Optimization of soil microbial fuel cell for sustainable bio-electricity production: combined effects of electrode material, electrode spacing, and substrate feeding frequency on power generation and microbial community diversity

BACKGROUND: Microbial fuel cells (MFCs) are among the leading research topics in the field of alternative energy sources due to their multifunctional potential. However, their low bio-energy production rate and unstable performance limit their application in the real world. Therefore, optimization is needed to deploy MFCs beyond laboratory-scale experiments. In this study, we investigated the combined influence of electrode material (EM), electrode spacing (ES), and substrate feeding interval (SFI) on microbial community diversity and the electrochemical behavior of a soil MFC (S-MFC) for sustainable bio-electricity generation. RESULTS: Two EMs (carbon felt (CF) and stainless steel/epoxy/carbon black composite (SEC)) were tested in an S-MFC under three levels of ES (2, 4, and 8 cm) and SFI (4, 6, and 8 days). After 30 days of operation, all MFCs achieved open-circuit voltage in the range of 782 + 12.2 mV regardless of the treatment. However, the maximum power of the SEC–MFC was 3.6 times higher than that of the CF–MFC under the same experimental conditions. The best solution, based on the interactive influence of the two discrete variables, was obtained with SEC at an ES of 4.31 cm and an SFI of 7.4 days during an operating period of 66 days. Analysis of the experimental treatment effects of the variables revealed the order SFI < ES < EM, indicating that EM is the most influential factor affecting the performance of S-MFC. The performance of S-MFC at a given ES value was found to be dependent on the levels of SFI with the SEC electrode, but this interactive influence was found to be insignificant with the CF electrode. The microbial bioinformatic analysis of the samples from the S-MFCs revealed that both electrodes (SEC and CF) supported the robust metabolism of electroactive microbes with similar morphological and compositional characteristics, independent of ES and SFI. The complex microbial community showed significant compositional changes at the anode and cathode over time. CONCLUSION: This study has demonstrated that the performance of S-MFC depends mainly on the electrode materials and not on the diversity of the constituent microbial communities. The performance of S-MFCs can be improved using electrode materials with pseudocapacitive properties and a larger surface area, instead of using unmodified CF electrodes commonly used in S-MFC systems. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13068-022-02224-9

Interactions of nitrogen-related, growth promoting bacteria with Miscanthus × giganteus : impact and mechanism

The highly nitrogen-use efficient biomass grass Miscanthus is a host of the bacterial endophyte Herbaspirillum frisingense. While Herbaspirillum frisingense has the genetic competence to fix nitrogen, the plant-associated microbiome may also contribute to this nitrogen efficiency. Furthermore, the costly field establishment of the sterile perennial Miscanthus × giganteus from rhizomes is a severe constraint for expanding the production area of this commercial biomass crop. In this study, the effect of Herbaspirillum frisingense inoculation on stem-cutting sprouting, shoot biomass and other yield parameters was investigated. I studied how the inoculation impacts on the M. × giganteus associated microbiome and how the long term differences in nitrogen fertilizer amount modulated the M. × giganteus associated microbiome. This was studied in a 14 year-old field trial of M. ×giganteus fertilized with various amounts of nitrogen. Stem cutting inoculation improved the shoot sprouting and establishment success of Miscanthus × giganteus in the greenhouse. In a small field trial, plant height and biomass from inoculated sites were significantly larger in the second year after establishment, but already after one year after inoculation, the bulk soil, rhizosphere, root and rhizome microbiomes were almost devoid of Herbaspirillum. This beta-proteobacterium may colonize the shoot of Miscanthus × giganteus more efficiently. Major differences between bacterial communities were determined by plant-soil compartments and less by the plant organs, while both inoculation and nitrogen had little effects on these communities. Compared to the little effect on the soil, rhizosphere and root microbiomes, the rhizome microbiome was massively modulated by both inoculation and nitrogen level. In the rhizome, several proteobacteria, which are associated with plant growth promoting functions, were enriched by inoculation, while N2-fixing-related bacterial families were favored by long-term nitrogen-deficiency plots, but denitrifier-related families were depleted. The studies suggest that H. frisingense inoculation may improve establishment of Miscanthus stem cuttings and has long-lasting effects on the rhizome microbiome diversity, despite low rhizocompetence and low root abundance. Meanwhile, the rhizome could be a potential nitrogen fixation factory. The organ-specific, nitrogen-related bacterial communities are modulated by long-term different nitrogen supply and are mainly shaped by the plant, which provides guidance for optimizing Miscanthus sustainable cultivation.Das stickstoffeffiziente Biomassegras Miscanthus wird unter anderem vom bakteriellen Endophyten Herbaspirillum frisingense besiedelt, welches die genetischen Grundlagen für Stickstoff-fixierung besitzt. Das mit Miscanthus assoziierte Mikrobiom, welches ebenso zu seiner Stickstoffeffizienz beitragen könnte, war zu Beginn der Arbeit noch nicht bekannt. Darüber hinaus ist das Etablieren des sterilen, mehrjährigen Miscanthus × giganteus aus Rhizomen ein hoher Kostenfaktor und damit ein schwerwiegendes Hindernis für die Erweiterung der Produktionsfläche dieser kommerziellen Biomassepflanze. In dieser Arbeit wurde die Wirkung der Inokulation mit Herbaspirillum frisingense auf das Keimen von Knospen an Stängeln, die Wirkung auf die Sprossbiomasse und auf andere Ertragsparameter untersucht. Darüber hinaus wurde untersucht, wie sich die Inokulation auf das mit M. × giganteus assoziierte Mikrobiom im Feld auswirkt. Das mit Miscanthus assoziierte Mikrobiom wurde ausserdem von einem 14-jährigen Dauerfeldversuch bestimmt, bei dem die Pflanzen ohne Stickstoff (N), oder jährlich mit 80 kg N gedüngt wurden. Die Beimpfung von Stängelabschnitten mit Herbaspirillum frisingense regte das Keimen von Knospen an und erhöhte den Etablierungserfolg von Miscanthus × giganteus im Gewächshaus. In einem kleinen Feldversuch waren Pflanzenhöhe und Biomasse von beimpften Rhizomen im zweiten Jahr nach der Etablierung signifikant größer, aber bereits nach einem Jahr nach der Inokulation waren die Mikrobiome des Bodens, der Rhizosphäre, der Wurzel und des Rhizoms nahezu frei vom beimften Herbaspirillum. Dieses betaProteobakterium kann offenbar den Spross von Miscanthus × giganteus effizienter besiedeln. Die Hauptunterschiede zwischen den Bakteriengemeinschaften wurden durch die unterschidlichen Umweltbedingungen der Kompartimente, also zwischen Pflanzen und Boden und weniger durch die Pflanzenorgane bestimmt. Sowohl die Inokulation, als auch die N-Düngung hatten nur geringe Auswirkungen auf diese Gemeinschaften. Im Vergleich zu den geringen Auswirkungen auf Boden, Rhizosphäre und Wurzelmikrobiome wurde das Rhizom-Mikrobiom sowohl durch Inokulation, als auch durch den N-Dünger, am meisten verändert. Im Rhizom wurden mehrere Proteobakterien, die bekanntermassen zur Förderung des Pflanzenwachstums beitragen, durch Inokulation angereichert, während N2- fixierende Bakterienfamilien im Rhizom durch Langzeit-N-Mangel begünstigt wurden. Familien, in denen Stickstoff-Denitrifizierer gefunden werden, waren weniger im Rhizom repräsentiert. Die Arbeit legt nahe, dass durch die Inokulation mit H. frisingense die Etablierung von Miscanthus-Stängelabschnitten verbessert werden kann. Trotz geringer Rhizokompetenz und geringer Abundanz hat das Inokulat lang-anhaltende Auswirkungen auf die Rhizom-Mikrobiom-Diversität. Das Rhizom könnte als eine potenzielle Stickstofffixierungsfabrik dienen, und somit langfristig zur Stickstoffeffizient beitragen. Die organspezifischen und wenig durch das N-Düngeniveau regulierten Bakteriengemeinschaften werden hauptsächlich von der Pflanze geprägt und könnten eine Rolle bei der Optimierung der nachhaltigen Kultivierung von Miscanthus spielen

Mining-impacted rice paddies select for Archaeal methylators and reveal a putative (Archaeal) regulator of mercury methylation

ABSTRACT: Methylmercury (MeHg) is a microbially produced neurotoxin derived from inorganic mercury (Hg), which accumulation in rice represents a major health concern to humans. However, the microbial control of MeHg dynamics in the environment remains elusive. Here, leveraging three rice paddy fields with distinct concentrations of Hg (Total Hg (THg): 0.21−513 mg kg−1 dry wt. soil; MeHg: 1.21−6.82 ng g−1 dry wt. soil), we resorted to metagenomics to determine the microbial determinants involved in MeHg production under contrasted contamination settings. We show that Hg methylating Archaea, along with methane-cycling genes, were enriched in severely contaminated paddy soils. Metagenome-resolved Genomes of novel putative Hg methylators belonging to Nitrospinota (UBA7883), with poorly resolved taxonomy despite high completeness, showed evidence of facultative anaerobic metabolism and adaptations to fluctuating redox potential. Furthermore, we found evidence of environmental filtering effects that influenced the phylogenies of not only hgcA genes under different THg concentrations, but also of two housekeeping genes, rpoB and glnA, highlighting the need for further experimental validation of whether THg drives the evolution of hgcAB. Finally, assessment of the genomic environment surrounding hgcAB suggests that this gene pair may be regulated by an archaeal toxin-antitoxin (TA) system, instead of the more frequently found arsR-like genes in bacterial methylators. This suggests the presence of distinct hgcAB regulation systems in bacteria and archaea. Our results support the emerging role of Archaea in MeHg cycling under mining-impacted environments and shed light on the differential control of the expression of genes involved in MeHg formation between Archaea and Bacteria

BIOGEOCHEMICAL RESPONSE TO VEGETATION AND HYDROLOGIC CHANGE IN AN ALASKAN BOREAL FEN ECOSYSTEM

Boreal peatlands store approximately one third of the earth’s terrestrial carbon, locked away in currently waterlogged and frozen conditions. Peatlands of boreal and arctic ecosystems are affected increasingly by shifting hydrology caused by climate change. The consequences of these relatively rapid ecosystem changes on carbon cycling between the landscape and the atmosphere could provide an amplifying feedback to climate warming. Alternatively, the advancement of terrestrial vegetation into once waterlogged soils could uptake carbon as a sink. Previous work suggests that fens will become an increasingly dominant landscape feature in the boreal. However, studies investigating fens, their response to hydrologic and vegetative change, and their carbon cycling dynamics are relatively few compared with other peatland types. This research investigates the biological and geochemical controls over carbon dioxide and methane cycling in a central Alaskan rich fen. The research concentrates on how these processes react to changes in water table and vegetation composition. The objectives of this body of research were to 1) Gain insights on how water table change affects carbon dioxide and methane transformation in a boreal rich fen from the pore water to the atmosphere; 2) Assess the mechanistic controls of specific boreal rich fen plant functional groups on carbon cycling; and 3) Profile the microbial community of a boreal rich fen and report on its response to water table change and specific plant functional groups. Although the oxidation of methane is prevalent in the studied rich fen, a raised water table and associated root exudates from greater sedge abundance fuels greater methane production than oxidation, for a net effect of greater methane production. However, the net methane that is released from the fen site is likely diminished compared with expected emissions due to the oxidizing nature of sedge, grass, and horsetail rhizospheres. Methanogens may also be in competition with other microorganisms for metabolic resources in this fen, which is recharged by the cyclic rewetting characteristic of these ecosystems. Overall, fens as a peatland type appear to have a resilience buffer in their carbon cycling response to hydrologic change more so than other peatland types

Microbial Communities and Biogeochemistry in Marine Sediments of the Baltic Sea and the High Arctic, Svalbard

Marine sediments contain more microorganisms than all of the world’s oceans, with current of estimates of 1×1029 microorganisms. Despite marine sediments being replete with microbial cells, the majority of these microorganisms remain uncultured in the laboratory. At present, it is estimated that over 99% of all microorganisms have evaded culture, although truer estimates likely depend upon environment. Factors responsible for the intractability of these microorganisms include very slow doubling times, predicted to be on the orders of years to centuries, as well as special physiological needs of extremophiles. Unsuccessful laboratory growth of these microorganisms requires us to rely on culture-independent tools, including molecular techniques, metagenomics, and bioinformatic tools to glean insight into their ecological structure and function.This dissertation combines molecular and bioinformatic techniques to evaluate the biosphere within deeply buried sediments of the Baltic Sea and shallow sediments in Arctic fjords. Quantification of microbial biomass within marine sediments lays the groundwork for questions related to organic carbon and element cycling. Although essential, reliable and reproducible estimates of microbial biomass within deeply buried sediments has proved challenging. Here we present an interlaboratory comparison of quantification results from International Ocean Discovery Program Exp. 347 sediments that allowed us to define best practices that lead to meaningful quantification estimates. We then transferred these best practices to marine sediments in a Svalbard fjord (Van Keulenfjorden) to understand how glacial proximity influences microbial communities. Through 16S rRNA gene libraries, organic geochemistry, and genome reconstruction, we illustrate that cross-fjord trends in organic matter influence community structure in the sediment. In addition, we argue that biological iron and sulfur cycling facilitates rapid recycling of electron acceptors crucial for carbon oxidation. We delved deeper into their metabolic pathways with metagenomic sequencing and contig binning. We reconstructed several genomes of the Woeseiaceae clade that can act both as a sink and a source of carbon. Ultimately, our work provides a framework for understanding how glacial proximity influences microbial community composition and metabolic function, which is important and timely with ongoing climate change and a strong threat of severe glacial retreat in this region

Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens

Background The role of the RNA polymerase sigma factor RpoN in regulation of gene expression in Geobacter sulfurreducens was investigated to better understand transcriptional regulatory networks as part of an effort to develop regulatory modules for genome-scale in silico models, which can predict the physiological responses of Geobacter species during groundwater bioremediation or electricity production. Results An rpoN deletion mutant could not be obtained under all conditions tested. In order to investigate the regulon of the G. sulfurreducens RpoN, an RpoN over-expression strain was made in which an extra copy of the rpoN gene was under the control of a taclac promoter. Combining both the microarray transcriptome analysis and the computational prediction revealed that the G. sulfurreducens RpoN controls genes involved in a wide range of cellular functions. Most importantly, RpoN controls the expression of the dcuB gene encoding the fumarate/succinate exchanger, which is essential for cell growth with fumarate as the terminal electron acceptor in G. sulfurreducens. RpoN also controls genes, which encode enzymes for both pathways of ammonia assimilation that is predicted to be essential under all growth conditions in G. sulfurreducens. Other genes that were identified as part of the RpoN regulon using either the computational prediction or the microarray transcriptome analysis included genes involved in flagella biosynthesis, pili biosynthesis and genes involved in central metabolism enzymes and cytochromes involved in extracellular electron transfer to Fe(III), which are known to be important for growth in subsurface environment or electricity production in microbial fuel cells. The consensus sequence for the predicted RpoN-regulated promoter elements is TTGGCACGGTTTTTGCT. Conclusion The G. sulfurreducens RpoN is an essential sigma factor and a global regulator involved in a complex transcriptional network controlling a variety of cellular processes

BIOFERTILIZERS FOR SUSTAINABLE AGRICULTURE: ISOLATION AND GENOMIC CHARACTERIZATION OF NITROGEN-FIXING BACTERIA FROM SUGARCANE

The goal of my thesis research was to explore the use of bacterial biofertilizers, as an alternative or complementary approach to chemical fertilizers, in support of more sustainable agricultural practices. To this end, I worked to discover and characterize native nitrogen-fixing bacteria that are associated with sugarcane crops cultivated in the Cauca Valley of Colombia. I hypothesized that native nitrogen-fixing bacteria, found in association with local sugarcane crops, could serve as potent biofertilizers with the potential to simultaneously increase crop yield while reducing the reliance of chemical fertilizers. I evaluated this hypothesis by isolating nitrogen-fixing bacteria isolated from Colombian sugarcane fields and characterizing their plant growth-promoting (PGP) potential using an integrated computational genomics and experimental approach. A high-throughput cultivation approach was developed and applied for the enrichment and isolation of nitrogen-fixing bacteria from environmental samples. Pure cultures of nitrogen-fixing bacteria were isolated and tested for diazotrophic potential by PCR amplification of nifH genes, a common molecular marker for nitrogen-fixing capacity, and twenty-two distinct nifH positive isolates were selected for genome sequencing and analysis. Genome sequence analysis confirmed the presence of intact nifH genes and operons in the genomes of 18 of the isolates, and isolate genomes were found to encode operons for phosphate solubilization, siderophore production, and other PGP phenotypes. I characterized 14 of the 22 nitrogen-fixing isolates as distinct strains of Klebsiella pneumoniae, and four others were members of genera that are closely related to Klebsiella. Computational phenotype predictions for PGP traits were validated with a series of experimental laboratory assays for nitrogen fixation and phosphate solubilization as well as the production of siderophores, gibberellic acid, and indole acetic acid. Results from the biochemical assays were consistent with the bioinformatic predictions for these isolates, in support of their PGP potential. The quantitative approach to computational phenotyping that I developed and applied to sugarcane bacterial isolates facilitates the screening for strains that have a high potential for nitrogen fixation and other PGP phenotypes while showing minimal risk for virulence and antibiotic resistance. Finally, I developed and validated an automated method to curate and continuously update a nifH reference sequence database, which can be used to support the characterization of metagenomic or environmental amplicon sequences. This process yields a far smaller, but much more reliable, set of ‘gold-standard’ nifH sequences, against which users can compare their metagenomic or amplicon sequence data for accurate functional prediction and taxonomic characterization of environmental samples.Ph.D

Operon Prediction Model Based on Markov Clustering Algorithm

There are many operon prediction models, but few methods can be applied to the operon prediction of new sequencing species effectively. In this paper, an operon prediction model based on Markov clustering algorithm is proposed. The model uses some generic attribute information of genomes and graph clustering algorithm instead of classifier to predict operon. Similarly to most operon prediction models, E. coli K12 and B. subtilis str. 168 were used to assess the prediction capability of the proposed model, the experiment results show that the proposed model has better capability of operon prediction than some other classical operon prediction methods