Sarah W.E.B. van den Broek


Last Name

van den Broek

First Name

Sarah W.E.B.

ORCID

0000-0003-0980-338X

Organisational unit

09646 - Dötterl, Sebastian / Dötterl, Sebastian

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2022 - 20258
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Publications 1 - 8 of 8
  • Current Challenges and Pitfalls in Soil Metagenomics
    Item type: Review Article
    Leite, Marcio F. A.; van den Broek, Sarah W.E.B.; Kuramae, Eiko E. (2022)
    Microorganisms
    Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicochemical properties; (2) incorporating untreated controls; and (3) sharing data. Accounting for soil physicochemical properties is crucial for better understanding the changes in soil microbial community composition, mechanisms, and abundance. Untreated controls provide a good baseline to measure changes in soil microbial communities and separate treatment effects from random effects. Sharing data increases reproducibility and enables meta-analyses, which are important for investigating overall effects. To overcome these challenges, we suggest establishing standard guidelines for the design of experiments for studying soil metagenomics. Addressing these challenges will promote a better understanding of soil microbial community composition and function, which we can exploit to enhance soil quality, health, and fertility.
  • Soil microbial and plant responses to increasing antibiotic concentration: a case study of five antibiotics
    Item type: Working Paper
    van den Broek, Sarah W.E.B.; Nybom, Inna; Conz, Rafaela Feola; et al. (2025)
    bioRxiv
    Antibiotic contamination from biogenic waste in agricultural soils poses a significant threat to soil health and crop productivity. We investigated the effect of antibiotics on the soil microbial community, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) and plant productivity in a six week greenhouse trial. Here, Spinacia oleracea (spinach) and Raphanus sativus (radish) were grown from seed and a mix of five antibiotics, namely sulfamethoxazole, trimethoprim, enrofloxacin, clarithromycin and chlortetracycline, were added to the soil at concentrations 0, 0.1, 1 and 10 mg kg−1 soil dry weight (c0, c0.1, c1 and c10, respectively). Overall, we found that the antibiotic treatments significantly impacted prokaryotic α-diversity and prokaryotic and fungal β-diversity. Human and plant pathogen abundance did not increase under antibiotic exposure, but there was a significant reduction of plant growth-promoting bacteria. Moreover, the c10 treatment significantly increased the abundance of MGE intI1 indicative of horizontal gene transfer and ARG sul1 antibiotic resistance and significantly lowered radish biomass and nitrogen uptake, while spinach biomass and nitrogen uptake were unaffected. In summary, our study showed that antibiotic exposure significantly changed prokaryotic community diversity and taxonomy, while fungi remained largely unaffected. The reduction of plant growth-promoting bacteria may have a significant impact on soil nutrient cycling and crop productivity, but more research is needed to understand the long-term impact of these co-applied antibiotics on food production. Additionally, more studies are needed to understand the effect of antibiotics on realistic, field scale, conditions to fully understand the impact on environmental and human health. Importance Agricultural soils are increasingly contaminated with complex mixtures of antibiotics from various biogenic sources, yet we lack a clear understanding of their specific ecological impact. While many studies investigate antibiotics, they often are studied in pollution sources like manure which contain confounding factors like heavy metals. To provide clear mechanistic insight, we investigated the effects of a complex, five-antibiotic mixture on the soil-plant system, independent of other contaminants. This revealed that the effect of antibiotics extends beyond selecting for antibiotic resistance. Specifically, the reduction of prokaryotic diversity and plant growth-promoting bacteria under antibiotic exposure can have potential detrimental effects on plant and soil health. Moreover, we found that antibiotic exposure can reduce plant biomass and nitrogen uptake, but this is highly plant dependent. This research highlights the critical need to monitor antibiotic pollution due to its potential detrimental effect on plant health and alterations to the soil microbiome.
  • The impact of antibiotics from human excreta-based fertilizers on soil bacterial and fungal communities, antibiotic resistance genes and mobile genetic elements
    Item type: Other Conference Item
    van den Broek, Sarah W.E.B.; Nybom, Inna; Conz, Rafaela Feola; et al. (2024)
    ASM MICROBE 2024. Abstracts Online
    The use of human excreta-based fertilizers to recycle valuable nutrients is an increasingly popular approach to enhance sustainable agriculture. Despite the many potential benefits, these fertilizers may introduce antibiotics and antibiotic resistant genes (ARGs). ARGs can disseminate among soil microorganisms through horizontal gene transfer using mobile genetic elements (MGEs), which can lead to antibiotic resistant pathogens that can spread to clinical settings. To investigate the potential impact of antibiotics on the soil microbial community structure and functioning, a six-week greenhouse trial was conducted where spinach and radish were grown in soils spiked with a mixture of five widespread antibiotics (clarithromycin, sulfamethoxazole, trimethoprim, chlortetracycline and enrofloxacin), applied at concentrations 0, 0.1, 1 and 10 mg kg-1 soil dry weight. Metabarcoding of bacterial and fungal ribosomal markers coupled to qPCR-based quantification of four ARGs (sul1, dfrA12, tetQ, qnrS1) and two MGEs (intI1, intI2) was performed on collected soil samples. In our study, a canonical analysis of principal coordinates of β-diversity showed distinct bacterial groups for each antibiotic concentration, while all fungal groups overlapped except for a distinct 10 mg kg-1 treatment cluster. Antibiotic concentration and soil pH had a significant impact on both bacterial and fungal β-diversity, but α-diversity remained unchanged. Sul1 and intI1 abundance significantly increased in the 10 mg kg-1 antibiotic concentration compared to the other treatments. This can likely be attributed to persistent selection pressure in the 10 mg kg-1 treatment, where sulfamethoxazole concentration remains high enough after 6 weeks to affect the sul1 and intI1 concentrations. Overall, our findings show that these five antibiotics only induced elevated sul1 and intI1 concentrations when applied in one to two orders of magnitude higher compared to commonly detected levels in agricultural soils. IntI1, suggested as an anthropogenic pollution indicator, did not increase in the lower antibiotic concentrations which is a promising step in the research investigating the environmental and human health risks of human excreta-derived fertilizers and advancing their safe use in the future. Nevertheless, monitoring antibiotic levels in fertilizers is crucial, as even low antibiotic concentrations may increase ARGs before and after application, potentially leading to antibiotic resistant pathogens and posing clinical risks.
  • Understanding soil organic carbon dynamics at larger scales
    Item type: Book Chapter
    Doetterl, Sebastian; Abramoff, Rose; Cornelis, Jean-Thomas; et al. (2023)
    Burleigh Dodds Series in Agricultural Science ~ Understanding and fostering soil carbon sequestration
  • Opportunities and challenges of using human excreta-derived fertilizers in agriculture: A review of suitability, environmental impact and societal acceptance
    Item type: Journal Article
    van den Broek, Sarah W.E.B.; Nybom, Inna; Hartmann, Martin; et al. (2024)
    Science of The Total Environment
    Human excreta-derived fertilizers (HEDFs) are organic fertilizers made from human excreta sources such as urine and feces. HEDFs can contribute to a sustainable and circular agriculture by reuse of valuable nutrients that would otherwise be discarded. However, HEDFs may contain contaminants such as pharmaceuticals, persistent organic compounds, heavy metals and pathogens which can negatively affect plant, water and soil quality. Moreover, consumer prejudice, farmer hesitance and strict regulations can discourage utilization of HEDFs. Here, we conducted a thorough review of published literature to explore the opportunities and challenges of using HEDFs in agricultural systems by evaluating the suitability of human excreta as a nutrient source, their typical contaminant composition, how they affect the quality of crops, soils and water and their societal impact and acceptance. We found that HEDFs are suitable nutrient-rich fertilizers, but may contain contaminants. Processing treatments increase the fertilizer quality by reducing these contaminants, but they do not remove all contaminants completely. Regarding the environmental impacts of these fertilizers, we found overall positive effects on crop yield, soil nutrients, plant-soil-microbe interactions and plant pathogen suppression. The use of HEDFs reduces water contamination from sewage waste dumping, but nutrient leaching dependent on soil type may still affect water quality. We found no increased risks with human pathogens compared to inorganic fertilizers but identified processing treatment as well as crop and soil type significantly affect these risks. Lastly, we found that public acceptance is possible with clear regulations and outreach to inform consumers and farmers of their multi-faceted benefits and safe usage after processing treatments. In summary, this review emphasizes the great potential of HEDFs and its positive impacts on society, especially in regions where conventional fertilizers are scarce, while also stressing the need for adaptation to specific soils and crops.
  • The effect of soil antibiotic contamination on the soil microbial community and its resistome
    Item type: Other Conference Item
    van den Broek, Sarah W.E.B.; Nybom, Inna; Conz, Rafaela Feola; et al. (2023)
    Human waste-based fertilizers contribute to sustainable agriculture by reusing valuable nutrients. However, these fertilizers may contain antibiotics and antibiotic resistance genes (ARGs) which spread among soil microorganisms by horizontal gene transfer using mobile genetic elements (MGEs). The goal of this study was to investigate the effect of antibiotics, commonly found in human waste-based fertilizers, on the soil microbial community and its resistome. A greenhouse trial was conducted where spinach and radish were exposed to a mix of five antibiotics (clarithromycin, sulfamethoxazole, trimethoprim, chlortetracycline and enrofloxacin). This mix was applied in four concentrations (0, 0.1, 1.0 and 10.0 mg/kg soil dry weight). The crops were grown for 6 weeks, after which samples were collected for metabarcoding (16S and ITS) and qPCR analysis. The metabarcoding data was analysed using a customised pipeline. For the qPCR, four ARG and two MGE targets were selected, namely sul1, dfrA12, tetQ, qnrS1, intI-1 and intI-2. Preliminary results of the metabarcoding show a shift of the soil bacterial community for both crops. Here, the 0 mg/kg treatment was significantly different than the 0.1 and 1.0 mg/kg treatment. For the resistome, sul1 and intI-1 were consistently found across all samples. Moreover, their abundance increased in the 0.1 and 1.0 mg/kg treatments compared to the 0 mg/kg control treatment. Detailed analysis of the soil microbial community, to be performed, will link the antibiotic distribution to the soil microbial community and its resistome. Our study shows that low antibiotic concentrations have the potential to increase ARG abundance. While these genes are not necessarily present in pathogens nor do they usually spread to clinical settings, soil antibiotic resistance has been linked to antibiotic resistant clinical pathogens. Therefore, it is important to better understand how these genes behave and disseminate in agriculture with waste-based fertilizers potentially containing antibiotics.
  • A comparison of antibiotic resistance genes from animal and human waste-based fertilizers: A case for changing farming practices?
    Item type: Other Conference Item
    van den Broek, Sarah W.E.B.; Hartmann, Martin; Doetterl, Sebastian; et al. (2022)
    Human excreta-derived fertilizers contribute to sustainable agriculture by reusing valuable nutrients. However, consumer prejudice, farmer hesitance and strict regulations discourage utilization of these fertilizers, while animal manure is widely accepted. Yet, both fertilizers may contain antibiotics and antibiotic resistance genes which spread among soil microorganisms by horizontal gene transfer. Here, we conducted a meta-analysis to compare antibiotic resistance gene presence, abundance and diversity in human excreta-derived fertilizers and animal manure. We created a co-occurrence keyword network using the litsearchr R package to find suitable papers and reduce bias. We collected data such as the antibiotic resistance gene determination method, fertilizer base (human or animal), fertilizer type (i.e. manure, sewage sludge), and assessed antibiotic resistance genes. This resulted in 7918 datapoints from 43 papers on human excreta-derived fertilizers, 7558 datapoints from 24 papers on animal manure and 3321 datapoints of untreated soil from 14 papers. Antibiotic resistance genes were most often detected in soil amended with animal manure (91.1%), followed by animal manure directly (81.6%), human excreta-derived fertilizers directly (68.2%), soil amended with human excreta-derived fertilizers (45.2%) and lastly in untreated soil (35.1%). Moreover, antibiotic resistance gene diversity was highest in animal manure, compared to human excreta-derived fertilizers and untreated soil. Animal manure and human excreta-derived fertilizers soil amendments added, respectively, 70 and 28 unique antibiotic resistance genes that were not detected in untreated soil. Our results indicate that, in the context of the soil resistome, human excreta-derived fertilizers are a safe alternative to animal manure. However, studies covering a larger diversity of soil and environmental settings are needed to better understand antibiotic resistance gene dissemination and to identify safe application rates for using human excreta as fertilizer.
Publications 1 - 8 of 8