Biology subjects

Nielsen, J. L.

Publications and source records attributed to Nielsen, J. L..

6 recordsLinked to original sources

bioRxiv2026

Elucidating redox-driven inhibition of methanogenesis by an artificial quinone in Methanosarcina barkeri: Integrated proteomic and physiological evidence

Methanogenesis is a crucial component of Earths carbon cycle and a source of methane for biofuel production. The presence of higher energy electron acceptors, such as iron(III) oxides and quinones, is believed to significantly impact methanogenesis. This study investigated the physiological and proteomic responses of the type I Methanosarcina, M. barkeri, to the artificial quinone 9,10-anthraquinone-2,7-disulfonate disodium (2,7-AQDS), using H2/CO2 as substrates. Our findings revealed that during 2,7-AQDS reduction, cellular growth ceased. The lack of energy conservation was associated with direct inhibition of both methanogenesis and CO2 utilization, corroborated by a significant downregulation of the enzymes involved in this metabolic pathway. Furthermore, the significant upregulation of specific subunits of the reversible Ech hydrogenase suggests that this enzyme redirects electrons from H2 towards the most energetically favorable reaction (2,7-AQDS reduction), rather than the reduction of ferredoxin, which is a highly energy-demanding process, essential for initiating the CO2 reduction pathway. Additionally, it is conceivable that Ech homologues in other hydrogenotrophic methanogens also participate in the reduction of higher energy-yielding electron acceptors. These findings provide novel insights into how quinones, particularly in their oxidized state, directly impact methanogenesis, thereby influencing both artificial and natural methanogenic environments.

microbiology↗

bioRxiv2025

Host genetics and diet jointly shape the microbiome of Drosophila melanogaster but do not predict lifespan or age-related traits

The microbiome is a key determinant of organismal health, yet inter-individual variability and heterogeneous responses to environmental conditions complicates the understanding of its effects on hosts. Here, we present a comprehensive analysis using the Drosophila Genetic Reference Panel (DGRP) to investigate how the interplay between host genetic variation and diet influences microbiome composition, and to assess whether microbiome features in young flies can be used to predict lifespan and age-related traits. Our findings show that adult flies reared on a nutritionally rich control diet exhibited higher microbial richness but lower evenness compared to those on a nutritionally poor restricted diet. Principal component analysis (PCA) highlighted substantial diversity among lines reared on the same diet, and this variation was heritable supported by high heritability estimates for all measured -diversity metrics, including Unique OTU counts, Shannon and Simpson indices, as well as the relative abundances of genera and species with relative abundances exceeding 1%. These results underscore the critical roles of both environmental factors and genetic variation in shaping microbiome composition under different dietary conditions. Moreover, we identified widespread genotype-by-diet interactions, suggesting that the genetic regulation of the microbiome is highly complex. Finally, we found that the microbiome features of young flies including diversity indices, taxonomic abundances, or ordination scores cannot predict age-associated phenotypes (lifespan, locomotor activity, dry weight, and heat knockdown time). Our findings offer valuable insights into the genetic architecture that governs microbiome composition, dietary responses, and aging in Drosophila melanogaster. Author SummaryThe community of microbes living on or inside animals - the microbiome - plays an important role in health and aging, but its composition varies greatly between individuals and across environments, making it challenging to fully understand its importance. In this study, we examined how host genetics and diet shape the microbiome of the fruit fly, Drosophila melanogaster, using a large panel of genetically diverse lines. We found that the microbiome of flies on a restricted nutritionally poor diet were relatively evenly distributed, while the microbiome of flies on a nutritionally rich diet had a higher species diversity. Many features of the microbiome were strongly influenced by the flies genes, and these genetic effects often depended on diet. Finally, we tested whether microbiome features obtained from young flies could predict age-related traits such as lifespan and activity at similar aged flies or later in life, but found no evidence for such links. These results highlight how genetic variation and diet interact to shape the microbiome and its role in aging.

genetics↗

bioRxiv2025

The Role of Genetic Variation in Shaping Phenotypic Responses to Diet in Aging Drosophila melanogaster

Nutrition plays a central role in healthy living, however, extensive variability in individual responses to dietary interventions complicates our understanding of its effects. Here we present a comprehensive study utilizing the Drosophila Genetic Reference Panel (DGRP), investigating how genetic variation influences responses to diet and aging. Quantitative genetic analyses of the impact of dietary restriction on lifespan, locomotor activity, dry weight, and heat knockdown time were performed. Locomotor activity, dry weight and heat knockdown time were measured on the same individual flies. We found significant genotype-by-diet interaction (GDI) and genotype-by-age interaction (GAI) for all traits. Therefore, environmental factors play a crucial role in shaping trait variation at different ages and diets, and/or distinct genetic variation influences these traits at different ages and diets. Our genome wide association study also identified a quantitative trait locus for age-dependent dietary response. The observed GDI and GAI indicates that susceptibility to environmental influences changes as organisms age, which could have significant implications for dietary recommendations and interventions aimed at promoting healthy aging in humans. The identification of associations between DNA sequence variation and age-dependent dietary responses opens new avenues for research into the genetic mechanisms underlying these interactions.

genetics↗

bioRxiv2023

The Selenoproteome as a dynamic response mechanism to oxidative stress in methanogenic communities

Methanogenesis is a critical process in the carbon cycle that is applied industrially in anaerobic digestion and biogas production. While naturally occurring in diverse environments, methanogenesis requires anaerobic and reduced conditions though varying degrees of oxygen tolerance have been described. Micro-aeration is touted as the next step to increase methane production and improve hydrolysis in digestion processes; therefore, a deeper understanding of the methanogenic response to oxygen stress is needed. In order to explore the drivers of oxygen tolerance in methanogenesis, two parallel enrichments were performed in an environment without reducing agents and in a redox-controlled environment by adding redox mediator AQDS. The cellular response to oxidative conditions is mapped using proteomic analysis. The resulting community showed remarkable tolerance to high-redox environments and was unperturbed in its methane production. Next to expressing pathways to mitigate reactive oxygen species, the higher redox potential environment showed an increased presence of selenocysteine and selenium-associated pathways. By including sulfur-to-selenium mass shifts in a proteomic database search, we provide the first evidence of dynamic and large-scale incorporation of selenocysteine as a response to oxidative stress by methanogenic organisms and the presence of a dynamic selenoproteome.

microbiology↗

bioRxiv2018

Biomass segregation between biofilm and flocs improves the control of nitrite-oxidizing bacteria in mainstream partial nitritation and anammox processes

The control of nitrite-oxidizing bacteria (NOB) challenges the implementation of partial nitritation and anammox (PN/A) processes under mainstream conditions. The aim of the present study was to understand how operating conditions impact microbial competition and the control of NOB in hybrid PN/A systems, where biofilm and flocs coexist. A hybrid PN/A moving-bed biofilm reactor (MBBR; also referred to as integrated fixed film activated sludge or IFAS) was operated at 15 {degrees}C on aerobically pre-treated municipal wastewater (23 mgNH4-N{middle dot}L-1). Ammonium-oxidizing bacteria (AOB) and NOB were enriched primarily in the flocs, and anammox bacteria (AMX) in the biofilm. After decreasing the dissolved oxygen concentration (DO) from 1.2 to 0.17 mgO2{middle dot}L-1 - with all other operating conditions unchanged - washout of NOB from the flocs was observed. The activity of the minor NOB fraction remaining in the biofilm was suppressed at low DO. As a result, low effluent NO3- concentrations (0.5 mgN{middle dot}L-1) were consistently achieved at aerobic nitrogen removal rates (80 mgN{middle dot}L-1{middle dot}d-1) comparable to those of conventional treatment plants. A simple dynamic mathematical model, assuming perfect biomass segregation with AOB and NOB in the flocs and AMX in the biofilm, was able to qualitatively reproduce the selective washout of NOB from the flocs in response to the decrease in DO-setpoint. Similarly, numerical simulations indicated that flocs removal is an effective operational strategy to achieve the selective washout of NOB. The direct competition for NO2- between NOB and AMX - the latter retained in the biofilm and acting as a \"NO2-sink\" - was identified by the model as key mechanism leading to a difference in the actual growth rates of AOB and NOB (i.e., NOB < AOB in flocs) and allowing for the selective NOB washout. Experimental results and model predictions demonstrate the increased operational flexibility, in terms of variables that can be easily controlled by operators, offered by hybrid systems as compared to solely biofilm systems for the control of NOB in mainstream PN/A applications.\n\nHighlightsO_LIHybrid PN/A systems provide increased operational flexibility for NOB control\nC_LIO_LIAOB and NOB enrich primarily in the flocs, and AMX in the biofilm (\"NO2-sink\")\nC_LIO_LIAMX use NO2- allowing to differentiate AOB and NOB growth rates\nC_LIO_LIA decrease in DO or an increase in floc removal leads to selective NOB washout from flocs\nC_LIO_LIThe activity of the minor NOB fraction in the biofilm is suppressed at limiting DO\nC_LI\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=63 SRC=\"FIGDIR/small/480780v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (21K):\norg.highwire.dtl.DTLVardef@cad5deorg.highwire.dtl.DTLVardef@9efef3org.highwire.dtl.DTLVardef@7409feorg.highwire.dtl.DTLVardef@3c1043_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2018

Resolving the individual contribution of key microbial populations to enhanced biological phosphorus removal with Raman-FISH

Enhanced biological phosphorus removal (EBPR) is a globally important biotechnological process and relies on the massive accumulation of phosphate within special microorganisms. Candidatus Accumulibacter conform to classical physiology model for polyphosphate accumulating organisms and are widely believed to be the most important player for the process in full-scale EBPR systems. However, it was impossible till now to quantify the contribution of specific microbial clades to EBPR. In this study, we have developed a new tool to directly link the identity of microbial cells to the absolute quantification of intracellular poly-P and other polymers under in situ conditions, and applied it to eight full-scale EBPR plants. Besides Ca. Accumulibacter, members of the genus Tetrasphaera were found to be important microbes for P accumulation, and in six plants they were the most important. As these Tetrasphaera cells did not exhibit the classical phenotype of poly-P accumulating microbes, our entire understanding of the microbiology of the EBPR process has to be revised. Furthermore, our new single-cell approach can now also be applied to quantify storage polymer dynamics in individual populations in situ in other ecosystems and might become a valuable tool for many environmental microbiologists.

ecology↗