Biology subjects

Wilhelm, R. C.

Publications and source records attributed to Wilhelm, R. C..

8 recordsLinked to original sources

bioRxiv2026

SIPdb: A stable isotope probing database and analytical dashboard for linking amplicon sequences to microbial activity using a reverse ecology approach

Stable isotope probing (SIP) provides a powerful means to connect microbial sequence data with diverse metabolic activities, but the lack of a framework for SIP-derived data has limited its integration into broader strategies for ecological inference. Here, we introduce the SIPdb, an extensible SQLite database of curated nucleic acid SIP experiments (also in phyloseq format) paired with an interactive RShiny dashboard for analysis and visualization. The initial release compiles 22 studies covering 21 isotopolog substrates across diverse environments, with data standardized using the MISIP metadata standard. In creating the SIPdb, we have provided a standardized pipeline that accommodates the three most common SIP gradient fractionation strategies (binary, multi-fraction, and density-resolved), two isotope incorporator designation strategies (fixed- and sliding-window), and four complementary differential abundance methods (DESeq2, edgeR, limma-voom, and ALDEx2). Using our pipeline, we identified more than 42,000 unique amplicon sequence variants as isotope incorporators across 62 phyla. Benchmarking with synthetic datasets demonstrated consistent performance across incorporator designation strategies, with ALDEx2 providing the highest specificity. Validation against original publications showed that, on average, SIPdb recovered 70.1% of author-reported incorporator taxa, with discrepancies arising from differences in phylotyping or classification approaches. Finally, our reanalysis of a non-SIP study of 1,4-dioxane degradation showed how SIPdb can both validate known degraders and uncover additional candidate taxa involved in community metabolism. The SIPdb establishes a scalable platform for reverse ecology, enabling hypothesis generation, cross-study meta-analysis, and linking taxa to metabolic processes, while serving as an open, extensible resource to accelerate ecological interpretation in microbiome research.

bioinformatics↗

bioRxiv2023

A data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence (MISIP)

DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, kinetics, and population dynamics, offering novel insights according to diverse research questions. Data re-use maximizes the information available from the time and resource intensive SIP experimental approach. Yet, a review of publicly available SIP sequencing metadata reveals that critical information necessary for reproducibility and reuse is often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) data standard framework and include examples of MISIP reporting for common SIP approaches. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires five metadata fields: isotope, isotopolog, isotopolog label and approach, and gradient position, and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (ex. gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will assure the reproducibility and reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.

bioinformatics↗

bioRxiv2022

Tracing carbon metabolism with stable isotope metabolomics reveals the legacy of diverse carbon sources in soil

Tracking the metabolic activity of whole soil communities can improve our understanding of the transformation and fate of carbon in soils. We used stable isotope metabolomics to trace 13C from nine labeled carbon sources into the water-soluble metabolite pool of an agricultural soil over time. Soil was amended with a mixture of all nine sources, with one source isotopically labeled in each treatment. We compared changes in the 13C-enrichment of metabolites with respects to carbon source and time over a 48-day incubation and contrasted differences between soluble versus insoluble sources. Whole soil metabolite profiles varied singularly by time, while the composition of 13C-labeled metabolites differed primarily by carbon source (R2 = 0.68) rather than time (R2 = 0.07) with source-specific differences persisting throughout incubations. The 13C-labeling of metabolites from insoluble carbon sources occurred at a slower rate than soluble sources but yielded a higher average atom % 13C in metabolite markers of biomass (amino acids and nucleic acids). The 13C-enrichment of metabolite markers of biomass stabilized at between 5 - 15 atom % 13C by the end of incubations. Temporal patterns in the 13C-enrichment of TCA cycle intermediates, nucleobases (uracil and thymine), and by-products of DNA salvage (allantoin) closely tracked microbial activity. Our results demonstrate that metabolite production in soils is driven by the carbon source supplied to the community, and that the fate of carbon in metabolite profiles do not tend to converge over time as a result of ongoing microbial processing and recycling. ImportanceCarbon metabolism in soil remains poorly described due to the inherent difficulty of obtaining information on the microbial metabolites produced by complex soil communities. Our study demonstrates the use of stable isotope probing (SIP) to study carbon metabolism in soil by tracking 13C from supplied carbon sources into metabolite pools and biomass. We show that differences in the metabolism of sources influences the fate of carbon in soils. Heterogeneity in 13C-metabolite profiles corresponded with compositional differences in the metabolically active populations, providing a basis for how microbial community composition is correlated with the quality of soil carbon. Our study demonstrates the application of SIP-metabolomics in studying soils and identifies several metabolite markers of growth, activity, and other aspects of microbial function.

microbiology↗

bioRxiv2022

The RNA Virome of Echinoderms

Echinoderms are a phylum of marine invertebrates that include model organisms, keystone species, and animals commercially harvested for seafood. Despite their scientific, ecological, and economic importance, there is little known about the diversity of RNA viruses that infect echinoderms compared to other invertebrates. We screened over 900 transcriptomes and viral metagenomes to characterize the RNA virome of 38 echinoderm species from all five classes (Crinoidea, Holothuroidea, Asteroidea, Ophiuroidea and Echinoidea). We identified 347 viral genome fragments that were classified to genera and families within nine viral orders - Picornavirales, Durnavirales, Martellivirales, Nodamuvirales, Reovirales, Amarillovirales, Ghabrivirales, Mononegavirales, and Hepelivirales. We compared the relative viral representation across three life stages (embryo, larvae, adult) and characterized the gene content of contigs which encoded complete or near-complete genomes. The proportion of viral reads in a given transcriptome was not found to significantly differ between life stages though the majority of viral contigs were discovered from transcriptomes of adult tissue. This study illuminates the biodiversity of RNA viruses from echinoderms, revealing the occurrence of viral groups in natural populations.

microbiology↗

bioRxiv2022

Ecological insights into soil health according to the life-history traits and environment-wide associations of bacteria in agricultural soils

Soil health assessment may be enhanced by monitoring changes in bacterial populations that are indicators of various biological, physical, and chemical properties of soil. However, the lack of ecological information for many abundant bacteria in agricultural soils limits our understanding of indicator responses and, thus, their utility for guiding management. We identified bacterial indicators of twelve conventional measures of soil health, and tillage intensity, from a 16S rRNA gene-based survey of farmland across North America. We then analyzed trends according to bacterial life-history frameworks and an environment-wide association survey (EWAS) to gain ecological insights. Life-history traits were assessed using genomic traits inferred from taxonomic classifications and included: genome size, rrn copy number, and coding density. An EWAS was conducted using 89 studies of agricultural land management. Most bacterial indicators were positively correlated with biological measures and negatively correlated with physical and chemical measures of soil health, revealing broad differences in the way management shapes bacterial associations with soil health. High soil health ratings corresponded with life-history traits associated with metabolic dependency (smaller genome and lower coding density), while lower health scores corresponded with traits selected for by environmental instability and disturbance (larger genome and multiple rrn). Trade-offs in community-weighted genome size explained most variation in overall health score. EWAS confirmed the importance of disturbance-adapted bacterial indicators, underscoring the impacts of tillage on soil bacterial communities. These findings provide insights into the ecological relationships between bacterial indicators and soil health and illustrate new approaches for interpreting patterns in microbiome data.

microbiology↗

bioRxiv2020

Phenolic acid-degrading Paraburkholderia prime decomposition in forest soil

Plant-derived phenolic acids are metabolized by soil microorganisms whose activity may enhance the decomposition of soil organic carbon (SOC). We characterized whether phenolic acid-degrading bacteria would enhance SOC mineralization in forest soils when primed with 13C-labeled p-hydroxybenzoic acid (PHB). We further investigated whether PHB-induced priming could explain differences in SOC content among mono-specific tree plantations in a 70-year-old common garden experiment. The activity of Paraburkholderia and Caballeronia dominated PHB degradation in all soils regardless of tree species or soil type. We isolated the principal PHB-degrading phylotype (Paraburkholderia madseniana RP11T), which encoded numerous oxidative enzymes, including secretion signal-bearing laccase, aryl-alcohol oxidase and DyP-type peroxidase, and confirmed its ability to degrade phenolics. The addition of PHB to soil led to significant enrichment (23-fold) of the RP11T phylotype (RP11ASV), as well as enrichment of other phylotypes of Paraburkholderia and Caballeronia. Metabolism of PHB primed significant loss of SOC (3 to 13 {micro}mols C g-1 dry wt soil over 7 days). In contrast, glucose addition reduced SOC mineralization (-3 to -8 {micro}mols C g-1 dry wt soil over 7 days). RP11ASV abundance and the expression of PHB monooxygenase (pobA) correlated with PHB respiration and were inversely proportional to SOC content in the field. We propose that plant-derived phenolics stimulate the activity of phenolic acid-degrading bacteria thereby causing soil priming and SOC loss. We show that Burkholderiaceae dominate soil priming in diverse forest soils and this observation counters the prevailing view that priming phenomena are a generalized non-specific response of community metabolism.

microbiology↗

bioRxiv2020

Diversity of sea star-associated densoviruses and transcribed endogenized viral elements of densovirus origin

A viral etiology of Sea Star Wasting Syndrome (SSWS) has been largely explored using metagenomics leading to the conclusion that a densovirus is the predominant DNA virus associated with this syndrome, and, thus, the most promising viral candidate pathogen. Single-stranded DNA viruses are however highly diverse and pervasive among eukaryotic organisms which we hypothesize may confound the association between densoviruses and SSWS in sea stars. To test this hypothesis and assess the association of densoviruses to SSWS, we compiled past metagenomic data with new metagenomic-derived viral genomes from sea stars collected from Antarctica, California, Washington, and Alaska. We used 179 publicly available sea star transcriptomes to complement our approaches for densovirus discovery. Lastly, we focus the study to SSaDV, the first sea star densovirus discovered, by documenting its biogeography and putative tissue tropism. Transcriptomes contained mostly endogenized densovirus elements similar to the NS1 gene, while >30 complete and near-complete densoviral genomes were recovered from viral metagenomes. SSaDV was associated with nearly all tested species from southern California to Alaska, and in contrast to previous work, we show SSaDV is one genotype among a high diversity of densoviruses present in sea stars across the west coast of the United States and globally that are commonly associated with grossly normal (i.e. healthy or asymptomatic) animals. The diversity and ubiquity of these viruses in wild sea stars confounds the original hypothesis that one densovirus was the etiologic agent of SSWD. ImportanceThe primary interest in sea star densoviruses, specifically SSaDV, has been their association with Sea Star Wasting Syndrome (SSWS), a disease that has decimated sea star populations across the west coast of the United States since 2013. The association of SSaDV to SSWS was originally drawn from metagenomic analyses concluding that it was (1) the only densovirus present in the metagenomic data and (2) the most likely viral candidate based on representation in symptomatic sea stars. We reassessed the original metagenomic data with additional genomic datasets and found that SSaDV was one of ten densoviruses present in the original dataset and was no more represented in symptomatic sea stars than in asymptomatic sea stars. Instead, SSaDV appears to be a widespread, generalist virus that exists among a large diversity of densoviruses present in sea star populations.

genomics↗

bioRxiv2018

Bacterial and fungal contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing

Delignification, or lignin-modification, facilitates the decomposition of lignocellulose in woody plant biomass. The extant diversity of lignin-degrading bacteria and fungi is underestimated by culture-dependent methods, limiting our understanding of the functional and ecological traits of decomposers populations. Here, we describe the use of stable isotope probing (SIP) coupled with amplicon and shotgun metagenomics to identify and characterize the functional attributes of lignin-, cellulose-and hemicellulose-degrading fungi and bacteria in coniferous forest soils from across North America. We tested the extent to which catabolic genes partitioned among different decomposer taxa; the relative roles of bacteria and fungi, and whether taxa or catabolic genes correlated with variation in lignocellulolytic activity, measured as the total assimilation of 13C-label into DNA and phospholipid fatty acids. We found high overall bacterial degradation of our model lignin substrate, particularly by gram-negative bacteria (Comamonadaceae and Caulobacteraceae), while fungi were more prominent in cellulose-degradation. Very few taxa incorporated 13C-label from more than one lignocellulosic polymer, suggesting specialization among decomposers. Collectively, members of Caulobacteraceae could degrade all three lignocellulosic polymers, providing new evidence for their importance in lignocellulose degradation. Variation in lignin-degrading activity was better explained by microbial community properties, such as catabolic gene content and community structure, than cellulose-degrading activity. SIP significantly improved shotgun metagenome assembly resulting in the recovery of several high-quality draft metagenome-assembled genomes and over 7,500 contigs containing unique clusters of carbohydrate-active genes. These results improve understanding of which organisms, conditions and corresponding functional genes contribute to lignocellulose decomposition.

molecular biology↗