX22141244; Archaeal consortium IV, PacBio Exp 4 – SRX22141246; RNA-seq data: Archaeal consortium I, Illumina-RNA Exp 1.1 – SRX22141247; Archaeal consortium I, Illumina-RNA Exp 1.2 – SRX22141248; Archaeal consortium II, Illumina-RNA Exp 2.1 – SRX22141249; Archaeal consortium I, Illumina-RNA Exp 2.2 – SRX22141236; Archaeal consortium III, Illumina-RNA Exp 3.1 – SRX22141237; Archaeal consortium III, Illumina-RNA Exp 3.2 – SRX22141238; Archaeal consortium IV; Archaeal consortium IV, Illumina-RNA Exp 4.1 – SRX22141239; Archaeal consortium IV, Illumina-RNA Exp 4.2 – SRX22141240; Illumina-RNA Exp 4.3 – SRX22141241; PacBio methylation data: H. lucentense Exp.I – SUPPF_0000005533; H. lucentense Exp.II – SUPPF_0000005534; H. lucentense Exp.III – SUPPF_0000005535; H. lucentense Exp.IV – SUPPF_0000005536; Ca. Nanohaloarchaeota archaeon SVXNc Exp.II – SUPPF_0000005537; Ca. Nanohaloarchaeota archaeon SVXNc Exp.IV – SUPPF_0000005538.SUPPLEMENTARY FIGURE S1. Atlas view of the genome of H. lucertense SVX82g composed of the chromosome and the three plasmids shown as brown and dark-green arcs. Genomic islands identified by the SeqWord Genome Island Sniffer and the respective metrics: GC content; the ratio of generalized relative variance (GRV) versus relative variance (RV) of distribution of nucleotide tetramers normalized by GC content (n1_4mer); and distance D between local and global tetramer frequency patterns calculated in a 5 kbp sliding window stepping 2 kbp used for detection of genomic islands (see http://seqword.bi.up.ac.za/sniffer/index.html for more detail) are shown respectively by pink blocks and coloured histograms as explained in the legend. Locations of methyltransferase (MT) and restriction endonuclease (RE) genes are depicted by triangle red marks.SUPPLEMENTARY FIGURE S2. Venn diagrams, contingency tables, and estimated Chi2 metrics visualize the distribution of unmethylated CTAG motifs on the chromosome (A) and the plasmids (B); and unmethylated CCTTG motifs on the chromosome (C) and the plasmids (D) of H. lucertense SVX82 in different experiments: (I) pure (axenic) culture on d-xylose; (II) binary culture with the ectosymbiont Ca. N. occultus SVXNc on d-xylose; (III) binary culture with Halorabdus sp. SVX81 on xylan; (IV) trinary culture with Halorabdus sp. SVX81 and the ectosymbiont Ca. N. occultus SVXNc on xylan.SUPPLEMENTARY FIGURE S3. Venn diagrams, contingency tables, and estimated Chi2 metrics visualize the distribution of unmethylated GTCGAGG motifs on the chromosome (A) and the plasmids (B); and unmethylated GRAGAAG motifs on the chromosome (C) and the plasmids (D) of H. lucertense SVX82 in different experiments: (I) pure (axenic) culture on d-xylose; (II) binary culture with the ectosymbiont Ca. N. occultus SVXNc on d-xylose; (III) binary culture with Halorabdus sp. SVX81 on xylan; (IV) trinary culture with Halorabdus sp. SVX81 and the ectosymbiont Ca. N. occultus SVXNc on xylan.SUPPLEMENTARY FIGURE S4. Venn diagrams, contingency tables, and estimated Chi2 metrics visualize the distribution of methylated GDGcHC motifs on the chromosome (A) and the plasmids (B) of H. lucertense SVX82 in different experiments: (I) pure (axenic) culture on d-xylose; (II) binary culture with the ectosymbiont Ca. N. occultus SVXNc on d-xylose; (III) binary culture with Halorabdus sp. SVX81 on xylan; (IV) trinary culture with Halorabdus sp. SVX81 and the ectosymbiont Ca. N. occultus SVXNc on xylan.SUPPLEMENTARY TABLE S1. Composition of consortia used in this study (120 h of cultivation).SUPPLEMENTARY TABLE S2. SRA NCBI database accession numbers of the raw SMRT PacBio genomic reads and Illumina RNA reads generated for this study.SUPPLEMENTARY TABLE S3. Protein coding genes H. lucertense SVX82 with cTAG methylation within 20 bp upstream of the start codon.SUPPLEMENTARY TABLE S4. Methylation and expression of genes with multiple GRAGa G methylation motifs within their sequences.SUPPLEMENTARY VIDEO S1. Three-dimensional (segmented) view of host (SVX82, maroon outer layer) and DPANN (SVXNc, cyan outer layer) interaction showing extensive membrane blebbing from the DPANN SVXNc at the DPANN-host interface.DNA methylation serves a variety of functions across all life domains. In this study, we investigated archaeal methylomics within a tripartite xylanolytic halophilic consortium. This consortium includes Haloferax lucertense SVX82, Halorhabdus sp. SVX81, and an ectosymbiotic Candidatus Nanohalococcus occultus SVXNc, a nano-sized archaeon from the DPANN superphylum. We utilized PacBio SMRT and Illumina cDNA sequencing to analyse samples from consortia of different compositions for methylomics and transcriptomics. Endogenous cTAG methylation, typical of Haloferax, was accompanied in this strain by methylation at four other motifs, including GDGcHC methylation, which is specific to the ectosymbiont. Our analysis of the distribution of methylated and unmethylated motifs suggests that autochthonous cTAG methylation may influence gene regulation. The frequency of GRAGAaG methylation increased in highly expressed genes, while CcTTG and GTCGaGG methylation could be linked to restriction-modification (RM) activity. Generally, the RM activity might have been reduced during the evolution of this archaeon to balance the protection of cells from intruders, the reduction of DNA damage due to self-restriction in stressful environments, and the benefits of DNA exchange under extreme conditions. Our methylomics, transcriptomics and complementary electron cryotomography (cryo-ET) data suggest that the nanohaloarchaeon exports its methyltransferase to methylate the Haloferax genome, unveiling a new aspect of the interaction between the symbiont and its host.National Health and Medical Research Council; Human Frontier Science Program (HFSP); Agence Nationale de la Recherche; HORIZON EUROPE European Research Council.http://wileyonlinelibrary.com/journal/emi4hj2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-15:Life on lan

Agricultura de precisión: integrando conocimientos para una agricultura moderna y sustentable

Este libro será de utilidad para nuestros países en su búsqueda de nuevas tecnologías que ayuden a nuestra agricultura a ser más competitiva y moderna, al mismo tiempo que sirva de estímulo a las nuevas generaciones de profesionales que tendrán la responsabilidad de continuar con el desarrollo de estas y otras nuevas tecnologías, que cada vez emergen con mayor frecuencia y velocida

Estrategias de biotecnología agropecuaria para el Cono Sur

154 páginas.En el documento se define la biotecnología como el uso integrado de la información científica desde una variedad de disciplinas, de forma de permitir el uso activo de organismos o sus componentes con objetivos médicos, agrícolas, industriales y ambientale