Biology subjects

Singer, G.

Publications and source records attributed to Singer, G..

11 recordsLinked to original sources

bioRxiv2025

Drying halves decomposition rates in river networks by disrupting structure-function linkages

River drying is intensifying worldwide due to climate change and water abstraction, with major consequences for biodiversity and ecosystem functioning. In river networks, drying not only alters local environmental conditions but also disrupts hydrological connectivity, reshaping the movement of organisms and resources at the network scale. Leaf litter decomposition--a key ecosystem function in freshwater systems--is particularly sensitive to changes in the structure of decomposer communities. We hypothesized that spatiotemporal patterns of drying regulate decomposition by altering the diversity and composition of detritivore macroinvertebrates, bacteria and fungi. We combined data from six European drying river networks (DRNs) spanning a wide latitudinal gradient to assess how local drying intensity and regional hydrological connectivity affect decomposition through changes in these decomposer groups. We found that short drying events ([≤] six dry days) reduced decomposition rates by up to 50% by shifting the control of decomposition from a balanced contribution of fungi, bacteria, and detritivores to one dominated by dry-tolerant but less efficient bacteria. These community shifts persisted after flow resumption, leading to sustained reductions in decomposition even under flowing conditions. Regional connectivity alleviated these negative effects of local drying by facilitating the recovery of more efficient aquatic decomposers through dispersal. However, this effect depended on DRN context. In particular, in southern, more arid DRNs, stronger fragmentation hindered the recovery of decomposer communities after flow resumption. Overall, our results provide mechanistic evidence that spatiotemporal patterns of drying can regulate the linkages between community structure and ecosystem functioning in river networks. As drying events become more frequent and prolonged, increasing disruption of these linkages will impact carbon cycling and energy fluxes in freshwater ecosystems under global change.

ecology↗

bioRxiv2024

Does method of field preparation affect survival and growth of juvenile Chinook salmon in agricultural floodplains?

There is growing interest to integrate conservation initiatives into agricultural practices using a reconciliation ecology framework. In Californias Central Valley, one approach to improving crucial nursery habitat for threatened and endangered fish species is by re-creating floodplain habitats through the inundation of agricultural fields during the non-growing season. We conducted a series of field experiments in agricultural floodplains (winter-flooded rice fields that were once natural floodplains) to explore whether different field preparation methods enhanced growth and survival of floodplain-dependent fish species. Approximately 8,000 juvenile fall-run Chinook Salmon (Oncorhynchus tshawytscha) were reared for at least 28 days on eight, 0.2 ha experimental fields. Each experimental field represented one of four treatments (two replicates per treatment): addition of large wood, addition of in-field canals, addition of both large wood and in-field canals, and control-where no additional field preparations were implemented beyond standard post-growing practices: i.e., chopping rice into stubble, baling and removing excess rice straw, and discing the field with a single pass by plowing rice straw into the ground to promote decomposition. We found no significant difference in water temperature, fish growth or fish survival among habitat treatments. Across treatments, survival ranged from 50.1%-78.3% and averaged 65.75% (/- 7.89% SE). These findings suggest agricultural floodplains require no additional modifications to promote fish growth and survival. Results illustrate the benefits of integrating working landscapes with conservation initiatives by creating more accessible and beneficial habitat for native fishes.

ecology↗

bioRxiv2022

Universal microbial reworking of dissolved organic matter along environmental gradients

Soils are losing increasing amounts of carbon annually to freshwaters as dissolved organic matter (DOM), which, if degraded, can accelerate climate change. DOM is more susceptible to degradation closer to its source and becomes increasingly dominated by the same, difficult-to-degrade compounds as degradation proceeds. However, the processes underlying DOM degradation across environments are poorly understood. Here we found DOM changed similarly along soil-aquatic gradients irrespective of differences in environmental conditions. Using ultra-high-resolution mass spectrometry, we tracked DOM along soil depths and hillslope positions in forest headwater catchments and related its composition to soil microbiomes and physical chemistry. Along depths and hillslopes, carbohydrate-like and unsaturated hydrocarbon-like compounds increased in mass, suggestive of microbial reworking of plant material. More than half of the variation in the abundance of these compounds was related to the expression of genes essential for degrading plant-derived carbohydrates. Our results implicate continuous microbial reworking in shifting DOM towards universal compounds in soils. By synthesising data from the land-to-ocean continuum, we suggest these processes can generalise across ecosystems and spatiotemporal scales. Such general degradation patterns can be leveraged to predict DOM composition and its downstream reactivity along environmental gradients to inform management of soil-to-stream carbon losses.

ecology↗

bioRxiv2022

Acute appendicitis manifests as two microbiome state types with oral pathogens influencing severity

Mounting evidence suggests that acute appendicitis (AA) is not one but two diseases: complicated appendicitis, which is associated with necrosis leading to perforation or periappendicular abscess, and uncomplicated appendicitis, which does not necessarily result in perforation. Even though AA is the most frequent cause of surgery from abdominal pain, little is known about the origins and etiopathogenesis of this disease, much less regarding the different disease types. In this study, we investigated the microbiome of samples from the appendix, rectum and peritoneum of 60 children and adolescents with AA to assess the composition and potential function of bacteria, archaea and fungi. The analysis of the appendix microbial community revealed a shift depending on the severity of the AA. This shift was reflected by two major community state types that represented the complicated and uncomplicated cases. We could demonstrate that complicated, but not uncomplicated, appendicitis is associated with a significant local expansion of oral, bacterial pathogens in the appendix, most strongly influenced by necrotizing Fusobacterium spp., Porphyromonas and Parvimonas. Uncomplicated appendicitis, however, was characterised by gut-associated microbiomes. Our findings support the hypothesis that two disease types exist in AA, which cannot be distinguished beyond doubt using standard clinical characterization methods or by analysis of the patients rectal microbiome. An advanced microbiome diagnosis, however, could improve non-surgical treatment of uncomplicated AA. ImportanceWith a lifetime risk of up to 17%, acute appendicitis is one of the most frequent causes of emergency abdominal surgery in westernized countries. Latest literature reports suggests that appendicitis manifests in two disease types: complicated and uncomplicated appendicitis with different, yet unknown, etiopathogenesis. In this study, we investigated the microbial composition (bacteria, archaea and fungi) from 60 children and adolescents that were diagnosed with acute appendicitis. Appendix, rectal and peritoneal samples were analysed using amplicon and metagenomic sequencing. Our results suggest that acute appendicitis manifests in three microbial state types that reflect complicated and uncomplicated appendicitis as well as special cases that are caused by bacterial overgrowth. Strikingly, uncomplicated appendicitis appears to be caused by gut-associated pathogens while complicated appendicitis is driven by oral-associated microbes such as Fusobacterium sp. or Porphyromonas sp. The findings provided in our study are of special interest to understand the etiopathogenesis of both complicated and uncomplicated appendicitis.

microbiology↗

bioRxiv2022

High-throughput Production of Diverse Xenobiotic Metabolites with P450-transduced Huh7 Hepatoma Cell Lines

Precision medicine requires methods to assess drug metabolism and distribution, including the identification of known and undocumented drug and chemical exposures as well as their metabolites. Recent work demonstrated high-throughput generation of xenobiotic metabolites with human liver S-9 fractions and detection in human plasma and urine. Here, we developed a panel of lentivirally transduced human hepatoma cell lines (Huh7) that stably express individual cytochrome P450 (P450) enzymes and generate P450-specific xenobiotic metabolites. We verified protein expression by immunoblotting and demonstrated that the cell lines generate P450-specific metabolites from probe substrates. To increase analytical throughput, we used a pooling strategy where 36 chemicals were grouped into 12 unique mixtures, each mixture containing 6 randomly selected compounds, and each compound being present in two separate mixtures. Each mixture of compounds was incubated with 8 different P450 cell lines with cell extracts analyzed at 0 and 2 h. Extracts were analyzed using liquid chromatography-high resolution mass spectrometry. Cell lines selectively metabolized test substrates, with pazopanib metabolized by CYP3A4 and CYP2C8 cells, bupropion by CYP2B6, and {beta}-naphthoflavone by CYP1A2 for example, showing substrate-enzyme specificity. Predicted metabolites from the remaining 33 compounds as well as many unidentified m/z features were detected. We also show that a specific metabolite generated by CYP2B6 cells, but not detected in the S9 system, was identified in human samples. Our data show that incubating these cell lines with chemical mixtures accelerated characterization of xenobiotic chemical space, while simultaneously allowing for the contributions of specific P450 enzymes to be identified. Significance statementHigh resolution mass spectrometry enables the identification of exposures to drugs and other xenobiotics in human samples. This paper demonstrates a workflow for high throughput production of xenobiotic metabolites using a panel of engineered cytochrome P450-expressing hepatoma cells. Active substrate-enzyme pairs can be identified using this workflow and generated metabolites can be used as surrogate standards to validate xenobiotic detection in humans.

pharmacology and toxicology↗

bioRxiv2021

Human Biopsies in Nanofibrillar Cellulose Hydrogel - A Novel Method for Long-term Tissue Culture

Advanced 3D in vitro models are laborious to prepare and susceptible to unintentional design errors due to culture adaptations, cell immaturity, xenofactors or yet incomplete knowledge of the dynamics within tissues or materials. In order to acquire cost-efficient research material with intact in vivo composition, we developed novel tissue culture method with plant-derived scaffolding. Human skin-, foreskin- and glioblastoma multiforme biopsies were dissected mechanically and cultivated for 28 days in plant-derived nanofibrillar cellulose hydrogel. Comparative cultures were done using mouse sarcoma tumor -derived Matrigel. Long-term preservation of cultivated tissues was evaluated against typical immunohistochemical biomarkers for each tissue type: skin tissues for cytokeratins 5/6, E-cadherin and vimentin for sustained tissue structures, and brain neoplasia for Olig2, S100, Nestin, NOTCH1, MAP2 and GFAP for preserved disease profile. Histological analysis from both culture conditions showed that until day 28, all cultivated biopsy types were able to sustain their characteristic protein expressions without signs of necrosis. We here conclude a novel tissue culture model in xeno-free 3D scaffolding, that can enable long-term sample storage in vitro, studies of human tumor tissues and their non-neoplastic microenvironment, and innovations in personalized medicine research.

cell biology↗

bioRxiv2021

Large herbivorous wildlife and livestock differentially influence the relative importance of different sources of carbon for riverine food webs

In many regions around the world, large populations of native wildlife have declined or been replaced by livestock grazing areas and farmlands, with consequences on terrestrial-aquatic ecosystems connectivity and trophic resources supporting food webs in aquatic ecosystems. The river continuum concept (RCC) and the riverine productivity model (RPM) predict a shift of carbon supplying aquatic food webs along the river: from terrestrial inputs in low-order streams to autochthonous production in mid-sized rivers. Here, we studied the influence of replacing large wildlife (mainly hippos) with livestock on the relative importance of C3 vegetation, C4 grasses and periphyton on macroinvertebrates in the Mara River, which is an African montane-savanna river known to receive large subsidy fluxes of terrestrial carbon and nutrients mediated by LMH, both wildlife and livestock. Using stable carbon ({delta}13C) and nitrogen ({delta}15N) isotopes, we identified spatial patterns of the relative importance of allochthonous carbon from C3 and C4 plants (woody vegetation and grasses, respectively) and autochthonous carbon from periphyton for macroinvertebrates at various sites of the Mara River and its tributaries. Potential organic carbon sources and invertebrates were sampled at 80 sites spanning stream orders 1 to 7, various catchment land uses (forest, agriculture and grasslands) and different loading rates of organic matter and nutrients by LMH (livestock and wildlife, i.e., hippopotamus). The importance of different sources of carbon along the river did not follow predictions of RCC and RPM. First, the importance of C3 and C4 carbon was not related to river order or location along the fluvial continuum but to the loading of organic matter (dung) by both wildlife and livestock. Notably, C4 carbon was important for macroinvertebrates even in large river sections inhabited by hippos. Second, even in small 1st -3rd order forested streams, autochthonous carbon was a major source of energy for macroinvertebrates, and this was fostered by livestock inputs fuelling aquatic primary production throughout the river network. Importantly, our results show that replacing wildlife (hippos) with livestock shifts river systems towards greater reliance on autochthonous carbon through an algae-grazer pathway as opposed to reliance on allochthonous inputs of C4 carbon through a detrital pathway.

ecology↗

bioRxiv2021

Livestock as vectors of organic matter and nutrient loading in aquatic ecosystems in African savannas

Populations of large wildlife have declined in many landscapes around the world, and have been replaced or displaced by livestock. The consequences of these changes on the transfer of organic matter (OM) and nutrients from terrestrial to aquatic ecosystems are not well understood. We used behavioural data, excretion and egestion rates and C: N: P stoichiometry of dung and urine of zebu cattle, to develop a metabolism-based estimate of loading rates of OM (dung), C, N and P into the Mara River, Kenya. We also directly measured the deposition of OM and urine by cattle into the river during watering. Per head, zebu cattle excrete and/or egest 25.6 g dry matter (DM, 99.6 g wet mass; metabolism) - 27.7 g DM (direct input) of OM, 16.0-21.8 g C, 5.9-9.6 g N, and 0.3-0.5 g P per day into the river. To replace loading rates OM of an individual hippopotamus by cattle, around 100 individuals will be needed, but much less for different elements. In parts of the investigated sub-catchments loading rates by cattle were equivalent to or higher than that of the hippopotamus. The patterns of increased suspended materials and nutrients as a result of livestock activity fit into historical findings on nutrients concentrations, dissolved organic carbon and other variables in agricultural and livestock areas in the Mara River basin. Changing these patterns of OM and nutrients transport and cycling are having significant effects on the structure and functioning of both terrestrial and aquatic ecosystems.

ecology↗

bioRxiv2019

Multiscale analysis of acne connects molecular subnetworks with disease status

Acne vulgaris affects millions of individuals and can lead to psychosocial impairment as well as permanent scarring. Previous studies investigating acne pathogenesis have either examined a targeted set of biological parameters in a modest-sized cohort or carried out high-throughput assays on a small number of samples. To develop a more comprehensive understanding of acne pathophysiology, we conducted an in-depth multi-omic study of 56 acne patients and 20 individuals without acne. We collected whole blood, skin punch biopsies, microbiota from skin follicles, and relevant clinical measurements to understand how multiple factors contribute to acne. We provide an integrative analysis of multi-omics data that results in a molecular network of acne. Comparisons of lesional and non-lesional skin highlighted multiple biological processes, including immune cell and inflammatory responses, response to stress, T cell activation, lipid biosynthesis, fatty acid metabolism, keratinocytes, antimicrobial activity, epithelial cell differentiation, and response to wounding, that are differentially altered in acne lesions compared to non-lesions. Our results suggest baseline differences in the skin that may predispose individuals to develop acne. These datasets and findings offer a framework for new target identification and reference for future studies.

systems biology↗

bioRxiv2019

Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater

1The characterization of biodiversity is a crucial element of ecological investigations as well as environmental assessment and monitoring activities. Increasingly, amplicon-based environmental DNA metabarcoding (alternatively, marker gene metagenomics) is used for such studies given its ability to provide biodiversity data from various groups of organisms simply from analysis of bulk environmental samples such as water, soil or sediments. The Illumina MiSeq is currently the most popular tool for carrying out this work, but we set out to determine whether typical studies were reading enough DNA to detect rare organisms (i.e., those that may be of greatest interest such as endangered or invasive species) present in the environment. We collected sea water samples along two transects in Conception Bay, Newfoundland and analyzed them on the MiSeq with a sequencing depth of 100,000 reads per sample (exceeding the 60,000 per sample that is typical of similar studies). We then analyzed these same samples on Illuminas newest high-capacity platform, the NovaSeq, at a depth of 7 million reads per sample. Not surprisingly, the NovaSeq detected many more taxa than the MiSeq thanks to its much greater sequencing depth. However, contrary to our expectations this pattern was true even in depth-for-depth comparisons. In other words, the NovaSeq can detect more DNA sequence diversity within samples than the MiSeq, even at the exact same sequencing depth. Even when samples were reanalyzed on the MiSeq with a sequencing depth of 1 million reads each, the MiSeqs ability to detect new sequences plateaued while the NovaSeq continued to detect new sequence variants. These results have important biological implications. The NovaSeq found 40% more metazoan families in this environment than the MiSeq, including some of interest such as marine mammals and bony fish so the real-world implications of these findings are significant. These results are most likely associated to the advances incorporated in NovaSeq especially patterned flow cell, which prevents similar sequences that are neighbours on the flow cell (common in metabarcoding studies) from being erroneously merged into single spots by the sequencing instrument. This study sets the stage for incorporating eDNA metabarcoding in comprehensive analysis of oceanic samples in a wide range of ecological and environmental investigations.

genomics↗

bioRxiv2018

Measuring the archaeome: detection and quantification of archaea signatures in the human body

Due to their fundamentally different biology, archaea are consistently overlooked in conventional 16S rRNA gene amplicon surveys. Herein, we evaluate different methodological set-ups to detect and quantify archaea signatures in human samples (nose, oral, appendix, stool, and skin) using amplicon sequencing and quantitative PCR.\n\nWith our optimized protocol, we were able to increase the detection of archaeal RSVs from one (using a so-called \"universal\" approach) to 81 RSVs in a representative sample set. Moreover, we confirmed the presence of about 5% archaeal signatures in the human gut, but found, unexpectedly, an almost 1:1 ratio of archaeal to bacterial 16S rRNA genes in appendix and nose samples. This finding indicates a high prevalence of archaeal signatures in body regions thus far not analyzed for the presence of archaea using appropriate methods.\n\nIn order to assess the archaeome diversity and archaeal abundance, a specific archaea-targeting methodology is required, for which we propose two standard procedures. These methodologies might not only prove useful for analyzing the human archaeome in more detail, but could also be used for other holobionts samples.

microbiology↗