Hydrogen-oxidizing bacteria and their applications in resource recovery and pollutant removal

Biological carbon capture from biogas streams: Insights into Cupriavidus necator autotrophic growth and transcriptional profile

Recycling carbon-rich wastes into high-value platform chemicals through biological processes provides a sustainable alternative to petrochemicals. Cupriavidus necator, known for converting carbon dioxide (CO2) into polyhydroxyalkanoates (PHA) was studied for the first time using biogas streams as the sole carbon source. The bacterium efficiently consumed biogenic CO2 from raw biogas with methane at high concentrations (50%) proving non-toxic. Continuous addition of H2 and O2 enabled growth trends comparable to glucose-based heterotrophic growth. Transcriptomic analysis revealed CO2-adaptated cultures exhibited upregulation of hydrogenases and Calvin cycle enzymes, as well as genes related to electron transport, nutrient uptake, and glyoxylate cycle. Non-adapted samples displayed activation of stress response mechanisms, suggesting potential lags in large-scale processes. These findings showcase the setting of growth parameters for a pioneering biological biogas upgrading strategy, emphasizing the importance of inoculum adaptation for autotrophic growth and providing potential targets for genetic engineering to push PHA yields in future applications.

The Calvin Benson cycle in bacteria: New insights from systems biology

The Calvin Benson cycle in phototrophic and chemolithoautotrophic bacteria has ecological and biotechnological importance, which has motivated study of its regulation. I review recent advances in our understanding of how the Calvin Benson cycle is regulated in bacteria and the technologies used to elucidate regulation and modify it, and highlight differences between and photoautotrophic and chemolithoautotrophic models. Systems biology studies have shown that in oxygenic phototrophic bacteria, Calvin Benson cycle enzymes are extensively regulated at post-transcriptional and post-translational levels, with multiple enzyme activities connected to cellular redox status through thioredoxin. In chemolithoautotrophic bacteria, regulation is primarily at the transcriptional level, with effector metabolites transducing cell status, though new methods should now allow facile, proteome-wide exploration of biochemical regulation in these models. A biotechnological objective is to enhance CO2 fixation in the cycle and partition that carbon to a product of interest. Flux control of CO2 fixation is distributed over multiple enzymes, and attempts to modulate gene Calvin cycle gene expression show a robust homeostatic regulation of growth rate, though the synthesis rates of products can be significantly increased. Therefore, de-regulation of cycle enzymes through protein engineering may be necessary to increase fluxes. Non-canonical Calvin Benson cycles, if implemented with synthetic biology, could have reduced energy demand and enzyme loading, thus increasing the attractiveness of these bacteria for industrial applications.

Syngas-driven sewage sludge conversion to microbial protein through H2S- and CO-tolerant hydrogen-oxidizing bacteria

Treating excess municipal sewage sludge (MSS) by means of thermochemical processes could enable its conversion into high-value microbial protein (MP) through syngas. Nevertheless, the variable composition and content of inhibitory compounds of the latter hinders the application potential of such a biorefinery scheme. Through a series of short- (48 to 96 h) and long-term (30 days) batch aerobic bioconversion tests, the present study aimed at investigating the potential of a mixed culture of hydrogen-oxidizing bacteria (HOB) to produce MP from a simulated syngas mixture characterized by variable H2 and CO2 concentrations, and different levels of CO and H2S as potential inhibitors of the HOB-driven process. Syngas was converted into MP with a protein content as high as 74 %, reaching biomass yields of 0.25 g VSS/g H2-COD, close to the maximum reported HOB yield of 0.28 g VSS/g H2-COD,  and volumetric productivities of 16 mg VSS/L/h. The potential of the process to provide between 50 and 100 % of the total nitrogen requirement of HOB solely by means of the gaseous ammonia nitrogen recovered through syngas was also preliminarily calculated. The presence of H2S and CO concentrations up to 0.4 % and up to 40 %, respectively, and a wide range of H2/CO2 ratios (2 - 10) had no negative influence on the main process performances. The role played by H2S- and CO-tolerant HOB species was fundamental to guarantee a high tolerance to microbial inhibitors, and demonstrated the high potential of mixed cultures for resource recovery and valorisation.

Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance

Democratizing genomic data science, including bioinformatics, can diversify the STEM workforce and may, in turn, bring new perspectives into the space sciences. In this respect, the development of education and research programs that bridge genome science with "place" and world-views specific to a given region are valuable for Indigenous students and educators. Through a multi-institutional collaboration, we developed an ongoing education program and model that includes Illumina and Oxford Nanopore sequencing, free bioinformatic platforms, and teacher training workshops to address our research and education goals through a place-based science education lens. High school students and researchers cultivated, sequenced, assembled, and annotated the genomes of 13 bacteria from Mars analog sites with cultural relevance, 10 of which were novel species. Students, teachers, and community members assisted with the discovery of new, potentially chemolithotrophic bacteria relevant to astrobiology. This joint education-research program also led to the discovery of species from Mars analog sites capable of producing N-acyl homoserine lactones, which are quorum-sensing molecules used in bacterial communication. Whole genome sequencing was completed in high school classrooms, and connected students to funded space research, increased research output, and provided culturally relevant, place-based science education, with participants naming three novel species described here. Students at St. Andrew's School (Honolulu, Hawai'i) proposed the name Bradyrhizobium prioritasuperba for the type strain, BL16AT, of the new species (DSM 112479T = NCTC 14602T). The nonprofit organization Kauluakalana proposed the name Brenneria ulupoensis for the type strain, K61T, of the new species (DSM 116657T = LMG = 33184T), and Hawai'i Baptist Academy students proposed the name Paraflavitalea speifideiaquila for the type strain, BL16ET, of the new species (DSM 112478T = NCTC 14603T).

Microbial gas fermentation technology for sustainable food protein production

The development of novel, sustainable, and robust food production technologies represents one of the major pillars to address the most significant challenges humanity is going to face on earth in the upcoming decades - climate change, population growth, and resource depletion. The implementation of microfoods, i.e., foods formulated with ingredients from microbial cultivation, into the food supply chain has a huge potential to contribute towards energy-efficient and nutritious food manufacturing and represents a means to sustainably feed a growing world population. This review recapitulates and assesses the current state in the establishment and usage of gas fermenting bacteria as an innovative feedstock for protein production. In particular, we focus on the most promising representatives of this taxon: the hydrogen-oxidizing bacteria (hydrogenotrophs) and the methane-oxidizing bacteria (methanotrophs). These unicellular microorganisms can aerobically metabolize gaseous hydrogen and methane, respectively, to provide the required energy for building up cell material. A protein yield over 70% in the dry matter cell mass can be reached with no need for arable land and organic substrates making it a promising alternative to plant- and animal-based protein sources. We illuminate the holistic approach to incorporate protein extracts obtained from the cultivation of gas fermenting bacteria into microfoods. Herein, the fundamental properties of the bacteria, cultivation methods, downstream processing, and potential food applications are discussed. Moreover, this review covers existing and future challenges as well as sustainability aspects associated with the production of microbial protein through gas fermentation.

In-situ microbial protein production by using nitrogen extracted from multifunctional bio-electrochemical system

Upgrading of waste nitrogen sources is considered as an important approach to promote sustainable development. In this study, a multifunctional bio-electrochemical system with three chambers was established, innovatively achieving 2.02 g/L in-situ microbial protein (MP) production via hydrogen-oxidizing bacteria (HOB) in the protein chamber (middle chamber), along with over 2.9 L CO2/(L·d) consumption rate. Also, 69% chemical oxygen demand was degraded by electrogenic bacteria in the anode chamber, resulting in the 394.67 J/L electricity generation. Focusing on the NH4+-N migration in the system, the current intensity contributed 4%-9% in the anode and protein chamber, whereas, the negative effect of -6.69% on contribution was shown in the cathode chamber. On the view of kinetics, NH4+-N migration in anode and cathode chambers was fitted well with Levenberg-Marquardt equation (R2 > 0.92), along with the well-matched results of HOB growth in the protein chamber based on Gompertz model (R2 > 0.99). Further evaluating MPs produced by HOB, 0.45 g/L essential amino acids was detected, showing the better amino acid profile than fish and soybean. Multifunctional bio-electrochemical system revealed the economic potential of producing 6.69 €/m3 wastewater according to a simplified economic evaluation.

Valorization of protein-rich waste and its application

Energy shortages present significant challenges with the rising population and dramatic urbanization development. The effective utilization of high-value products generated from massive protein-rich waste has emerged as an excellent solution for mitigating the growing energy crisis. However, the traditional disposal and treatment of protein-rich waste, have been proven to be ineffective in resource utilization, which led to high chemical oxygen demand and water eutrophication. To effectively address this issue, hydrolysate and bioconversion products from protein-rich waste have been widely investigated. Herein, we aim to provide an overview of the valorization of protein-rich waste based on a comprehensive analysis of publicly available literature. Firstly, the sources of protein-rich waste with various quantities and qualities are systematically summarized. Then, we scrutinize and analyze the hydrolysis approaches of protein-rich waste and the versatile applications of hydrolyzed products. Moreover, the main factors influencing protein biotransformation and the applications of bioconversion products are covered and extensively discussed. Finally, the potential prospects and future directions for the valorization of protein-rich waste are proposed pertinently.

Enrichment of biofertilizer-type hydrogen-oxidizing bacteria on urea containing Cu(II)

With the utilization of pesticides and fertilizers (e.g. urea), the presence of nitrogen and heavy metals (e.g. copper) can enter and pollute the environment. Biofertilizers can be used to replace chemical fertilizers to increase crop yields and reduce environmental stress. The utilization of hydrogen-oxidizing bacteria (HOB) to be biofertilizers has recently attracted more attention. However, the enrichment of HOB on urea and the effect of copper are undetermined. HOB were successfully enriched using urea in this investigation. The average urea conversion rate (AUCR) was 180.08 mgN/L/d with a hydraulic retention time of 10 h. Microbial community (R1) was dominated by Hydrogenophaga (83.92%), a biofertilizer-type HOB. After addition of 5.47 mg/L Cu2+, the AUCR was decreased by 16%-151.18 mgN/L/d, and the growth of HOB was inhibited by 48%. Meanwhile, inhibition was also reflected by the increase of polysaccharide content (20.27 ± 0.57 to 33.45 ± 2.53 mg/gVSS) and protein content (106.19 ± 19.39 to 125.14 ± 24.73 mg/gVSS) of extracellular polymeric substances in the HOB. The resulting microbial community (R2) was changed to Azospiralium-dominated flora (91.33%). Both enriched microbial communities (R1 and R2) exhibited the abilities of ACC degradation and phosphate solubilization. This study demonstrates that employing urea can directly enrich biofertilizer-type HOB and copper-tolerant HOB can be obtained in a 5.47 mg/L Cu2+ environment. The results provide potential methods to obtain biofertilizer from copper-containing urea wastewater via HOB.

From anaerobic digestion to single cell protein synthesis: A promising route beyond biogas utilization

The accumulation of a large amount of organic solid waste and the lack of sufficient protein supply worldwide are two major challenges caused by rapid population growth. Anaerobic digestion is the main force of organic waste treatment, and the high-value utilization of its products (biogas and digestate) has been widely concerned. These products can be used as nutrients and energy sources for microorganisms such as microalgae, yeast, methane-oxidizing bacteria(MOB), and hydrogen-oxidizing bacteria(HOB) to produce single cell protein(SCP), which contributes to the achievement of sustainable development goals. This new model of energy conversion can construct a bioeconomic cycle from waste to nutritional products, which treats waste without additional carbon emissions and can harvest high-value biomass. Techno-economic analysis shows that the SCP from biogas and digestate has higher profit than biogas electricity generation, and its production cost is lower than the SCP using special raw materials as the substrate. In this review, the case of SCP-rich microorganisms using anaerobic digestion products for growth was investigated. Some of the challenges faced by the process and the latest developments were analyzed, and their potential economic and environmental value was verified.

Construction of Cupriavidus necator displayed with superoxide dismutases for enhanced growth in bioelectrochemical systems

It is of great significance to utilize CO2 as feedstock to synthesize biobased products, particularly single cell protein (SCP) as the alternative food and feed. Bioelectrochemical system (BES) driven by clean electric energy has been regarded as a promising way for Cupriavidus necator to produce SCP from CO2 directly. At present, the key problem of culturing C. necator in BES is that reactive oxygen species (ROS) generated in cathode chamber are harmful to bacterial growth. Therefore, it is necessary to find a solution to mitigate the negative effect of ROS. In this study, we constructed a number of C. necator strains displayed with superoxide dismutase (SOD), which allowed the decomposition of superoxide anion radical. The effects of promoters and signal peptides on the cell surface displayed SOD were analyzed. The proteins displayed on the surface were further verified by the fluorescence experiment. Finally, the growth of C. necator CMS incorporating a pBAD-SOD-E-tag-IgAβ plasmid could achieve 4.9 ± 1.0 of OD600 by 7 days, equivalent to 1.7 ± 0.3 g/L dry cell weight (DCW), and the production rate was 0.24 ± 0.04 g/L/d DCW, around 2.7-fold increase than the original C. necator CMS (1.8 ± 0.3 of OD600). This study can provide an effective and novel strategy of cultivating strains for the production of CO2-derived SCP or other chemicals in BES.

Non-photosynthetic chemoautotrophic CO2 assimilation microorganisms carbon fixation efficiency and control factors in deep-sea hydrothermal vent

Non-photosynthetic chemoautotrophic microorganisms in deep-sea hydrothermal vent can obtain energy by oxidation reducing substances and synthesize CO₂ into organic carbon, and the development and utilization of microbial resources in this environment for CO₂ fixation under ordinary environmental conditions is of great significance to understand the carbon cycle and microbial carbon fixation in deep-sea hydrothermal vent. In this study, a set of spiral-stirred bioreactor (SSB) was developed to cultivate a group of non-photosynthetic chemoautotrophic CO₂ assimilation microorganisms (NPCAM), mainly Sphingomonadaceae (unclassified, the mean of which was 31.16 %), from deep-sea hydrothermal vent sediments, which have the characteristics of halophilic, acid-base and heavy metal resistant. The maximum carbon fixation efficiency (calculated by CO₂) was 6.209 mg·CO₂/(L·h) after 96 h of incubation in the presence of mixed electron donors (MEDs, 0.46 % NaNO₂, 0.50 % Na₂S₂O₃ and 1.25 % Na₂S, w/v), mixed inorganic carbon sources (CO₂, Na₂CO₃ and NaHCO₃) and aerobic conditions. The detection of NPCAM synthetic organic fraction in SSB system, the study of single bacteria culturability and carbon fixation efficiency, the analysis of CO₂ fixation pathway and the development of coupled carbon fixation technology are the prospective works that need to be further developed.

C1-based biomanufacturing: Advances, challenges and perspectives

One-carbon (C1) compounds have emerged as a key research focus due to the growth of metabolic engineering and synthetic biology as affordable and sustainable nonfood sugar feedstocks for energy-efficient and environmentally friendly biomanufacturing. This paper summarizes and discusses current developments in C1 compounds for biomanufacturing. First, two primary groups of microbes that use C1 compounds (native and synthetic) are introduced, and the traits, categorization, and functions of C1 microbes are summarized. Second, engineering strategies for C1 utilization are compiled and reviewed, including reconstruction of C1-utilization pathway, enzyme engineering, cofactor engineering, genome-scale modeling, and adaptive laboratory evolution. Third, a review of C1 compounds' uses in the synthesis of biofuels and high-value compounds is presented. Finally, potential obstacles to C1-based biomanufacturing are highlighted along with future research initiatives.