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The biological route of nitrate reduction has important implications for the bioavailability of nitrogen within ecosystems. Nitrate reduction via nitrite, either to ammonium (ammonification) or to nitrous oxide or dinitrogen (denitrification), determines whether nitrogen is retained within the system or lost as a gas. The acidophilic sulfate-reducing bacterium (aSRB) Acididesulfobacillus acetoxydans can perform dissimilatory nitrate reduction to ammonium (DNRA). While encoding a Nar-type nitrate reductase, A. acetoxydans lacks recognized nitrite reductase genes. In this study, A. acetoxydans was cultivated under conditions conducive to DNRA. During cultivations, we monitored the production of potential nitrogen intermediates (nitrate, nitrite, nitric oxide, hydroxylamine, and ammonium). Resting cell experiments were performed with nitrate, nitrite, and hydroxylamine to confirm their reduction to ammonium, and formed intermediates were tracked. To identify the enzymes involved in DNRA, comparative transcriptomics and proteomics were performed with A. acetoxydans growing under nitrate- and sulfate-reducing conditions. Nitrite is likely reduced to ammonia by the previously undescribed nitrite reductase activity of the NADH-linked sulfite reductase AsrABC, or by a putatively ferredoxin-dependent homolog of the nitrite reductase NirA (DEACI_1836), or both. We identified enzymes and intermediates not previously associated with DNRA and nitrosative stress in aSRB. This increases our knowledge about the metabolism of this type of bacteria and helps the interpretation of (meta)genome data from various ecosystems on their DNRA potential and the nitrogen cycle.

The aim of this study is to describe the Dissimilatory Nitrate Reduction to Ammonium (DNRA) pathway of an acidophilic sulfate reducing bacterium, Acididesulfobacillus acetoxydans. While encoding a Nar-type nitrate reductase, A. acetoxydans does not encode any of the known nitrite reductases. To identify the enzymes involved in DNRA we performed comparative transcriptomics and proteomics. This was followed by cultivation of A. acetoxydans performing DNRA during which we measured all potential nitrogen intermediates. Several intermediates not previously associated with DNRA were identified. For each identified intermediate, resting cell experiments were performed to investigate the biological transformation of nitrogenous compounds by A. acetoxydans. In summary, we demonstrate that the DNRA pathway of A. acetoxydans proceeds via intermediates not previously associated to DNRA and provide data-driven hypotheses which enzymes might be involved in this DNRA pathway., The aim of this study is to describe the Dissimilatory Nitrate Reduction to Ammonium (DNRA) pathway of an acidophilic sulfate reducing bacterium, Acididesulfobacillus acetoxydans. While encoding a Nar-type nitrate reductase, A. acetoxydans does not encode any of the known nitrite reductases. To identify the enzymes involved in DNRA we performed comparative transcriptomics and proteomics. This was followed by cultivation of A. acetoxydans performing DNRA during which we measured all potential nitrogen intermediates. Several intermediates not previously associated with DNRA were identified. For each identified intermediate, resting cell experiments were performed to investigate the biological transformation of nitrogenous compounds by A. acetoxydans. In summary, we demonstrate that the DNRA pathway of A. acetoxydans proceeds via intermediates not previously associated to DNRA and provide data-driven hypotheses which enzymes might be involved in this DNRA pathway.

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Radboud University, 26 mei 2023, Promotores : Lamers, L.P.M., Welte, C.U. Co-promotor : Veraart, A.J., Contains fulltext : 292806.pdf (Publisher’s version ) (Open Access), Methane is the second most important greenhouse gas and is responsible for around 20 percent of global warming. Unlike carbon dioxide (CO2), most methane comes from natural systems, and more specifically from shallow lakes. Yet as a society we have a huge impact on this, because nutrients from agriculture production and increases in temperature that are caused by climate change increase methane emissions. However, why this is so, and whether this process can be reversed, is not yet clear. This PhD thesis therefore focused on the methane cycle in lakes, and the way in which this is influenced by warming, nutrients and carbon. Evidence showed that warming causes a different type of methane-consuming bacteria in lake beds, which resulted in less methane being consumed. Extra nutrients increased methane consumption, but only at low concentrations. Methane production is therefore likely to increase at high concentrations, which would cause a greater emission of methane. Extra carbon increased methane production but did not affect methane consumption. It was ultimately found that methane emissions from shallow lakes can be cut down by control measures that reduce nutrients in shallow lakes. Although global warming is a universal problem, increases in nutrients and carbon are mostly caused by local factors. As a result, it is vital that their availability in shallow lakes is locally reduced in order to cut methane emissions and combat climate change.

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14 juni 2023, Item does not contain fulltext

Radboud University, 10 november 2023, Promotores : Welte, C.U., Jetten, M.S.M., Contains fulltext : 297620.pdf (Publisher’s version ) (Closed access)

Item does not contain fulltext, Supporting information for article https://doi.org/10.1002/anie.202311981, 11 oktober 2023

Contains fulltext : 299121.pdf (Publisher’s version ) (Closed access), Humans are highly skilled at manipulating natural landscapes to their own ends. Examples include deforestation to create more agricultural land, building dykes against flooding rivers, and the construction of cities. Changes to the landscape mean that the landscape often emits more greenhouse gases and therefore contributes more to climate change. In this PhD thesis, we focused on the last example, the city, and specifically on methane emissions from canals. Methane, also known as swamp gas, is the result of microbial decomposition of organic waste and a stronger greenhouse gas than carbon dioxide. We mapped the methane cycle in six Dutch cities. In Amsterdam, we found a biofilm on the quay wall containing methane-eating bacteria. The same bacteria were also present in four other cities, indicating a biological methane filter. In Amsterdam's canal bed, we also discovered another way to filter methane, which occurs in the absence of oxygen and alongside the microbes that emit methane. This second methane filter is special because it appears to rely on the same organic material that methane bacteria use to make methane. This PhD thesis contributes to the knowledge of methane and provides new insights for the use of microbes as methane filters., Radboud University, 13 december 2023, Promotores : Welte, C.U., Jetten, M.S.M., xi, 138 p.

Item does not contain fulltext, The data set includes the results of biogeochemical and sedimentary analyses on 4 sediment cores (69.5 cm - 113 cm) from two thermokarst lakes in Far East Siberia near the town of Chokurdakh. The analysis include lake depth measurements, linescan imaging, XRF scans, grainsize distribution, loss-on-ignition, porewater content, magnetic susceptibility, dissolved organic carbon (DOC) concentration, sediment density, stable carbon isotope measurements of DOC and soil organic carbon and radiocarbon ages., 11 oktober 2023

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Radboud University, 14 september 2022, Promotores : Welte, C.U., Jetten, M.S.M., Contains fulltext : 252648.pdf (Publisher’s version ) (Open Access)

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29 maart 2021, Contains fulltext : 240227.pdf (Publisher’s version ) (Open Access)

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Radboud University, 09 december 2020, Promotor : Jetten, M.S.M. Co-promotor : Welte, C.U., Contains fulltext : 226903.pdf (publisher's version ) (Open Access), Summary We live in a microbial world. Microorganisms were the first life forms on our planet, shaping the Earth as we know it today. During Earth's history, a set of metabolic processes evolved exclusively in microorganisms that thrived in the absence of oxygen. One of these processes is the last step in the anaerobic degradation of organic matter: methanogenesis. This process is performed by methanogenic archaea belonging to the phylum Euryarchaeota. Although several studies indicated the potential for methanogenesis outside of this phylum, so far, no experimental evidence exists. The methane (CH4), which is the terminal product of the methanogenic pathway, contains a lot of energy and is therefore an ideal substrate for a wide range of methanotrophic organisms which constitute the biological CH4 sink. Methanotrophs occur in both the archaeal and bacterial domain, and several terminal electron acceptors can be used in the process. Anaerobic methanotrophic archaea (or ANME archaea) use the reverse methanogenesis pathway for CH4 activation and subsequent oxidation to carbon dioxide (CO2). Aerobic methanotrophic bacteria including the intra-aerobic “Candidatus Methylomirabilis sp.” species use oxygen and methane monooxygenases (MMOs) to activate CH4. The aim of this thesis was to investigate the interplay between CH4 producing and consuming organisms of the microbial CH4 cycle in a warming world. It is important to investigate climate impacts, since the balance between methanogens and methanotrophs determines the CH4 fluxes into the atmosphere. In turn, this largely determines the greenhouse gas (GHG) potential of an ecosystem, mainly due to the significantly higher climate impact of CH4, which has a 34-fold higher warming potential than CO2. To assess environmental impacts such as warming and increased nutrient availability, their effects on the microbial CH4 cycle, their interactions, and net GHG fluxes within a variety of manmade and natural methanogenic ecosystems

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Contains fulltext : 205818.pdf (publisher's version ) (Open Access), The anaerobic oxidation of methane (AOM) is a microbial process present in marine and freshwater environments. AOM is important for reducing the emission of the second most important greenhouse gas methane. In marine environments anaerobic methanotrophic archaea (ANME) are involved in sulfate-reducing AOM. In contrast, Ca. Methanoperedens of the ANME-2d cluster carries out nitrate AOM in freshwater ecosystems. Despite the importance of those organisms for AOM in non-marine environments little is known about their lipid composition or carbon sources. To close this gap, we analysed the lipid composition of ANME-2d archaea and found that they mainly synthesise archaeol and hydroxyarchaeol as well as different (hydroxy-) glycerol dialkyl glycerol tetraethers, albeit in much lower amounts. Abundant lipid headgroups were dihexose, monomethyl-phosphatidyl ethanolamine and phosphatidyl hexose. Moreover, a monopentose was detected as a lipid headgroup that is rare among microorganisms. Batch incubations with 13C labelled bicarbonate and methane showed that methane is the main carbon source of ANME-2d archaea varying from ANME-1 archaea that primarily assimilate dissolved inorganic carbon (DIC). ANME-2d archaea also assimilate DIC, but to a lower extent than methane. The lipid characterisation and analysis of the carbon source of Ca. Methanoperedens facilitates distinction between ANME-2d and other ANMEs.

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Radboud University, 27 november 2019, Promotor : Jetten, M.S.M. Co-promotores : Welte, C.U., Lücker, S., Contains fulltext : 214400.pdf (publisher's version ) (Open Access)

16 augustus 2019, Contains fulltext : 207232.pdf (Publisher’s version ) (Open Access)

Radboud University, 11 december 2019, Promotor : Jetten, M.S.M. Co-promotor : Welte, C.U., Contains fulltext : 213681.pdf (publisher's version ) (Open Access)

Contains fulltext : 205822.pdf (Publisher’s version ) (Closed access), Methanomassiliicoccus luminyensis was originally isolated from human feces and belongs to the seventh order of methanogens, the Methanomassiliicoccales, which are only distantly related to other methanogenic archaea. The organism forms methane from the reduction of methylamines or methanol using molecular hydrogen as reductant. The energy-conserving system in M. luminyensis is unique and the enzymes involved in this process are not found in this combination in members of the other methanogenic orders. In this context our central question was how the organism is able to generate ATP. Energy transduction was dependent on a membrane-bound ferredoxin: heterodisulfide oxidoreductase composed of reduced ferredoxin as an electron donor, at least one protein in the membrane fraction and the heterodisulfide reductase HdrD, which reduced the electron acceptor CoM-S-S-CoB. Electron transfer of this respiratory chain proceeded with a rate of 145 nmol reduced heterodisulfide min(-1) .mg(-1) membrane protein. Methanomassiliicoccus luminyensis is the first example of a methanogenic archaeon that does not require Na(+) ions for energy conservation. Only protons were used as coupling ions for the generation of the electrochemical ion gradient. The membrane-bound F420 H2 :phenazine oxidoreductase complex (without the electron input module FpoF) probably catalyzed the oxidation of reduced ferredoxin and potentially acted as primary proton pump in this electron transport system. In summary, the energy-conserving system of M. luminyensis possesses features found in the pathways of hydrogenotrophic and methylotrophic/aceticlastic methanogenesis. Consequently, the composition of the enzymes involved in ion translocation across the cytoplasmic membrane is different from all other methanogenic archaea.

Contains fulltext : 176750.pdf (publisher's version ) (Open Access), Coal mining is responsible for 11% of total anthropogenic methane emission thereby contributing considerably to climate change. Attempts to harvest coalbed methane for energy production are challenged by relatively low methane concentrations. In this study, we investigated whether nutrient and acetate amendment of a non-producing sub-bituminous coal well could transform the system to a methane source. We tracked cell counts, methane production, acetate concentration and geochemical parameters for 25 months in one amended and one unamended coal well in Australia. Additionally, the microbial community was analysed with 16S rRNA gene amplicon sequencing at 17 and 25 months after amendment and complemented by metagenome sequencing at 25 months. We found that cell numbers increased rapidly from 3.0 x 104 cells ml-1 to 9.9 x 107 in the first 7 months after amendment. However, acetate depletion with concomitant methane production started only after 12-19 months. The microbial community was dominated by complex organic compound degraders (Anaerolineaceae, Rhodocyclaceae and Geobacter spp.), acetoclastic methanogens (Methanothrix spp.) and fungi (Agaricomycetes). Even though the microbial community had the functional potential to convert coal to methane, we observed no indication that coal was actually converted within the time frame of the study. Our results suggest that even though nutrient and acetate amendment stimulated relevant microbial species, it is not a sustainable way to transform non-producing coal wells into bioenergy factories.

25 april 2018, Promotores : Jetten, M.S.M., Camp, H.J.M. op den Co-promotor : Welte, C.U., Contains fulltext : 190339.pdf (publisher's version ) (Open Access)

01 december 2018, Contains fulltext : 198842.pdf (publisher's version ) (Open Access), Arctic permafrost soils store large amounts of organic matter that is sensitive to temperature increases and subsequent microbial degradation to methane (CH 4 ) and carbon dioxide (CO 2 ). Here, we studied methanogenic and methanotrophic activity and community composition in thermokarst lake sediments from Utqiag vik (formerly Barrow), Alaska. This experiment was carried out under in situ temperature conditions (4 degrees C) and the IPCC 2013 Arctic climate change scenario (10 degrees C) after addition of methanogenic and methanotrophic substrates for nearly a year. Trimethylamine (TMA) amendment with warming showed highest maximum CH 4 production rates, being 30% higher at 10 degrees C than at 4 degrees C. Maximum methanotrophic rates increased by up to 57% at 10 degrees C compared to 4 degrees C. 16S rRNA gene sequencing indicated high relative abundance of Methanosarcinaceae in TMA amended incubations, and for methanotrophic incubations Methylococcaeae were highly enriched. Anaerobic methanotrophic activity with nitrite or nitrate as electron acceptor was not detected. This study indicates that the methane cycling microbial community can adapt to temperature increases and that their activity is highly dependent on substrate availability.

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