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1.
Nature ; 630(8018): 899-904, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38723661

RESUMEN

Nitrogen (N2) fixation in oligotrophic surface waters is the main source of new nitrogen to the ocean1 and has a key role in fuelling the biological carbon pump2. Oceanic N2 fixation has been attributed almost exclusively to cyanobacteria, even though genes encoding nitrogenase, the enzyme that fixes N2 into ammonia, are widespread among marine bacteria and archaea3-5. Little is known about these non-cyanobacterial N2 fixers, and direct proof that they can fix nitrogen in the ocean has so far been lacking. Here we report the discovery of a non-cyanobacterial N2-fixing symbiont, 'Candidatus Tectiglobus diatomicola', which provides its diatom host with fixed nitrogen in return for photosynthetic carbon. The N2-fixing symbiont belongs to the order Rhizobiales and its association with a unicellular diatom expands the known hosts for this order beyond the well-known N2-fixing rhizobia-legume symbioses on land6. Our results show that the rhizobia-diatom symbioses can contribute as much fixed nitrogen as can cyanobacterial N2 fixers in the tropical North Atlantic, and that they might be responsible for N2 fixation in the vast regions of the ocean in which cyanobacteria are too rare to account for the measured rates.


Asunto(s)
Diatomeas , Fijación del Nitrógeno , Nitrógeno , Océanos y Mares , Rhizobium , Agua de Mar , Simbiosis , Carbono/metabolismo , Diatomeas/metabolismo , Diatomeas/fisiología , Nitrógeno/metabolismo , Fotosíntesis , Filogenia , Rhizobium/clasificación , Rhizobium/metabolismo , Rhizobium/fisiología , Agua de Mar/microbiología , Agua de Mar/química , Cianobacterias/aislamiento & purificación , Cianobacterias/metabolismo , Océano Atlántico
2.
Proc Natl Acad Sci U S A ; 121(10): e2311321121, 2024 Mar 05.
Artículo en Inglés | MEDLINE | ID: mdl-38408251

RESUMEN

Since their discovery, extracellular vesicles (EVs) have changed our view on how organisms interact with their extracellular world. EVs are able to traffic a diverse array of molecules across different species and even domains, facilitating numerous functions. In this study, we investigate EV production in Euryarchaeota, using the model organism Haloferax volcanii. We uncover that EVs enclose RNA, with specific transcripts preferentially enriched, including those with regulatory potential, and conclude that EVs can act as an RNA communication system between haloarchaea. We demonstrate the key role of an EV-associated small GTPase for EV formation in H. volcanii that is also present across other diverse evolutionary branches of Archaea. We propose the name, ArvA, for the identified family of archaeal vesiculating GTPases. Additionally, we show that two genes in the same operon with arvA (arvB and arvC) are also involved in EV formation. Both, arvB and arvC, are closely associated with arvA in the majority of other archaea encoding ArvA. Our work demonstrates that small GTPases involved in membrane deformation and vesiculation, ubiquitous in Eukaryotes, are also present in Archaea and are widely distributed across diverse archaeal phyla.


Asunto(s)
Euryarchaeota , Vesículas Extracelulares , Haloferax volcanii , Proteínas de Unión al GTP Monoméricas , Euryarchaeota/genética , Archaea/genética , ARN , Haloferax volcanii/genética , Vesículas Extracelulares/genética
3.
PLoS Biol ; 21(9): e3002292, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-37747940

RESUMEN

Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.


Asunto(s)
Archaea , Sulfatos , Anaerobiosis , Sulfatos/metabolismo , Sedimentos Geológicos/microbiología , Bacterias/genética , Oxidación-Reducción , Filogenia
4.
PLoS Biol ; 20(1): e3001508, 2022 01.
Artículo en Inglés | MEDLINE | ID: mdl-34986141

RESUMEN

The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.


Asunto(s)
Archaea , Electrones , Anaerobiosis , Archaea/genética , Archaea/metabolismo , Genómica , Sedimentos Geológicos/microbiología , Metano/metabolismo , Oxidación-Reducción , Filogenia , Sulfatos/metabolismo
5.
Appl Environ Microbiol ; 88(11): e0210921, 2022 06 14.
Artículo en Inglés | MEDLINE | ID: mdl-35604226

RESUMEN

Syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Anoxic Percoll density gradients and size-selective filtration were used to separate ANME-SRB consortia from sediment particles and single cells to accelerate the cultivation process. Over a 3-year period, a subset of the sediment-associated ANME and SRB lineages, predominantly comprised of ANME-2a/2b ("Candidatus Methanocomedenaceae") and their syntrophic bacterial partners, SEEP-SRB1/2, adapted and grew under defined laboratory conditions. Metagenome-assembled genomes from several enrichments revealed that ANME-2a, SEEP-SRB1, and Methanococcoides in different enrichments from the same inoculum represented distinct species, whereas other coenriched microorganisms were closely related at the species level. This suggests that ANME, SRB, and Methanococcoides are more genetically diverse than other members in methane seeps. Flow cytometry sorting and sequencing of cell aggregates revealed that Methanococcoides, Anaerolineales, and SEEP-SRB1 were overrepresented in multiple ANME-2a cell aggregates relative to the bulk metagenomes, suggesting they were physically associated and possibly interacting. Overall, this study represents a successful case of selective cultivation of anaerobic slow-growing microorganisms from sediments based on their physical characteristics, introducing new opportunities for detailed genomic, physiological, biochemical, and ecological analyses. IMPORTANCE Biological anaerobic oxidation of methane (AOM) coupled with sulfate reduction represents a large methane sink in global ocean sediments. Methane consumption is carried out by syntrophic archaeal-bacterial consortia and fuels a unique ecosystem, yet the interactions in these slow-growing syntrophic consortia and with other associated community members remain poorly understood. The significance of this study is the establishment of sediment-free enrichment cultures of anaerobic methanotrophic archaea and sulfate-reducing bacteria performing AOM with sulfate using selective cultivation approaches based on size, density, and metabolism. By reconstructing microbial genomes and analyzing community composition of the enrichment cultures and cell aggregates, we shed light on the diversity of microorganisms physically associated with AOM consortia beyond the core syntrophic partners. These enrichment cultures offer simplified model systems to extend our understanding of the diversity of microbial interactions within marine methane seeps.


Asunto(s)
Ecosistema , Metano , Anaerobiosis , Archaea/metabolismo , Bacterias/genética , Bacterias/metabolismo , Sedimentos Geológicos/microbiología , Metano/metabolismo , Oxidación-Reducción , Filogenia , Sulfatos/metabolismo
6.
Nature ; 528(7583): 555-9, 2015 Dec 24.
Artículo en Inglés | MEDLINE | ID: mdl-26610025

RESUMEN

Nitrification is a two-step process where ammonia is first oxidized to nitrite by ammonia-oxidizing bacteria and/or archaea, and subsequently to nitrate by nitrite-oxidizing bacteria. Already described by Winogradsky in 1890, this division of labour between the two functional groups is a generally accepted characteristic of the biogeochemical nitrogen cycle. Complete oxidation of ammonia to nitrate in one organism (complete ammonia oxidation; comammox) is energetically feasible, and it was postulated that this process could occur under conditions selecting for species with lower growth rates but higher growth yields than canonical ammonia-oxidizing microorganisms. Still, organisms catalysing this process have not yet been discovered. Here we report the enrichment and initial characterization of two Nitrospira species that encode all the enzymes necessary for ammonia oxidation via nitrite to nitrate in their genomes, and indeed completely oxidize ammonium to nitrate to conserve energy. Their ammonia monooxygenase (AMO) enzymes are phylogenetically distinct from currently identified AMOs, rendering recent acquisition by horizontal gene transfer from known ammonia-oxidizing microorganisms unlikely. We also found highly similar amoA sequences (encoding the AMO subunit A) in public sequence databases, which were apparently misclassified as methane monooxygenases. This recognition of a novel amoA sequence group will lead to an improved understanding of the environmental abundance and distribution of ammonia-oxidizing microorganisms. Furthermore, the discovery of the long-sought-after comammox process will change our perception of the nitrogen cycle.


Asunto(s)
Amoníaco/metabolismo , Bacterias/metabolismo , Nitratos/metabolismo , Nitrificación , Nitritos/metabolismo , Bacterias/enzimología , Bacterias/genética , Evolución Molecular , Genoma Bacteriano/genética , Nitrificación/genética , Oxidación-Reducción , Oxidorreductasas/genética , Oxidorreductasas/metabolismo , Filogenia
7.
Proc Natl Acad Sci U S A ; 113(45): 12792-12796, 2016 Nov 08.
Artículo en Inglés | MEDLINE | ID: mdl-27791118

RESUMEN

Anaerobic oxidation of methane (AOM) is crucial for controlling the emission of this potent greenhouse gas to the atmosphere. Nitrite-, nitrate-, and sulfate-dependent methane oxidation is well-documented, but AOM coupled to the reduction of oxidized metals has so far been demonstrated only in environmental samples. Here, using a freshwater enrichment culture, we show that archaea of the order Methanosarcinales, related to "Candidatus Methanoperedens nitroreducens," couple the reduction of environmentally relevant forms of Fe3+ and Mn4+ to the oxidation of methane. We obtained an enrichment culture of these archaea under anaerobic, nitrate-reducing conditions with a continuous supply of methane. Via batch incubations using [13C]methane, we demonstrated that soluble ferric iron (Fe3+, as Fe-citrate) and nanoparticulate forms of Fe3+ and Mn4+ supported methane-oxidizing activity. CO2 and ferrous iron (Fe2+) were produced in stoichiometric amounts. Our study connects the previous finding of iron-dependent AOM to microorganisms detected in numerous habitats worldwide. Consequently, it enables a better understanding of the interaction between the biogeochemical cycles of iron and methane.

8.
Microb Ecol ; 74(1): 1-5, 2017 07.
Artículo en Inglés | MEDLINE | ID: mdl-28074246

RESUMEN

Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua. Phylogenetic analysis of the 16S rRNA gene indicated that this Scalindua sp. belongs to a distinct group, separate from the anammox bacteria in the seawater column, that contains mostly sequences retrieved from high-salt environments. Using coverage- and composition-based binning, we extracted and assembled the draft genome of the dominant anammox bacterium. Comparative genomic analysis indicated that this Scalindua species uses compatible solutes for osmoadaptation, in contrast to other marine anammox bacteria that likely use a salt-in strategy. We propose the name Candidatus Scalindua rubra for this novel species, alluding to its discovery in the Red Sea.


Asunto(s)
Bacterias/clasificación , Genoma Bacteriano , Filogenia , Agua de Mar/microbiología , Bacterias/genética , Océano Índico , Oxidación-Reducción , Compuestos de Amonio Cuaternario , ARN Ribosómico 16S/genética , Sales (Química)
9.
Microb Ecol ; 72(3): 503-9, 2016 10.
Artículo en Inglés | MEDLINE | ID: mdl-27457652

RESUMEN

Microbial methane oxidizers play a crucial role in the oxidation of methane in marine ecosystems, as such preventing the escape of excessive methane to the atmosphere. Despite the important role of methanotrophs in marine ecosystems, only a limited number of isolates are described, with only four genomes available. Here, we report on two genomes of gammaproteobacterial methanotroph cultures, affiliated with the deep-sea cluster 2, obtained from North Sea sediment. Initial enrichments using methane as sole source of carbon and energy and mimicking the in situ conditions followed by serial subcultivations and multiple extinction culturing events over a period of 3 years resulted in a highly enriched culture. The draft genomes of the methane oxidizer in both cultures showed the presence of genes typically found in type I methanotrophs, including genes encoding particulate methane monooxygenase (pmoCAB), genes for tetrahydromethanopterin (H4MPT)- and tetrahydrofolate (H4F)-dependent C1-transfer pathways, and genes of the ribulose monophosphate (RuMP) pathway. The most distinctive feature, when compared to other available gammaproteobacterial genomes, is the absence of a calcium-dependent methanol dehydrogenase. Both genomes reported here only have a xoxF gene encoding a lanthanide-dependent XoxF5-type methanol dehydrogenase. Thus, these genomes offer novel insight in the genomic landscape of uncultured diversity of marine methanotrophs.


Asunto(s)
Oxidorreductasas de Alcohol/genética , Proteínas Bacterianas/genética , Sedimentos Geológicos/microbiología , Elementos de la Serie de los Lantanoides/farmacología , Methylococcaceae/enzimología , Methylococcaceae/genética , Proteínas Bacterianas/metabolismo , Composición de Base , Calcio , ADN Bacteriano/genética , Ecosistema , Regulación Bacteriana de la Expresión Génica , Regulación Enzimológica de la Expresión Génica , Genoma Bacteriano , Redes y Vías Metabólicas/genética , Metano/metabolismo , Methylococcaceae/clasificación , Methylococcaceae/efectos de los fármacos , Nitrógeno/metabolismo , Mar del Norte , Oxidación-Reducción , Oxigenasas/genética , Filogenia , Agua de Mar/microbiología , Tetrahidrofolatos/genética
10.
J Bacteriol ; 196(1): 80-9, 2014 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-24142254

RESUMEN

Anammox bacteria perform anaerobic ammonium oxidation (anammox) and have a unique compartmentalized cell consisting of three membrane-bound compartments (from inside outwards): the anammoxosome, riboplasm, and paryphoplasm. The cell envelope of anammox bacteria has been proposed to deviate from typical bacterial cell envelopes by lacking both peptidoglycan and a typical outer membrane. However, the composition of the anammox cell envelope is presently unknown. Here, we investigated the outermost layer of the anammox cell and identified a proteinaceous surface layer (S-layer) (a crystalline array of protein subunits) as the outermost component of the cell envelope of the anammox bacterium "Candidatus Kuenenia stuttgartiensis." This is the first description of an S-layer in the phylum of the Planctomycetes and a new addition to the cell plan of anammox bacteria. This S-layer showed hexagonal symmetry with a unit cell consisting of six protein subunits. The enrichment of the S-layer from the cell led to a 160-kDa candidate protein, Kustd1514, which has no homology to any known protein. This protein is present in a glycosylated form. Antibodies were generated against the glycoprotein and used for immunogold localization. The antiserum localized Kustd1514 to the S-layer and thus verified that this protein forms the "Ca. Kuenenia stuttgartiensis" S-layer.


Asunto(s)
Bacterias/química , Bacterias/ultraestructura , Membrana Celular/química , Membrana Celular/ultraestructura , Glicoproteínas de Membrana/análisis , Compuestos de Amonio/metabolismo , Bacterias/metabolismo , Procesamiento de Imagen Asistido por Computador , Microscopía Electrónica , Oxidación-Reducción , Multimerización de Proteína , Subunidades de Proteína/química , Subunidades de Proteína/metabolismo
11.
Environ Microbiol ; 16(11): 3487-98, 2014 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-24750895

RESUMEN

Fixed nitrogen is released by anaerobic ammonium oxidation (anammox) and/or denitrification from (marine) ecosystems. Nitrite, the terminal electron acceptor of the anammox process, occurs in nature at very low concentrations and is produced via (micro)aerobic oxidation of ammonium or nitrate reduction. The coupling of sulfide-dependent denitrification to anammox is particularly interesting because besides hydrogen, sulfide is the most important reductant at the chemocline of anoxic marine basins and is abundant within sediments. Although at µM concentrations, sulfide may be toxic and inhibiting anammox activity, a denitrifying microorganism could convert sulfide and nitrate at sufficiently high rates to allow anammox bacteria to stay active despite an influx of sulfide. To test this hypothesis, a laboratory scale model system containing a co-culture of anammox bacteria and the autotrophic denitrifier Sulfurimonas denitrificans DSM1251 was started. Complementary techniques revealed that the gammaproteobacterial Sedimenticola sp. took over the intended role of Su. denitrificans. A stable coculture of anammox bacteria and Sedimenticola sp. consumed sulfide, nitrate, ammonium and CO2 . Anammox bacteria contributed 65-75% to the nitrogen loss from the reactor. The cooperation between anammox and sulfide-dependent denitrification may play a significant role in environments where sulfur cycling is active and where actual sulfide concentrations stay below µM range.


Asunto(s)
Compuestos de Amonio/metabolismo , Bacterias/metabolismo , Desnitrificación , Epsilonproteobacteria/metabolismo , Azufre/metabolismo , Anaerobiosis , Procesos Autotróficos , Bacterias/efectos de los fármacos , Técnicas de Cocultivo , Gammaproteobacteria/metabolismo , Interacciones Microbianas , Modelos Biológicos , Nitratos/metabolismo , Nitritos/metabolismo , Oxidación-Reducción , Sulfuros/metabolismo , Sulfuros/toxicidad
12.
Nat Commun ; 15(1): 5293, 2024 Jun 21.
Artículo en Inglés | MEDLINE | ID: mdl-38906896

RESUMEN

Lacustrine methane emissions are strongly mitigated by aerobic methane-oxidizing bacteria (MOB) that are typically most active at the oxic-anoxic interface. Although oxygen is required by the MOB for the first step of methane oxidation, their occurrence in anoxic lake waters has raised the possibility that they are capable of oxidizing methane further anaerobically. Here, we investigate the activity and growth of MOB in Lake Zug, a permanently stratified freshwater lake. The rates of anaerobic methane oxidation in the anoxic hypolimnion reached up to 0.2 µM d-1. Single-cell nanoSIMS measurements, together with metagenomic and metatranscriptomic analyses, linked the measured rates to MOB of the order Methylococcales. Interestingly, their methane assimilation activity was similar under hypoxic and anoxic conditions. Our data suggest that these MOB use fermentation-based methanotrophy as well as denitrification under anoxic conditions, thus offering an explanation for their widespread presence in anoxic habitats such as stratified water columns. Thus, the methane sink capacity of anoxic basins may have been underestimated by not accounting for the anaerobic MOB activity.


Asunto(s)
Lagos , Metano , Oxidación-Reducción , Metano/metabolismo , Lagos/microbiología , Anaerobiosis , Methylococcaceae/metabolismo , Methylococcaceae/genética , Metagenómica , Oxígeno/metabolismo
13.
Environ Microbiol ; 15(5): 1275-89, 2013 May.
Artículo en Inglés | MEDLINE | ID: mdl-22568606

RESUMEN

Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the 'Candidatus Scalindua' species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by 'Candidatus Scalindua profunda' to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater 'Candidatus Kuenenia stuttgartiensis'. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K.stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm.


Asunto(s)
Organismos Acuáticos/genética , Organismos Acuáticos/metabolismo , Genoma Bacteriano , Metagenoma , Ciclo del Nitrógeno , Planctomycetales/genética , Planctomycetales/metabolismo , Organismos Acuáticos/clasificación , Nitrito Reductasas/metabolismo , Océanos y Mares , Oxidación-Reducción , Planctomycetales/clasificación , Compuestos de Amonio Cuaternario/metabolismo , ARN Ribosómico 16S/genética , Microbiología del Agua
14.
BMC Microbiol ; 13: 265, 2013 Nov 23.
Artículo en Inglés | MEDLINE | ID: mdl-24267221

RESUMEN

BACKGROUND: Anaerobic ammonium oxidizing (anammox) bacteria may contribute up to 50% to the global nitrogen production, and are, thus, key players of the global nitrogen cycle. The molecular mechanism of anammox was recently elucidated and is suggested to proceed through a branched respiratory chain. This chain involves an exceptionally high number of c-type cytochrome proteins which are localized within the anammoxosome, a unique subcellular organelle. During transport into the organelle the c-type cytochrome apoproteins need to be post-translationally processed so that heme groups become covalently attached to them, resulting in mature c-type cytochrome proteins. RESULTS: In this study, a comparative genome analysis was performed to identify the cytochrome c maturation system employed by anammox bacteria. Our results show that all available anammox genome assemblies contain a complete type II cytochrome c maturation system. CONCLUSIONS: Our working model suggests that this machinery is localized at the anammoxosome membrane which is assumed to be the locus of anammox catabolism. These findings will stimulate further studies in dissecting the molecular and cellular basis of cytochrome c biogenesis in anammox bacteria.


Asunto(s)
Compuestos de Amonio/metabolismo , Bacterias/genética , Bacterias/metabolismo , Citocromos c/metabolismo , Redes y Vías Metabólicas/genética , Procesamiento Proteico-Postraduccional , Biología Computacional , Genoma Bacteriano , Proteínas de la Membrana/metabolismo , Orgánulos/enzimología , Orgánulos/metabolismo , Oxidación-Reducción
15.
Nat Microbiol ; 8(2): 231-245, 2023 02.
Artículo en Inglés | MEDLINE | ID: mdl-36658397

RESUMEN

'Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus-host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, 'Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.


Asunto(s)
Archaea , Ecosistema , Filogenia , Viroma , Sedimentos Geológicos , Anaerobiosis , Metano/metabolismo , Alcanos/metabolismo
16.
Nat Microbiol ; 8(8): 1574-1586, 2023 08.
Artículo en Inglés | MEDLINE | ID: mdl-37429908

RESUMEN

Nitric oxide (NO) is a highly reactive and climate-active molecule and a key intermediate in the microbial nitrogen cycle. Despite its role in the evolution of denitrification and aerobic respiration, high redox potential and capacity to sustain microbial growth, our understanding of NO-reducing microorganisms remains limited due to the absence of NO-reducing microbial cultures obtained directly from the environment using NO as a substrate. Here, using a continuous bioreactor and a constant supply of NO as the sole electron acceptor, we enriched and characterized a microbial community dominated by two previously unknown microorganisms that grow at nanomolar NO concentrations and survive high amounts (>6 µM) of this toxic gas, reducing it to N2 with little to non-detectable production of the greenhouse gas nitrous oxide. These results provide insight into the physiology of NO-reducing microorganisms, which have pivotal roles in the control of climate-active gases, waste removal, and evolution of nitrate and oxygen respiration.


Asunto(s)
Microbiota , Óxido Nítrico , Desnitrificación , Nitrógeno/química , Gases , Reactores Biológicos
17.
Appl Environ Microbiol ; 78(22): 8033-44, 2012 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-22961894

RESUMEN

Poly(3-hydroxybutyrate) (PHB) production and mobilization in Ralstonia eutropha are well studied, but in only a few instances has PHB production been explored in relation to other cellular processes. We examined the global gene expression of wild-type R. eutropha throughout the PHB cycle: growth on fructose, PHB production using fructose following ammonium depletion, and PHB utilization in the absence of exogenous carbon after ammonium was resupplied. Our results confirm or lend support to previously reported results regarding the expression of PHB-related genes and enzymes. Additionally, genes for many different cellular processes, such as DNA replication, cell division, and translation, are selectively repressed during PHB production. In contrast, the expression levels of genes under the control of the alternative sigma factor σ(54) increase sharply during PHB production and are repressed again during PHB utilization. Global gene regulation during PHB production is strongly reminiscent of the gene expression pattern observed during the stringent response in other species. Furthermore, a ppGpp synthase deletion mutant did not show an accumulation of PHB, and the chemical induction of the stringent response with DL-norvaline caused an increased accumulation of PHB in the presence of ammonium. These results indicate that the stringent response is required for PHB accumulation in R. eutropha, helping to elucidate a thus-far-unknown physiological basis for this process.


Asunto(s)
Cupriavidus necator/genética , Cupriavidus necator/metabolismo , Regulación Bacteriana de la Expresión Génica , Polihidroxialcanoatos/metabolismo , Carbono/metabolismo , Medios de Cultivo/química , Cupriavidus necator/crecimiento & desarrollo , Fructosa/metabolismo , Eliminación de Gen , Perfilación de la Expresión Génica , Compuestos de Amonio Cuaternario/metabolismo
19.
Nat Microbiol ; 7(2): 200-212, 2022 02.
Artículo en Inglés | MEDLINE | ID: mdl-35027677

RESUMEN

Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation-decentralized innovation-hierarchical import model that accounts for the emergence of eukaryotic complexity.


Asunto(s)
Archaea/genética , Eucariontes/genética , Evolución Molecular , Flujo Génico , Genoma Arqueal , Células Procariotas/metabolismo , Proteínas Arqueales/genética , Bacterias/genética , Metagenómica , Filogenia
20.
ISME J ; 16(7): 1750-1764, 2022 07.
Artículo en Inglés | MEDLINE | ID: mdl-35352015

RESUMEN

Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those currently known, showing the microbial community in Auka hydrothermal sediments is highly diverse. 16S rRNA gene amplicon screening of 224 sediment samples across the vent field indicates that the MAGs retrieved from a single site are representative of the microbial community in the vent field sediments. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison between Auka MAGs and MAGs from Guaymas Basin revealed a remarkable 20% species-level overlap, suggestive of long-distance species transfer over 400 km and subsequent sediment colonization. Optimal growth temperature prediction on the Auka MAGs, and thousands of reference genomes, shows that thermophily is a trait that has evolved frequently. Taken together, our Auka vent field results offer new perspectives on our understanding of hydrothermal vent microbiology.


Asunto(s)
Respiraderos Hidrotermales , Microbiota , Sedimentos Geológicos/microbiología , Respiraderos Hidrotermales/microbiología , Metagenómica , Filogenia , ARN Ribosómico 16S/genética
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