Ferredoxin reduction by hydrogen with iron functions as an evolutionary precursor of flavin-based electron bifurcation.

Autotrophic theories for the origin of metabolism posit that the first cells satisfied their carbon needs from CO2 and were chemolithoautotrophs that obtained their energy and electrons from H2. The acetyl-CoA pathway of CO2 fixation is central to that view because of its antiquity: Among known CO2 fixing pathways it is the only one that is i) exergonic, ii) occurs in both bacteria and archaea, and iii) can be functionally replaced in full by single transition metal catalysts in vitro. In order to operate in cells at a pH close to 7, however, the acetyl-CoA pathway requires complex multi-enzyme systems capable of flavin-based electron bifurcation that reduce low potential ferredoxin-the physiological donor of electrons in the acetyl-CoA pathway-with electrons from H2. How can the acetyl-CoA pathway be primordial if it requires flavin-based electron bifurcation? Here, we show that native iron (Fe0), but not Ni0, Co0, Mo0, NiFe, Ni2Fe, Ni3Fe, or Fe3O4, promotes the H2-dependent reduction of aqueous Clostridium pasteurianum ferredoxin at pH 8.5 or higher within a few hours at 40 °C, providing the physiological function of flavin-based electron bifurcation, but without the help of enzymes or organic redox cofactors. H2-dependent ferredoxin reduction by iron ties primordial ferredoxin reduction and early metabolic evolution to a chemical process in the Earth's crust promoted by solid-state iron, a metal that is still deposited in serpentinizing hydrothermal vents today.

Exploring Acetogenesis in Firmicutes: From Phylogenetic Analysis to Solid Medium Cultivation with Solid-Phase Electrochemical Isolation Equipments.

This study introduces a groundbreaking approach for the exploration and utilization of electrotrophic acetogens, essential for advancing microbial electrosynthesis systems (MES). Our initial focus was the development of Solid-Phase Electrochemical Isolation Equipment (SPECIEs), a novel cultivation method for isolating electrotrophic acetogens directly from environmental samples on a solid medium. SPECIEs uses electrotrophy as a selection pressure, successfully overcoming the traditional cultivation method limitations and enabling the cultivation of diverse microbial communities with enhanced specificity towards acetogens. Following the establishment of SPECIEs, we conducted a genome-based phylogenetic analysis using the Genome Taxonomy Database (GTDB) to identify potential electrotrophic acetogens within the Firmicutes phylum and its related lineages. Subsequently, we validated the electrotrophic capabilities of selected strains under electrode-oxidizing conditions in a liquid medium. This sequential approach, integrating innovative cultivation techniques with detailed phylogenetic analysis, paves the way for further advances in microbial cultivation and the identification of new biocatalysts for sustainable energy applications.

Isolation, draft genome sequence, and identification of Paenibacillus glycanilyticus subsp. hiroshimensis CCS26.

To isolate the useful strain for fermentation to produce bioactive compounds, we screened oligotrophic bacteria, and then strain CCS26 was isolated from leaf soil collected in Japan. This strain was capable of growth on low-nutrient medium. To elucidate the taxonomy of strain CCS26, we determined the 16S rRNA gene and draft genome sequences, respectively. A phylogenetic tree based on 16S rRNA gene sequences showed that strain CCS26 clustered with Paenibacillus species. The draft genome sequence of strain CCS26 consisted of a total of 90 contigs containing 6,957,994 bp, with a GC content of 50.8% and comprising 6,343 predicted coding sequences. Based on analysis of the average nucleotide identity with the draft genome sequence, the strain was identified as P. glycanilyticus subsp. hiroshimensis CCS26.

Isolation and draft genome sequence of Paenibacillus sp. CCS19.

Here, we describe the isolation and draft genome sequence of Paenibacillus sp. CCS19. Paenibacillus sp. CCS19 was isolated from leaf soil collected in Japan and identified based on similarity of the 16S rRNA sequence with related Paenibacillus type strains. The draft genome sequence of Paenibacillus sp. CCS19 consisted of a total of 107 contigs containing 6,816,589 bp, with a GC content of 51.5% and comprising 5,935 predicted coding sequences.

Biogas purification and ammonia load reduction in sewage treatment by two-stage down-flow hanging sponge reactor.

In this study, a two-stage down-flow hanging sponge (TSDHS) reactor was used as biotrickling filter for biogas desulfurization by utilizing the anaerobic digester supernatant (ADS) of sewage sludge of an activated sludge process (ASP). The reactor comprises a closed-type first-stage down-flow hanging sponge (1st DHS) and an open-type second-stage down-flow hanging sponge (2nd DHS) reactors. In the 1st DHS, hydrogen sulfide in biogas was dissolved into the ADS, and then it was oxidized into elemental sulfur and sulfate by microbe using dissolved oxygen and nitrite in the ADS. More than 99.9 % of hydrogen sulfide was removed within 400 s of empty bed residence time, and >50 % of removed hydrogen sulfide was oxidized into elemental sulfur and accumulated at the surface of the sponge carrier in the 1st DHS. The 1st DHS effluent was fed into the 2nd DHS for nitrogen removal via nitrification and sulfur-based denitrification with the recirculation of the 2nd DHS effluent under nonaeration condition. In the 2nd DHS, 36.8 % of ammonia and 5.3 % of total inorganic nitrogen were removed. Sulfurimonas and Halothiobacillus were increased and contributed to the sulfur-based denitrification as well as the accumulation of elemental sulfur in the 1st DHS, respectively. In the 2nd DHS, Nitrosococcus, Nitrobacter, and Sulfuritalea were considered as the contributors of nitrogen removal via nitrification and sulfur-based denitrification. Further, this study shows that a TSDHS reactor can achieve not only desulfurization of biogas in the 1st DHS but also a 3.5 %-15 % reduction of the ammonia load in the 2nd DHS by effective utilization of the ADS during sewage treatment, assuming that the ADS is returned to the ASP.

Draft Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae CCI2, Isolated from Leaf Soil.

Klebsiella pneumoniae subsp. pneumoniae CCI2 was isolated from leaf soil collected in Hiroshima Prefecture, Japan. The draft genome sequence comprises 78 contigs and contains 5,075,115 bp with a G+C content of 57.7%.

Seeding the drainage canal of a wastewater treatment system for the natural rubber industry with rubber for the enhanced removal of organic matter and nitrogen.

Current pretreatment methods for wastewater from natural rubber (NR) factories either have low rubber recovery efficiency or are costly to operate. A wastewater treatment system was developed that combines a pretreatment canal (PTC) seeded with rubber, an anaerobic baffled reactor (ABR), and a down-flow hanging sponge (DHS) reactor. The PTC is simple to implement and contributes to not only rubber recovery but also organic matter removal in the ABR and nitrogen removal in the DHS reactor. In experiments, the PTC recovered 16.6% of residual rubber through coagulation. The ABR increased the chemical oxygen demand removal efficiency and methane recovery compared with other anaerobic reactors treating raw NR wastewater. The DHS reactor removed 30.7% of total inorganic nitrogen (TIN) by nitrification, anaerobic ammonia oxidation and denitrification. Feeding the bottom stage of the DHS reactor with sodium acetate solution increased the TIN removal efficiency to 87.8%. The water quality of the final effluent achieved the Vietnamese standards for the NR industry. Microbial community analysis was performed to identify the dominant microorganisms and mechanisms in the PTC, ABR, and DHS reactor.

Draft Genome Sequence of Enterobacter sp. AS-1, a Potential Eurytrophic Recombination Host.

Strain AS-1 was isolated from laboratory-scale activated sludge collected in Japan. This strain not only grows on rich medium, including R2A medium, but also forms colonies on medium lacking organic matter other than agar (water agar), indicating it could be used as a eurytrophic recombinant host in material production processes. Here, we present a draft genome sequence of Enterobacter sp. AS-1, which consists of a total of 24 contigs containing 5,207,146 bp, with a GC content of 55.64%, and comprising 4,921 predicted coding sequences. Based on 16S rRNA gene sequence analysis, strain AS-1 was designated as Enterobacter sp. AS-1.

Isolation, draft genome sequencing and identification of Enterobacter roggenkampii CCI9.

Strain CCI9, which was isolated from leaf soil collected in Japan, was capable of growth on poor-nutrient medium, at temperatures of 10°C to 45°C, at pHs of 4.5 to 10, and in the presence of 7.0% NaCl. We determined a draft genome sequence of strain CCI9, which consists of a total of 28 contigs containing 4,644,734 bp with a GC content of 56.1%. This assembly yielded 4,154 predicted coding sequences. Multilocus sequence analysis (MLSA) based on atpD, gyrB, infB, and rpoB gene sequences were performed to further identify strain CCI9. The MLSA revealed that strain CCI9 clustered tightly with Enterobacter roggenkampii EN-117T. Moreover, the average nucleotide identity value (98.6%) between genome sequences of strain CCI9 and E. roggenkampii EN-117T exceeds the cutoff value for prokaryotic subspecies delineation. Therefore, strain CCI9 was identified as E. roggenkampii CCI9. To clarify differences between E. roggenkampii EN-117T and CCI9, the coding proteins were compared against the eggNOG database.

Draft Genome Sequence of Enterobacter oligotrophicus CCA3, Isolated from Leaf Soil.

Enterobacter oligotrophicus CCA3 was isolated from leaf soil collected in Hiroshima Prefecture, Japan. Here, we report the draft genome sequence of E. oligotrophicus CCA3. The draft genome sequence of E. oligotrophicus CCA3 consists of 29 contigs of 4,425,100 bp, with a GC content of 54.2%.

Paenibacillus glycanilyticus subsp. hiroshimensis subsp. nov., isolated from leaf soil collected in Japan.

Strain CCI5, an oligotrophic bacterium, was isolated from leaf soil collected in Japan. Strain CCI5 grew at temperatures between 25 °C and 43 °C (optimum temperature, 40 °C) and at pHs between 6.0 and 10.0 (optimum pH, 9.0). Its major fatty acids were anteiso-C15:0 and iso-C16:0, and menaquinone 7 was the only detected quinone system. In a phylogenetic analysis based on 16S rRNA gene sequences, strain CCI5 presented as a member of the genus Paenibacillus. Moreover, multilocus sequence analysis based on partial sequences of the atpD, dnaA, gmk, and infB genes showed that strain CCI5 tightly clustered with P. glycanilyticus DS-1T. The draft genome of strain CCI5 consisted of 6,864,972 bp with a G+C content of 50.7% and comprised 6,189 predicted coding sequences. The genome average nucleotide identity value (97.8%) between strain CCI5 and P. glycanilyticus DS-1T was below the cut-off value for prokaryotic subspecies delineation. Based on its phenotypic, chemotaxonomic, and phylogenetic features, strain CCI5 (= HUT-8145T = KCTC 43270T) can be considered as a novel subspecies within the genus Paenibacillus with the proposed name Paenibacillus glycanilyticus subsp. hiroshimensis subsp. nov.

Deinococcus kurensis sp. nov., isolated from pond water collected in Japan.

An aerobic, oligotrophic, Gram-positive, non-sporulating, motile, rod-shaped, palladium-leaching bacterial strain, Deinococcus sp. KR-1, was previously isolated from pond water collected in Japan. This strain grew at 10 °C to 40 °C (optimum 30 °C), at pH 4.5 to 11.5 (optimum pH 8.0), and in the presence of 2.0% NaCl. Its major cellular fatty acids were C15: 1ω6 and C16 : 1ω7c. The quinone system was menaquinone 8. Multilocus sequence analysis based on partial sequences of four housekeeping genes (atpD, dnaA, gyrB and rpoB) showed that branching of Deinococcus sp. KR-1 was distant to those of Deinococcus type strains. The genome average nucleotide identity value between strain KR-1 and its closest related Deinococcus type strain was less than 95.69%. Based on its phenotypic, chemotaxonomic and phylogenetic data, strain KR-1 (= HUT-8138T = KCTC 33977T) can be considered a novel species within the genus Deinococcus with the proposed name Deinococcus kurensis sp. nov.

Draft genome sequence of Deinococcus sp. KR-1, a potential strain for palladium-leaching.

Strain KR-1 was isolated from pond water collected in Japan. Because this strain was capable of adsorbing palladium particles in sterilized water, strain KR-1 will be a useful biocatalyst for palladium-leaching from metal waste. Here we present a draft genome sequence of Deinococcus sp. KR-1, which consists of a total of 7 contigs containing 4,556,772 bp with a GC content of 70.0% and comprises 4,450 predicted coding sequences. Based on the 16S rRNA gene sequence analysis, strain KR-1 was identified as Deinococcus sp. KR-1.

Enterobacter oligotrophica sp. nov., a novel oligotroph isolated from leaf soil.

A novel oligotrophic bacterium, designated strain CCA6, was isolated from leaf soil collected in Japan. Cells of the strain were found to be a Gram-negative, non-sporulating, motile, rod-shaped bacterium. Strain CCA6 grew at 10-45°C (optimum 20°C) and pH 4.5-10.0 (optimum pH 5.0). The strain was capable of growth in poor-nutrient (oligotrophic) medium, and growth was unaffected by high-nutrient medium. The major fatty acid and predominant quinone system were C16:0 and ubiquinone-8. Phylogenetic analysis based on 16S rRNA gene sequences indicated strain CCA6 presented as a member of the family Enterobacteriaceae. Multilocus sequence analysis (MLSA) based on fragments of the atpD, gyrB, infB, and rpoB gene sequences was performed to further identify strain CCA6. The MLSA showed clear branching of strain CCA6 with respect to Enterobacter type strains. The complete genome of strain CCA6 consisted of 4,476,585 bp with a G+C content of 54.3% and comprising 4,372 predicted coding sequences. The genome average nucleotide identity values between strain CCA6 and the closest related Enterobacter type strain were <88.02%. Based on its phenotypic, chemotaxonomic and phylogenetic features, strain CCA6 (=HUT 8142T =KCTC 62525T ) can be considered as a novel species within the genus Enterobacter with the proposed name Enterobacter oligotrophica.

Pseudomonas humi sp. nov., isolated from leaf soil.

An aerobic, Gram-negative, non-sporulating, motile, rod-shaped and lignin-degrading bacterial strain, Pseudomonas sp. CCA1, was isolated from leaf soil collected in Japan. This strain grew at 20-45 °C (optimum 20 °C), at pH 5.0-10.0 (optimum pH 5.0), and in the presence of 2% NaCl. Its major cellular fatty acids were C16:0 and summed feature 8 (C18:1ω6c and/or C18:1ω7c). The predominant quinone system was ubiquinone-9. Comparative 16S rRNA gene sequence analysis showed that Pseudomonas sp. CCA1 was related most closely to P. citronellolis NBRC 103043T (98.9%), but multilocus sequence analysis based on fragments of the atpD, gyrA, gyrB and rpoB gene sequences showed strain CCA1 to branch separately from its most closely related Pseudomonas type strains. DNA-DNA hybridization values between Pseudomonas sp. CCA1 and type strains of closely related Pseudomonas species were less than 53%. Based on its phenotypic, chemotaxonomic and phylogenetic features, we propose that Pseudomonas sp. CCA1 represents a novel species within the genus Pseudomonas, for which the name Pseudomonas humi sp. nov. is proposed. The type strain is CCA1 (= HUT 8136T = TBRC 8616T).

Enrichment and physiological characterization of an anaerobic ammonium-oxidizing bacterium 'Candidatus Brocadia sapporoensis'.

We successfully enriched a novel anaerobic ammonium-oxidizing (anammox) bacterium affiliated with the genus 'Candidatus Brocadia' with high purity (>90%) in a membrane bioreactor (MBR). The enriched bacterium was distantly related to the hitherto characterized 'Ca. Brocadia fulgida' and 'Ca. Brocadia sinica' with 96% and 93% of 16S ribosomal RNA gene sequence identity, respectively. The bacterium exhibited the common structural features of anammox bacteria and produced hydrazine in the presence of hydroxylamine under anoxic conditions. The temperature range of anammox activity was 20-45°C with a maximum activity at 37°C. The maximum specific growth rate (µmax) was 0.0082h-1 at 37°C, corresponding to a doubling time of 3.5 days. The half-saturation constant (KS) for nitrite was 5±2.5µM. The anammox activity was inhibited by nitrite (IC50=11.6mM) but not by formate and acetate. The major respiratory quinone was identified to be menaquinone-7 (MK-7). The enriched anammox bacterium shared nearly half of genes with 'Ca. Brocadia sinica' and 'Ca. Brocadia fulgida'. The enriched bacterium showed all known physiological characteristics of anammox bacteria and can be distinguished from the close relatives by its 16S rRNA gene sequence. Therefore, we proposed the name 'Ca. Brocadia sapporoensis' sp. nov.

Complete Genome Sequence of Ureibacillus thermosphaericus A1, a Thermophilic Bacillus Isolated from Compost.

Ureibacillus thermosphaericus A1 was isolated from compost collected in Munakata City, Fukuoka Prefecture, Japan. Here, we report the first complete genome sequence of U. thermosphaericus The complete genome of this strain consists of 3,488,104 bp with a GC content of 36.3% and comprises 3,362 predicted coding sequences.

Genetic diversity of marine anaerobic ammonium-oxidizing bacteria as revealed by genomic and proteomic analyses of 'Candidatus Scalindua japonica'.

Anaerobic ammonium-oxidizing (anammox) bacteria affiliated with the genus 'Candidatus Scalindua' are responsible for significant nitrogen loss in oceans, and thus their ecophysiology is of great interest. Here, we enriched a marine anammox bacterium, 'Ca. S. japonica' from a Hiroshima bay sediment in Japan, and comparative genomic and proteomic analyses of 'Ca. S. japonica' were conducted. Sequence of the 4.81-Mb genome containing 4019 coding regions of genes (CDSs) composed of 47 contigs was determined. In the proteome, 1762 out of 4019 CDSs in the 'Ca. S. japonica' genome were detected. Based on the genomic and proteomic data, the core anammox process and carbon fixation of 'Ca. S. japonica' were further investigated. Additionally, the present study provides the first detailed insights into the genetic background responsible for iron acquisition and menaquinone biosynthesis in anammox bacterial cells. Comparative analysis of the 'Ca. Scalindua' genomes revealed that the 1502 genes found in the 'Ca. S. japonica' genome were not present in the 'Ca. S. profunda' and 'Ca. S. rubra' genomes, showing a high genomic diversity. This result may reflect a high phylogenetic diversity of the genus 'Ca. Scalindua'.

Identification and characterization of Burkholderia multivorans CCA53.

OBJECTIVE: A lignin-degrading bacterium, Burkholderia sp. CCA53, was previously isolated from leaf soil. The purpose of this study was to determine phenotypic and biochemical features of Burkholderia sp. CCA53. RESULTS: Multilocus sequence typing (MLST) analysis based on fragments of the atpD, gltD, gyrB, lepA, recA and trpB gene sequences was performed to identify Burkholderia sp. CCA53. The MLST analysis revealed that Burkholderia sp. CCA53 was tightly clustered with B. multivorans ATCC BAA-247T. The quinone and cellular fatty acid profiles, carbon source utilization, growth temperature and pH were consistent with the characteristics of B. multivorans species. Burkholderia sp. CCA53 was therefore identified as B. multivorans CCA53.

Oxidation of glucose by syntrophic association between Geobacter and hydrogenotrophic methanogens in microbial fuel cell.

OBJECTIVE: To investigate a syntrophic interaction between Geobacter sulfurreducens and hydrogenotrophic methanogens in sludge-inoculated microbial fuel cell (MFC) systems running on glucose with an improved electron recovery at the anode. RESULTS: The presence of archaea in MFC reduces Coulombic efficiency (CE) due to their electron scavenging capability but, here, we demonstrate that a syntrophic interaction can occur between G. sulfurreducens and hydrogenotrophic methanogens via interspecies H2 transfer with improvement in CE and power density. The addition of the methanogenesis inhibitor, 2-bromoethanesulfonate (BES), resulted in the reduction in power density from 5.29 to 2 W/m3, and then gradually increased to the peak value of 5.5 W/m3 when BES addition was stopped. CONCLUSION: Reduction of H2 partial pressure by archaea is an efficient approach in improving power output in a glucose-fed MFC system using Geobacter sp. as an inoculum.