Genomic characterization of three novel Desulfobacterota classes expand the metabolic and phylogenetic diversity of the Phylum

An overwhelming majority of bacterial life remains uncharacterized. Recent efforts to assemble genomes from metagenomes have provided invaluable insights into these yet-uncultured bacterial lineages. We report on the characterization of 30 genomes belonging to three novel classes within the phylum Desulfobacterota. One class (proposed name Candidatus “Anaeroferrophillalia”) was characterized by the capacity for heterotrophic growth, either fermentatively or utilizing polysulfide, tetrathionate and thiosulfate as electron acceptors. Autotrophic growth using the Wood Ljungdahl pathway and hydrogen or Fe(II) as an electron donor could also occur in absence of organic carbon sources. The second class (proposed name Candidatus “Anaeropigmentia”) was characterized by its capacity for fermentative or aerobic growth at low oxygen thresholds using a broad range of sugars and amino acids, and the capacity to synthesize the methyl/alkyl carrier CoM, an ability that is prevalent in the archaeal but rare in the bacterial domain. Pigmentation is inferred from the capacity for carotenoids (lycopene) production, as well as the occurrence of the majority of genes involved in bacteriochlorophyll a biosynthesis. The third class (proposed name Candidatus “Zymogenia”) was characterized by the capacity for heterotrophic growth fermentatively using broad sugars and amino acids as carbon sources, and the adaptation of some of its members to hypersaline habitats. Analysis of the distribution pattern of all three classes showed their occurrence as rare community members in multiple habitats, with preferences for anaerobic terrestrial (e.g. hydrocarbon contaminated environments, wetlands, bioreactors), freshwater (e.g. ground water and gas-saturated temperate lakes), and marine (e.g. hydrothermal vents, marine sediments, and coastal sediments) environments, over oxygenated (e.g. pelagic ocean and agricultural land) settings. Special preference for some members of the class Candidatus “Zymogenia” to hypersaline environments, e.g. hypersaline microbial mats and lagoons was observed.ImportanceCulture-independent diversity surveys conducted in the last three decades have clearly demonstrated that the scope of microbial diversity is much broader than that inferred from isolation efforts. Multiple reasons have been put forth to explain the refractiveness of a wide range of the earth’s microbiome to isolation efforts. Documenting the scope of high-rank phylogenetic diversity on earth, as well as deciphering and documenting the metabolic capacities, physiological preferences, and putative ecological roles of these yet-uncultured lineages represents one of the central goals in current microbial ecology research. Recent efforts to assemble genomes from metagenomes have provided invaluable insights into these yet-uncultured lineages. This study expands our knowledge of the phylum Desulfobacterota through the characterization of 30 genomes belonging to three novel classes. The analyzed genomes were either recovered from Zodletone Spring in southwestern Oklahoma in this study, or recently binned from public metagenomes as part of the Global Earth Microbiome initiative. Our results expand the high-rank diversity within the bacterial tree of life by describing three novel classes within the phylum Desulfobacterota, document the utilization of multiple metabolic processes, e.g. iron-oxidation, aromatic hydrocarbon degradation, reduction of sulfur-cycling intermediates, and features, e.g. coenzyme M biosynthesis, and pigmentation, as salient characteristics in these novel Desulfobacterota classes.

Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator

SummaryBacteria must balance the different needs for substrate assimilation, growth functions, and resilience in order to thrive in their environment. Of all cellular macromolecules, the bacterial proteome is by far the most important resource and its size is limited. Here, we investigated how the highly versatile ‘knallgas’ bacterium Cupriavidus necator reallocates protein resources when grown on different limiting substrates and with different growth rates. We determined protein quantity by mass spectrometry and estimated enzyme utilization by resource balance analysis modeling. We found that C. necator invests a large fraction of its proteome in functions that are hardly utilized. Of the enzymes that are utilized, many are present in excess abundance. One prominent example is the strong expression of CBB cycle genes such as Rubisco during growth on fructose. Modeling and mutant competition experiments suggest that CO2-reassimilation through Rubisco does not provide a fitness benefit for heterotrophic growth, but is rather an investment in readiness for autotrophy.HighlightsA large fraction of the C. necator proteome is related to environmental readinessHighly utilized enzymes are more abundant and less variableAutotrophy related enzymes are largely underutilizedKnockout of Calvin cycle genes increases growth rate on sugar but decreases affinity

Synthesis of glycogen by Chlorobium limicola IMV K-8 while growth in wastewater

Due to the high content of organic compounds, the distillery wastewater can be a good substrate for the production of glycogen during cultivation of green photosynthetic bacteria. Green photosynthetic bacteria Chlorobium limicola IMV K-8 are producers of glycogen and show exoelectrogenic properties when grown alone or inside the co-culture with heterotrophic bacteria-exoelectrogens in wastewater of various origins. In our previous works it was found that due to the phototrophic growth of C. limicola IMV K-8 in the distillery wastewater significantly reduces the content of compounds of nitrogen, sulfur, Ca2+, Mg2+ and others. The study of the patterns of glycogen synthesis by green photosynthetic bacteria during growth in such an extreme environment as the wastewater of a distillery has prospects for the development of biotechnology for the production of this polysaccharide. The aim of the study was to investigate the glycogen content in C. limicola IMV K-8 cells under different growth conditions in the wastewater of the distillery. Bacteria were grown in the wastewater of the distillery under light (phototrophic growth) and without light exposure (heterotrophic growth). Bacterial cells grown on GSB medium under light (phototrophic growth) and without light (heterotrophic growth) exposure were used as controls. Glycogen content was determined at 7, 14, 21 and 30 days of growth by the glucose oxidase method. Glucose or glycogen in the wastewater of the distillery without the introduction of bacteria was not detected. It was found that the content of glycogen in cells of C. limicola IMV K-8 grown in the wastewater of the distillery, under light exposure increased from 3.8 % to 39.8 % of cells dry weight from the seventh to third day of growth during 30 days of cultivation and was 2 times higher the glycogen content of cells on GSB medium. It is assumed that the bacteria C. limicola IMV K-8 use available in the water sources of carbon and other compounds necessary for cell metabolism along with glycogen biosynthesis and bioremediation of wastewater. During C. limicola IMV K-8 growth in the darkness there is an assimilation of organic sources of carbon (acetate, pyruvate and probably organic compounds of wastewater), which allows cells to remain viable for 30 days without additional sources of carbon, nitrogen, etc., but significant glycogen synthesis does not occur. The glycogen formed under phototrophic conditions can be further a source of carbon or a substrate for electric current generation by exoelectrogenic bacteria.

Valorization of CO2 through lithoautotrophic production of sustainable chemicals in Cupriavidus necator

Coupling recent advancements in genetic engineering of diverse microbes and gas-driven fermentation provides a path towards sustainable commodity chemical production. Cupriavidus necator H16 is a suitable species for this task because it effectively utilizes H2 and CO2 and is genetically tractable. Here, we demonstrate the versatility of C. necator for chemical production by engineering it to produce three products from CO2 under lithotrophic conditions: sucrose, polyhydroxyalkanoates (PHAs), and lipochitooligosaccharides (LCOs). We engineered sucrose production in a co-culture system with heterotrophic growth 30 times that of WT C. necator. We engineered PHA production (20-60% DCW) and selectively altered product composition by combining different thioesterases and phaCs to produce copolymers directly from CO2. And, we engineered C. necator to convert CO2 into the LCO, a plant growth enhancer, with titers of ∼1.4 mg/L—equivalent to yields in its native source, Bradyrhizobium. We applied the LCOs to germinating seeds as well as corn plants and observed increases in a variety of growth parameters. Taken together, these results expand our understanding f how a gas-utilizing bacteria can promote sustainable production.

Heterotrophic growth of Aphanothece microscopica Nägeli in calcium alginate beads from BG11 medium and vinasse

A aplicação de microalgas e cianobactérias imobilizadas no tratamento de efluentes tem sido objeto de diversas pesquisas nos últimos anos, visando principalmente a remoção de carbono e nitrogênio simultaneamente, além de outros nutrientes como fósforo. Quanto aos métodos de imobilização de microalgas, o sistema de encapsulação em matrizes de macromoléculas como o alginato tem despertado interesse devido às suas características de biodegradabilidade, biocompatibilidade e não toxicidade. Neste contexto, o objetivo da pesquisa foi o desenvolvimento de esferas de alginato para a imobilização da cianobactéria Aphanothece microscopica Nägeli, bem como a avaliação do crescimento e capacidade de remoção de glicose, como exemplo de composto orgânico, da fase líquida “bulk”. Os resultados indicaram elevadas velocidades específicas de crescimento para Aphanothece microscopica Nägeli imobilizada em alginato de cálcio tanto para o meio BG11 e vinhaça de cana-de-açúcar, sugerindo a viabilidade do processo, com perspectivas de remoção contínua de matéria orgânica de efluentes a partir deste sistema de cultivo microalgal