Biology subjects

Sousa, D. Z.

Publications and source records attributed to Sousa, D. Z..

7 recordsLinked to original sources

bioRxiv2026

Carbon monoxide utilisation by Thermanaeromonas species and description of Thermobium azorense gen. nov., sp. nov.

Syngas fermentation by carbon monoxide (CO)-utilising acetogens offers a sustainable route for converting gasified waste materials into value-added chemicals. In this study, we isolated a novel thermophilic CO-utilising bacterium, strain AZ2, from marine hydrothermal sediment collected on the island of Sao Miguel, Azores, Portugal. Strain AZ2 is an obligately anaerobic, spore-forming bacterium. Average nucleotide identity (ANI; 78.4-86.7%) and digital DNA-DNA hybridization (dDDH; 23.4-32.5 %) analyses indicate that strain AZ2 represents a novel species within a previously uncharacterised lineage represented by the GTDB placeholder genus UBA2545 in the Neomoorellaceae family. Strain AZ2 was able to grow fermentatively on CO, producing acetate. We further demonstrated that its closest isolated relatives - Thermanaeromonas toyohensis, T. burensis, and Thermanaeromonas sp. strain 9S - are capable of growing on CO, producing either acetate or hydrogen gas (H2). Additionally, we unveiled the genomic potential for CO utilisation within other members of the GTDB placeholder class DSM-521 (previously Moorellia) to which our isolate belongs, expanding the list of possible thermophilic CO-utilising acetogens. We propose that strain AZ2T represents the type strain of a novel genus and species, named Thermobium azorense gen. nov., sp. nov. (= DSM 121889T = JCM 39698T).

microbiology↗

bioRxiv2025

Proton stress adaptation in acidophilic sulfate-reducing bacteria: insights from Acididesulfobacillus acetoxydans for acid mine drainage bioremediation

Acid mine drainage (AMD) waters are a global environmental threat due to their extremely low pH (<3) and high metal loads. Acidophilic sulfate-reducing bacteria (aSRB) can mitigate AMD by reducing sulfate to sulfide, a proton-consuming process that also precipitates metals as metal sulfides. Although sulfate reduction has been observed in AMD waters, most characterized aSRB are only moderately acidophilic and originate from protected microniches. Here, we examined the pH tolerance and proton stress adaptation of the complete organic acid-oxidizing aSRB Acididesulfobacillus acetoxydans. Continuous chemostat cultivations were operated across a pH gradient, achieving steady states from pH 5.0 (optimum) down to 2.9, with microcosms showing metabolic activity even at pH 2.5 which is typical AMD-acidity. Transcriptomic profiles remained remarkably stable across conditions, except for upregulation of the K+-transporting ATPase (kdpABC) at lower pH, suggesting an increased reliance on the chemiosmotic gradient to impede proton influx. Lipid analysis revealed increased core lipid saturation, mid-chain methylation and a shift in priming precursors from leucine to valine at low pH, indicating reduced membrane permeability and more energy-efficient biosynthetic pathways. These adaptations impede proton entry demonstrating adaptation of aSRB to AMD-like acidity and removes the critical pH bottleneck for AMD bioremediation and metal recovery. SynopsisThis study shows acidophilic sulfate-reducing bacteria can adapt to AMD-like acidity while retaining metabolic activity, underscoring their potential for AMD bioremediation and biotechnology.

microbiology↗

bioRxiv2024

FT-IR micro-spectroscopy for imaging the extracellular matrix composition in biofilms

Microorganisms form granules by embedding themselves in an extracellular matrix through the secretion of extracellular polymeric substances (EPS). The extracellular matrix is a complex structure comprising of e.g. proteins, polysaccharides, lipids, and extracellular DNA. Understanding the function of individual EPS components within the matrix not only requires knowledge on the composition of the extracellular matrix, but also on the spatial distribution of said components. Molecular imaging like e.g. fluorescence microscopy have been used for the visualization of the extracellular matrix, but these target specific molecules. Untargeted approaches like FT-IR micro-spectroscopy would allow for a broader exploration. In this study FT-IR micro-spectroscopy analysis was implemented on sliced anaerobic granular sludge to explore the EPS distribution. Visualization of single wavenumber absorbance showed a higher polysaccharide content in the EPS at the granule perimeter, shifting to a higher protein concentration toward the centre. The boundary of this shift was approximately 150 {micro}m from the surface, which was in accordance with the layer of fermentative bacteria described in literature. The complexity in the polymer composition meant that many functional groups were overlapping, making FT-IR annotation challenging. To address this, principal component analysis and two-dimensional correlation spectroscopy analysis were included in the analysis. These methods enabled the identification of overlapping functional groups and correlations between functional groups. Positive correlations between protein and polysaccharide functional groups suggested the presence of glycoproteins, which has been regularly described in chemical EPS analysis studies. Additionally, correlations between sulfated compounds and protein/polysaccharide functional groups indicated potential co-localization in the extracellular matrix. Differences in positive correlations of sialic acids with polysaccharides suggest variations in polysaccharide compositions, possibly caused by differences in the microbial community.

microbiology↗

bioRxiv2022

Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum

BackgroundMicrobial production of propionate from diluted streams of ethanol (e.g., deriving from syngas fermentation) is a sustainable alternative to the petrochemical production route. Yet, few ethanol-fermenting propionigenic bacteria are known, and understanding of their metabolism is limited. Anaerotignum neopropionicum is a propionate-producing bacterium that uses the acrylate pathway to ferment ethanol and CO2 to propionate and acetate. In this work, we used computational and experimental methods to study the metabolism of A. neopropionicum and, in particular, the pathway for conversion of ethanol into propionate. ResultsOur work describes iANEO_SB607, the first genome-scale metabolic model (GEM) of A. neopropionicum. The model was built combining the use of automatic tools with an extensive manual curation process, and it was validated with experimental data from this and published studies. The model predicted growth of A. neopropionicum on ethanol, lactate, sugars and amino acids, matching observed phenotypes. In addition, the model was used to implement a dynamic flux balance analysis (dFBA) approach that accurately predicted the fermentation profile of A. neopropionicum during batch growth on ethanol. A systematic analysis of the metabolism of A. neopropionicum combined with model simulations shed light into the mechanism of ethanol fermentation via the acrylate pathway, and revealed the presence of the electron-transferring complexes NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (Nfn) and acryloyl-CoA reductase-EtfAB, identified for the first time in this bacterium. ConclusionsThe realisation of the GEM iANEO_SB607 is a stepping stone towards the understanding of the metabolism of the propionate-producer A. neopropionicum. With it, we have gained insight into the functioning of the acrylate pathway and energetic aspects of the cell, with focus on the fermentation of ethanol. Overall, this study provides a basis to further exploit the potential of propionigenic bacteria as microbial cell factories.

systems biology↗

bioRxiv2021

Large scale function-based genome prospecting for industrial traits applied to 1,3-propanediol production.

Due to the success of next-generation sequencing, there has been a vast build-up of microbial genomes in the public repositories. FAIR genome prospecting of this huge genomic potential for biotechnological benefiting, require new efficient and flexible methods. In this study, Semantic Web technologies are applied to develop a function-based genome mining approach that follows a knowledge and discovery in database (KDD) protocol. Focusing on the industrial important trait of 1,3-propanediol (1,3-PD) production 187 new candidate species were identified. Furthermore, the genetic architecture of the particular trait was resolved, and persistent domains identified.

bioinformatics↗

bioRxiv2020

Modeling a co-culture of Clostridium autoethanogenum and Clostridium kluyveri to increase syngas conversion to medium-chain fatty-acids

Microbial fermentation of synthesis gas (syngas) is becoming more attractive for sustainable production of commodity chemicals. To date, syngas fermentation focuses mainly on the use of Clostridium species for the production of small organic molecules such as ethanol and acetate. The cocultivation of syngas-fermenting microorganisms with chain-elongating bacteria can expand the range of possible products, allowing, for instance, the production of medium-chain fatty acids (MCFA) and alcohols from syngas. To explore these possibilities, we report herein a genome-scale, constraint-based metabolic model to describe growth of a co-culture of Clostridium autoethanogenum and Clostridium kluyveri on syngas for the production of valuable compounds. Community flux balance analysis was used to gain insight into the metabolism of the two strains and their interactions, and to reveal potential strategies enabling production of butyrate and hexanoate. The model suggests that addition of succinate is one strategy to optimize the production of medium-chain fatty-acids from syngas with this co-culture. According to the predictions, addition of succinate increases the pool of crotonyl-CoA and the ethanol/acetate uptake ratio in C. kluyveri, resulting in the flux of up to 60% of electrons into hexanoate. Other potential way to optimize butyrate and hexanoate is to increase ethanol production by C. autoethanogenum. Deletion of either formate transport, acetaldehyde dehydrogenase or formate dehydrogenase (ferredoxin) from the metabolic model of C. autoethanogenum leads to a (potential) increase in ethanol production up to 150%, which is clearly very attractive.Competing Interest StatementThe authors have declared no competing interest.View Full Text

synthetic biology↗

bioRxiv2019

Elucidating syntrophic butyrate-degrading populations in anaerobic digesters using stable isotope-informed genome-resolved metagenomics

Linking the genomic content of uncultivated microbes to their metabolic functions remains a critical challenge in microbial ecology. Resolving this challenge has implications for improving our management of key microbial interactions in biotechnologies such as anaerobic digestion, which relies on slow-growing syntrophic and methanogenic communities to produce renewable methane from organic waste. In this study, we combined DNA stable isotope probing (SIP) with genome-centric metagenomics to recover the genomes of populations enriched in 13C after feeding 13C-labeled butyrate. Differential abundance analysis on recovered genomic bins across the SIP metagenomes identified two metagenome-assembled genomes (MAGs) that were significantly enriched in the heavy 13C DNA. Phylogenomic analysis assigned one MAG to the genus Syntrophomonas, and the other MAG to the genus Methanothrix. Metabolic reconstruction of the annotated genomes showed that the Syntrophomonas genome encoded all the enzymes for beta-oxidizing butyrate, as well as several mechanisms for interspecies electron transfer via electron transfer flavoproteins, hydrogenases, and formate dehydrogenases. The Syntrophomonas genome shared low average nucleotide identity (< 95%) with any cultured representative species, indicating it is a novel species that plays a significant role in syntrophic butyrate degradation within anaerobic digesters. The Methanothrix genome contained the complete pathway for aceticlastic methanogenesis, indicating that it was enriched in 13C from syntrophic acetate transfer. This study demonstrates the potential of stable-isotope-informed genome-resolved metagenomics to elucidate the nature of metabolic cooperation in slow-growing uncultured microbial populations, such as syntrophic bacteria and methanogens, that are important to waste treatment as well as global carbon cycling. ImportancePredicting the metabolic potential and ecophysiology of mixed microbial communities remains a major challenge, especially for slow-growing anaerobes that are difficult to isolate. Unraveling the in-situ metabolic activities of uncultured species could enable a more descriptive framework to model substrate transformations by microbiomes, which has broad implications for advancing the fields of biotechnology, global biogeochemistry, and human health. Here, we investigated the in-situ function of mixed microbiomes by combining DNA-stable isotope probing with metagenomics to identify the genomes of active syntrophic populations converting butyrate, a C4 fatty acid, into methane within anaerobic digesters. This approach thus moves beyond the mere presence of metabolic genes to resolve who is doing what by obtaining confirmatory assimilation of labeled substrate into the DNA signature. Our findings provide a framework to further link the genomic identities of uncultured microbes with their ecological function within microbiomes driving many important biotechnological and global processes.

microbiology↗