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1.
Nature ; 583(7816): 453-458, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32669693

RESUMO

Manganese is one of the most abundant elements on Earth. The oxidation of manganese has long been theorized1-yet has not been demonstrated2-4-to fuel the growth of chemolithoautotrophic microorganisms. Here we refine an enrichment culture that exhibits exponential growth dependent on Mn(II) oxidation to a co-culture of two microbial species. Oxidation required viable bacteria at permissive temperatures, which resulted in the generation of small nodules of manganese oxide with which the cells associated. The majority member of the culture-which we designate 'Candidatus Manganitrophus noduliformans'-is affiliated to the phylum Nitrospirae (also known as Nitrospirota), but is distantly related to known species of Nitrospira and Leptospirillum. We isolated the minority member, a betaproteobacterium that does not oxidize Mn(II) alone, and designate it Ramlibacter lithotrophicus. Stable-isotope probing revealed 13CO2 fixation into cellular biomass that was dependent upon Mn(II) oxidation. Transcriptomic analysis revealed candidate pathways for coupling extracellular manganese oxidation to aerobic energy conservation and autotrophic CO2 fixation. These findings expand the known diversity of inorganic metabolisms that support life, and complete a biogeochemical energy cycle for manganese5,6 that may interface with other major global elemental cycles.


Assuntos
Bactérias/metabolismo , Crescimento Quimioautotrófico , Manganês/metabolismo , Bactérias/classificação , Bactérias/genética , Bactérias/crescimento & desenvolvimento , Ciclo do Carbono , Dióxido de Carbono/metabolismo , Técnicas de Cocultura , Perfilação da Expressão Gênica , Isótopos , Manganês/química , Compostos de Manganês/química , Compostos de Manganês/metabolismo , Oxirredução , Óxidos/química , Óxidos/metabolismo , Filogenia
2.
Bioresour Technol ; 315: 123863, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32717518

RESUMO

Anammox as a novel biological process in natural nitrogen cycle has been introduced into wastewater treatment process. However, the regulation mechanism of anammox metabolism remained to be investigated. In this study, the specific quorum sensing (QS) signaling molecules for mediating anammox were identified in anammox activity tests. Anammox was valve-regulated by the collaboration of QS signaling molecules N-butyryl-homoserine lactone (C14-HSL) and N-(3-oxotetradecanoyl)-homoserine lactone (3-oxo-C14-HSL), and prompted with the C14-HSL/3-oxo-C14-HSL mole ratio above 1.0. Moreover, the ratio of chemical oxygen demand to total nitrogen (C/N) was identified as an effective regulator for the distribution of C14-HSL and 3-oxo-C14-HSL. An engineering method for control anammox through regulating C/N ratio was proposed and demonstrated based on the performance of two microaerobic reactors treating piggery wastewater and anammox activity tests. The discovery should be of great significance to understanding the social behaviors of anammox bacteria in organic wastewater treatment processes.


Assuntos
4-Butirolactona , Percepção de Quorum , Bactérias , Crescimento Quimioautotrófico , Nitrogênio , Transdução de Sinais
3.
Bioresour Technol ; 312: 123608, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32531736

RESUMO

An integrated investigation to structural, activity and microbial diversity of anammox granular sludge (AnGS) in a wastewater treatment system with high ammonia nitrogen load was performed and aimed to establish the relationship between granular size and performance. With the increase in granule size, the main component of extracellular polymeric substances (EPS) changed from slime EPS to tightly-bound EPS, while the organic component remained the same, and the specific anammox activity increased. However, the results of qPCR and high-throughput sequencing showed that for granules with sizes inferior than 4.75 mm, the abundance of ammonia-oxidizing bacteria (AnAOB) increased as the size increased, and the copies of AnAOB decreased when the granule size increased above 4.75 mm, and the community complexity increased. According to the correlation analysis results, AnAOB first accumulated and then optimized the flora structure to improve efficiency and 2.8 mm to 4.75 mm was the optimal size of AnGS.


Assuntos
Reatores Biológicos , Esgotos , Bactérias , Crescimento Quimioautotrófico , Nitrogênio , Oxirredução , Águas Residuárias
4.
Bioresour Technol ; 309: 123325, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32330801

RESUMO

This work investigated the effects of integration of floc, aggregate and carrier (IFAC) on anammox biofilm quality and development mechanisms. The IFAC system harvested high-quality anammox biofilm with a reduction of 60% in the formation period, an increment of 282.14%~397.26% in mechanical stability, an enhancement of 10.18 ~ 21.56% in ecological stability and an improvement of 9.44%~46.18% in abundance of the phylum Planctomycetes. Aggregates enabled carriers to accumulate initial biomass efficiently and equipped biofilm with additional joint forces. Floc promoted accumulation of terminal biomass, enhanced ecological stability by improving community diversity and raised abundance of the phylum Planctomycetes by assisting anammox consortium settlement. A model of the development procedure of high-quality anammox biofilm was established and a strategy for pre-designing the IFAC system to reap high-quality biofilm was proposed. We expect our findings to provide theoretical guidance for designs and applications of anammox process with excellent stability.


Assuntos
Reatores Biológicos , Nitrogênio , Anaerobiose , Biofilmes , Crescimento Quimioautotrófico , Oxirredução , Esgotos
5.
Water Res ; 170: 115306, 2020 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-31770650

RESUMO

Groundwater ecosystems face the challenge of energy limitation due to the absence of light-driven primary production. Lack of space and low oxygen availability might further contribute to generally assumed low food web complexity. Chemolithoautotrophy provides additional input of carbon within the subsurface, however, we still do not understand how abundances of chemolithoautotrophs, differences in surface carbon input, and oxygen availability control subsurface food web complexity. Using a molecular approach, we aimed to disentangle the different levels of potential trophic interactions in oligotrophic groundwater along a hillslope setting of alternating mixed carbonate-/siliciclastic bedrock with contrasting hydrochemical conditions and hotspots of chemolithoautotrophy. Across all sites, groundwater harbored diverse protist communities including Ciliophora, Cercozoa, Centroheliozoa, and Amoebozoa but correlations with hydrochemical parameters were less pronounced for eukaryotes compared to bacteria. Ciliophora-affiliated reads dominated the eukaryotic data sets across all sites. DNA-based evidence for the presence of metazoan top predators such as Cyclopoida (Arthropoda) and Stenostomidae (Platyhelminthes) was only found at wells where abundances of functional genes associated with chemolithoautotrophy were 10-100 times higher compared to wells without indications of these top predators. At wells closer to recharge areas with presumably increased inputs of soil-derived substances and biota, fungi accounted for up to 85% of the metazoan-curated eukaryotic sequence data, together with a low potential for chemolithoautotrophy. Although we did not directly observe higher organisms, our results point to the existence of complex food webs with several trophic levels in oligotrophic groundwater. Chemolithoautotrophy appears to provide strong support to more complex trophic interactions, feeding in additional biomass produced by light-independent CO2-fixation.


Assuntos
Cadeia Alimentar , Água Subterrânea , Animais , Biota , Crescimento Quimioautotrófico , Ecossistema
6.
ISME J ; 14(2): 649-656, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31680119

RESUMO

Deep-sea Bathymodiolus mussels and their chemoautotrophic symbionts are well-studied representatives of mutualistic host-microbe associations. However, how host-symbiont interactions vary on the molecular level between related host and symbiont species remains unclear. Therefore, we compared the host and symbiont metaproteomes of Pacific B. thermophilus, hosting a thiotrophic symbiont, and Atlantic B. azoricus, containing two symbionts, a thiotroph and a methanotroph. We identified common strategies of metabolic support between hosts and symbionts, such as the oxidation of sulfide by the host, which provides a thiosulfate reservoir for the thiotrophic symbionts, and a cycling mechanism that could supply the host with symbiont-derived amino acids. However, expression levels of these processes differed substantially between both symbioses. Backed up by genomic comparisons, our results furthermore revealed an exceptionally large repertoire of attachment-related proteins in the B. thermophilus symbiont. These findings imply that host-microbe interactions can be quite variable, even between closely related systems.


Assuntos
Bactérias/genética , Bactérias/metabolismo , Mytilidae/microbiologia , Simbiose/genética , Aminoácidos/genética , Aminoácidos/metabolismo , Animais , Anidrases Carbônicas/metabolismo , Crescimento Quimioautotrófico , Genoma Bacteriano/genética , Brânquias/metabolismo , Interações entre Hospedeiro e Microrganismos , Mytilidae/metabolismo , Proteômica , Simbiose/fisiologia
7.
Microbiol Res ; 230: 126345, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31585234

RESUMO

Chemolithotrophic bacteria oxidize various sulfur species for energy and electrons, thereby operationalizing biogeochemical sulfur cycles in nature. The best-studied pathway of bacterial sulfur-chemolithotrophy involves direct oxidation of thiosulfate (S2O32-) to sulfate (SO42-) without any free intermediate. This pathway mediated by SoxXAYZBCD is apparently the exclusive mechanism of thiosulfate oxidation in facultatively chemolithotrophic alphaproteobacteria. Here we explore the molecular mechanisms of sulfur oxidation in the thiosulfate- and tetrathionate(S4O62-)-oxidizing alphaproteobacterium Paracoccus thiocyanatus SST, and compare them with the prototypical Sox process of Paracoccus pantotrophus. Our results reveal a unique case where an alphaproteobacterium has Sox as its secondary pathway of thiosulfate oxidation converting ∼10% of the thiosulfate supplied, whilst ∼90% of the substrate is oxidized via a pathway that produces tetrathionate as an intermediate. Sulfur oxidation kinetics of a deletion mutant showed that thiosulfate-to-tetrathionate conversion, in SST, is catalyzed by a thiosulfate dehydrogenase (TsdA) homolog that has far-higher substrate-affinity than the Sox system of this bacterium, which in turn is also less efficient than the P. pantotrophus Sox. Deletion of soxB abolished sulfate-formation from thiosulfate/tetrathionate, while thiosulfate-to-tetrathionate conversion remained unperturbed. Physiological studies revealed the involvement of glutathione in SST tetrathionate oxidation. However, zero impact of the insertional mutation of a thiol dehydrotransferase (thdT) homolog, together with the absence of sulfite as an intermediate, indicated that SST tetrathionate oxidation is mechanistically novel, and distinct from its betaproteobacterial counterpart mediated by glutathione, ThdT, SoxBCD and sulfite:acceptor oxidoreductase. The present findings highlight extensive functional diversification of sulfur-oxidizing enzymes across phylogenetically close, as well as distant, bacteria.


Assuntos
Paracoccus/metabolismo , Tiossulfatos/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Crescimento Quimioautotrófico , Oxirredução , Oxirredutases/genética , Oxirredutases/metabolismo , Paracoccus/genética , Enxofre/metabolismo
8.
J Environ Sci (China) ; 86: 141-153, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31787178

RESUMO

With the increasing application of anammox for the treatment of high-strength industrial wastewater, application of anammox in municipal sewage has been gaining more attention. Sludge granulation in particular enhances the enrichment and retention of anammox bacteria in municipal sewage treatment systems. However, the performance of granular sludge under continuous and varying hydraulic loading shock remains little understood. In this study, the robustness of anammox granular sludge in treating low-strength municipal sewage under various shock loadings was investigated. Results showed that an upflow anaerobic sludge blanket (UASB) reactor with anammox granules performed well, with anammox specific activity up to 0.28 kg N/kg VSS/day and anti-loading shock capability up to 187.2 L/day during the 8-month testing period. The accumulation rate of N2O (<0.01 kg N/kg VSS/day) in the liquid phase was seven times higher than that of the gas phase, which could be mainly attributed to the incomplete denitrification and insufficient carbon source. However, only a small part of the produced N2O escaped into the atmosphere. High-throughput sequencing and molecular ecological network analyses also identified the bacterial diversity and community structure, indicating the potential resistance against loading shock. The composition and structural analyses showed that polysaccharides were an important functional component in the tightly bound extracellular polymeric substances (TB-EPS), which was the major EPS layer of anammox granules. Scanning electron microscopy (SEM) also showed that the gaps in between the anammox-clusters in the granules inhibit the flotation of the sludge and ensure efficient settling and retention of anammox granules.


Assuntos
Dióxido de Nitrogênio/análise , Eliminação de Resíduos Líquidos/métodos , Bactérias/metabolismo , Crescimento Quimioautotrófico , Desnitrificação , Águas Residuárias
9.
J Environ Sci (China) ; 86: 97-106, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31787194

RESUMO

Knowledge on methanogenic microbial communities associated with the degradation of polycyclic aromatic hydrocarbons (PAHs) is crucial to developing strategies for PAHs bioremediation. In this study, the linkage between the type of PAHs and microbial community structure was fully investigated through 16S rRNA gene sequencing on four PAH-degrading cultures. Putative degradation products were also detected. Our results indicated that naphthalene (Nap)/2-methylnaphthalene (2-Nap), phenanthrene (Phe) and anthracene (Ant) sculpted different microbial communities. Among them, Nap and 2-Nap selected for similar degrading bacteria (i.e., Alicycliphilus and Thauera) and methanogens (Methanomethylovorans and Methanobacterium). Nap and 2-Nap were probably activated via carboxylation, producing 2-naphthoic acid. In contrast, Phe and Ant shaped different bacterial and archaeal communities, with Arcobacter and Acinetobacter being Phe-degraders and Thiobacillus Ant-degrader. Methanogenic archaea Methanobacterium and Methanomethylovorans predominated Phe-degrading and Ant-degrading culture, respectively. These findings can improve our understanding of natural PAHs attenuation and provide some guidance for PAHs bioremediation in methanogenic environment.


Assuntos
Microbiota , Hidrocarbonetos Policíclicos Aromáticos/metabolismo , Poluentes do Solo/metabolismo , Archaea , Bactérias , Biodegradação Ambiental , Crescimento Quimioautotrófico , Euryarchaeota
10.
J Microbiol ; 57(12): 1095-1104, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31758395

RESUMO

Subglacial ecosystems harbor diverse chemoautotrophic microbial communities in areas with limited organic carbon, and lithological H2 produced during glacial erosion has been considered an important energy source in these ecosystems. To verify the H2-utilizing potential there and to identify the related energy-converting metabolic mechanisms of these communities, we performed metagenomic analysis on subglacial sediment samples from East Antarctica with and without H2 supplementation. Genes coding for several [NiFe]-hydrogenases were identified in raw sediment and were enriched after H2 incubation. All genes in the dissimilatory nitrate reduction and denitrification pathways were detected in the subglacial community, and the genes coding for these pathways became enriched after H2 was supplied. Similarly, genes transcribing key enzymes in the Calvin cycle were detected in raw sediment and were also enriched. Moreover, key genes involved in H2 oxidization, nitrate reduction, oxidative phosphorylation, and the Calvin cycle were identified within one metagenome-assembled genome belonging to a Polaromonas sp. As suggested by our results, the microbial community in the subglacial environment we investigated consisted of chemoautotrophic populations supported by H2 oxidation. These results further confirm the importance of H2 in the cryosphere.


Assuntos
Sedimentos Geológicos/microbiologia , Hidrogênio/metabolismo , Metagenoma , Microbiota/fisiologia , Regiões Antárticas , Archaea/classificação , Archaea/enzimologia , Archaea/genética , Archaea/metabolismo , Bactérias/classificação , Bactérias/enzimologia , Bactérias/genética , Bactérias/metabolismo , Ciclo do Carbono , Crescimento Quimioautotrófico , Comamonadaceae/enzimologia , Comamonadaceae/metabolismo , Genes Arqueais/genética , Genes Bacterianos/genética , Hidrogenase/classificação , Hidrogenase/genética , Hidrogenase/isolamento & purificação , Redes e Vias Metabólicas , Microbiota/genética , Nitratos/metabolismo , Fosforilação Oxidativa , Fotossíntese , Análise de Sequência de DNA
11.
BMC Biol ; 17(1): 91, 2019 11 18.
Artigo em Inglês | MEDLINE | ID: mdl-31739792

RESUMO

BACKGROUND: Symbiotic relationships between microbes and their hosts are widespread and diverse, often providing protection or nutrients, and may be either obligate or facultative. However, the genetic mechanisms allowing organisms to maintain host-symbiont associations at the molecular level are still mostly unknown, and in the case of bacterial-animal associations, most genetic studies have focused on adaptations and mechanisms of the bacterial partner. The gutless tubeworms (Siboglinidae, Annelida) are obligate hosts of chemoautotrophic endosymbionts (except for Osedax which houses heterotrophic Oceanospirillales), which rely on the sulfide-oxidizing symbionts for nutrition and growth. Whereas several siboglinid endosymbiont genomes have been characterized, genomes of hosts and their adaptations to this symbiosis remain unexplored. RESULTS: Here, we present and characterize adaptations of the cold seep-dwelling tubeworm Lamellibrachia luymesi, one of the longest-lived solitary invertebrates. We sequenced the worm's ~ 688-Mb haploid genome with an overall completeness of ~ 95% and discovered that L. luymesi lacks many genes essential in amino acid biosynthesis, obligating them to products provided by symbionts. Interestingly, the host is known to carry hydrogen sulfide to thiotrophic endosymbionts using hemoglobin. We also found an expansion of hemoglobin B1 genes, many of which possess a free cysteine residue which is hypothesized to function in sulfide binding. Contrary to previous analyses, the sulfide binding mediated by zinc ions is not conserved across tubeworms. Thus, the sulfide-binding mechanisms in sibgolinids need to be further explored, and B1 globins might play a more important role than previously thought. Our comparative analyses also suggest the Toll-like receptor pathway may be essential for tolerance/sensitivity to symbionts and pathogens. Several genes related to the worm's unique life history which are known to play important roles in apoptosis, cell proliferation, and aging were also identified. Last, molecular clock analyses based on phylogenomic data suggest modern siboglinid diversity originated in 267 mya (± 70 my) support previous hypotheses indicating a Late Mesozoic or Cenozoic origins of approximately 50-126 mya for vestimentiferans. CONCLUSIONS: Here, we elucidate several specific adaptations along various molecular pathways that link phenome to genome to improve understanding of holobiont evolution. Our findings of adaptation in genomic mechanisms to reducing environments likely extend to other chemosynthetic symbiotic systems.


Assuntos
Crescimento Quimioautotrófico , Genoma/fisiologia , Poliquetos/genética , Poliquetos/microbiologia , Simbiose/fisiologia , Animais , Fontes Hidrotermais
12.
Geobiology ; 17(6): 628-642, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31496030

RESUMO

Permanently anoxic regions in the ocean are widespread and exhibit unique microbial metabolic activity exerting substantial influence on global elemental cycles and climate. Reconstructing microbial metabolic activity rates in these regions has been challenging, due to the technical difficulty of direct rate measurements. In Cariaco Basin, which is the largest permanently anoxic marine basin and an important model system for geobiology, long-term monitoring has yielded time series for the concentrations of biologically important compounds; however, the underlying metabolite fluxes remain poorly quantified. Here, we present a computational approach for reconstructing vertical fluxes and in situ net production/consumption rates from chemical concentration data, based on a 1-dimensional time-dependent diffusive transport model that includes adaptive penalization of overfitting. We use this approach to estimate spatiotemporally resolved fluxes of oxygen, nitrate, hydrogen sulfide, ammonium, methane, and phosphate within the sub-euphotic Cariaco Basin water column (depths 150-900 m, years 2001-2014) and to identify hotspots of microbial chemolithotrophic activity. Predictions of the fitted models are in excellent agreement with the data and substantially expand our knowledge of the geobiology in Cariaco Basin. In particular, we find that the diffusivity, and consequently fluxes of major reductants such as hydrogen sulfide, and methane, is about two orders of magnitude greater than previously estimated, thus resolving a long-standing apparent conundrum between electron donor fluxes and measured dark carbon assimilation rates.


Assuntos
Archaea/metabolismo , Bactérias/metabolismo , Microbiota , Água do Mar/química , Anaerobiose , Crescimento Quimioautotrófico , Modelos Teóricos , Venezuela
13.
Microbes Environ ; 34(3): 278-292, 2019 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-31413226

RESUMO

Hydrothermal systems, including terrestrial hot springs, contain diverse geochemical conditions that vary over short spatial scales due to progressive interactions between reducing hydrothermal fluids, the oxygenated atmosphere, and, in some cases, seawater. At Jinata Onsen on Shikinejima Island, Japan, an intertidal, anoxic, iron-rich hot spring mixes with the oxygenated atmosphere and seawater over short spatial scales, creating diverse chemical potentials and redox pairs over a distance of ~10 m. We characterized geochemical conditions along the outflow of Jinata Onsen as well as the microbial communities present in biofilms, mats, and mineral crusts along its traverse using 16S rRNA gene amplicon and genome-resolved shotgun metagenomic sequencing. Microbial communities significantly changed downstream as temperatures and dissolved iron concentrations decreased and dissolved oxygen increased. Biomass was more limited near the spring source than downstream, and primary productivity appeared to be fueled by the oxidation of ferrous iron and molecular hydrogen by members of Zetaproteobacteria and Aquificae. The microbial community downstream was dominated by oxygenic Cyanobacteria. Cyanobacteria are abundant and active even at ferrous iron concentrations of ~150 µM, which challenges the idea that iron toxicity limited cyanobacterial expansion in Precambrian oceans. Several novel lineages of Bacteria are also present at Jinata Onsen, including previously uncharacterized members of the phyla Chloroflexi and Calditrichaeota, positioning Jinata Onsen as a valuable site for the future characterization of these clades.


Assuntos
Bactérias/metabolismo , Biodiversidade , Fontes Termais/química , Fontes Termais/microbiologia , Ferro/metabolismo , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Biomassa , Crescimento Quimioautotrófico , Geografia , Ferro/análise , Metagenômica , Microbiota/genética , Oxigênio/análise , Oxigênio/metabolismo , Processos Fototróficos , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Temperatura
14.
ISME J ; 13(12): 3131-3134, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31395953

RESUMO

In many seagrass sediments, lucinid bivalves and their sulfur-oxidizing symbionts are thought to underpin key ecosystem functions, but little is known about their role in nutrient cycles, particularly nitrogen. We used natural stable isotopes, elemental analyses, and stable isotope probing to study the ecological stoichiometry of a lucinid symbiosis in spring and fall. Chemoautotrophy appeared to dominate in fall, when chemoautotrophic carbon fixation rates were up to one order of magnitude higher as compared with the spring, suggesting a flexible nutritional mutualism. In fall, an isotope pool dilution experiment revealed carbon limitation of the symbiosis and ammonium excretion rates up to tenfold higher compared with fluxes reported for nonsymbiotic marine bivalves. These results provide evidence that lucinid bivalves can contribute substantial amounts of ammonium to the ecosystem. Given the preference of seagrasses for this nitrogen source, lucinid bivalves' contribution may boost productivity of these important blue carbon ecosystems.


Assuntos
Bivalves/metabolismo , Nitrogênio/metabolismo , Plantas/metabolismo , Animais , Carbono/metabolismo , Ciclo do Carbono , Crescimento Quimioautotrófico , Ecologia , Ecossistema , Simbiose
15.
PLoS One ; 14(8): e0220706, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31393920

RESUMO

Fetida Cave is an active sulfuric acid cave influenced by seawater, showing abundant microbial communities that organize themselves under three main different morphologies: water filaments, vermiculations and moonmilk deposits. These biofilms/deposits have different cave distribution, pH, macro- and microelement and mineralogical composition, carbon and nitrogen content. In particular, water filaments and vermiculations had circumneutral and slightly acidic pH, respectively, both had abundant organic carbon and high microbial diversity. They were rich in macro- and microelements, deriving from mineral dissolution, and, in the case of water filaments, from seawater composition. Vermiculations had different color, partly associated with their mineralogy, and unusual minerals probably due to trapping capacities. Moonmilk was composed of gypsum, poor in organic matter, had an extremely low pH (0-1) and low microbial diversity. Based on 16S rRNA gene analysis, the microbial composition of the biofilms/deposits included autotrophic taxa associated with sulfur and nitrogen cycles and biomineralization processes. In particular, water filaments communities were characterized by bacterial taxa involved in sulfur oxidation and reduction in aquatic, aphotic, microaerophilic/anoxic environments (Campylobacterales, Thiotrichales, Arenicellales, Desulfobacterales, Desulforomonadales) and in chemolithotrophy in marine habitats (Oceanospirillales, Chromatiales). Their biodiversity was linked to the morphology of the water filaments and their collection site. Microbial communities within vermiculations were partly related to their color and showed high abundance of unclassified Betaproteobacteria and sulfur-oxidizing Hydrogenophilales (including Sulfuriferula), and Acidiferrobacterales (including Sulfurifustis), sulfur-reducing Desulfurellales, and ammonia-oxidizing Planctomycetes and Nitrospirae. The microbial community associated with gypsum moonmilk showed the strong dominance (>60%) of the archaeal genus Thermoplasma and lower abundance of chemolithotrophic Acidithiobacillus, metal-oxidizing Metallibacterium, Sulfobacillus, and Acidibacillus. This study describes the geomicrobiology of water filaments, vermiculations and gypsum moonmilk from Fetida Cave, providing insights into the microbial taxa that characterize each morphology and contribute to biogeochemical cycles and speleogenesis of this peculiar seawater-influenced sulfuric acid cave.


Assuntos
Cavernas/microbiologia , Microbiota , Água do Mar/química , Ácidos Sulfúricos/metabolismo , Bactérias/isolamento & purificação , Biodiversidade , Biofilmes , Crescimento Quimioautotrófico , Oxirredução , Filogenia , Enxofre/metabolismo
16.
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
17.
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
18.
Environ Microbiol ; 21(10): 3696-3710, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31188531

RESUMO

Species in the archaeal order Sulfolobales thrive in hot acid and exhibit remarkable metabolic diversity. Some species are chemolithoautotrophic, obtaining energy through the oxidation of inorganic substrates, sulphur in particular, and acquiring carbon through the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) CO2 -fixation cycle. The current model for sulphur oxidation in the Sulfolobales is based on the biochemical analysis of specific proteins from Acidianus ambivalens, including sulphur oxygenase reductase (SOR) that disproportionates S° into H2 S and sulphite (SO3 2- ). Initial studies indicated SOR catalyses the essential first step in oxidation of elemental sulphur, but an ancillary role for SOR as a 'recycle' enzyme has also been proposed. Here, heterologous expression of both SOR and membrane-bound thiosulphate-quinone oxidoreductase (TQO) from Sulfolobus tokodaii 'restored' sulphur oxidation capacity in Sulfolobus acidocaldarius DSM639, but not autotrophy, although earlier reports indicate this strain was once capable of chemolithoautotrophy. Comparative transcriptomic analyses of Acidianus brierleyi, a chemolithoautotrophic sulphur oxidizer, and S. acidocaldarius DSM639 showed that while both share a strong transcriptional response to elemental sulphur, S. acidocaldarius DSM639 failed to upregulate key 3-HP/4-HB cycle genes used by A. brierleyi to drive chemolithoautotrophy. Thus, the inability for S. acidocaldarius DSM639 to grow chemolithoautotrophically may be rooted more in gene regulation than the biochemical capacity.


Assuntos
Crescimento Quimioautotrófico , Sulfolobales/metabolismo , Enxofre/metabolismo , Processos Autotróficos , Oxirredução , Oxirredutases/metabolismo , Tiossulfatos/metabolismo
19.
mBio ; 10(3)2019 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-31064824

RESUMO

Sulfur-oxidizing bacteria from the SUP05 clade are abundant in anoxic and oxygenated marine waters that appear to lack reduced sources of sulfur for cell growth. This raises questions about how these chemosynthetic bacteria survive across oxygen and sulfur gradients and how their mode of survival impacts the environment. Here, we use growth experiments, proteomics, and cryo-electron tomography to show that a SUP05 isolate, "Candidatus Thioglobus autotrophicus," is amorphous in shape and several times larger and stores considerably more intracellular sulfur when it respires oxygen. We also show that these cells can use diverse sources of reduced organic and inorganic sulfur at submicromolar concentrations. Enhanced cell size, carbon content, and metabolic activity of the aerobic phenotype are likely facilitated by a stabilizing surface-layer (S-layer) and an uncharacterized form of FtsZ-less cell division that supports morphological plasticity. The additional sulfur storage provides an energy source that allows cells to continue metabolic activity when exogenous sulfur sources are not available. This metabolic flexibility leads to the production of more organic carbon in the ocean than is estimated based solely on their anaerobic phenotype.IMPORTANCE Identifying shifts in microbial metabolism across redox gradients will improve efforts to model marine oxygen minimum zone (OMZ) ecosystems. Here, we show that aerobic morphology and metabolism increase cell size, sulfur storage capacity, and carbon fixation rates in "Ca Thioglobus autotrophicus," a chemosynthetic bacterium from the SUP05 clade that crosses oxic-anoxic boundaries.


Assuntos
Organismos Aquáticos/metabolismo , Ciclo do Carbono , Gammaproteobacteria/metabolismo , Bactérias Redutoras de Enxofre/metabolismo , Enxofre/metabolismo , Carbono/metabolismo , Crescimento Quimioautotrófico , Microscopia Crioeletrônica , Ecossistema , Gammaproteobacteria/ultraestrutura , Oxirredução , Oxigênio/metabolismo , Filogenia , Proteômica , Água do Mar/microbiologia , Bactérias Redutoras de Enxofre/ultraestrutura
20.
ISME J ; 13(9): 2264-2279, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31073213

RESUMO

There are many unknowns regarding the distribution, activity, community composition, and metabolic repertoire of microbial communities in the subseafloor of deep-sea hydrothermal vents. Here we provide the first characterization of subseafloor microbial communities from venting fluids along the central Mariana back-arc basin (15.5-18°N), where the slow-spreading rate, depth, and variable geochemistry along the back-arc distinguish it from other spreading centers. Results indicated that diverse Epsilonbacteraeota were abundant across all sites, with a population of high temperature Aquificae restricted to the northern segment. This suggests that differences in subseafloor populations along the back-arc are associated with local geologic setting and resultant geochemistry. Metatranscriptomics coupled to stable isotope probing revealed bacterial carbon fixation linked to hydrogen oxidation, denitrification, and sulfide or thiosulfate oxidation at all sites, regardless of community composition. NanoSIMS (nanoscale secondary ion mass spectrometry) incubations at 80 °C show only a small portion of the microbial community took up bicarbonate, but those autotrophs had the highest overall rates of activity detected across all experiments. By comparison, acetate was more universally utilized to sustain growth, but within a smaller range of activity. Together, results indicate that microbial communities in venting fluids from the Mariana back-arc contain active subseafloor communities reflective of their local conditions with metabolisms commonly shared across geologically disparate spreading centers throughout the ocean.


Assuntos
Bactérias/isolamento & purificação , Bactérias/metabolismo , Fontes Hidrotermais/microbiologia , Bactérias/classificação , Bactérias/genética , Ciclo do Carbono , Crescimento Quimioautotrófico , Hidrogênio/metabolismo , Fontes Hidrotermais/química , Microbiota , Filogenia , RNA Ribossômico 16S/metabolismo , Sulfetos/metabolismo
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