Understanding aerobic/anaerobic metabolism in Caldibacillus debilis through a comparison with model organisms

Bacterial synergy and relay for thermophilic hydrogen production through dark fermentation using food waste

BACKGROUND

Food waste is a significant global issue, with 1.3 billion tons generated annually, a figure expected to rise to 2.1 billion tons by 2030. Conventional disposal methods, such as landfilling and incineration, present environmental challenges, including methane emissions and pollution. Hydrogen production through dark fermentation presents a sustainable alternative, offering both waste management and renewable energy generation. This study investigates the bacterial synergy and relay mechanisms involved in thermophilic H2 production using food waste as a substrate.

PURPOSE

The primary aim of this research was to analyze the metabolic pathways and dynamics of functional genes prediction during thermophilic H2 production from food waste, focusing on the role of bacterial consortia in enhancing H2 yields.

METHODS

A continuous stirred-tank reactor (CSTR) was operated using food waste as the substrate and a thermophilic bacterial consortium as the inoculum. The study utilized genomic analysis to monitor changes in bacteriobiome composition over time and to correlate these changes with H2 production. Volatile fatty acids (VFAs) and H2 production rates were analyzed using gas chromatography and high-performance liquid chromatography (HPLC). The Kyoto Encyclopedia of Genes and Genomes (KEGG) database was employed to identify functional genes involved in the fermentation process.

RESULTS

The study identified key bacterial species, including Caproiciproducens and Caproicibacter, that dominated during the later stages of H2 production, replacing earlier dominant species such as Clostridium. These shifts in bacterial dominance were strongly correlated with sustained H2 production rates ranging from 353 to 403 mL·L-1·h-1, with H2 concentrations between 55 % and 62 % (v/v). Functional gene analysis revealed significant pathways related to polysaccharide degradation, glycolysis, and dark fermentation.

CONCLUSIONS

This study highlights the importance of bacterial synergy and relay in maintaining continuous H2 production from food waste under thermophilic conditions. The findings provide insights into optimizing biohydrogen production processes, emphasizing the role of specific bacterial species in enhancing efficiency. These results contribute to the development of sustainable waste management strategies and renewable energy production.

Enhancing aerobic composting of food waste by adding hydrolytically active microorganisms

The biomass of native microorganisms in food waste (FW) suitable for accelerated composting is initially low and requires time for adaptation. Adding of efficient hydrolytic microorganisms should be able to enhance compost-specific microbial activity, adjust microbial community structure, and potentially hasten FW biodegradation. This study aimed to identify bacterial and fungal strains with growth characteristics suitable for accelerating FW composting. Over 7 weeks, FW was composted in a pilot-scale test, either inoculated at the start or on day 28 with three different mixtures of 10 autochthonous Bacillus and Penicillium spp. strains known for their high hydrolytic activity. The effects of inoculation were assessed by measuring the rate of carbon dioxide (CO2) and ammonia (NH3) production and also the increase in temperature due to spontaneous exothermic activity of the enhanced microbial population degrading FW. Inoculation with Bacillus spp., particularly B. amyloliquefaciens and B. subtilis, at the beginning of composting increased CO2 production nearly 3-fold while maintaining stable ammonia production and temperature. The high concentration of Bacillus relative to native FW microorganisms led to dominant fermentation processes even in the presence of oxygen, resulting in moderate heat release and elevated production of volatile organic compounds. Introducing Penicillium spp. at a later stage (day 28) increased CO2 production nearly 2-fold, along with higher NH3 levels and temperature. These findings highlight the significance of inoculation timing and microbial composition in regulating metabolic pathways during FW composting degradation, offering insights for designing effective microbial formulations for composting.

Metagenomic analysis of a thermophilic bacterial consortium and its use in the bioremediation of a petroleum-contaminated soil

Biodegradation is difficult at high temperatures due to the limited capacity of microorganisms to survive and function outside their optimum temperature range. Here, a thermophilic petroleum-degrading consortium was enriched from compost at a temperature of 55 °C. 16S rDNA and metagenomic techniques were used to analyze the composition of the consortium and the mechanisms of degradation. The consortium degraded 17000 mg total petroleum hydrocarbons (TPHs) L-1 with a degradation efficiency of 81.5% in 14 days. The consortium utilized a range of substrates such as n-hexadecane, n-docosane, naphthalene and pyrene and grew well over a wide range of pH (4-10) and salinity (0-90 g L-1). The hydrocarbon-degrading extremophilic consortium contained, inter alia, (relative abundance >1%) Caldibacillus, Geobacillus, Mycolicibacterium, Bacillus, Chelatococcus, and Aeribacillus spp. Metagenomic analysis was conducted to discover the degradation and environmental tolerance functional genes of the consortium. Two alkane hydroxylase genes, alkB and ladA, were found. A microcosm study shows that the consortium promoted the bioremediation of soil TPHs. The results indicate that the consortium may be a good candidate for the high-temperature bioremediation of petroleum-contaminated soils.

Effect of oxygen deficiency on organic matter decomposition during the early stage of composting

This study aimed to elucidate the recovery of organic matter decomposition after oxygen deficiency in the early stage was replaced by aerobic conditions during composting. Oxygen deficiency at the early stage was created by supplying nitrogen gas into the composting for 3 days (LN3dA) and 5 days (LN5dA). Subsequently, air was introduced until the end of composting instead of nitrogen gas. Runs LN3dA and LN5dA had lower organic matter decomposition by 10% and 19%, respectively, compared with fully aerobic composting (LA) after oxygen deficiency was changed to aerobic conditions. Compared with fully aerobic composting, composting with oxygen deficiency at the early thermophilic stage had a different bacterial community, as analyzed by high-throughput sequencing. During vigorous organic matter decomposition, Bacillus was dominant in Run LA, whereas Caldibacillus proliferated in Runs LN3dA and LN5dA. Bacillus thermoamylovorans, Bacillus arbutinivorans, and Bacillus kokeshiiformis were hypothesized to be inhibited by Caldibacillus. Moreover, dissimilarity analysis indicated that different bacterial communities remained until the end of composting, which could be a reason for the incomplete recovery of organic matter decomposition. As analyzed by the API-ZYM kit, the enzymatic activities were also different between all composting runs. One of the characterized enzymes, α-galactosidase, displayed low activity during oxygen deficiency and could not achieve high activity with sufficient oxygen until composting was completed. Overall, our study showed that oxygen deficiency at the early thermophilic stage caused incomplete recovery of organic matter decomposition.

Proteomic Shifts Reflecting Oxidative Stress and Reduced Capacity for Protein Synthesis, and Alterations to Mitochondrial Membranes in Neurospora crassa Lacking VDAC

Voltage-dependent anion-selective channels (VDAC) maintain the bidirectional flow of small metabolites across the mitochondrial outer membrane and participate in the regulation of multiple cellular processes. To understand the roles of VDAC in cellular homeostasis, preliminary proteomic analyses of S100 cytosolic and mitochondria-enriched fractions from a VDAC-less Neurospora crassa strain (ΔPor-1) were performed. In the variant cells, less abundant proteins include subunits of translation initiation factor eIF-2, enzymes in the shikimate pathway leading to precursors of aromatic amino acids, and enzymes involved in sulfate assimilation and in the synthesis of methionine, cysteine, alanine, serine, and threonine. In contrast, some of the more abundant proteins are involved in electron flow, such as the α subunit of the electron transfer flavoprotein and lactate dehydrogenase, which is involved in one pathway leading to pyruvate synthesis. Increased levels of catalase and catalase activity support predicted increased levels of oxidative stress in ΔPor-1 cells, and higher levels of protein disulfide isomerase suggest activation of the unfolded protein response in the endoplasmic reticulum. ΔPor-1 cells are cold-sensitive, which led us to investigate the impact of the absence of VDAC on several mitochondrial membrane characteristics. Mitochondrial membranes in ΔPor-1 are more fluid than those of wild-type cells, the ratio of C18:1 to C18:3n3 acyl chains is reduced, and ergosterol levels are lower. In summary, these initial results indicate that VDAC-less N. crassa cells are characterized by a lower abundance of proteins involved in amino acid and protein synthesis and by increases in some associated with pyruvate metabolism and stress responses. Membrane lipids and hyphal morphology are also impacted by the absence of VDAC.

Production of n-caproate using food waste through thermophilic fermentation without addition of external electron donors

The effectiveness of producing n-caproate from food waste without external electron donors (EDs) was investigated through batch and semi-continuous fermentation. The maximum concentration of n-caproate reached 10,226.28 mg COD/L during semi-continuous fermentation. The specificity for n-caproate was the highest at 40.19 ± 3.95%, and the soluble COD conversion rate of n-caproate reached up to 22.50 ± 1.09% at the end of batch fermentation. The production of n-caproate was coupled with the generation of lactate as an ED to facilitate chain elongation reactions. When lactate was used as the only substrate, n-butyrate (64.12 ± 20.11%) markedly dominated the products, instead of n-caproate (0.63 ± 0.07%). Microbial community analysis revealed that Caproiciproducens, Rummeliibacillus, and Clostridium_sensu_stricto_12 were the key genera related to n-caproate production. In addition to n-caproate, n-butyrate dominated the products in batch and semi-continuous fermentation with a maximum specificity of 47.59 ± 3.39%. Clostridium_sensu_stricto_7 was committed to producing n-butyrate from lactate.

Effects of carbon concentration, oxygen, and controlled pH on the engineering strain Lactiplantibacillus casei E1 in the production of bioethanol from sugarcane molasses

Sugarcane molasses are considered a potential source for bioethanol's commercial production because of its availability and low market price. It contains high concentrations of fermentable sugars that can be directly metabolized by microbial fermentation. Heterofermentative lactic acid bacteria, especially Lactiplantibacillus casei, have a high potential to be a biocatalyst in ethanol production that they are characterized by strong abilities of carbohydrate metabolism, ethanol synthesis, and high alcohol tolerance. This study aimed to evaluate the feasibility of producing ethanol by Lactiplantibacillus casei used the ethanologen engineering strain L. casei E1 as a starter culture and cane molasses as substrate medium. The effects of environmental factors on the metabolism of L. casei E1 were analyzed by high-performance liquid chromatography (HPLC) system, and the gene expression of key enzymes in carbon source metabolism was detected using quantitative real-time PCR (RT-qPCR). Results showed that the strain could grow well, ferment sugar quickly in cane molasses. By fermenting this bacterium anaerobically at 37 °C for 36 h incubation in 5 °BX molasses when the fermenter's pH was controlled at 6.0, ethanol yield reached 13.77 g/L, and carbohydrate utilization percentage was 78.60%. RT-qPCR results verified the strain preferentially ferment glucose and fructose of molasses to ethanol at the molecular level. In addition, the metabolism of sugars, especially fructose, would be inhibited by elevating acidity. Our findings support the theoretical basis for exploring Lactic acid bacteria as a starter culture for converting sugarcane molasses into ethanol.

Genomic comparison of facultatively anaerobic and obligatory aerobic Caldibacillus debilis strains GB1 and Tf helps explain physiological differences

Caldibacillus debilis strains GB1 and Tf display distinct phenotypes. Caldibacillus debilis GB1 is capable of anaerobic growth and can synthesize ethanol while C. debilis Tf cannot. Comparison of the GB1 and Tf genome sequences revealed that the genomes were highly similar in gene content and showed a high level of synteny. At the genome scale, there were several large sections of DNA that appeared to be from lateral gene transfer into the GB1 genome. Tf did have unique genetic content but at a much smaller scale: 300 genes in Tf verses 857 genes in GB1 that matched at ≤90% sequence similarity. Gene complement and copy number of genes for the glycolysis, tricarboxylic acid cycle, and electron transport chain pathways were identical in both strains. While Tf is an obligate aerobe, it possesses the gene complement for an anaerobic lifestyle (ldh, ak, pta, adhE, pfl). As a species, other strains of C. debilis should be expected to have the potential for anaerobic growth. Assaying the whole cell lysate for alcohol dehydrogenase activity revealed an approximately 2-fold increase in the enzymatic activity in GB1 when compared with Tf.

A metabolic and genomic assessment of sugar fermentation profiles of the thermophilic Thermotogales, Fervidobacterium pennivorans

A metabolic, genomic and proteomic assessment of Fervidobacterium pennivorans strains was undertaken to clarify the metabolic and genetic capabilities of this Thermotogales species. The type strain Ven5 originally isolated from a hot mud spa in Italy, and a newly isolated strain (DYC) from a hot spring at Ngatamariki, New Zealand, were compared for metabolic and genomic differences. The fermentation profiles of both strains on cellobiose generated similar major end products (acetate, alanine, glutamate, H₂, and CO₂). The vast majority of end products produced were redox neutral, and carbon balances were in the range of 95-115%. Each strain showed distinct fermentation profiles on sugar substrates. The genome of strain DYC was sequenced and shown to have high sequence similarity and synteny with F. pennivorans Ven5 genome, suggesting they are the same species. The unique genome regions in Ven5, corresponded to genes involved in the Entner-Doudoroff pathway confirming our observation of DYC's inability to utilize gluconate. Genome analysis was able to elucidate pathways involved in production of the observed end-products with the exception of alanine and glutamate synthesis which were resolved with less clarity due to poor sequence identity and missing critical enzymes within the pathway, respectively.

Description of a cryptic thermophilic (pro)phage, CBP1 from Caldibacillus debilis strain GB1

This study characterizes a cryptic (pro)phage-related sequence within the Caldibacillus debilis GB1 genome, designated CBP1.CBP1 is a Siphoviridae-like genome highly related to GBVS1 from Geobacillus sp. 6k51. The CBP1genome is a 37,315 bp region containing 69 putative ORFs with a GC content of 42% flanked on both sides by host DNA integrated into the main bacterial chromosome (contig 16). Bioinformatic analyses identified cassettes of genes within the CBP1 genome that were similar in function, yet distinct in sequence, from genes previously identified in GBVS1. All of CBP1 genes had less than 60% amino acid sequence identity with GBVS1by tBLASTx, with the exception of the TMP repeat gene. CBP1 possessed all the necessary genes to undergo a temperate/lytic phage life cycle, including excision, replication, structural genes, DNA packaging, and cell lyses. Proteomic analysis of CBP1 revealed the expression of 5 proteins. One of the expressed proteins was a transcriptional regulator protein homologous to the bacteriophage λ repressor protein (cI) expressed in high amounts from the CBP1 region, consistent with a lysogenic phage in a repressed state. The CBP1 protein expression profile during host growth provides unique insight into thermophilic Siphoviridae-like phages in the repressed state within their host cells.