Microbial Carbonation of Monocalcium Silicate.

Biocement formed through microbially induced calcium carbonate precipitation (MICP) is an emerging biotechnology focused on reducing the environmental impact of concrete production. In this system, CO2 species are provided via ureolysis by Sporosarcina pasteurii (S. pasteurii) to carbonate monocalcium silicate for MICP. This is one of the first studies of its kind that uses a solid-state calcium source, while prior work has used highly soluble forms. Our study focuses on microbial physiological, chemical thermodynamic, and kinetic studies of MICP. Monocalcium silicate incongruently dissolves to form soluble calcium, which must be coupled with CO2 release to form calcium carbonate. Chemical kinetic modeling shows that calcium solubility is the rate-limiting step, but the addition of organic acids significantly increases the solubility, enabling extensive carbonation to proceed up to 37 mol %. The microbial urease activity by S. pasteurii is active up to pH 11, 70 °C, and 1 mol L-1 CaCl2, producing calcite as a means of solidification. Cell-free extracts are also effective albeit less robust at extreme pH, producing calcite with different physical properties. Together, these data help determine the chemical, biological, and thermodynamic parameters critical for scaling microbial carbonation of monocalcium silicate to high-density cement and concrete.

Complete Genome Sequence of Acidithiobacillus ferriphilus GT2, Isolated from Gold Mill Tailings.

We report the complete genome sequence of Acidithiobacillus ferriphilus GT2, an acidophile isolated from gold mill tailings. The circular genome of GT2 contains 2,489 predicted protein-coding units and a single plasmid. Functional analysis indicates the metabolic potential to oxidize iron and reduced sulfur compounds and to fix N2 and CO2.

Photoferrotrophy and phototrophic extracellular electron uptake is common in the marine anoxygenic phototroph Rhodovulum sulfidophilum.

Photoferrotrophy allows anoxygenic phototrophs to use reduced iron as an electron donor for primary productivity. Recent work shows that freshwater photoferrotrophs can use electrons from solid-phase conductive substances via phototrophic extracellular electron uptake (pEEU), and the two processes share the underlying electron uptake mechanism. However, the ability of marine phototrophs to perform photoferrotrophy and pEEU, and the contribution of these processes to primary productivity is largely unknown. To fill this knowledge gap, we isolated 15 new strains of the marine anoxygenic phototroph Rhodovulum sulfidophilum on electron donors such as acetate and thiosulfate. We observed that all of the R. sulfidophilum strains isolated can perform photoferrotrophy. We chose strain AB26 as a representative strain to study further, and find that it can also perform pEEU from poised electrodes. We show that during pEEU, AB26 transfers electrons to the photosynthetic electron transport chain. Furthermore, systems biology-guided mutant analysis shows that R. sulfidophilum AB26 uses a previously unknown diheme cytochrome c protein, which we call EeuP, for pEEU but not photoferrotrophy. Homologs of EeuP occur in a range of widely distributed marine microbes. Overall, these results suggest that photoferrotrophy and pEEU contribute to the biogeochemical cycling of iron and carbon in marine ecosystems.

Extracellular electron uptake by autotrophic microbes: physiological, ecological, and evolutionary implications.

Microbes exchange electrons with their extracellular environment via direct or indirect means. This exchange is bidirectional and supports essential microbial oxidation-reduction processes, such as respiration and photosynthesis. The microbial capacity to use electrons from insoluble electron donors, such as redox-active minerals, poised electrodes, or even other microbial cells is called extracellular electron uptake (EEU). Autotrophs with this capability can thrive in nutrient and soluble electron donor-deficient environments. As primary producers, autotrophic microbes capable of EEU greatly impact microbial ecology and play important roles in matter and energy flow in the biosphere. In this review, we discuss EEU-driven autotrophic metabolisms, their mechanism and physiology, and highlight their ecological, evolutionary, and biotechnological implications.

Draft Genome Sequence of a Marine Photoferrotrophic Bacterium, Rhodovulum robiginosum DSM 12329T.

Here, we report the draft genome sequence of Rhodovulum robiginosum DSM 12329T, an anoxygenic phototroph isolated from a marine sediment in the North Sea (Jadebusen, Germany). This is the first genome for a marine photoferrotrophic bacterium, and it provides a genetic basis to understand the mechanistic underpinnings of photoferrotrophy in future studies.

Towards sustainable bioplastic production using the photoautotrophic bacterium Rhodopseudomonas palustris TIE-1.

Bacterial synthesis of polyhydroxybutyrates (PHBs) is a potential approach for producing biodegradable plastics. This study assessed the ability of Rhodopseudomonas palustris TIE-1 to produce PHBs under various conditions. We focused on photoautotrophy using a poised electrode (photoelectroautotrophy) or ferrous iron (photoferroautotrophy) as electron donors. Growth conditions were tested with either ammonium chloride or dinitrogen gas as the nitrogen source. Although TIE-1's capacity to produce PHBs varied fairly under different conditions, photoelectroautotrophy and photoferroautotrophy showed the highest PHB electron yield and the highest specific PHB productivity, respectively. Gene expression analysis showed that there was no differential expression in PHB biosynthesis genes. This suggests that the variations in PHB accumulation might be post-transcriptionally regulated. This is the first study to systematically quantify the amount of PHB produced by a microbe via photoelectroautotrophy and photoferroautotrophy. This work could lead to sustainable bioproduction using abundant resources such as light, electricity, iron, and carbon dioxide.

Phototrophic extracellular electron uptake is linked to carbon dioxide fixation in the bacterium Rhodopseudomonas palustris.

Extracellular electron uptake (EEU) is the ability of microbes to take up electrons from solid-phase conductive substances such as metal oxides. EEU is performed by prevalent phototrophic bacterial genera, but the electron transfer pathways and the physiological electron sinks are poorly understood. Here we show that electrons enter the photosynthetic electron transport chain during EEU in the phototrophic bacterium Rhodopseudomonas palustris TIE-1. Cathodic electron flow is also correlated with a highly reducing intracellular redox environment. We show that reducing equivalents are used for carbon dioxide (CO2) fixation, which is the primary electron sink. Deletion of the genes encoding ruBisCO (the CO2-fixing enzyme of the Calvin-Benson-Bassham cycle) leads to a 90% reduction in EEU. This work shows that phototrophs can directly use solid-phase conductive substances for electron transfer, energy transduction, and CO2 fixation.

Draft Genome Sequences of Four Rhodobacter sphaeroides Strains Isolated from a Marine Ecosystem.

Rhodobacter sphaeroides is an alphaproteobacterium found in freshwater and marine ecosystems. To better understand the metabolic diversity within this species, we isolated and sequenced four R. sphaeroides isolates obtained from Trunk River in Woods Hole, Massachusetts. Here, we report the draft genome sequences of R. sphaeroides AB24, AB25, AB27, and AB29.

Draft Genome Sequences of Two Closely Related Marichromatium Isolates, Photosynthetic Gammaproteobacteria from Marine Ecosystems.

Marichromatium species are photosynthetic gammaproteobacteria found in marine environments. Only two Marichromatium genomes are publicly available. Here, we report the draft genome sequences of two new Marichromatium strains isolated from Woods Hole, MA. These strains share >99% similarity to Marichromatium gracile and M. indicum based on 16S rRNA gene sequence analysis.

Anaerobic Oxidation of Ethane, Propane, and Butane by Marine Microbes: A Mini Review.

The deep ocean and its sediments are a continuous source of non-methane short-chain alkanes (SCAs) including ethane, propane, and butane. Their high global warming potential, and contribution to local carbon and sulfur budgets has drawn significant scientific attention. Importantly, microbes can use gaseous alkanes and oxidize them to CO2, thus acting as effective biofilters. A relative decrease of these gases with a concomitant 13C enrichment of propane and n-butane in interstitial waters vs. the source suggests microbial anaerobic oxidation. The reported uncoupling of sulfate-reduction (SR) from anaerobic methane oxidation supports their microbial consumption. To date, strain BuS5 isolated from the sediments of Guaymas Basin, Gulf of California, is the only pure culture that can anaerobically degrade propane and n-butane. This organism belongs to a metabolically diverse cluster within the Deltaproteobacteria called Desulfosarcina/Desulfococcus. Other phylotypes involved in gaseous alkane degradation were identified based on stable-isotope labeling and fluorescence in-situ hybridization. A novel syntrophic association of the archaeal genus, Candidatus Syntrophoarchaeum, and a thermophilic SR bacterium, HotSeep-1 was recently discovered from the Guaymas basin, Gulf of California that can anaerobically oxidize n-butane. Strikingly, metagenomic data and the draft genomes of ca. Syntrophoarchaeum suggest that this organism uses a novel mechanism for n-butane oxidation, distinct from the well-established fumarate addition mechanism. These recent findings indicate that a lot remains to be understood about our understanding of anaerobic SCA degradation. This mini-review summarizes our current understanding of microbial anaerobic SCA degradation, and provides an outlook for future research.

Draft Genome Sequences of Three Closely Related Isolates of the Purple Nonsulfur Bacterium Rhodovulum sulfidophilum.

We report here the draft genome sequences of three isolates of Rhodovulum sulfidophilum from a single population that will serve as a model system for understanding genomic traits that underlie metabolic variation within closely related marine purple nonsulfur bacteria in natural microbial communities.