Biology subjects

Jurburg, S. D.

Publications and source records attributed to Jurburg, S. D..

6 recordsLinked to original sources

bioRxiv2026

The illusion of diversity: sampling design drives conflicting estimates of soil bacterial richness

Soil microbial diversity is shaped by the spatial scale at which communities are sampled, yet standard sampling practices often homogenize samples, obscuring fine-scale spatial structure and diversity patterns. To better understand how sampling effort, spatial extent, and physical homogenization influence plot-level microbial richness estimates, we sampled 57 forest and grassland sites across three regions in Germany using a 14-core cross-transect design, and performed 16S rRNA gene metabarcoding. We simulated sampling efforts of 1-14 cores and a range of spatial extents, and compared diversity estimates to those from physically homogenized composite samples. Plot-level richness increased continuously with sampling effort and spatial extent, with no evidence of saturation. However, when sequencing depth was held constant, sampling completeness declined with increasing sampling effort, meaning that more diversity is not captured. Composite samples substantially underestimated plot-level richness and altered apparent diversity relationships between ecosystems; individual cores identified forests as richer than grasslands, whereas homogenized samples suggested the opposite relationship. These results demonstrate that sampling effort, spatial extent, and homogenization fundamentally shape soil microbial diversity estimates. Homogenized composite samples cannot substitute for individual cores when the goal is to reliably quantify plot-level richness or compare diversity across ecosystems.

ecology↗

bioRxiv2025

HVRLocator: A Computationally Efficient Tool for Identifying Hypervariable Regions in 16S rRNA Big Datasets

BackgroundAmplicon sequencing of the 16S rRNA gene is widely used to assess microbial diversity due to its cost-effectiveness and efficiency. However, public 16S rRNA datasets often lack standardized metadata, particularly information on the sequenced hypervariable regions or primers used, which are critical for accurate analysis and data reuse. To address this, we present the HVRLocator, a computational tool that reliably identifies sequenced hypervariable regions, enhancing metadata quality and enabling more robust large-scale microbiome studies. ResultsThe HVRLocator tool processed samples at an average rate of 0.147 per minute. Validation confirmed 100% accuracy in predicting alignment positions, correctly matching sequences to the expected primer regions based on literature. We demonstrated how to use the tool to select appropriate and comparable sequences for building a global bacterial database from V4 region amplicons of the 16S rRNA gene. Using HVRLocator, we selected 36,217 valid samples out of 45,882 runs, enabling us to identify cases where metadata incorrectly labeled sequences as targeting the V4 region. ConclusionEven when metadata is available, it can be inaccurate or misleading. HVRLocator offers a reliable and efficient method to identify the exact hypervariable sequenced region, ensuring accurate processing of large-scale 16S rRNA amplicon data. By bypassing inconsistent metadata and literature, it streamlines data curation and enhances the reliability of microbial studies, syntheses, and meta-analyses. Its use is essential for critically evaluating published data and enabling accurate and reproducible research in microbial ecology.

bioinformatics↗

bioRxiv2025

Soil protist diversity enhances prokaryotic diversity, and regulates dominant prokaryotes and the abundance of key nitrogen cycling genes

Soil protists play crucial roles in soil microbial food-webs by preying on bacteria and other microorganisms. However, the effect of protist diversity on soil prokaryotic communities remains poorly understood. This study aimed to elucidate how different protist diversity treatments affect the composition and functionality of soil prokaryotic communities. We established soil microcosms with increasingly complex protist communities, including a control without protists, a medium diversity treatment with three small bacterivorous protists, and a high diversity treatment with seven protists of diverse trophic styles and sizes. Over 21 days, we monitored changes in the prokaryotic community using 16S rRNA gene sequencing and assessed the effects on nitrifiers and denitrifiers by qPCR of nitrogen-cycling genes. Protist diversity explained 23 % of the observed prokaryotic community differentiation over time, with the high-diversity treatment causing the greatest divergence from the control. The most abundant prokaryotes were preferentially predated in all protist treatments. Unexpectedly, the absolute abundance of the nirK gene, which is widely distributed among bacterial taxa and thus associated with high functional redundancy, decreased. The differential response of genes with lower distribution and redundancy, such as the bacterial and archaeal amoA and the Nitrospira-associated nxrB genes, to protist diversity indicated selective predation on archaea. High protist diversity systematically enhanced these effects compared to the medium diversity treatment. Overall, protist diversity was positively associated with prokaryotic diversity, which is crucial for maintaining ecosystem stability. These findings highlight the critical role of protist diversity and likely complementary predation in shaping soil prokaryotic communities and their functioning.

ecology↗

bioRxiv2024

Analysis of predation-driven inoculum loss and carbon flow in bioaugmented soils through DNA-SIP

Bioaugmentation is considered as a sustainable and cost-effective methodology to recover contaminated environments, but its outcome is highly variable. Predation is a key top-down control mechanism affecting inoculum establishment, however its effects on this process have received little attention. This study focused on the impact of trophic interactions on bioaugmentation success in two soils with different pollution exposure histories We inoculated a 13C-labelled pollutant-degrading consortium in these soils and tracked the fate of the labelled biomass through stable isotope probing (SIP) of DNA. We identified active bacterial and eukaryotic inoculum-biomass consumers through amplicon sequencing of 16S rRNA and 18S rRNA genes coupled to modified enrichment factor calculation. Inoculation effectively increased PAH removal in short-term polluted soils but not in long-term polluted soils. A decrease in the relative abundance of the inoculated genera was observed already on day 15 in the long-term polluted soil, while growth of these genera was observed in the short-term polluted soil, indicating establishment of the inoculum. In both soils, eukaryotic genera dominated as early incorporators of 13C-labelled biomass, while bacteria incorporated the labelled biomass at the end of the incubation period, probably through cross-feeding. We also found different successional patterns between the two soils. In the short-term polluted soil, Cercozoa and Fungi genera predominated as early incorporators, whereas Ciliophora, Ochrophyta and Amoebozoa were the predominant genera in the long-term polluted soil. Our results showed differences in the inoculum establishment and predator community behaviours, affecting bioaugmentation efficiency. This highlights the need to further study predation effects on inoculum survival to increase the applicability of inoculation-based technologies.

microbiology↗

bioRxiv2022

Temperature seasonality and nutrient enrichment drive intra-annual community turnover in global grasslands

In many grasslands, species with specific traits occupy unique temporal positions within communities. Such intra-annual segregation is predicted to be greatest in systems with high intra-annual climate variability because fluctuating environmental conditions provide opportunities for temporal niche partitioning among species. However, because most studies on intra-annual community dynamics have been conducted at individual sites, relationships between intra-annual climate variability and seasonal community dynamics at global scales have not yet been identified. Furthermore, the same characteristics that promote species-specific responses to fluctuations in environmental conditions may also drive species-specific responses to global change drivers such as eutrophication. Research provides evidence that eutrophication alters inter-annual plant community dynamics yet understanding of how it alters intra-annual dynamics remains limited. We used early-season and late-season compositional data collected from 10 grassland sites around the world to ask how intra-annual variability in precipitation and temperature as well as nutrient enrichment shape intra-annual species segregation, or seasonal {beta}-diversity, in plant communities. We also assessed whether changes in the abundances of specific functional groups including annual forbs, perennial forbs, C3 and C4 graminoids, and legumes underpin compositional differences between early- and late-season communities and treatments. We found that intra-annual temperature variability and seasonal {beta}-diversity were positively related but observed no relationship between intra-annual precipitation variability and seasonal {beta}-diversity. This suggests that positive relationships between -diversity and intra-annual temperature variability identified in earlier studies may be underpinned by the positive influence of intra-annual temperature variability on temporal segregation of species within growing seasons. We found that nutrient enrichment increased seasonal {beta}-diversity via increased turnover of species between early- and late-season communities. This finding mirrors patterns observed at inter-annual scales and suggests fertilization can alter compositional dynamics via similar mechanisms at varied temporal scales. Finally, fertilization reduced the abundance of C4 graminoids and legumes and eliminated intra-annual differences in these groups. In contrast, fertilization resulted in intra-annual differences in C3 graminoids which were not observed in control conditions, and increased abundance of C3 graminoids and annual forbs overall. Our study provides new insight into how intra-annual climate variability and nutrient enrichment influence biodiversity and seasonal dynamics in global grasslands.

ecology↗

bioRxiv2020

The archives are half-empty: a field-wide assessment of the availability of microbial community sequencing data

The sequencing revolution has resulted in the explosive growth of public genetic repositories. These repositories now hold invaluable collections of 16S rRNA gene amplicon sequences, but the extent to which the currently archived data is findable, accessible, and reusable has not been evaluated. We conducted a field-wide assessment of the availability and state of publicly archived 16S rRNA gene amplicon sequencing data. Using custom-built pattern-based text extraction algorithms, we searched 26,927 publications in 17 microbiology or microbial ecology journals, and identified 2,015 studies which performed 16S rRNA gene amplicon sequencing. We found, for example, that 7.2% of these had not been made public at the time of analysis, a trend which increased over time. Of the 635 studies targeting the V3-V4 region of the 16S rRNA gene, 40.3% contained data which was not available or not reusable, and for 25.5% of the studies, faults in data formatting or data labelling were likely to create obstacles in data reuse. Taken together, only 34% of these datasets had potentially reusable data. Our study reveals significant gaps in the availability of currently deposited community sequencing data, identifies major contributors to data loss, and offers suggestions for improving data archiving practices in the future.

ecology↗