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1.
Nat Commun ; 11(1): 5733, 2020 11 12.
Artigo em Inglês | MEDLINE | ID: mdl-33184291

RESUMO

Microbial methanogenesis in anaerobic soils contributes greatly to global methane (CH4) release, and understanding its response to temperature is fundamental to predicting the feedback between this potent greenhouse gas and climate change. A compensatory thermal response in microbial activity over time can reduce the response of respiratory carbon (C) release to temperature change, as shown for carbon dioxide (CO2) in aerobic soils. However, whether microbial methanogenesis also shows a compensatory response to temperature change remains unknown. Here, we used anaerobic wetland soils from the Greater Khingan Range and the Tibetan Plateau to investigate how 160 days of experimental warming (+4°C) and cooling (-4°C) affect the thermal response of microbial CH4 respiration and whether these responses correspond to changes in microbial community dynamics. The mass-specific CH4 respiration rates of methanogens decreased with warming and increased with cooling, suggesting that microbial methanogenesis exhibited compensatory responses to temperature changes. Furthermore, changes in the species composition of methanogenic community under warming and cooling largely explained the compensatory response in the soils. The stimulatory effect of climate warming on soil microbe-driven CH4 emissions may thus be smaller than that currently predicted, with important consequences for atmospheric CH4 concentrations.


Assuntos
Respiração Celular/fisiologia , Crescimento Quimioautotrófico/fisiologia , Mudança Climática , Metano/metabolismo , Microbiologia do Solo , Temperatura , Biomassa , Carbono/metabolismo , Ciclo do Carbono , Dióxido de Carbono/análise , Crescimento Quimioautotrófico/genética , China , Ecologia , Aquecimento Global , Gases de Efeito Estufa , Metano/análise , Solo , Áreas Alagadas
2.
Proc Natl Acad Sci U S A ; 117(36): 22452-22461, 2020 09 08.
Artigo em Inglês | MEDLINE | ID: mdl-32820073

RESUMO

Carbon fixation via the Calvin cycle is constrained by the side activity of Rubisco with dioxygen, generating 2-phosphoglycolate. The metabolic recycling of phosphoglycolate was extensively studied in photoautotrophic organisms, including plants, algae, and cyanobacteria, where it is referred to as photorespiration. While receiving little attention so far, aerobic chemolithoautotrophic bacteria that operate the Calvin cycle independent of light must also recycle phosphoglycolate. As the term photorespiration is inappropriate for describing phosphoglycolate recycling in these nonphotosynthetic autotrophs, we suggest the more general term "phosphoglycolate salvage." Here, we study phosphoglycolate salvage in the model chemolithoautotroph Cupriavidus necator H16 (Ralstonia eutropha H16) by characterizing the proxy process of glycolate metabolism, performing comparative transcriptomics of autotrophic growth under low and high CO2 concentrations, and testing autotrophic growth phenotypes of gene deletion strains at ambient CO2 We find that the canonical plant-like C2 cycle does not operate in this bacterium, and instead, the bacterial-like glycerate pathway is the main route for phosphoglycolate salvage. Upon disruption of the glycerate pathway, we find that an oxidative pathway, which we term the malate cycle, supports phosphoglycolate salvage. In this cycle, glyoxylate is condensed with acetyl coenzyme A (acetyl-CoA) to give malate, which undergoes two oxidative decarboxylation steps to regenerate acetyl-CoA. When both pathways are disrupted, autotrophic growth is abolished at ambient CO2 We present bioinformatic data suggesting that the malate cycle may support phosphoglycolate salvage in diverse chemolithoautotrophic bacteria. This study thus demonstrates a so far unknown phosphoglycolate salvage pathway, highlighting important diversity in microbial carbon fixation metabolism.


Assuntos
Crescimento Quimioautotrófico/fisiologia , Glicolatos/metabolismo , Fotossíntese/fisiologia , Acetilcoenzima A/metabolismo , Proteínas de Bactérias/metabolismo , Ciclo do Carbono/fisiologia , Cupriavidus necator/genética , Cupriavidus necator/metabolismo , Malato Sintase/metabolismo , Malatos/metabolismo , Oxirredução
3.
Appl Environ Microbiol ; 86(1)2019 12 13.
Artigo em Inglês | MEDLINE | ID: mdl-31628148

RESUMO

Use of hydrogen gas (H2) as an electron donor is common among free-living chemolithotrophic microorganisms. Given the presence of this dissolved gas at deep-sea hydrothermal vents, it has been suggested that it may also be a major electron donor for the free-living and symbiotic chemolithoautotrophic bacteria that are the primary producers at these sites. Giant Riftia pachyptila siboglinid tubeworms and their symbiotic bacteria ("Candidatus Endoriftia persephone") dominate many vents in the Eastern Pacific, and their use of sulfide as a major electron donor has been documented. Genes encoding hydrogenase are present in the "Ca Endoriftia persephone" genome, and proteome data suggest that these genes are expressed. In this study, high-pressure respirometry of intact R. pachyptila and incubations of trophosome homogenate were used to determine whether this symbiotic association could also use H2 as a major electron donor. Measured rates of H2 uptake by intact R. pachyptila in high-pressure respirometers were similar to rates measured in the absence of tubeworms. Oxygen uptake rates in the presence of H2 were always markedly lower than those measured in the presence of sulfide, as was the incorporation of 13C-labeled dissolved inorganic carbon. Carbon fixation by trophosome homogenate was not stimulated by H2, nor was hydrogenase activity detectable in these samples. Though genes encoding [NiFe] group 1e and [NiFe] group 3b hydrogenases are present in the genome and transcribed, it does not appear that H2 is a major electron donor for this system, and it may instead play a role in intracellular redox homeostasis.IMPORTANCE Despite the presence of hydrogenase genes, transcripts, and proteins in the "Ca Endoriftia persephone" genome, transcriptome, and proteome, it does not appear that R. pachyptila can use H2 as a major electron donor. For many uncultivable microorganisms, omic analyses are the basis for inferences about their activities in situ However, as is apparent from the study reported here, there are dangers in extrapolating from omics data to function, and it is essential, whenever possible, to verify functions predicted from omics data with physiological and biochemical measurements.


Assuntos
Crescimento Quimioautotrófico/fisiologia , Gammaproteobacteria/metabolismo , Hidrogênio/metabolismo , Fontes Hidrotermais , Poliquetos/microbiologia , Animais , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Carbono/metabolismo , Genes Bacterianos , Genoma Bacteriano , Interações entre Hospedeiro e Microrganismos/fisiologia , Hidrogenase/genética , Hidrogenase/metabolismo , Fontes Hidrotermais/química , Fontes Hidrotermais/microbiologia , Poliquetos/metabolismo , Substâncias Redutoras/metabolismo , Simbiose
4.
Environ Microbiol ; 21(11): 4062-4075, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31336026

RESUMO

Ammonia-oxidizing archaea (AOA) constitute a considerable fraction of microbial biomass in the global ocean, comprising 20%-40% of the ocean's prokaryotic plankton. However, it remains enigmatic to what extent these chemolithoautotrophic archaea release dissolved organic carbon (DOC). A combination of targeted and untargeted metabolomics was used to characterize the exometabolomes of three model AOA strains of the Nitrosopumilus genus. Our results indicate that marine AOA exude a suite of organic compounds with potentially varying reactivities, dominated by nitrogen-containing compounds. A significant fraction of the released dissolved organic matter (DOM) consists of labile compounds, which typically limit prokaryotic heterotrophic activity in open ocean waters, including amino acids, thymidine and B vitamins. Amino acid release rates corresponded with ammonia oxidation activity and the three Nitrosopumilus strains predominantly released hydrophobic amino acids, potentially as a result of passive diffusion. Despite the low contribution of DOC released by AOA (~0.08%-1.05%) to the heterotrophic prokaryotic carbon demand, the release of physiologically relevant metabolites could be crucial for microbes that are auxotrophic for some of these compounds, including members of the globally abundant and ubiquitous SAR11 clade.


Assuntos
Amônia/metabolismo , Archaea/metabolismo , Processos Heterotróficos/fisiologia , Compostos Orgânicos/metabolismo , Carbono/metabolismo , Crescimento Quimioautotrófico/fisiologia , Oceanos e Mares , Oxirredução , Filogenia
5.
Environ Microbiol ; 21(10): 3831-3854, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31271506

RESUMO

Marine sponges represent one of the few eukaryotic groups that frequently harbour symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However, in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of ammonia-oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope-based functional assays. 'Candidatus Nitrosospongia ianthellae' is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbour nitrite-oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system, represent important adaptations of AOA to life within these ancient filter-feeding animals.


Assuntos
Amônia/metabolismo , Archaea/genética , Archaea/metabolismo , Poríferos/microbiologia , Animais , Archaea/isolamento & purificação , Crescimento Quimioautotrófico/fisiologia , Hibridização in Situ Fluorescente , Nitrificação/fisiologia , Nitritos/metabolismo , Oxirredução , Filogenia , Microbiologia do Solo
6.
Proc Natl Acad Sci U S A ; 116(17): 8505-8514, 2019 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-30962361

RESUMO

Hosts of chemoautotrophic bacteria typically have much higher biomass than their symbionts and consume symbiont cells for nutrition. In contrast to this, chemoautotrophic Candidatus Riegeria symbionts in mouthless Paracatenula flatworms comprise up to half of the biomass of the consortium. Each species of Paracatenula harbors a specific Ca Riegeria, and the endosymbionts have been vertically transmitted for at least 500 million years. Such prolonged strict vertical transmission leads to streamlining of symbiont genomes, and the retained physiological capacities reveal the functions the symbionts provide to their hosts. Here, we studied a species of Paracatenula from Sant'Andrea, Elba, Italy, using genomics, gene expression, imaging analyses, as well as targeted and untargeted MS. We show that its symbiont, Ca R. santandreae has a drastically smaller genome (1.34 Mb) than the symbiont´s free-living relatives (4.29-4.97 Mb) but retains a versatile and energy-efficient metabolism. It encodes and expresses a complete intermediary carbon metabolism and enhanced carbon fixation through anaplerosis and accumulates massive intracellular inclusions such as sulfur, polyhydroxyalkanoates, and carbohydrates. Compared with symbiotic and free-living chemoautotrophs, Ca R. santandreae's versatility in energy storage is unparalleled in chemoautotrophs with such compact genomes. Transmission EM as well as host and symbiont expression data suggest that Ca R. santandreae largely provisions its host via outer-membrane vesicle secretion. With its high share of biomass in the symbiosis and large standing stocks of carbon and energy reserves, it has a unique role for bacterial symbionts-serving as the primary energy storage for its animal host.


Assuntos
Genoma Bacteriano/genética , Platelmintos , Rhodospirillaceae , Simbiose , Animais , Crescimento Quimioautotrófico/genética , Crescimento Quimioautotrófico/fisiologia , Redes e Vias Metabólicas , Platelmintos/metabolismo , Platelmintos/microbiologia , Platelmintos/fisiologia , Rhodospirillaceae/genética , Rhodospirillaceae/fisiologia , Simbiose/genética , Simbiose/fisiologia
7.
Biochemistry ; 58(11): 1470-1477, 2019 03 19.
Artigo em Inglês | MEDLINE | ID: mdl-30395445

RESUMO

Alarming changes in environmental conditions have prompted significant research into producing renewable commodities from sources other than fossil fuels. One such alternative is CO2, a determinate greenhouse gas with historically high atmospheric levels. If sequestered, CO2 could be used as a highly renewable feedstock for industrially relevant products and fuels. The vast majority of atmospheric CO2 fixation is accomplished by photosynthetic organisms, which have unfortunately proven difficult to utilize as chassis for industrial production. Nonphotosynthetic CO2 fixing microorganisms and pathways have recently attracted scientific and commercial interest. This Perspective will review promising alternate CO2 fixation strategies and their potential to supply microbially produced fuels and commodity chemicals, such as higher alcohols. Acetogenic fermentation and microbial electrosynthesis are the primary focuses of this review.


Assuntos
Ciclo do Carbono/fisiologia , Dióxido de Carbono/isolamento & purificação , Dióxido de Carbono/metabolismo , Biocombustíveis/microbiologia , Crescimento Quimioautotrófico/fisiologia , Fermentação , Fotossíntese , Engenharia de Proteínas/métodos , Engenharia de Proteínas/tendências
8.
FEMS Microbiol Ecol ; 94(8)2018 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-29931252

RESUMO

The deep biosphere is the largest 'bioreactor' on earth, and microbes inhabiting this biome profoundly influence global nutrient and energy cycles. An important question for deep biosphere microbiology is whether or not specific populations are viable. To address this, we used quantitative PCR and high throughput 16S rRNA gene sequencing of total and viable cells (i.e. with an intact cellular membrane) from three groundwaters with different ages and chemical constituents. There were no statistically significant differences in 16S rRNA gene abundances and microbial diversity between total and viable communities. This suggests that populations were adapted to prevailing oligotrophic conditions and that non-viable cells are rapidly degraded and recycled into new biomass. With higher concentrations of organic carbon, the modern marine and undefined mixed waters hosted a community with a larger range of predicted growth strategies than the ultra-oligotrophic old saline water. These strategies included fermentative and potentially symbiotic lifestyles by candidate phyla that typically have streamlined genomes. In contrast, the old saline waters had more 16S rRNA gene sequences in previously cultured lineages able to oxidize hydrogen and fix carbon dioxide. This matches the paradigm of a hydrogen and carbon dioxide-fed chemolithoautotrophic deep biosphere.


Assuntos
Bactérias/metabolismo , Crescimento Quimioautotrófico/fisiologia , Água Subterrânea/microbiologia , Nutrientes/metabolismo , Bactérias/classificação , Bactérias/genética , Biodiversidade , Biomassa , Ecossistema , Filogenia , RNA Ribossômico 16S/genética , Reciclagem
9.
World J Microbiol Biotechnol ; 34(7): 89, 2018 Jun 09.
Artigo em Inglês | MEDLINE | ID: mdl-29886519

RESUMO

With rapid technology progress and cost reduction, clean hydrogen from water electrolysis driven by renewable powers becomes a potential feedstock for CO2 fixation by hydrogen-oxidizing bacteria. Cupriavidus necator (formally Ralstonia eutropha), a representative member of the lithoautotrophic prokaryotes, is a promising producer of polyhydroxyalkanoates and single cell proteins. This paper reviews the fundamental properties of the hydrogen-oxidizing bacterium, the metabolic activities under limitation of individual gases and nutrients, and the value-added products from CO2, including the products with large potential markets. Gas fermentation and bioreactor safety are discussed for achieving high cell density and high productivity of desired products under chemolithotrophic conditions. The review also updates the recent research activities in metabolic engineering of C. necator to produce novel metabolites from CO2.


Assuntos
Bactérias/metabolismo , Ciclo do Carbono , Dióxido de Carbono/metabolismo , Cupriavidus necator/metabolismo , Hidrogênio/metabolismo , Reatores Biológicos , Crescimento Quimioautotrófico/fisiologia , Cupriavidus necator/genética , Proteínas na Dieta/metabolismo , Fermentação , Gases/metabolismo , Hidrogenase/metabolismo , Hidroxibutiratos/metabolismo , Metabolismo dos Lipídeos , Engenharia Metabólica , Oxirredução , Poliésteres/metabolismo , Poli-Hidroxialcanoatos/metabolismo
10.
FEMS Microbiol Ecol ; 94(6)2018 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-29873717

RESUMO

Microorganisms are the drivers of biogeochemical methane and nitrogen cycles. Essential roles of chemolithoautotrophic microorganisms in these cycles were predicted long before their identification. Dedicated enrichment procedures, metagenomics surveys and single-cell technologies have enabled the identification of several new groups of most-wanted spookmicrobes, including novel methoxydotrophic methanogens that produce methane from methylated coal compounds and acetoclastic 'Candidatus Methanothrix paradoxum', which is active in oxic soils. The resultant energy-rich methane can be oxidized via a suite of electron acceptors. Recently, 'Candidatus Methanoperedens nitroreducens' ANME-2d archaea and 'Candidatus Methylomirabilis oxyfera' bacteria were enriched on nitrate and nitrite under anoxic conditions with methane as an electron donor. Although 'Candidatus Methanoperedens nitroreducens' and other ANME archaea can use iron citrate as an electron acceptor in batch experiments, the quest for anaerobic methane oxidizers that grow via iron reduction continues. In recent years, the nitrogen cycle has been expanded by the discovery of various ammonium-oxidizing prokaryotes, including ammonium-oxidizing archaea, versatile anaerobic ammonium-oxidizing (anammox) bacteria and complete ammonium-oxidizing (comammox) Nitrospira bacteria. Several biogeochemical studies have indicated that ammonium conversion occurs under iron-reducing conditions, but thus far no microorganism has been identified. Ultimately, iron-reducing and sulfate-dependent ammonium-oxidizing microorganisms await discovery.


Assuntos
Compostos de Amônio/metabolismo , Bactérias/metabolismo , Crescimento Quimioautotrófico/fisiologia , Metano/metabolismo , Methanosarcinales/metabolismo , Anaerobiose , Bactérias/crescimento & desenvolvimento , Methanosarcinales/crescimento & desenvolvimento , Nitratos/metabolismo , Nitritos/metabolismo , Ciclo do Nitrogênio , Oxirredução , Solo
11.
Nat Commun ; 9(1): 1729, 2018 04 30.
Artigo em Inglês | MEDLINE | ID: mdl-29712903

RESUMO

Members of the gammaproteobacterial clade SUP05 couple water column sulfide oxidation to nitrate reduction in sulfidic oxygen minimum zones (OMZs). Their abundance in offshore OMZ waters devoid of detectable sulfide has led to the suggestion that local sulfate reduction fuels SUP05-mediated sulfide oxidation in a so-called "cryptic sulfur cycle". We examined the distribution and metabolic capacity of SUP05 in Peru Upwelling waters, using a combination of oceanographic, molecular, biogeochemical and single-cell techniques. A single SUP05 species, U Thioglobus perditus, was found to be abundant and active in both sulfidic shelf and sulfide-free offshore OMZ waters. Our combined data indicated that mesoscale eddy-driven transport led to the dispersal of U T. perditus and elemental sulfur from the sulfidic shelf waters into the offshore OMZ region. This offshore transport of shelf waters provides an alternative explanation for the abundance and activity of sulfide-oxidizing denitrifying bacteria in sulfide-poor offshore OMZ waters.


Assuntos
Crescimento Quimioautotrófico/fisiologia , Gammaproteobacteria/metabolismo , Redes e Vias Metabólicas/fisiologia , Água do Mar/química , Enxofre/metabolismo , Organismos Aquáticos , Gammaproteobacteria/classificação , Gammaproteobacteria/crescimento & desenvolvimento , Nitrogênio/metabolismo , Oxirredução , Oxigênio/metabolismo , Peru , Filogenia , Água do Mar/microbiologia
12.
Proc Natl Acad Sci U S A ; 115(23): 6022-6027, 2018 06 05.
Artigo em Inglês | MEDLINE | ID: mdl-29773709

RESUMO

Members of the archaeal phylum Bathyarchaeota are among the most abundant microorganisms on Earth. Although versatile metabolic capabilities such as acetogenesis, methanogenesis, and fermentation have been suggested for bathyarchaeotal members, no direct confirmation of these metabolic functions has been achieved through growth of Bathyarchaeota in the laboratory. Here we demonstrate, on the basis of gene-copy numbers and probing of archaeal lipids, the growth of Bathyarchaeota subgroup Bathy-8 in enrichments of estuarine sediments with the biopolymer lignin. Other organic substrates (casein, oleic acid, cellulose, and phenol) did not significantly stimulate growth of Bathyarchaeota Meanwhile, putative bathyarchaeotal tetraether lipids incorporated 13C from 13C-bicarbonate only when added in concert with lignin. Our results are consistent with organoautotrophic growth of a bathyarchaeotal group with lignin as an energy source and bicarbonate as a carbon source and shed light into the cycling of one of Earth's most abundant biopolymers in anoxic marine sediment.


Assuntos
Sedimentos Geológicos/química , Sedimentos Geológicos/microbiologia , Lignina/metabolismo , Archaea/metabolismo , Carbono/metabolismo , Crescimento Quimioautotrófico/fisiologia , DNA Arqueal/metabolismo , Fontes Geradoras de Energia , Lignina/química , Metano/metabolismo , RNA Ribossômico 16S/metabolismo
13.
Microb Ecol ; 76(2): 387-403, 2018 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-29354879

RESUMO

The organisms inhabiting the deep-seafloor are known to play a crucial role in global biogeochemical cycles. Chemolithoautotrophic prokaryotes, which produce biomass from single carbon molecules, constitute the primary source of nutrition for the higher organisms, being critical for the sustainability of food webs and overall life in the deep-sea hydrothermal ecosystems. The present study investigates the metabolic profiles of chemolithoautotrophs inhabiting the sediments of Menez Gwen and Rainbow deep-sea vent fields, in the Mid-Atlantic Ridge. Differences in the microbial community structure might be reflecting the distinct depth, geology, and distance from vent of the studied sediments. A metagenomic sequencing approach was conducted to characterize the microbiome of the deep-sea hydrothermal sediments and the relevant metabolic pathways used by microbes. Both Menez Gwen and Rainbow metagenomes contained a significant number of genes involved in carbon fixation, revealing the largely autotrophic communities thriving in both sites. Carbon fixation at Menez Gwen site was predicted to occur mainly via the reductive tricarboxylic acid cycle, likely reflecting the dominance of sulfur-oxidizing Epsilonproteobacteria at this site, while different autotrophic pathways were identified at Rainbow site, in particular the Calvin-Benson-Bassham cycle. Chemolithotrophy appeared to be primarily driven by the oxidation of reduced sulfur compounds, whether through the SOX-dependent pathway at Menez Gwen site or through reverse sulfate reduction at Rainbow site. Other energy-yielding processes, such as methane, nitrite, or ammonia oxidation, were also detected but presumably contributing less to chemolithoautotrophy. This work furthers our knowledge of the microbial ecology of deep-sea hydrothermal sediments and represents an important repository of novel genes with potential biotechnological interest.


Assuntos
Sedimentos Geológicos/microbiologia , Fontes Hidrotermais/microbiologia , Metagenômica , Microbiota/fisiologia , Archaea/classificação , Archaea/genética , Archaea/metabolismo , Processos Autotróficos , Açores , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Biodiversidade , Carbono/metabolismo , Ciclo do Carbono , Crescimento Quimioautotrófico/fisiologia , Ciclo do Ácido Cítrico , Epsilonproteobacteria/metabolismo , Metagenoma/fisiologia , Metano/metabolismo , Nitrogênio/metabolismo , Oxirredução , Fotossíntese , Filogenia , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Enxofre/metabolismo
14.
Proc Natl Acad Sci U S A ; 115(1): E92-E101, 2018 01 02.
Artigo em Inglês | MEDLINE | ID: mdl-29183985

RESUMO

Dissimilatory phosphite oxidation (DPO), a microbial metabolism by which phosphite (HPO32-) is oxidized to phosphate (PO43-), is the most energetically favorable chemotrophic electron-donating process known. Only one DPO organism has been described to date, and little is known about the environmental relevance of this metabolism. In this study, we used 16S rRNA gene community analysis and genome-resolved metagenomics to characterize anaerobic wastewater treatment sludge enrichments performing DPO coupled to CO2 reduction. We identified an uncultivated DPO bacterium, Candidatus Phosphitivorax (Ca. P.) anaerolimi strain Phox-21, that belongs to candidate order GW-28 within the Deltaproteobacteria, which has no known cultured isolates. Genes for phosphite oxidation and for CO2 reduction to formate were found in the genome of Ca. P. anaerolimi, but it appears to lack any of the known natural carbon fixation pathways. These observations led us to propose a metabolic model for autotrophic growth by Ca. P. anaerolimi whereby DPO drives CO2 reduction to formate, which is then assimilated into biomass via the reductive glycine pathway.


Assuntos
Dióxido de Carbono/metabolismo , Crescimento Quimioautotrófico/fisiologia , Deltaproteobacteria , Metagenômica , Fosfitos/metabolismo , Esgotos/microbiologia , Águas Residuárias/microbiologia , Microbiologia da Água , Deltaproteobacteria/genética , Deltaproteobacteria/metabolismo , Oxirredução , Purificação da Água
15.
Curr Biol ; 27(21): 3390-3395.e4, 2017 Nov 06.
Artigo em Inglês | MEDLINE | ID: mdl-29107553

RESUMO

The ecology of microbes frequently involves the mixing of entire communities (community coalescence), for example, flooding events, host excretion, and soil tillage [1, 2], yet the consequences of this process for community structure and function are poorly understood [3-7]. Recent theory suggests that a community, due to coevolution between constituent species, may act as a partially cohesive unit [8-11], resulting in one community dominating after community coalescence. This dominant community is predicted to be the one that uses resources most efficiently when grown in isolation [11]. We experimentally tested these predictions using methanogenic communities, for which efficient resource use, quantified by methane production, requires coevolved cross-feeding interactions between species [12]. After propagation in laboratory-scale anaerobic digesters, community composition (determined from 16S rRNA sequencing) and methane production of mixtures of communities closely resembled that of the single most productive community grown in isolation. Analysis of each community's contribution toward the final mixture suggests that certain combinations of taxa within a community might be co-selected as a result of coevolved interactions. As a corollary of these findings, we also show that methane production increased with the number of inoculated communities. These findings are relevant to the understanding of the ecological dynamics of natural microbial communities, as well as demonstrating a simple method of predictably enhancing microbial community function in biotechnology, health, and agriculture [13].


Assuntos
Anaerobiose/fisiologia , Bactérias/metabolismo , Metano/biossíntese , Consórcios Microbianos/fisiologia , Bactérias/classificação , Bactérias/genética , Crescimento Quimioautotrófico/fisiologia , RNA Ribossômico 16S/genética , Esgotos/microbiologia , Silagem/microbiologia
16.
Microbiol Res ; 205: 1-7, 2017 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-28942835

RESUMO

Molecular mechanisms of chemolithotrophic tetrathionate oxidation are not clearly understood. Here we used transposon(Tn5-mob)-insertion mutagenesis to search for novel tetrathionate oxidation genes in the facultatively chemolithoautotrophic betaproteobacterium Advenella kashmirensis that not only oxidizes tetrathionate, but also produces the same as an intermediate during thiosulfate oxidation. Genome-wide random insertion of Tn5-mob occurred at a frequency of one per 104 donor E. coli cells. A library of 8000 transconjugants yielded five tetrathionate-oxidation-impaired mutants, of which, the one named Ak_Tn_16 was studied here in detail. When grown chemolithoautotrophically on thiosulfate, Ak_Tn_16 converted the total thiosulfate supplied to equivalent amount of tetrathionate, exactly in the same way as the wild type. It could not, however, oxidize the intermediary tetrathionate to sulfate; Ak_Tn_16 could not also oxidize tetrathionate when it was supplied as the starting chemolithotrophic substrate. In the Ak_Tn_16 genome, Tn5-mob was found to have transposed in a novel soxO gene, located just-upstream of soxB, within the sox gene cluster. SoxO was predicted, via iterative threading assembly simulation, to be a glutathione-disulfide (GSSG) reductase. When Ak_Tn_16 was grown in tetrathionate-based chemolithoautotrophic medium supplemented with reduced glutathione (GSH) its tetrathionate-oxidation deficiency, remarkably, was ameliorated. Implications for a key role of GSH in tetrathionate oxidation are discussed in the light of other molecular evidences available for A. kashmirensis.


Assuntos
Alcaligenaceae/genética , Alcaligenaceae/metabolismo , Glutationa Redutase/genética , Oxirredução , Ácido Tetratiônico/metabolismo , Sequência de Bases , Crescimento Quimioautotrófico/genética , Crescimento Quimioautotrófico/fisiologia , Elementos de DNA Transponíveis , DNA Bacteriano , Escherichia coli/genética , Genes Bacterianos/genética , Glutationa/metabolismo , Mutagênese Insercional , Análise de Sequência , Enxofre/metabolismo , Tiossulfatos/metabolismo
17.
Environ Microbiol ; 19(11): 4432-4446, 2017 11.
Artigo em Inglês | MEDLINE | ID: mdl-28805344

RESUMO

Viruses are the most abundant life forms in the world's oceans and they are key drivers of biogeochemical cycles, but their impact on the microbial assemblages inhabiting hydrothermal vent ecosystems is still largely unknown. Here, we analysed the viral life strategies and virus-host interactions in the sediments of a newly discovered shallow-water hydrothermal field of the Mediterranean Sea. Our study reveals that temperate viruses, once experimentally induced to replicate, can cause large mortality of vent microbes, significantly reducing the chemoautotrophic carbon production, while enhancing the metabolism of microbial heterotrophs and the re-cycling of the organic matter. These results provide new insights on the factors controlling primary and secondary production processes in hydrothermal vents, suggesting that the inducible provirus-host interactions occurring in these systems can profoundly influence the functioning of the microbial food web and the efficiency in the energy transfer to the higher trophic levels.


Assuntos
Bactérias/virologia , Crescimento Quimioautotrófico/fisiologia , Sedimentos Geológicos/virologia , Fontes Hidrotermais/microbiologia , Água do Mar/microbiologia , Carbono , Ciclo do Carbono , Ecossistema , Mar Mediterrâneo , Microbiologia da Água
18.
Environ Microbiol ; 19(7): 2754-2768, 2017 07.
Artigo em Inglês | MEDLINE | ID: mdl-28474482

RESUMO

While mechanisms of different carbon dioxide (CO2 ) assimilation pathways in chemolithoautotrohic prokaryotes are well understood for many isolates under laboratory conditions, the ecological significance of diverse CO2 fixation strategies in the environment is mostly unexplored. Six stratified freshwater lakes were chosen to study the distribution and diversity of the Calvin-Benson-Bassham (CBB) cycle, the reductive tricarboxylic acid (rTCA) cycle, and the recently discovered archaeal 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) pathway. Eleven primer sets were used to amplify and sequence genes coding for selected key enzymes in the three pathways. Whereas the CBB pathway with different forms of RubisCO (IA, IC and II) was ubiquitous and related to diverse bacterial taxa, encompassing a wide range of potential physiologies, the rTCA cycle in Epsilonproteobacteria and Chloribi was exclusively detected in anoxic water layers. Nitrifiying Nitrosospira and Thaumarchaeota, using the rTCA and HP/HB cycle respectively, are important residents in the aphotic and (micro-)oxic zone of deep lakes. Both taxa were of minor importance in surface waters and in smaller lakes characterized by an anoxic hypolimnion. Overall, this study provides a first insight on how different CO2 fixation strategies and chemical gradients in lakes are associated to the distribution of chemoautotrophic prokaryotes with different functional traits.


Assuntos
Ciclo do Carbono/fisiologia , Dióxido de Carbono/metabolismo , Crescimento Quimioautotrófico/fisiologia , Chlorobi/metabolismo , Ciclo do Ácido Cítrico/fisiologia , Epsilonproteobacteria/metabolismo , Fotossíntese/fisiologia , Archaea/metabolismo , Chlorobi/genética , Epsilonproteobacteria/genética , Hidroxibutiratos/metabolismo , Ácido Láctico/análogos & derivados , Ácido Láctico/metabolismo , Lagos/química , Lagos/microbiologia , Ribulose-Bifosfato Carboxilase/genética , Ribulose-Bifosfato Carboxilase/metabolismo
19.
Environ Microbiol ; 19(6): 2495-2506, 2017 06.
Artigo em Inglês | MEDLINE | ID: mdl-28464419

RESUMO

Chemolithoautotrophic sulfur-oxidizing and denitrifying Gamma- (particularly the SUP05 cluster) and Epsilonproteobacteria (predominantly Sulfurimonas subgroup GD17) are assumed to compete for substrates (electron donors and acceptors) in marine pelagic redox gradients. To elucidate their ecological niche separation we performed 34 S0 , 15 NO3- and H13 CO3- stable-isotope incubations with water samples from Baltic Sea suboxic, chemocline and sulfidic zones followed by combined phylogenetic staining and high-resolution secondary ion mass spectrometry of single cells. SUP05 cells were small-sized (0.06-0.09 µm3 ) and most abundant in low-sulfidic to suboxic zones, whereas Sulfurimonas GD17 cells were significantly larger (0.26-0.61 µm3 ) and most abundant at the chemocline and below. Together, SUP05 and GD17 cells accumulated up to 48% of the labelled substrates but calculation of cell volume-specific rates revealed that GD17 cells incorporated labelled substrates significantly faster throughout the redox zone, thereby potentially outcompeting SUP05 especially at high substrate concentrations. Thus, in synopsis with earlier described features of SUP05/GD17 we conclude that their spatially overlapping association in stratified sulfidic zones is facilitated by their different lifestyles: whereas SUP05 cells are streamlined, non-motile K-strategists adapted to low substrate concentrations, GD17 cells are motile r-strategists well adapted to fluctuating substrate and redox conditions.


Assuntos
Crescimento Quimioautotrófico/fisiologia , Epsilonproteobacteria/crescimento & desenvolvimento , Enxofre/metabolismo , Desnitrificação , Epsilonproteobacteria/classificação , Marcação por Isótopo , Oceanos e Mares , Oxirredução , Oxigênio , Filogenia , Água do Mar/microbiologia
20.
Proc Natl Acad Sci U S A ; 114(18): E3652-E3658, 2017 05 02.
Artigo em Inglês | MEDLINE | ID: mdl-28416684

RESUMO

The "wooden-steps" hypothesis [Distel DL, et al. (2000) Nature 403:725-726] proposed that large chemosynthetic mussels found at deep-sea hydrothermal vents descend from much smaller species associated with sunken wood and other organic deposits, and that the endosymbionts of these progenitors made use of hydrogen sulfide from biogenic sources (e.g., decaying wood) rather than from vent fluids. Here, we show that wood has served not only as a stepping stone between habitats but also as a bridge between heterotrophic and chemoautotrophic symbiosis for the giant mud-boring bivalve Kuphus polythalamia This rare and enigmatic species, which achieves the greatest length of any extant bivalve, is the only described member of the wood-boring bivalve family Teredinidae (shipworms) that burrows in marine sediments rather than wood. We show that K. polythalamia harbors sulfur-oxidizing chemoautotrophic (thioautotrophic) bacteria instead of the cellulolytic symbionts that allow other shipworm species to consume wood as food. The characteristics of its symbionts, its phylogenetic position within Teredinidae, the reduction of its digestive system by comparison with other family members, and the loss of morphological features associated with wood digestion indicate that K. polythalamia is a chemoautotrophic bivalve descended from wood-feeding (xylotrophic) ancestors. This is an example in which a chemoautotrophic endosymbiosis arose by displacement of an ancestral heterotrophic symbiosis and a report of pure culture of a thioautotrophic endosymbiont.


Assuntos
Bactérias/metabolismo , Bivalves/microbiologia , Crescimento Quimioautotrófico/fisiologia , Simbiose/fisiologia , Madeira/metabolismo , Animais , Madeira/microbiologia
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