Syntrophic growth of alkaliphilic anaerobes controlled by ferric and ferrous minerals transformation coupled to acetogenesis

Impact of steel slag, gypsum, and coal gangue on microbial immobilization of metal(loid)s in non-ferrous mine waste dumps

Non-ferrous mine waste dumps globally generate soil pollution characterized by low pH and high metal(loid)s content. In this study, the steel slag (SS), gypsum (G), and coal gangue (CG) combined with functional bacteria consortium (FB23) were used for immobilizing metal(loid)s in the soil. The result shown that FB23 can effectively decrease As, Pb, and Zn concentrations within 10 d in an aqueous medium experiment. In a 310-day field column experiment, solid waste including SS, G, and CG combined with FB23 decreased As, Cd, Cu, and Pb concentrations in the aqueous phase. Optimized treatment was obtained by combining FB23 with 1% SS, 1% G, and 1.5% CG. Furthermore, the application of solid waste (SS, G, and CG) increased the top 20 functional bacterial consortium (FB23) abundance at the genus level from 1% to 21% over 50 days in the soil waste dump. Moreover, dissolved organic carbon (DOC) and pH were identified as the main factors influencing the reduction in bioavailable As, Cd, Cu, and Pb in the combination remediation. Additionally, the reduction of Fe and sulfur S was crucial for decreasing the mobilization of the metal(loid)s. This study provides valuable insights into the remediation of metal contamination on a larger scale.

Genomic Insights into Syntrophic Lifestyle of 'Candidatus Contubernalis alkaliaceticus' Based on the Reversed Wood-Ljungdahl Pathway and Mechanism of Direct Electron Transfer

The anaerobic oxidation of fatty acids and alcohols occurs near the thermodynamic limit of life. This process is driven by syntrophic bacteria that oxidize fatty acids and/or alcohols, their syntrophic partners that consume the products of this oxidation, and the pathways for interspecies electron exchange via these products or direct interspecies electron transfer (DIET). Due to the interdependence of syntrophic microorganisms on each other's metabolic activity, their isolation in pure cultures is almost impossible. Thus, little is known about their physiology, and the only available way to fill in the knowledge gap on these organisms is genomic and metabolic analysis of syntrophic cultures. Here we report the results of genome sequencing and analysis of an obligately syntrophic alkaliphilic bacterium 'Candidatus Contubernalis alkaliaceticus'. The genomic data suggest that acetate oxidation is carried out by the Wood-Ljungdahl pathway, while a bimodular respiratory system involving an Rnf complex and a Na+-dependent ATP synthase is used for energy conservation. The predicted genomic ability of 'Ca. C. alkaliaceticus' to outperform interspecies electron transfer both indirectly, via H2 or formate, and directly, via pili-like appendages of its syntrophic partner or conductive mineral particles, was experimentally demonstrated. This is the first indication of DIET in the class Dethiobacteria.

Perspectives on Microbial Electron Transfer Networks for Environmental Biotechnology

The overlap of microbiology and electrochemistry provides plenty of opportunities for a deeper understanding of the redox biogeochemical cycle of natural-abundant elements (like iron, nitrogen, and sulfur) on Earth. The electroactive microorganisms (EAMs) mediate electron flows outward the cytomembrane via diverse pathways like multiheme cytochromes, bridging an electronic connection between abiotic and biotic reactions. On an environmental level, decades of research on EAMs and the derived subject termed “electromicrobiology” provide a rich collection of multidisciplinary knowledge and establish various bioelectrochemical designs for the development of environmental biotechnology. Recent advances suggest that EAMs actually make greater differences on a larger scale, and the metabolism of microbial community and ecological interactions between microbes play a great role in bioremediation processes. In this perspective, we propose the concept of microbial electron transfer network (METN) that demonstrates the “species-to-species” interactions further and discuss several key questions ranging from cellular modification to microbiome construction. Future research directions including metabolic flux regulation and microbes–materials interactions are also highlighted to advance understanding of METN for the development of next-generation environmental biotechnology.

Effect of Humin and Chemical Factors on CO2-Fixing Acetogenesis and Methanogenesis

Acetogenesis and methanogenesis have attracted attention as CO₂-fixing reactions. Humin, a humic substance insoluble at any pH, has been found to assist CO₂-fixing acetogenesis as the sole electron donor. Here, using two CO₂-fixing consortia with acetogenic and methanogenic activities, the effect of various parameters on these activities was examined. One consortium utilized humin and hydrogen (H₂) as electron donors for acetogenesis, either separately or simultaneously, but with a preference for the electron use from humin. The acetogenic activity was accelerated 14 times by FeS at 0.2 g/L as the optimal concentration, while being inhibited by MgSO₄ at concentration above 0.02 g/L and by NaCl at concentrations higher than 6 g/L. Another consortium did not utilize humin but H₂ as electron donor, suggesting that humin was not a universal electron donor for acetogenesis. For methanogenesis, both consortia did not utilize extracellular electrons from humin unless H₂ was present. The methanogenesis was promoted by FeS at 0.2 g/L or higher concentrations, especially without humin, and with NaCl at 2 g/L or higher concentrations regardless of the presence of humin, while no significant effect was observed with MgSO₄. Comparative sequence analysis of partial 16S rRNA genes suggested that minor groups were the humin-utilizing acetogens in the consortium dominated by Clostridia, while Methanobacterium was the methanogen utilizing humin with H₂.

Bioanalytical applications of Mössbauer spectroscopy

Data on the applications of Mössbauer spectroscopy in the transmission (mainly on 57Fe nuclei) and emission (on 57Co nuclei) variants for analytical studies at the molecular level of metal-containing components in a wide range of biological objects (from biocomplexes and biomacromolecules to supramolecular structures, cells, tissues and organisms) and of objects that are participants or products of biological processes, published in the last 15 years are discussed and systematized. The prospects of the technique in its biological applications, including the developing fields (emission variant, use of synchrotron radiation), are formulated.

The bibliography includes 248 references.

Casting Light on the Adaptation Mechanisms and Evolutionary History of the Widespread Sumerlaeota

In recent years, the tree of life has expanded substantially. Despite this, many abundant yet uncultivated microbial groups remain to be explored.

Sumerlaeota is a mysterious, putative phylum-level lineage distributed globally but rarely reported. As such, their physiology, ecology, and evolutionary history remain unknown. The 16S rRNA gene survey reveals that Sumerlaeota is frequently detected in diverse environments globally, especially cold arid desert soils and deep-sea basin surface sediments, where it is one dominant microbial group. Here, we retrieved four Sumerlaeota metagenome-assembled genomes (MAGs) from two hot springs and one saline lake. Including another 12 publicly available MAGs, they represent six of the nine putative Sumerlaeota subgroups/orders, as indicated by 16S rRNA gene-based phylogeny. These elusive organisms likely obtain carbon mainly through utilization of refractory organics (e.g., chitin and cellulose) and proteinaceous compounds, suggesting that Sumerlaeota act as scavengers in nature. The presence of key bidirectional enzymes involved in acetate and hydrogen metabolisms in these MAGs suggests that they are acetogenic bacteria capable of both the production and consumption of hydrogen. The capabilities of dissimilatory nitrate and sulfate reduction, nitrogen fixation, phosphate solubilization, and organic phosphorus mineralization may confer these heterotrophs great advantages to thrive under diverse harsh conditions. Ancestral state reconstruction indicated that Sumerlaeota originated from chemotrophic and facultatively anaerobic ancestors, and their smaller and variably sized genomes evolved along dynamic pathways from a sizeable common ancestor (2,342 genes), leading to their physiological divergence. Notably, large gene gain and larger loss events occurred at the branch to the last common ancestor of the order subgroup 1, likely due to niche expansion and population size effects.

Siderite-based anaerobic iron cycle driven by autotrophic thermophilic microbial consortium

Using a sample from a terrestrial hot spring (pH 6.8, 60 °C), we enriched a thermophilic microbial consortium performing anaerobic autotrophic oxidation of hydrothermal siderite (FeCO₃), with CO₂/bicarbonate as the electron acceptor and the only carbon source, producing green rust and acetate. In order to reproduce Proterozoic environmental conditions during the deposition of banded iron formation (BIF), we incubated the microbial consortium in a bioreactor that contained an unmixed anoxic layer of siderite, perfectly mixed N₂/CO₂-saturated liquid medium and microoxic (2% O₂) headspace. Long-term incubation (56 days) led to the formation of magnetite (Fe₃O₄) instead of green rust as the main product of Fe(II) oxidation, the precipitation of newly formed metabolically induced siderite in the anoxic zone, and the deposition of hematite (Fe₂O₃) on bioreactor walls over the oxycline boundary. Acetate was the only metabolic product of CO₂/bicarbonate reduction. Thus, we have demonstrated the ability of autotrophic thermophilic microbial consortium to perform a short cycle of iron minerals transformation: siderite–magnetite–siderite, accompanied by magnetite and hematite accumulation. This cycle is believed to have driven the evolution of the early biosphere, leading to primary biomass production and deposition of the main iron mineral association of BIF.

Metabolic regulation of ethanol-type fermentation of anaerobic acidogenesis at different pH based on transcriptome analysis of Ethanoligenens harbinense

BACKGROUND

Ethanol-type fermentation, one of the fermentation types in mixed cultures of acidogenesis with obvious advantages such as low pH tolerance and high efficiency of H₂ production, has attracted widespread attentions. pH level greatly influences the establishment of the fermentation of carbohydrate acidogenesis by shaping community assembly and the metabolic activity of keystone populations. To explore the adaptation mechanisms of ethanol-type fermentation to low pH, we report the effects of initial pH on the physiological metabolism and transcriptomes of Ethanoligenens harbinense-a representative species of ethanol-type fermentation.

RESULTS

Different initial pH levels significantly changed the cell growth and fermentation products of E. harbinense. Using transcriptomic analysis, we identified and functionally categorized 1753 differentially expressed genes (DEGs). By mining information on metabolic pathways, we probed the transcriptional regulation of ethanol-H₂ metabolism relating to pH responses. Multiple pathways of E. harbinense were co-regulated by changing gene expression patterns. Low initial pH down-regulated the expression of cell growth- and acidogenesis-related genes but did not affect the expression of H₂ evolution-related hydrogenase and ferredoxin genes. High pH down-regulated the expression of H₂ evolution- and acidogenesis-related genes. Multiple resistance mechanisms, including chemotaxis, the phosphotransferase system (PTS), and the antioxidant system, were regulated at the transcriptional level under pH stress.

CONCLUSIONS

Ethanoligenens adapted to low pH by regulating the gene expression networks of cell growth, basic metabolism, chemotaxis and resistance but not H₂ evolution-related genes. Regulation based on pH shifts can represent an important approach to establish and enhance ethanol-type fermentation. The complete gene expression network of ethanol fermentative bacteria for pH response provides valuable insights into the acidogenic fermentation, and offers an effective regulation strategy for the sustainable energy recovery from wastewater and solid waste.