Biology subjects

Dijkstra, P.

Publications and source records attributed to Dijkstra, P..

12 recordsLinked to original sources

bioRxiv2026

Quantitative stable isotope probing to measure in situ growth of protist populations

Soil protists shape microbial food webs and nutrient cycling, yet methods for measuring their population growth in soil have lagged behind the taxonomic resolution available from 18S rRNA gene sequencing. Microscopy-based approaches can estimate abundance and growth, but with limited taxonomic resolution. Here, we tested whether quantitative stable isotope probing (qSIP) can provide reproducible, sequencing-resolved growth measurements for soil protists. We incubated soil with natural-abundance or {superscript 1} O-labeled water and measured taxon-specific 18O enrichment in DNA using three common 18S rRNA gene primer sets. 18O enrichment values were positively correlated across datasets, with relationships closest to 1:1 after poorly resolved taxonomic assignments were excluded, indicating that qSIP provides reproducible population-level growth signals across marker choices. We then compared 18S amplicon profiles from unfractionated DNA with qSIP-derived growth measurements across a soil moisture gradient. Amplicon profiles showed small shifts in relative abundances of major protist groups, whereas qSIP revealed a large moisture response in the growing community: 7 ASVs were growing at 20% field capacity compared with 143 at 80% field capacity, representing 1.6% and 63.3% of total protist relative abundance, respectively. Average growth was <1% day{square}1 in the two driest treatments, increasing to 2.1% day{square}1 at 60% and 5.6% day{square}1 at 80% field capacity; among growing taxa, rates averaged 8.7% and 8.3% day{square}1 in the two wetter treatments. By pairing taxonomic resolution with isotope-based growth estimates, qSIP with 18O-H2O moves soil protist ecology toward quantitative population dynamics: identifying which taxa grow, how fast, and how growth responds to the environment.

microbiology↗

bioRxiv2026

Rapid Changes in Transcription During a Feast-Famine Event

AbstractSoil microbes have sophisticated mechanisms to detect and respond to short pulses of C inputs, often involving changes in gene-expression. We studied gene transcription in a soil microbial community before, and 8, 24, and 48h after glucose addition (0.7 mg C g-1 dry soil) to understand how microbes react to periods of substrate excess and subsequent starvation. The relative transcript abundance of genes associated with energy metabolism and biosynthesis of amino acids, lipids, nucleotides, and cell wall components increased 8h after glucose addition. By 24 and 48h, the abundances of these transcripts reversed. Transcript abundance for genes associated with degradation of lipids, nucleotides, and (hetero)cyclic hydrocarbons decreased at 8h, but increased 24 and 48h after glucose addition. Simultaneously with a rise in transcripts for energy production and biosynthesis at 8h, transcription of regulatory genes for the exponential growth phase and ribosome assembly and maturation increased. In contrast, at 24 and 48h, transcript abundance for genes associated with ribosomal hibernation, sporulation, and regulation of the stationary phase increased, while transcripts for regulators for the exponential phase, and ribosome activation decreased. Based on changes in transcript abundance of phosphoenolpyruvate carboxylase and pyruvate carboxylase, it appeared that 8h after glucose addition glycolytic activity was high, however, gluconeogenesis returned at 24 and 48h. High levels of transcripts for nrtC-ntrB indicated N limitation 8 and 24h after glucose addition. Transcripts associated with Type VI Secretion Systems increased 24 and 48h after start of the experiment, suggesting a short lag between primary consumers and predatory bacteria. These results illustrate how metatranscriptome analysis can be used to study the ecophysiology of soil microbes providing details on the timing of exponential and stationary phase processes, coordination between anabolism and catabolism, and emerging nutrient limitations in natural soil communities. Research HighlightsO_LIWe studied gene transcription of a soil microbial community after glucose addition C_LIO_LITranscript abundances for biosynthesis and energy production initially increased, while those for degradation decreased C_LIO_LITranscripts of regulators and sporulation genes indicated start of stationary phase at 24h C_LIO_LINitrogen limitation induced transcription of nitrogen stress genes C_LI

ecology↗

bioRxiv2026

Neuroendocrine Stress Induces Differential Oxidative Stress and Antioxidant Profiles between Proactive and Reactive Stress Coping Styles

Neuroendocrine stressors can disrupt the brains redox equilibrium by generating high levels of reactive oxygen species (ROS) that lead to oxidative stress. The magnitude of the effect of neuroendocrine stressors on brain redox equilibrium can be influenced by many internal and external factors. To what extent the relationship between neuroendocrine and oxidative stress is modulated by an individuals stress coping style is only beginning to be understood. To explore this, we subjected proactive and reactive zebrafish to an acute novelty stressor and subsequently quantified changes in behavior and whole brain biomarkers of oxidative stress and antioxidants (DNA damage, total glutathione (GSH), glutathione ratio, oxygen radical absorbance capacity (ORAC), and superoxide dismutase (SOD). Stressed fish had significantly higher total glutathione, trends higher ORAC, DNA damage, and glutathione ratio, and trend for lower SOD levels compared to controls. In addition, individuals with a reactive stress coping style exhibited significantly higher levels of SOD and glutathione ratio, and a trend for ORAC compared to proactive individuals. From a principal component analysis, we also found that the reactive individuals had significantly higher PC1 scores (antioxidant axis) compared to the proactive, and a trend for stressed fish having higher PC1 scores than control. The oxidative stress axis (PC2) showed that the stressed fish had a significantly higher PC2 score relative to control fish. Our results show that neuroendocrine stress-induced disruption of redox equilibrium in the brain differs by stress coping style. Those with a reactive stress coping style have elevated antioxidant capabilities and capacities. Overall, our findings suggest that elevated reactivity to neuroendocrine stressors commonly seen in reactive stress coping styles may be mitigated through the glutathione buffering system and other antioxidants.

animal behavior and cognition↗

bioRxiv2025

Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland

Changes in global patterns can leave a lasting legacy in semi-arid grasslands by reshaping microbial growth dynamics and carbon cycling during the first wet-up in the autumn--a period known for intense microbial activity and significant carbon emissions. To study the lasting impacts of decreased winter rain, we implemented two precipitation regimes (100% vs. 50% mean annual precipitation) in California Mediterranean-climate grassland field plots. After the dry season, soils were rewetted in the laboratory with H218O, and sampled at 0 h, 3 h, 24 h, 48 h, 72 h, and 168 h post rewet. We quantified CO2 efflux; measured microbial growth and mortality via quantitative 18O stable isotope probing and 16S rRNA gene amplicon sequencing; and characterized the soil organic carbon chemical composition, metagenomes, and metatranscriptomes. We found that reduced winter precipitation imposed a strong legacy effect on microbial turnover; despite maintaining similar respiration rates, microbial growth declined by [~]1 order of magnitude, yielding decreased community growth efficiency (CGE = gross community growth/net respiration), and microbial mortality declined by [~]2 orders of magnitude. Soil organic carbon also shifted from lipid-like, amino-sugar-like, and protein-like compounds (indicative of microbial necromass) to more oxidized lignin-like and tannin-like compounds (indicative of decomposing plant-derived compounds). Meta-omics revealed distinct metabolic strategies linked to CGE. At high-CGE, microbes appeared to consume more energetically favorable N-rich necromass (released via high microbial turnover), this allowed for increased amino acids and peptidoglycan biosynthesis and greater aromatic compound degradation, fueling further energy production and growth efficiency. At low-CGE, communities had elevated carbohydrate metabolism and lipid turnover, consistent with increased investment in plant detritus degradation and membrane repair and maintenance rather than growth. Together, our findings demonstrate that reduced winter rainfall decreases microbial turnover following rewetting. Persistent decreases in CGE due to reduced winter rainfall result in consistent carbon loss as CO2, which, if sustained over multiple years, could ultimately lead to a net decline in total soil organic carbon.

microbiology↗

bioRxiv2025

Intersectional roles of trait covariation and phenotypic plasticity in the coloration and behavior of an African cichlid

An animals ability to adapt to a changing environment often requires the coordination of various traits. Across these traits, many covary with one another to generate a diversity of complex phenomes tuned to a given ecology. While many reports have documented trait covariation in populations, less is known about how plastic traits co-vary to facilitate adaptation in an individual. In African cichlids, morphology and behavior are two hallmarks driving the adaptive speciation of lineages within the East African Great Lakes. Here, we leverage social rank and body coloration as plastic model traits to understand the intersectional relationship shaping male competition in the African cichlid Astatotilapia burtoni. Addressing the need to disentangle the influence of environmental adaptation from social dynamics on color morphology, we conducted experiments rearing cichlids in visually distinct environments using blue and yellow gravel substrates to induce blue/yellow color morphs. Our results demonstrate that the visual environment significantly influences the emergence of male color morphs: yellow territorial males were more prevalent on brown gravel, whereas blue males predominantly appeared in blue backgrounds. Contrary to previous reports, we found that blue males consistently outcompete yellow males in direct contests. Furthermore, behavioral patterns changed over time, with blue males adjusting their aggression strategies based on their visual environment, while yellow males exhibited a higher propensity to flee. These findings indicate that animal coloration and behavior are intersectional plastic traits that interact to shape male competition and behavioral ecology. This study provides new insights into the dynamics of phenotypic plasticity, adaptive strategies in fluctuating environments, and trait covariation.

animal behavior and cognition↗

bioRxiv2024

Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil

In soils, the first rain after a prolonged dry period greatly impacts soil microbial community function, yet we lack a full understanding of the genomic traits associated with the microbial response to rewetting. Genomic traits such as codon usage bias and genome size have been linked to bacterial growth in soils--however this is often through measurements in culture. Here, we used metagenome-assembled genomes in combination with metatranscriptomics and 18O- water stable isotope probing to track genomic traits associated with transcriptional activity and growth of soil microorganisms over the course of one week following rewetting of a grassland soil. We found that the codon bias in ribosomal protein genes was the strongest predictor of growth rate. We also observed higher growth rates in bacteria with smaller genomes, demonstrating that reduced genome size contributes to bacterial growth responses to sudden changes in water or nutrient availability--potentially explaining why smaller genomes are more prevalent in arid and carbon poor systems. High levels of codon bias corresponded to faster transcriptional upregulation of ribosomal protein genes. In early transcribing taxa, nucleotides requiring less energy to produce were more common at synonymous substitution sites--where nucleotide substitutions did not change the encoded amino acid. We found several of these relationships also existed within a phylum, suggesting that association between genomic traits and activity could be a generalized characteristic of soil bacteria. These results provide in situ evidence that following rewetting, certain genomic characteristics affect soil microbial growth rate and transcription, and points towards the fitness advantages that these traits might pose for bacteria under changing conditions in soil.

microbiology↗

bioRxiv2021

Edaphic controls on genome size and GC content of bacteria in soil microbial communities

Bacteria in soil microbial communities are crucial to terrestrial ecosystem function, yet our understanding of the fundamental characteristics of their genomes, such as GC content and genome size, is not complete. Much of our understanding of the mechanisms which shape their genomic traits is derived from other systems or from isolated bacteria. Here we determined average genome size, GC content, codon usage, and amino acid content from 398 soil metagenomes across a broad geographic range and used machine-learning to determine which environmental parameters most strongly explain the distribution of these traits. We found that genomic trait averages were most related to pH, which we suggest is primarily due to the correlation of pH with several environmental parameters, especially soil carbon content. Low pH soils had higher carbon to nitrogen ratios (C:N) and tended to have communities with lower GC content and larger genomes, potentially a response to increased physiological stress and a requirement for metabolic diversity. Conversely, smaller genomes with high GC content were associated with high pH and low soil C:N, indicating potential resource driven selection against AT base pairs. As soil bacteria tend to be more carbon limited, smaller genomes with higher GC content may reduce the cost of reproduction in carbon-limited soils. Similarly, we found that nutrient conservation also applied to amino acid stoichiometry, where bacteria in soils with low C:N ratios tended to code for amino acids with lower C:N. Together, these relationships point towards fundamental mechanisms that underpin nucleotide and amino acid selection in soil bacterial communities.

ecology↗

bioRxiv2021

Soil, ocean, hot spring, and host-associated environments reveal unique selection pressures on genomic features of bacteria in microbial communities

Free-living bacteria in nutrient limited environments often exhibit small genomes which curb the cost of reproduction - a phenomenon known as genomic streamlining. Streamlining has been associated with a suite of traits such as reduced GC content, fewer 16S rRNA copies, and a lower abundance of regulatory genes, such as sigma ({sigma}) factors. Here, we analyzed these traits from 116 publicly available metagenomes derived from marine, soil, host associated, and thermophilic communities. In marine and thermophilic communities, genome size and GC content declined in parallel, but GC content was higher in thermophilic communities. In soils, the relationship between genome size and GC content was negative, suggesting a different selection pressure on genome size and GC content in soil bacteria. The abundance of {sigma}-factors varied with average genome size, ecosystem type, and the specific functions regulated by the sigma factor. In marine environments, housekeeping and heat-shock {sigma}-factor genes (rpoD and rpoH respectively) increased as genome size declined, and {sigma}-factor responsible for flagella biosynthesis (fliA) decreased, suggesting a trade-off between nutrient conservation and chemotaxis. In soils, a high abundance of fliA and the stress response {sigma}-factor gene (rpoS) was associated with smaller average genome size and often located in harsh and/or carbon-limited environments such as deserts or agricultural fields - suggesting an increased capacity for stress response and mobility in nutrient-poor soils. This work showcases how ecosystem-specific environmental constraints force trade-offs which are then embedded in the genomic features of bacteria in microbial communities, specifically genome size, GC content, and regulatory genes, and further highlights the importance of considering these features in microbial community analysis.

microbiology↗

bioRxiv2021

Rapid response of nitrogen cycling gene transcription to labile carbon amendments in a soil microbial community

Episodic inputs of labile carbon (C) to soil can rapidly stimulate nitrogen (N) immobilization by soil microorganisms. However, the transcriptional patterns that underlie this process remain unclear. In order to better understand the regulation of N cycling in soil microbial communities, we conducted a 48 h laboratory incubation with an agricultural soil where we stimulated the uptake of inorganic N by amending the soil with glucose. We analyzed the metagenome and metatranscriptome of the microbial communities at four timepoints that corresponded with changes in N availability. The relative abundances of genes remained largely unchanged throughout the incubation. In contrast, glucose addition rapidly increased transcription of genes encoding for ammonium and nitrate transporters, enzymes responsible for N assimilation into biomass, and genes associated with the N regulatory network. This upregulation coincided with an increase in transcripts associated with glucose breakdown and oxoglutarate production, demonstrating a connection between C and N metabolism. When concentrations of ammonium were low, we observed a transient upregulation of genes associated with the nitrogen fixing enzyme nitrogenase. Transcripts for nitrification and denitrification were downregulated throughout the incubation, suggesting that dissimilatory transformations of N may be suppressed in response to labile C inputs in these soils. These results demonstrate that soil microbial communities can respond rapidly to changes in C availability by drastically altering the transcription of N cycling genes. IMPORTANCEA large portion of activity in soil microbial communities occurs in short time frames in response to an increase in C availability, affecting the biogeochemical cycling of nitrogen. These changes are of particular importance as nitrogen represents both a limiting nutrient for terrestrial plants as well as a potential pollutant. However, we lack a full understanding of the short-term effects of labile carbon inputs on the metabolism of microbes living in soil. Here, we found that soil microbial communities responded to labile carbon addition by rapidly transcribing genes encoding proteins and enzymes responsible for inorganic nitrogen acquisition, including nitrogen fixation. This work demonstrates that soil microbial communities respond within hours to carbon inputs through altered gene expression. These insights are essential for improved understanding of the microbial processes governing soil organic matter production, decomposition, and nutrient cycling in natural and agricultural ecosystems.

microbiology↗

bioRxiv2021

Genomics-informed insights into microbial degradation of N,N-dimethylformamide

Effective degradation of N,N-Dimethylformamide (DMF), an important industrial waste product, is challenging as only few bacterial isolates are known to be capable of degrading DMF. Aerobic remediation of DMF has typically been used, whereas anoxic remediation attempts are recently made, using nitrate as one electron acceptor, and ideally include methane as a byproduct. Here, we analyzed 20,762 complete genomes and 28 constructed draft genomes for the genes associated with DMF degradation. We identified 952 genomes that harbor genes involved in DMF degradation, expanding the known diversity of prokaryotes with these metabolic capabilities. Our findings suggest acquisition of DMF-degrading gene via plasmids are important in the order Rhizobiales and genus Paracoccus, but not in most other lineages. Degradation pathway analysis reveals that most putative DMF degraders using aerobic Pathway I will accumulate methylamine intermediate, while members of Paracoccus, Rhodococcus, Achromobacter, and Pseudomonas could potentially mineralize DMF completely under aerobic conditions. The aerobic DMF degradation via Pathway II is more common than thought and is primarily present in -and {beta}-Proteobacteria and Actinobacteria. Most putative DMF degraders could grow with nitrate anaerobically (Pathway III), however, genes for the use of methyl-CoM to produce methane were not found. These analyses suggest that microbial consortia could be more advantageous in DMF degradation than pure culture, particularly for methane production under the anaerobic condition. The identified genomes and plasmids form an important foundation for optimizing bioremediation of DMF-containing wastewaters. ImportanceDMF is extensively used as a solvent in industries, and is classified as a probable carcinogen. DMF is a refractory compound resistant to degradation, and until now, only few bacterial isolates have been reported to degrade DMF. To achieve effective microbial degradation of DMF from wastewater, it is necessary to identify genomic diversity with the potential to degrade DMF and characterize the genes involved in two aerobic degradation pathways and potential anaerobic degradation for methane production. A wide diversity of organisms has the potential to degrade DMF. Plasmid-mediated degradation of DMF is important for Rhizobiales and Paracoccus. Most DMF degraders could grow anaerobically with nitrate as electron acceptor, while co-cultures are required to complete intermediate methanogenesis for methane production. This is the first genomics-based global investigation into DMF degradation pathways. The genomic database generated by this study provides an important foundation for the bioremediation of DMF in industrial waste waters. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC="FIGDIR/small/435917v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@e46e1dorg.highwire.dtl.DTLVardef@f93887org.highwire.dtl.DTLVardef@1ee5ce8org.highwire.dtl.DTLVardef@15a529_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures

Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-degrading microbial communities, which were enriched from 7 contaminated soils or sediments with a range of xenobiotic compounds. We show that multiple microbial strategies likely drive the development of xenobiotic degrading communities, notably (i) presence of genes encoding catabolic enzymes to degrade xenobiotics; (ii) presence of genes encoding efflux pumps; (iii) auxiliary catabolic genes on plasmids; and (iv) positive interactions dominate microbial communities with efficient degradation. Overall, the integrated analyses of microbial ecological strategies advance our understanding of microbial processes driving the biodegradation of xenobiotics and promote the design of bioremediation systems.

microbiology↗

bioRxiv2021

The Functional Significance of Bacterial Predators

Predation structures food webs, influences energy flow, and alters rates and pathways of nutrient cycling through ecosystems, effects that are well documented for macroscopic predators. In the microbial world, predatory bacteria are common, yet little is known about their rates of growth and roles in energy flows through microbial food webs, in part because these are difficult to quantify. Here, we show that growth and carbon uptake were higher in predatory bacteria compared to non-predatory bacteria, a finding across 15 sites, synthesizing 82 experiments and over 100,000 taxon-specific measurements of element flow into newly synthesized bacterial DNA. Obligate predatory bacteria grew 36% faster and assimilated carbon at rates 211% higher than non-predatory bacteria. These differences were less pronounced for facultative predators (6% higher growth rates, 17% higher carbon assimilation rates), though high growth and carbon assimilation rates were observed for some facultative predators, such as members of the genera Lysobacter and Cytophaga, both capable of gliding motility and wolfpack hunting behavior. Added carbon substrates disproportionately stimulated growth of obligate predators, with responses 63% higher than non-predators for the Bdellovibrionales and 81% higher for the Vampirovibrionales, whereas responses of facultative predators to substrate addition were no different from non-predators. This finding supports ecological theory that higher productivity increases predator control of lower trophic levels. These findings also indicate that the functional significance of bacterial predators increases with energy flow, and that predatory bacteria influence element flow through microbial food webs.

ecology↗