Draft Genome Sequences of Sulfurovum spp. TSL1 and TSL6, Two Sulfur-Oxidizing Bacteria Isolated from Marine Sediment

Sulfurovum spp. TSL1 and TSL6 are sulfur-oxidizing chemolithoautotrophic bacteria isolated from the tsunami-launched marine sediment in the Great East Japan earthquake. This announcement describes the draft genome sequences of the two isolates that possess the gene sets for the sulfur oxidation pathway.

Planetary Atmospheres and Surface simulation Chamber (PASC): A platform for planetary exploration and astrobiology applications

<p>Even though space missions provide fundamental and unique knowledge for planetary exploration, they are always costly and extremely time-consuming. Due to the obvious technical and economical limitations for <em>in-situ</em> planetary exploration; laboratory simulations are one of the most feasible research options to make advances both in planetary science and in a consistent description of the origin of life.  Planetary Atmosphere and Surfaces Chamber (PASC) are able to simulated atmosphere and surface temperature for the majority of the planetary objects and they are especially appropriate to study physico-chemical and biological changes induced in a particular sample due to in-situ irradiation in a controlled environment (1). Number of relevant applications in planetary exploration will be described in order to provide an understanding about the potential and flexibility of planetary simulation chambers systems: mainly, stability and presence of certain minerals on Mars surface; photochemistry process on molecules and microorganisms potential habitability under planetary environmental conditions would be studied. Furthermore, UV-photocatalytic process on mineral surfaces has shown species potential fixation (2-6). Therefore, simulation chambers assess several multidisciplinary and challenging planetary and astrobiological studies. Furthermore, will be a promising tools and necessary platform to design future planetary space mission and to validate in-situ measurements from orbital or rover observations.</p> <p>References:</p> <p>1.- Mateo-Martí, E.; Prieto-Ballesteros, O.; Sobrado, J. M.; Gómez-Elvira, J. and Martín-Gago, J. A. 2006. “A chamber for studying planetary environments and its applications to astrobiology”. <strong><em>Measurement and Science Technology</em> </strong>17, 2274-2280.</p> <p>2.- E. Mateo-Marti*, S. Galvez-Martinez, C. Gil-Lozano and María-Paz Zorzano. “Pyrite-induced uv-photocatalytic abiotic nitrogen fixation: implications for early atmospheres and Life”.<strong> </strong><strong>Scientific reports</strong>  9: 15311-1--9 (2019).</p> <p>3.- E. J. Cueto Díaz, S. Galvez-Martinez, Mª C.Torquemada Vico, M. P. Valles González and E. Mateo-Marti*. ”2-D organization of silica nanoparticles on gold surfaces: CO<sub>2</sub> marker detection and storage”. <strong>RSC Advances</strong>,<strong> </strong>10, 31758 (2020).</p> <p>4.- C. Gil‑Lozano*, A. G. Fairén*, V.Muñoz‑Iglesias, M. Fernández‑Sampedro, O. Prieto‑Ballesteros, L. Gago‑Duport, E.Losa‑Adams, D.Carrizo, Janice L. Bishop, T.Fornaro and E. Mateo-Marti<strong> </strong>“Constraining the preservation of organic compounds in Mars analog nontronites after exposure to acid and alkaline fluids”<strong> </strong><strong>Scientific reports,</strong>  20, 71657-9 (2020).</p> <p>5.- Zorzano, M. P.; Mateo-Martí, E.; Prieto-Ballesteros, O.; Osuna, S. and Renno, N. 2009. “The stability of liquid saline water on present day Mars”.<em> <strong>Geophys. Res. Lett.</strong></em><strong> </strong> 36, L20201.</p> <p>6.- Gomez, F., Mateo-Martı´, E., Prieto-Ballesteros, O., Martın-Gago, J.A., Amils, R., 2010. “Protection of chemolithoautotrophic bacteria exposed to simulated mars environmental conditions”. <strong>Icarus</strong> 209, 482–487.</p>

Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow)

Pelagic aggregates function as biological carbon pumps for transporting fixed organic carbon to sediments. In iron-rich (ferruginous) lakes, photoferrotrophic and chemolithoautotrophic bacteria contribute to CO2 fixation by oxidizing reduced iron, leading to the formation of iron-rich pelagic aggregates (iron snow). The significance of iron oxidizers in carbon fixation, their general role in iron snow functioning and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis of iron snow collected from an acidic lake with protein-based stable isotope probing to determine general metabolic activities and to trace 13CO2 incorporation in iron snow over time under oxic and anoxic conditions. mRNA-derived metatranscriptome of iron snow identified four key players (Leptospirillum, Ferrovum, Acidithrix, Acidiphilium) with relative abundances (59.6–85.7%) encoding ecologically relevant pathways, including carbon fixation and polysaccharide biosynthesis. No transcriptional activity for carbon fixation from archaea or eukaryotes was detected. 13CO2 incorporation studies identified active chemolithoautotroph Ferrovum under both conditions. Only 1.0–5.3% relative 13C abundances were found in heterotrophic Acidiphilium and Acidocella under oxic conditions. These data show that iron oxidizers play an important role in CO2 fixation, but the majority of fixed C will be directly transported to the sediment without feeding heterotrophs in the water column in acidic ferruginous lakes.

Nitrate removal by a novel lithoautotrophic nitrate-reducing iron(II)-oxidizing culture enriched from a pyrite-rich limestone aquifer

Nitrate removal in oligotrophic environments is often limited by the availability of suitable organic electron donors. Chemolithoautotrophic bacteria may play a key role in denitrification in aquifers depleted in organic carbon. Under anoxic and circumneutral pH conditions, iron(II) was hypothesized to serve as an electron donor for microbially mediated nitrate reduction by Fe(II)-oxidizing (NRFeOx) microorganisms. However, lithoautotrophic NRFeOx cultures have never been enriched from any aquifer and as such there are no model cultures available to study the physiology and geochemistry of this potentially environmentally relevant process. Using iron(II) as an electron donor, we enriched a lithoautotrophic NRFeOx culture from nitrate-containing groundwater of a pyrite-rich limestone aquifer. In the enriched NRFeOx culture that does not require additional organic co-substrates for growth, within 7-11 days 0.3-0.5 mM of nitrate was reduced and 1.3-2 mM of iron(II) was oxidized leading to a stoichiometric NO 3 - /Fe(II) ratio of 0.2, with N 2 and N 2 O identified as the main nitrate reduction products. Short-range ordered Fe(III) (oxyhydr)oxides were the product of iron(II) oxidation. Microorganisms were observed to be closely associated with formed minerals but only few cells were encrusted, suggesting that most of the bacteria were able to avoid mineral precipitation at their surface. Analysis of the microbial community by long-read 16S rRNA gene sequencing revealed that the culture is dominated by members of the Gallionellaceae family that are known as autotrophic, neutrophilic, microaerophilic iron(II)-oxidizers. In summary, our study suggests that NRFeOx mediated by lithoautotrophic bacteria can lead to nitrate removal in anthropogenically impacted aquifers. Importance Removal of nitrate by microbial denitrification in groundwater is often limited by low concentrations of organic carbon. In these carbon-poor ecosystems, nitrate-reducing bacteria that can use inorganic compounds such as Fe(II) (NRFeOx) as electron donors could play a major role in nitrate removal. However, no lithoautotrophic NRFeOx culture has been successfully isolated or enriched from this type of environment and as such there are no model cultures available to study the rate-limiting factors of this potentially important process. Here we present the physiology and microbial community composition of a novel lithoautotrophic NRFeOx culture enriched from a fractured aquifer in southern Germany. The culture is dominated by a putative Fe(II)-oxidizer affiliated with the Gallionellaceae family and performs nitrate reduction coupled to Fe(II) oxidation leading to N 2 O and N 2 formation without the addition of organic substrates. Our analyses demonstrate that lithoautotrophic NRFeOx can potentially lead to nitrate removal in nitrate-contaminated aquifers.

Engineering lithoheterotrophy in an obligate chemolithoautotrophic Fe(II) oxidizing bacterium

Neutrophilic Fe(II) oxidizing bacteria like Mariprofundus ferrooxydans are obligate chemolithoautotrophic bacteria that play an important role in the biogeochemical cycling of iron and other elements in multiple environments. These bacteria generally exhibit a singular metabolic mode of growth which prohibits comparative “omics” studies. Furthermore, these bacteria are considered non-amenable to classical genetic methods due to low cell densities, the inability to form colonies on solid medium, and production of copious amounts of insoluble iron oxyhydroxides as their metabolic byproduct. Consequently, the molecular and biochemical understanding of these bacteria remains speculative despite the availability of substantial genomic information. Here we develop the first genetic system in neutrophilic Fe(II) oxidizing bacterium and use it to engineer lithoheterotrophy in M. ferrooxydans, a metabolism that has been speculated but not experimentally validated. This synthetic biology approach could be extended to gain physiological understanding and domesticate other bacteria that grow using a single metabolic mode.

Engineering lithoheterotrophy in an obligate chemolithoautotrophic Fe(II) oxidizing bacterium

ABSTRACTNeutrophilic Fe(II) oxidizing bacteria like Mariprofundus ferrooxydans are obligate chemolithoautotrophic bacteria that play an important role in the biogeochemical cycling of iron and other elements in multiple environments. These bacteria generally exhibit a singular metabolic mode of growth which prohibits comparative “omics” studies. Furthermore, these bacteria are considered non-amenable to classical genetic methods due to low cell densities, the inability to form colonies on solid medium, and production of copious amounts of insoluble iron oxyhydroxides as their metabolic byproduct. Consequently, the functional understanding of these bacteria remains speculative despite the availability of substantial genomic information. Here we develop the first genetic system in neutrophilic Fe(II) oxidizing bacterium and use it to engineer lithoheterotrophy in M. ferrooxydans, a metabolism that has been speculated but not experimentally validated. Our work suggests that M. ferroxydans partitions energy generation from carbon oxidation. This synthetic biology approach could be extended to gain physiological understanding and domesticate other bacteria that grow using a single metabolic mode.

Phosphoglycolate salvage in a chemolithoautotroph using the Calvin cycle

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 chemolithoautotrophCupriavidus necatorH16 (Ralstonia eutrophaH16) by characterizing the proxy process of glycolate metabolism, performing comparative transcriptomics of autotrophic growth under low and high CO2concentrations, and testing autotrophic growth phenotypes of gene deletion strains at ambient CO2. We find that the canonical plant-like C2cycle 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.

Photorespiration pathways in a chemolithoautotroph

Carbon fixation via the Calvin cycle is constrained by the side activity of Rubisco with dioxygen, generating 2-phosphoglycolate. The metabolic recycling of 2-phosphoglycolate, an essential process termed photorespiration, was extensively studied in photoautotrophic organisms, including plants, algae, and cyanobacteria, but remains uncharacterized in chemolithoautotrophic bacteria. Here, we study photorespiration in the model chemolithoautotroph Cupriavidus necator (Ralstonia eutropha) 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 photorespiratory pathway. Upon disruption of the glycerate pathway, we find that an oxidative pathway, which we term the malate cycle, supports photorespiration. In this cycle, glyoxylate is condensed with 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 photorespiration in diverse chemolithoautotrophic bacteria. This study thus demonstrates a so-far unknown photorespiration pathway, highlighting important diversity in microbial carbon fixation metabolism.

Hydrogen Does Not Appear To Be a Major Electron Donor for Symbiosis with the Deep-Sea Hydrothermal Vent Tubeworm Riftia pachyptila

ABSTRACT 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.

Molecular techniques applied to investigations of abundance of the ammonia oxidizing bacteria and ammonia oxidizing archaea microorganisms in the environment

<p>This review shows regards of the recently experienced concerning the environments of ammonia oxidizing bacteria (AOB), ammonia oxidizing archaea (AOA) microorganisms, and denitrifying microbes. The advancements of molecular biology techniques have encouraged staggeringly to the fast recent developments in the sector. Various methods for implementing so are discussed. The function of AOB, AOA, and denitrifying microorganism composition was investigated through a high throughput of the 16S rRNA amplicon sequencing protocol. There is potential to observe the specific species appearance of these microorganisms in each environment and get to the evaluated relative abundance of several kinds. There is information indicated which the structure of denitrifying and nitrifying group was monitored field to significant fluctuations and the complexes, together in space and in time. More effort is required to enhance and isolate those microorganisms that common of the progressions and to function them through the compound of molecular techniques, biochemical and physiological. However, the investigation with deoxyribonucleic acid (DNA), antibodies, and the polymerase chain reaction (PCR) was preferred mainly to report the composition of chemolithoautotrophic bacteria, surveys of their characteristics in environmental that needed quantification at the transcriptional level is presently not available.</p>