Biology subjects

Kappler, A.

Publications and source records attributed to Kappler, A..

8 recordsLinked to original sources

bioRxiv2026

Towards understanding nitrate-reducing Fe(II) oxidation in Ferrigenium straubiae: spotlight on old and new key protein candidates

3.Autotrophic Fe(II) oxidation is a key microbial process linking iron cycling to global carbon and nitrogen turnover in anoxic and low-oxygen environments. While Fe(II) oxidation, and electron utilization by canonical denitrification or oxygen-reducing pathways have been proposed, the whole electron transport chain via the periplasm is unknown. To address this gap, we compared the transcriptome of Ferrigenium straubiae strain KS (= KCTC 25982; = DSM 118991) cultivated under autotrophic conditions using Fe(II) as the electron donor and either nitrate or oxygen as the terminal electron acceptor. Additionally, we reanalyzed the genome using bioinformatic tools (FeGenie, MHCScan, Foldseek, AlphaFold, COFACTOR, and InterProScan) to classify known, putative, and previously uncharacterized proteins. Using these analyses, we (i) identified a form II RubisCO-mediated, sedoheptulose-7-phosphate-forming transaldolase variant of the Calvin-Benson-Bassham cycle, (ii) revealed the metabolic possibility of a reversed oxidative TCA cycle and an alternative CO2 fixation route via 10-formyl-tetrahydrofolate, (iii) found novel structural features of the proposed Fe(II) oxidases (Cyc2 and MtoA/B: {beta}-barrel outer membrane cytochromes), (iv) uncovered a nitric oxide reductase (eNOR-family) and two redox complexes specifically upregulated under nitrate-reducing Fe(II)-oxidizing conditions, including one comprising a sphaeroides heme protein homolog, and (v) reveal a cytochrome c rich gene area encoding ten heme proteins and (iv) proposed a conserved nonaheme cytochrome c to link Fe(II) oxidation to quinone reduction. 2. RepositoriesGenBank whole genome sequence of strain KS: JAGRPI00000000 IMG Taxon ID of strain KS: 2878407288 NCBI BioProject ID of RNA-Seq data: PRJNA1399691 Strain availability: KCTC 25982 and DSM 118991 Normalized transcripts and Log2FoldChanges (Excel file), and supplementary information are available with the online version of this article.

microbiology↗

bioRxiv2025

Alpine peatlands: spatially and temporally complex ecosystems with year-round methane cycling activity

Peatlands are well-known emitters of methane. European alpine peatlands share certain characteristics with boreal peatlands, despite being located at temperate latitudes, such as a strong seasonality with snowfall in winter and a short summer and growing season. Unlike boreal peatlands, they experience relatively large temperature fluctuations between day and night and are more likely to be sloping. It is unknown how these factors affect methane dynamics. Furthermore, winter methane dynamics have rarely been studied. We therefore quantified the soil-atmosphere methane flux at an alpine peatland in Austria (1700 m a.s.l), with a focus on the spatial and temporal heterogeneity in this ecosystem. In summer, methane emissions were high (49 mg m2 h-1), whereas in spring, shortly after snowmelt, both methane uptake and emissions were observed at different locations within the alpine peatland. In winter, a local snow-free patch persisted at the peatland due to the year-round influx of 5{degrees}C spring water. We compared the methane flux from this snow-free patch to another alpine peatland which also contained such a snow-free area and observed methane emissions at the one peatland (1.2 mg m2 h-1) and methane uptake at the other (-0.06 mg m2 h-1). The input of spring water in combination with the sloping nature of the peatlands resulted in a large spatial heterogeneity, likely as a result of the input of redox-active components such as sulfate by the spring water. The microbial community composition also suggested the presence of active sulfur, iron and methane cycling in the peat soil. Overall, our research shows that alpine peatlands are unique systems due to the year-round spring water throughput, altering biogeochemical cycles and creating local snow-free conditions, with implications for methane cycling.

microbiology↗

bioRxiv2024

Environmental versus litter traits as drivers of microbial decomposer functions

Plant litter decomposition is a key ecosystem process with significant implications for global carbon cycling, soil fertility and plant productivity. Given that microbial decomposers are the main players in the decomposition process, it is surprising how little is known about their functional diversity in different habitats or their ability to respond to environmental changes. To fill this knowledge gap, we conducted a litterbag decomposition experiment along a pronounced climate and vegetation gradient in the Chilean Coastal Cordillera (26{degrees}S to 38{degrees}S), ranging from hyper-arid to temperate, using mixtures of four plant species, native to the respective ecosystems. We analyzed potential decomposition functions of bacterial and fungal litter communities along with their biotic (litter traits) and abiotic (meteorological conditions and soil properties) environments, to determine the relative importance of these environmental factors for microbial community functioning. We also tested the impact of the functional diversity of the decomposer communities (i.e., the diversity of decomposition related functions) on litter mass loss. Functional composition was related most strongly to the temporal variation of precipitation and radiation, explaining about 19 % and 6 % of variation in bacteria and fungi, respectively. In contrast, functional diversity was quite strongly related to litter chemical traits (C:N, C:P, tannins, phenols). Litter mass loss after six months of decomposition was not correlated to the functional diversity of decomposer communities but increased with the presence of habitat generalists like Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Taken together, these results highlight i) the interplay between abiotic factors and chemical litter traits on litter microbial functions and functional diversity and ii) the importance of microbial generalists for litter decomposition across different ecosystems. These results enhance our ability to predict changes in microbial decomposer communities and litter decomposition under future climate-change scenarios.

ecology↗

bioRxiv2022

Nitrate leaching and its implication for Fe and As mobility in a Southeast Asian aquifer

The drinking water quality of millions of people in South and Southeast Asia is at risk due to arsenic (As) contamination of groundwater and insufficient access to water treatment facilities. Intensive use of nitrogen (N) fertilizer increases the possibility of nitrate (NO3-) leaching into aquifers, yet very little is known about how the N cycle will interact with and affect the iron (Fe) and As mobility in aquifers. We hypothesized that input of NO3- into highly methanogenic aquifers can stimulate nitrate-dependent anaerobic methane oxidation (N-DAMO) and subsequently help to remove NO3- and decrease CH4 emission. We, therefore, investigated the effects of N input into aquifers and its effect on Fe and As mobility, by running a set of microcosm experiments using aquifer sediment from Van Phuc, Vietnam supplemented with 15NO3- and 13CH4. Additionally, we assessed the effect of N-DAMO by inoculating the sediment with two different N-DAMO enrichment cultures (N-DAMO(O) and N-DAMO(V)). We found that native microbial communities and both N-DAMO enrichments could efficiently consume nearly 5 mM NO3- in 5 days. In an uninoculated setup, NO3- was preferentially used over Fe(III) as electron acceptor and consequently inhibited Fe(III) reduction and As mobilization. The addition of N-DAMO(O) and N-DAMO(V) enrichment cultures led to substantial Fe(III) reduction followed by the release of Fe2+ (0.190{+/-}0.002 mM and 0.350{+/-}0.007 mM, respectively) and buildup of sedimentary Fe(II) (11.20{+/-}0.20 mM and 10.91{+/-}0.47 mM, respectively) at the end of the experiment (day 64). Only in the N-DAMO(O) inoculated setup, As was mobilized (27.1{+/-}10.8 g/L), while in the setup inoculated with N-DAMO(V) a significant amount of Mn (24.15{+/-}0.41 mg/L) was released to the water. Methane oxidation and 13CO2 formation were observed only in the inoculated setups, suggesting that the native microbial community did not have sufficient potential for N-DAMO. An increase of NH4+ implied that dissimilatory nitrate reduction to ammonium (DNRA) took place in both inoculated setups. The archaeal community in all treatments was dominated by Ca. Methanoperedens while the bacterial community consisted largely of various denitrifiers. Overall, our results suggest that input of N fertilizers to the aquifer decreases As mobility and that CH4 cannot serve as an electron donor for the native NO3- reducing community. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/511258v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1ac9adborg.highwire.dtl.DTLVardef@eaa3ccorg.highwire.dtl.DTLVardef@a7d1a1org.highwire.dtl.DTLVardef@1b3dee9_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

Carbon oxidation with sacrificial anodes to inhibit O2 evolution in membrane-less bioelectrochemical systems for microbial electrosynthesis

Microbial electrosynthesis is an emerging biosynthesis technology that produces value-added chemicals and fuels and, at the same time, reduces the environmental carbon footprint. However, constraints, such as low current densities and high inner resistance, disfavor this technology for industrial-scale purposes. The cathode performance has been strongly improved in recent years, while the anode performance has not been given enough attention despite its importance in closing the electric circuit. For traditional water electrolysis, O2 is produced at the anode, which is toxic to the anaerobic autotrophs that engage in microbial electrosynthesis. To overcome O2 toxicity in conventional microbial electrosynthesis, the anode and the cathode chamber have been separated by an ion-exchange membrane to avoid contact between the microbes and O2. However, ion-exchange membranes increase the maintenance costs and compromise the production efficiency by introducing an additional internal resistance. Furthermore, O2 is inevitably transferred to the catholyte due to diffusion and electro-osmotic fluxes that occur within the membrane. Here, we proved the concept of integrating carbon oxidation with sacrificial anodes and microbes to simultaneously inhibit the O2 evolution reaction (OER) and circumvent membrane application, which allows microbial electrosynthesis to proceed in a single chamber. The carbon-based anodes performed carbon oxidation as the alternative reaction to the OER. This enables microbial electrosynthesis to be performed with cell voltages as low as 1.8-2.1 V at 10 A{middle dot}m-2. We utilized Methanothermobacter thermautotrophicus {Delta}H in a single-chamber Bioelectrochemical system (BES) with the best performing carbon-based anode (i.e., activated-carbon anode with soluble iron) to achieve a maximum cathode-geometric CH4 production rate of 27.3 L{middle dot}m-2{middle dot}d-1, which is equal to a volumetric methane production rate of 0.11 L{middle dot}L-1{middle dot}d-1 in our BES, at a coulombic efficiency of 99.4%. In this study, Methanothermobacter thermautotrophicus {Delta}H was majorly limited by sulfur that inhibited electromethanogenesis. However, this proof-of-concept study allows microbial electrosynthesis to be performed more energy-efficiently and can be immediately utilized for research purposes in microbial electrosynthesis.

bioengineering↗

bioRxiv2022

Resolving the fate of trace metals during microbial remineralization of phytoplankton biomass in precursor banded iron formation sediments

Banded Iron Formations (BIFs) have long been considered a sedimentary record of seawater trace metal composition during the Precambrian. However, recent work has suggested that the trace metal composition of BIFs was derived from phytoplankton biomass, not seawater. In this model, phytoplankton biomass settles from the photic zone to the seafloor sediments, where it is then oxidized by heterotrophic microbes, such as dissimilatory Fe(III) reducing (DIR) bacteria, for energy generation. Remineralization of this biomass released the trace metals associated with organic molecules from phytoplankton (i.e., in metalloproteins), allowing these metals to be captured by Fe (oxyhydr)oxides and preserved in BIFs. While there is compelling evidence that the phytoplankton biomass served as a trace metal shuttle to precursor BIF sediments, it is unclear whether the degradation of biomass by DIR bacteria would liberate the biogenic trace metals as the model proposes. This work tests this hypothesis by using anoxic incubations of a model DIR bacterium (Shewanella oneidensis MR-1) with phytoplankton biomass as energy and carbon sources and ferrihydrite, a poorly crystalline Fe(III) oxyhydroxide (Fe(OH)3), as electron acceptor. Our results show that while S. oneidensis MR-1 can consume some of the carbon substrates found in phytoplankton biomass, there is no evidence that S. oneidensis MR-1 degraded metalloproteins which would have liberated trace metals. In the context of the Precambrian, these data imply that other heterotrophic bacteria, such as fermenters, may have had a larger role in the liberation of trace metals from dead biomass during early BIF development. HighlightsO_LIPhytoplankton are the proposed source of trace metals to banded iron formations C_LIO_LIIron reducers are hypothesized to release metals from phytoplankton biomass C_LIO_LIExperiments show that iron reducers do not liberate metals when degrading biomass C_LIO_LIOther microbial heterotrophs must have liberated the biogenic trace metals C_LI

microbiology↗

bioRxiv2019

Metagenomic- and cultivation-based exploration of anaerobic chloroform biotransformation in hypersaline sediments as natural source of chloromethanes

Chloroform (CF) is an environmental contaminant that can be naturally formed in various environments ranging from forest soils to salt lakes. Here we investigated CF removal potential in sediments obtained from hypersaline lakes in Western Australia. Reductive dechlorination of CF to dichloromethane (DCM) was observed in enrichment cultures derived from sediments of Lake Strawbridge, which has been reported as a natural source of CF. The lack of CF removal in the abiotic control cultures without artificial electron donors indicated that the observed CF removal is a biotic process. Metabolite analysis with 13C labelled CF in the sediment-free enrichment cultures (pH 8.5, salinity 5%) revealed that increasing the vitamin B12 concentration from 0.04 to 4 M enhanced CF removal, reduced DCM formation, and increased 13CO2 production, which is likely a product of CF oxidation. Known organohalide-respiring bacteria and reductive dehalogenase genes were neither detected by quantitative PCR nor metagenomic analysis. Rather, members of the order Clostridiales, known to co-metabolically transform CF to DCM and CO2, were detected in the enrichment cultures. Genome-resolved metagenome analysis indicated that their genomes encode enzymatic repertoires for the Wood-Ljungdahl pathway and cobalamin biosynthesis that are known to be involved in co-metabolic CF transformation. ImportanceMore than 90% of the global CF emission to the atmosphere originates from natural sources, including saline environments such as salt lake sediments. However, knowledge about the microbial metabolism of CF in such extreme environments is lacking. Here we showed CF transformation potential in a hypersaline lake that was reported as a natural source of CF production. Application of interdisciplinary approaches of microbial cultivation, stable isotope labelling, and metagenomics aided in defining potential chloroform transformation pathways. This study indicates that microbiota may act as a filter to reduce CF emission from hypersaline lakes to the atmosphere, and expands our knowledge of halogen cycling in extreme hypersaline environments.

microbiology↗

bioRxiv2018

Pyrite formation from FeS and H2S is mediated by a novel type of microbial energy metabolism

The exergonic reaction of FeS with H2S to form FeS2 (pyrite) and H2 was postulated to have operated as an early form of energy metabolism on primordial Earth. Since the Archean, sedimentary pyrite formation played a major role in the global iron and sulfur cycles, with direct impact on the redox chemistry of the atmosphere. To date, pyrite formation was considered a purely geochemical reaction. Here, we present microbial enrichment cultures, which grew with FeS, H2S, and CO2 as their sole substrates to produce FeS2 and CH4. Cultures grew over periods of three to eight months to cell densities of up to 2-9x106 cells mL-1. Transformation of FeS with H2S to FeS2 was followed by 57Fe Mossbauer spectroscopy and showed a clear biological temperature profile with maximum activity at 28{degrees}C and decreasing activities towards 4{degrees}C and 60{degrees}C. CH4 was formed concomitantly with FeS2 and exhibited the same temperature dependence. Addition of either penicillin or 2-bromoethanesulfonate inhibited both FeS2 and CH4 production, indicating a syntrophic coupling of pyrite formation to methanogenesis. This hypothesis was supported by a 16S rRNA gene-based phylogenetic analysis, which identified at least one archaeal and five bacterial species. The archaeon was closely related to the hydrogenotrophic methanogen Methanospirillum stamsii while the bacteria were most closely related to sulfate-reducing Deltaproteobacteria, as well as uncultured Firmicutes and Actinobacteria. We identified a novel type of microbial metabolism able to conserve energy from FeS transformation to FeS2, which may serve as a model for a postulated primordial iron-sulfur world.\n\nSignificance statementPyrite is the most abundant iron-sulfur mineral in sediments. Over geological times, its burial controlled oxygen levels in the atmosphere and sulfate concentrations in seawater. Its formation in sediments is so far considered a purely geochemical process that is at most indirectly supported by microbial activity. We show that lithotrophic microorganisms can directly transform FeS and H2S to FeS2 and use this exergonic reaction as a novel form of energy metabolism that is syntrophically coupled to methanogenesis. Our results provide insights into a syntrophic relationship that could sustain part of the deep biosphere and lend support to the iron-sulfur-world theory that postulated FeS transformation to FeS2 as a key energy-delivering reaction for life to emerge.

microbiology↗